Mercurial > repos > czouaoui > circoletto
changeset 0:f2b96501291a draft
Uploaded
| author | czouaoui |
|---|---|
| date | Tue, 13 Mar 2018 05:06:56 -0400 |
| parents | |
| children | 90b72b3a5bad |
| files | circoletto.pl circoletto.xml test-data/blast_170144 test-data/circoletto.png |
| diffstat | 4 files changed, 8248 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circoletto.pl Tue Mar 13 05:06:56 2018 -0400 @@ -0,0 +1,1176 @@ +#!/usr/bin/perl -w + +$version = localtime((stat($0))[9]); +$circos_compatibility = '0.69-3'; + +$| = 1; + +use POSIX; +use Getopt::Long; +use Bio::SearchIO; +use Bio::Seq; + +$randomer = int(rand(1001)) . $$; +$randomer = sprintf "%010s", $randomer; + +$usage = "# Circoletto - visualising sequence similarity with Circos +# Darzentas N. +# $version +# http://bat.infspire.org | bat\@infspire.org + +welcome + +before you run Circoletto, be sure to: +- have Circos (tested with $circos_compatibility, http://circos.ca/software/download/circos/), BLAST (tested with 2.2.25) in your path, and BioPerl (tested with 1.6.901) installed +- check / edit (in the code) the two paths to Circos and Circos tools - if we cannot find them, we'll print a warning and exit +- if you need to increase the max_sequences > 200, you also need to edit max_ideograms in Circos' housekeeping.conf + +circoletto.pl + + either +--query or --q (path to) the queries +--database or --db (path to) the database + or +--blastout or --bl (path to) the BLAST output + + other (optional) arguments +--out_dir output directory, otherwise pwd +--out_name output basename (extension will be added automatically) +--best_hit set to show only best hit per query +--best_hit_type best hit type, 'entry' to show all HSPs per best hit [default], or 'local' to show single best HSP +--w_hits set if you want to show only entries with BLAST hits +--z_by depth-order ribbons by 'score' (highest at top) [default] / 'score_rev' / 'alnlen' (longest at top) / 'alnlen_rev' +--e_value E-value [default: 1e-10] +--gep gap extension penalty, set to >=2 if you need to constrain it e.g. for genomic data [default: -1] +--flt set to enable pre-filtering of query sequences +--html_out set to provide BLAST HTML output (runs BLAST again...) +--no_labels set to switch off labels +--out_size set radius of output in pixels, so set to '1000' for a 2000x2000 output [default: 1000] +--out_type output type, either 'svg', or 'png' [default] +--score2colour score to colour ribbons with, 'bit' for bitscore [default], or 'eval' for E-value, or 'id' for % identity +--scoreratio2colour score ratio to use for colouring, 'max' for score/max [default], 'minmax' for (score-min)/(max-min) that should give more colour range esp. for % identity +--abscolour use absolute scores for colouring, currently only allowed with % identity +--maxB1 max score for blue +--maxG2 max score for green +--maxO3 max score for orange, then it's red +--annotation user provided annotation file, see 'example_annotation.txt' +--annocolour colour ribbons by 'query' or 'database' default ideogram colours or annotation (see --annotation), or by 'query_rainbow_(colour|grey)' or 'database_rainbow_(colour|grey)' +--invertcolour set to colour ribbons by SEQUENCE (i.e. not ORDER) invertion (or reverse complementarity or plus/minus), normal in black, inverted in lime +--untangling_off set to turn off ribbon untangling +--revcomp_q set to reverse complement query DNA sequences +--revcomp_d set to reverse complement database DNA sequences +--reverse_qorder set to reverse ORDER of query sequences, may help clarity +--reverse_dorder set to reverse ORDER of database sequences, may help clarity +--reverse_qorient set to reverse ORIENTATION of query sequences which then need to be read anticlockwisely, may help clarity +--reverse_dorient set to reverse ORIENTATION of database sequences which then need to be read anticlockwisely, may help clarity +--hide_orient_lights set to hide orientation lights at edges of ideograms, read from green (=beginning) to red (=end) +--ribocolours2allow blue, green, orange, red in a format like this (including parentheses) '(green|orange)' or '(blue)' - histograms are not affected +--tblastx run 6-frame tBLASTx for DNA vs DNA +--cpus number of CPUs to use with BLAST + +"; + +my $options_res = GetOptions( + "query|q:s" => \$query, + "database|db:s" => \$database, + "blastout|bl:s" => \$blastout, + "out_dir:s" => \$out_dir, + "out_name:s" => \$out_name, + "out_size:f" => \$out_size, + "out_type:s" => \$out_type, + "e_value|e-value|evalue:s" => \$e_value, + "gep:s" => \$gep, + "flt!" => \$flt, + "best_hit!" => \$best_hit, + "best_hit_type:s" => \$best_hit_type, + "z_by:s" => \$z_by, + "w_hits!" => \$w_hits, + "untangling_off|tangle!" => \$untangling_off, + "revcomp_q!" => \$revcomp_q, + "revcomp_d!" => \$revcomp_d, + "reverse_qorder!" => \$reverse_qorder, + "reverse_dorder!" => \$reverse_dorder, + "reverse_qorient!" => \$reverse_qorient, + "reverse_dorient!" => \$reverse_dorient, + "hide_orient_lights!" => \$hide_orient_lights, + "ribocolours2allow:s" => \$ribocolours2allow, + "annotation:s" => \$annotation, + "score2colour:s" => \$score2colour, + "scoreratio2colour:s" => \$scoreratio2colour, + "abscolour!" => \$abscolour, + "maxB1:s" => \$maxB1, + "maxG2:s" => \$maxG2, + "maxO3:s" => \$maxO3, + #"maxR4:s" => \$maxR4, + "annocolour|annotate_by:s" => \$annocolour, + "invertcolour!" => \$invertcolour, + "no_labels!" => \$no_labels, + "dirty_labels!" => \$dirty_labels, + "tblastx!" => \$tblastx, + "override!" => \$override, + "ltrphyler!" => \$ltrphyler, + "cpus:f" => \$cpus, + "mhits:f" => \$mhits, + "online!" => \$online + ); + + +############################################################# +$path2circos = '/home/czouaoui/circos/circos-0.69-3'; # path to Circos +$path2circostools = '/home/czouaoui/circos/circos-tools-0.22'; # path to Circos utilities +############################################################# +if (-e "$path2circos/bin/circos") { $path2circos_ok = 1; } else { print "(!) path to Circos not OK\n"; } +if (-e "$path2circostools/tools/orderchr/bin/orderchr") { $path2circostools_ok = 1; } else { print "(!) path to Circos tools not OK\n"; } +unless ($path2circos_ok && $path2circostools_ok) { print "(!) please edit paths in circoletto.pl and try again - exiting\n"; exit; } + +#if (`which blast2` !~ /blast2/) { print "(!) cannot find blast2 - exiting\n"; exit; } +#if (`which formatdb` !~ /formatdb/) { print "(!) cannot find formatdb - exiting\n"; exit; } +# +#if (`perl -MBio::SearchIO -e 0` ne '') { print "(!) cannot find Bio::SearchIO - exiting\n"; exit; } +#if (`perl -MBio::Seq -e 0` ne '') { print "(!) cannot find Bio::Seq - exiting\n"; exit; } + + +unless ($online) { # ... i.e. offline + + unless ((defined($query) && defined($database)) || defined($blastout)) { die $usage; } + $out_dir = defined $out_dir ? "$out_dir/" : '.'; + $dir = "dir = $out_dir"; + if ($override) { $factor = 50; + } else { $factor = 1; } + $max_sequences = 200 * $factor; + $max_ribbons = 1000 * $factor; + $max_ribbons2untangle = 100; + $max_total_length = 2000000000; $max_total_length_in_mb = 2000; + $max_his_data = 500000; + +} else { + + $out_dir = '/labs/bat/www/tools/results/circoletto/'; + $dir = 'dir = /labs/bat/www/tools/results/circoletto'; + $gep = '-1'; + if ($override) { $factor = 50; + } else { $factor = 1; } + $max_sequences = 200 * $factor; + $max_ribbons = 1000 * $factor; + $max_ribbons2untangle = 100; + $max_total_length = 2000000000; $max_total_length_in_mb = 2000; + $max_his_data = 500000; + +} + +unless (defined $max_label_len) { $max_label_len = 20; } # 20 +unless (defined $out_type) { $out_type = 'png'; } +unless (defined $e_value) { $e_value = '1e-10'; } +unless (defined $gep) { $gep = '-1'; } +unless (defined $flt) { $flt = 0; } +unless (defined $score2colour) { $score2colour = 'bit'; } +unless (defined $scoreratio2colour) { $scoreratio2colour = 'max'; } +unless (defined $abscolour) { $abscolour = 0; } +unless (defined $maxB1) { $maxB1 = 50; } +unless (defined $maxG2) { $maxG2 = 75; } +unless (defined $maxO3) { $maxO3 = 99.9999; } +unless (defined $best_hit) { $best_hit = 0; } +unless (defined $best_hit_type) { $best_hit_type = 'entry'; } +unless (defined $w_hits) { $w_hits = 0; } +unless (defined $annocolour) { $annocolour = 'scores'; } +unless (defined $invertcolour) { $invertcolour = 0; } +unless (defined $no_labels) { $no_labels = 0; } +unless (defined $dirty_labels) { $dirty_labels = 0; } +unless (defined $untangling_off) { $untangling_off = 0; } +unless (defined $revcomp_q) { $revcomp_q = 0; } +unless (defined $revcomp_d) { $revcomp_d = 0; } +unless (defined $reverse_qorder) { $reverse_qorder = 0; } +unless (defined $reverse_dorder) { $reverse_dorder = 0; } +unless (defined $reverse_qorient) { $reverse_qorient = 0; } +unless (defined $reverse_dorient) { $reverse_dorient = 0; } +unless (defined $hide_orient_lights) { $hide_orient_lights = 0; } +unless (defined $out_size) { $out_size = '1000p'; } else { $out_size .= 'p'; } +unless (defined $tblastx) { $tblastx = 0; } +unless (defined $override) { $override = 0; } +unless (defined $ltrphyler) { $ltrphyler = 0; } +unless (defined $cpus) { $cpus = 1; } +unless (defined $ribocolours2allow) { $ribocolours2allow = "(blue|green|orange|red)"; } +unless (defined $z_by) { $z_by = "score"; } +if ($ltrphyler && $tblastx) { $lc_flt = '-U T'; } else { $lc_flt = ''; } + +open STDERR, '>/dev/null'; + +#green fully opaque +#green_a1 16% transparent +#green_a2 33% transparent +#green_a3 50% transparent +#green_a4 66% transparent +#green_a5 83% transparent +%kolours = ( +'query' , 'vvlgrey', +'database', 'dgrey', +'defdom' , 'black' +); +%ribocolours = ( +'q1' , 'blue', +'q2' , 'green', +'q3' , 'orange', +'q4' , 'red' +); +%score2colour4report = ( +'bit' , 'bitscore', +'eval' , 'E-value', +'id' , '% identity' +); +%scoreratio2colour4report = ( +'max' , 'score/max', +'minmax' , '(score-min)/(max-min)' +); +$greenlight = 'lgreen'; +$redlight = 'lred'; + +$chr_order = 'chromosomes_order = '; +if ($reverse_qorient || $reverse_dorient) { $chr2rev = 'chromosomes_reverse = '; } else { $chr2rev = ''; } + +if (defined($query) && defined($database)) { + + print "(?) going through the FASTA files\n"; + + #`perl -pi -e 's/\r//g' $query` unless $online; + $flag = 0; + open (FASTA, "$query"); + while (<FASTA>) { + chomp; + if (/^>/) { + $label = (split / /, $_)[0]; +# update annotation FASTA loading when you change these + $label =~ s/^>//; + $label =~ s/[^\w\-.]/_/g unless $dirty_labels; + $label =~ s/_{1,}/./g unless $dirty_labels; + $uniq_label = substr($label,0,$max_label_len); + while (defined($uniq_labels{$uniq_label})) { + $randomer4label = int(rand(1001)); + $randomer4label = sprintf "%04s", $randomer4label; + $uniq_label = substr($label,0,$max_label_len-4) . "$randomer4label"; + } + $uniq_labels{$label} = $uniq_label; + $uniq_labels{$uniq_label} = $uniq_label; + $original_labels{$uniq_label} = $_; + $original_labels{$uniq_label} =~ s/^>//; + $label = $uniq_label; + ++$query_entries{$label}; + push(@{$ordered{query}}, $label); + $flag = 1; + } elsif (/\w/) { + s/\s//g; + $sequences{$label} .= $_; + $flag = 0; + } + } + close FASTA; + + foreach $label (keys %query_entries) { + if (length($sequences{$label}) > 20) { + $seq = Bio::Seq->new(); + if(! $seq->validate_seq($sequences{$label}) ) { + print "(!) query $label has invalid sequence - exiting\n"; exit; + } else { + $seq->seq($sequences{$label}); + ++$q_seq_types{$seq->alphabet}; + } + } + } + if (keys(%q_seq_types) == 1) { + foreach $type (keys %q_seq_types) { + $q_seq_type = $type; + } + } else { + print "(!) your query file apparently has no sequence label(s), or both nucleotide and amino acid sequences,\nor confusing/invalid characters, or too little sequence - exiting\n"; exit; + } + + if ($flag) { print "(!) your query file is incomplete (most probably) - exiting\n"; exit; + } else { + if (keys(%query_entries) == 0) { print "(!) your query file is either empty or not in right format - exiting\n"; exit; + } elsif (keys(%query_entries) > $max_sequences) { print "(!) your query file contains too many sequences (" . keys(%query_entries) . " - we allow up to $max_sequences) - exiting\n"; exit; + } else { print "(=) " . keys(%query_entries) . " entries found in query file\n"; } + } + + if ($q_seq_type eq 'dna' && $revcomp_q) { print "(?) reverse complementing query DNA sequences\n"; } + $clean = ''; + $#non_uniq_labels = -1; + foreach $label (sort keys %query_entries) { + if ($q_seq_type eq 'dna' && $revcomp_q) { $clean_seq = revcomp($sequences{$label}); + } else { $clean_seq = $sequences{$label}; } + $clean .= ">$label\n$clean_seq\n"; + + if ($query_entries{$label} > 1) { + push(@non_uniq_labels, $label); + } + } + if (scalar(@non_uniq_labels) > 0) { + print "(!) the max label length (currently $max_label_len) causes some query sequence labels\n(" . join(", ",@non_uniq_labels) . ") to be redundant... please change the first $max_label_len characters accordingly - exiting\n"; exit; + } + + if ($reverse_qorder) { + print "(?) reversing order of query ideograms\n"; + @{$ordered{query}} = reverse(@{$ordered{query}}); + } + + open (CLEAN, ">$query.clean"); + print CLEAN $clean; + close CLEAN; + + if ($query ne $database) { + + $flag = 0; + #`perl -pi -e 's/\r//g' $database` unless $online; + open (FASTA, "$database"); + while (<FASTA>) { + chomp; + if (/^>/) { + $label = (split / /, $_)[0]; + $label =~ s/^>//; + $label =~ s/[^\w\-.]/_/g unless $dirty_labels; + $label =~ s/_{1,}/./g unless $dirty_labels; + $uniq_label = substr($label,0,$max_label_len); + while (defined($uniq_labels{$uniq_label})) { + $randomer4label = int(rand(1001)); + $randomer4label = sprintf "%04s", $randomer4label; + $uniq_label = substr($label,0,$max_label_len-4) . "$randomer4label"; + } + $uniq_labels{$label} = $uniq_label; + $uniq_labels{$uniq_label} = $uniq_label; + $original_labels{$uniq_label} = $_; + $original_labels{$uniq_label} =~ s/^>//; + $label = $uniq_label; + ++$database_entries{$label}; + push(@{$ordered{database}}, $label); + $flag = 1; + } elsif (/\w/) { + s/\s//g; + unless (defined($query_entries{$label})) { + $sequences{$label} .= $_; + } + $flag = 0; + } + } + close FASTA; + + foreach $label (keys %database_entries) { + if (length($sequences{$label}) > 20) { + $seq = Bio::Seq->new(); + if(! $seq->validate_seq($sequences{$label}) ) { + print "(!) database entry $label has invalid sequence - exiting\n"; exit; + } else { + $seq->seq($sequences{$label}); + ++$d_seq_types{$seq->alphabet}; + #print $seq->alphabet . "\t$original_labels{$label}\n"; + } + } + } + if (keys(%d_seq_types) == 1) { + foreach $type (keys %d_seq_types) { + $d_seq_type = $type; + } + } else { + print "(!) your database file apparently has no sequence label(s), or both nucleotide and amino acid sequences,\nor confusing/invalid characters, or too little sequence - exiting\n"; exit; + } + + if ($flag) { print "(!) your database file is incomplete (most probably)\n"; + } else { + if (keys(%database_entries) == 0) { print "(!) your database file is either empty or not in right format - exiting\n"; exit; + } elsif (keys(%database_entries) > $max_sequences) { print "(!) your database file contains too many sequences (" . keys(%database_entries) . " - we allow up to $max_sequences) - exiting\n"; exit; + } else { print "(=) " . keys(%database_entries) . " entries found in database file\n"; } + } + + if ($d_seq_type eq 'dna' && $revcomp_d) { print "(?) reverse complementing database DNA sequences\n"; } + $clean = ''; + $#non_uniq_labels = -1; + foreach $label (sort keys %database_entries) { + if ($d_seq_type eq 'dna' && $revcomp_d) { $clean_seq = revcomp($sequences{$label}); + } else { $clean_seq = $sequences{$label}; } + $clean .= ">$label\n$clean_seq\n"; + + if ($database_entries{$label} > 1) { + push(@non_uniq_labels, $label); + } + } + if (scalar(@non_uniq_labels) > 0) { print "(!) the max label length (currently $max_label_len) causes some database sequence labels\n(" . join(", ",@non_uniq_labels) . ") to be redundant... please change the first $max_label_len characters accordingly - exiting\n"; exit; } + + if ($reverse_dorder) { + print "(?) reversing order of database ideograms\n"; + @{$ordered{database}} = reverse(@{$ordered{database}}); + } + + open (CLEAN, ">$database.clean"); + print CLEAN $clean; + close CLEAN; + + } else { + print "(?) query and database seem the same (filename and/or content), we assume you're running an all against all\n"; + $d_seq_type = $q_seq_type; + } + + if (keys(%sequences) > $max_sequences) { + print "(!) you have too many sequences in total (" . keys(%sequences) . " - we allow up to $max_sequences) - exiting\n"; exit; + } + $max_hits_per_query = sprintf "%.0f", $max_ribbons / keys(%sequences); + $lensum = 0; + foreach $label (keys %sequences){ + $lengths{$label} = length($sequences{$label}); + $lensum += length($sequences{$label}); + } + %sequences = (); + + + if ($q_seq_type eq 'dna' && $d_seq_type eq 'dna') { + $seq_type4formatdb = 'F'; + $database4formatdb2check = "$database.clean.nsq"; + if ($tblastx) { + if ($lensum > $max_total_length/200 && !$tblastx) { + print "(!) running tBLASTx with your sequences may overload our server,\neither load less data (<".($max_total_length_in_mb/200)."Mb) or tBLASTx-it-yourself and come back - exiting\n"; exit; + } elsif ($lensum > $max_total_length/500 && !$tblastx) { + print "(!) running tBLASTx with only one CPU due to your largish dataset - may take a while\n"; + $cpus = 1; + } + $program = 'tblastx'; + } else { + $program = 'blastn'; + } + } elsif ($q_seq_type eq 'protein' && $d_seq_type eq 'protein') { + $seq_type4formatdb = 'T'; + $database4formatdb2check = "$database.clean.psq"; + $program = 'blastp'; + } elsif ($q_seq_type eq 'dna' && $d_seq_type eq 'protein') { + $seq_type4formatdb = 'T'; + $database4formatdb2check = "$database.clean.psq"; + $program = 'blastx'; + } elsif ($q_seq_type eq 'protein' && $d_seq_type eq 'dna') { + $seq_type4formatdb = 'F'; + $database4formatdb2check = "$database.clean.nsq"; + $program = 'tblastn'; + } + print "(?) formatdb is running\n"; + my $formatdb = `nice formatdb -i $database.clean -p $seq_type4formatdb -l $database.clean.formatdb.log`; + $status = $? >> 8; unless ($status==0) { print "(!) there was an error running formatdb on your database - exiting\n"; exit; } + if ($flt) {$flt = 'T'; + } else { $flt = 'F'; } + $blastout = "$out_dir" . "cl$randomer.blasted"; + if ($best_hit) { + $v4blast = 1; + $b4blast = 1; + } else { + if (defined($mhits)) { + $v4blast = $mhits; + $b4blast = $mhits; + } else { + $v4blast = $max_sequences; + $b4blast = $max_sequences; + } + } + print "(?) $program is running with -F $flt -e $e_value -E $gep -v $v4blast -b $b4blast $lc_flt\n"; + my $blast = `nice blastall -p $program -i $query.clean -d $database.clean -F $flt -e $e_value -E $gep -v $v4blast -b $b4blast -a $cpus $lc_flt > $blastout`; + $status = $? >> 8; unless ($status==0) { print "(!) there was an error running $program with your files - exiting\n"; exit; } + +} + +print "(?) going through the BLAST output\n"; +#`perl -pi -e 's/\r//g' $blastout` unless $online; +$grep4queries = `grep -c '^Query=' $blastout`; +chomp $grep4queries; +unless ($grep4queries =~ /\d/ && $grep4queries > 0) { print "(!) could not find any queries, or BLAST output is in wrong format - exiting\n"; exit; } +$max_hits_per_query = sprintf "%.0f", $max_ribbons / $grep4queries; +%hsp = (); +my $in = new Bio::SearchIO(-format => 'blast', + -file => "$blastout"); +while( my $result = $in->next_result ) { + $blastout_query = $result->query_name; + $uniq_label = substr($blastout_query,0,$max_label_len); + if (defined($uniq_labels{$uniq_label})) { + $blastout_query = $uniq_labels{$uniq_label}; + } else { + $blastout_query =~ s/[^\w\-.]/_/g unless $dirty_labels; + $blastout_query =~ s/_{1,}/./g unless $dirty_labels; + $uniq_label = substr($blastout_query,0,$max_label_len); + while (defined($uniq_labels{$uniq_label})) { + $randomer4label = int(rand(1001)); + $randomer4label = sprintf "%04s", $randomer4label; + $uniq_label = substr($blastout_query,0,$max_label_len-4) . "$randomer4label"; + } + $uniq_labels{$blastout_query} = $uniq_label; + $uniq_labels{$uniq_label} = $uniq_label; + $original_labels{$blastout_query} = $result->query_name; + $blastout_query = $uniq_label; + } + if ($blastout_query =~ /\w/) { + $lengths{$blastout_query} = $result->query_length; + unless (defined($query_entries{$blastout_query})) { + push(@{$ordered{query}}, $blastout_query); + } + $query_entries{$blastout_query} = 1; + while( my $hit = $result->next_hit ) { + $blastout_hit = $hit->name; + $uniq_label = substr($blastout_hit,0,$max_label_len); + if (defined($uniq_labels{$uniq_label})) { + $blastout_hit = $uniq_labels{$uniq_label}; + } else { + $blastout_hit =~ s/[^\w\-.]/_/g unless $dirty_labels; + $blastout_hit =~ s/_{1,}/./g unless $dirty_labels; + $uniq_label = substr($blastout_hit,0,$max_label_len); + while (defined($uniq_labels{$uniq_label})) { + $randomer4label = int(rand(1001)); + $randomer4label = sprintf "%04s", $randomer4label; + $uniq_label = substr($blastout_hit,0,$max_label_len-4) . "$randomer4label"; + } + $uniq_labels{$blastout_hit} = $uniq_label; + $uniq_labels{$uniq_label} = $uniq_label; + $original_labels{$blastout_hit} = $hit->name; + $blastout_hit = $uniq_label; + } + if ($blastout_hit =~ /\w/) { + $lengths{$blastout_hit} = $hit->length; + unless (defined($database_entries{$blastout_hit})) { + push(@{$ordered{database}}, $blastout_hit); + } + $database_entries{$blastout_hit} = 1; + while( my $hithsp = $hit->next_hsp ) { + if ($blastout_query eq $blastout_hit && $hithsp->hsp_length/$lengths{$blastout_query} <= 0.5 ) { $go = 1; + } elsif ($blastout_query ne $blastout_hit) { $go = 1; + } else { $go = 0; } + if ($go) { + if ($score2colour eq 'eval') { + if ($hithsp->evalue == 0) { + $score = 181; + } else { + $conv2e = sprintf "%.0e", $hithsp->evalue; + @split = split("e-", $conv2e); + $score = "$split[1].$split[0]"; + } + } elsif ($score2colour eq 'bit') { $score = $hithsp->bits; + } elsif ($score2colour eq 'id') { $score = $hithsp->percent_identity; + } else { $score = $hithsp->bits; } + $qstart = $hithsp->start('query'); + $qend = $hithsp->end('query'); + #$qstrand = $hithsp->strand('query'); + $hstrand = $hithsp->strand('hit'); + if ($hstrand == 0 || $hstrand == 1) { + $hstart = $hithsp->start('hit'); + $hend = $hithsp->end('hit'); + } elsif ($hstrand == -1) { + $hend = $hithsp->start('hit'); + $hstart = $hithsp->end('hit'); + } + $mem{all}{$blastout_query}{$score}{$blastout_hit}{"$qstart $qend"}{"$hstart $hend"} = $hithsp->hsp_length; + $entries_per_set{all}{$blastout_query} = 1; + $entries_per_set{all}{$blastout_hit} = 1; + $alnlens{all}{$hithsp->hsp_length} = 1; + $scores{all}{$score} += $hithsp->hsp_length; + ++$hsp{all}; + ++$hsp_per_query{$blastout_query}; + if ($hsp_per_query{$blastout_query} <= $max_hits_per_query) { + $mem{max}{$blastout_query}{$score}{$blastout_hit}{"$qstart $qend"}{"$hstart $hend"} = $hithsp->hsp_length; + $entries_per_set{max}{$blastout_query} = 1; + $entries_per_set{max}{$blastout_hit} = 1; + $alnlens{max}{$hithsp->hsp_length} = 1; + $scores{max}{$score} += $hithsp->hsp_length; + ++$hsp{max}; + } + } + } + } + } + } +} +unless (defined($query) && defined($database)) { + if (keys(%query_entries) == 0) { print "(!) could not find any queries, or BLAST output is in wrong format - exiting\n"; exit; + } elsif (keys(%query_entries) > $max_sequences) { print "(!) there are too many queries (" . keys(%query_entries) . " - we allow up to $max_sequences) - exiting\n"; exit; + } else { print "(=) " . keys(%query_entries) . " queries found\n"; } + + if (keys(%database_entries) == 0) { print "(!) could not find any database entries, or BLAST output is in wrong format - exiting\n"; exit; + } elsif (keys(%database_entries) > $max_sequences) { print "(!) there are too many database entries (" . keys(%database_entries) . " - we allow up to $max_sequences) - exiting\n"; exit; + } else { print "(=) " . keys(%database_entries) . " database entries found\n"; } + + if (keys(%lengths) > $max_sequences) { print "(!) you have too many entries in total (" . keys(%lengths) . " - we allow up to $max_sequences) - exiting\n"; exit; } + + if ($reverse_qorder) { + print "(?) reversing order of query ideograms\n"; + @{$ordered{query}} = reverse(@{$ordered{query}}); + } + if ($reverse_dorder) { + print "(?) reversing order of database ideograms\n"; + @{$ordered{database}} = reverse(@{$ordered{database}}); + } +} + +if ($hsp{all} == 0) { + print "(!) no hits found so maybe you can try different datasets or a more relaxed E-value - exiting\n"; exit; +} elsif ($hsp{all} > $max_ribbons) { + print "(!) $hsp{all} local alignments are too many (we allow up to $max_ribbons for clarity),\n\tso please consider stricter E-value or smaller input datasets\n"; + print "(?) in the meantime, we are switching to $max_hits_per_query hits per query\n"; + if ($hsp{max} > $max_ribbons) { + print "(!) $hsp{max} local alignments are still too many (we allow up to $max_ribbons) - exiting\n"; exit; + } else { + $set2consider = 'max'; + } +} else { + $set2consider = 'all'; +} + +$lensum2show = 0; +foreach $label (keys %{$entries_per_set{$set2consider}}) { $lensum2show += $lengths{$label}; } +if ($lensum2show > $max_total_length) { print "(!) the total length of your sequences to show is more than $max_total_length_in_mb megabases (currently $lensum2show bp) - exiting\n"; exit; } +$orient_light_width = int($lensum2show * 0.004); + +if (defined($annotation)) { + print "(?) loading annotation\n"; + open (ANNOTATION, "$annotation"); + while (<ANNOTATION>) { + if (!/^\#/ && /\w/) { + chomp; + @tabs = (split /\s+/); + $label = shift(@tabs); + $label = (split / /, $_)[0]; +# always update from above + $label =~ s/^>//; + $label =~ s/[^\w\-.]/_/g unless $dirty_labels; + $label =~ s/_{1,}/./g unless $dirty_labels; + if (defined($uniq_labels{$label})) { + $label = $uniq_labels{$label}; + } else { + $label = substr($label,0,$max_label_len); + } + if (defined($lengths{$label})) { + $kolour = shift(@tabs); + if ($kolour ne '-') { + $annotations{$label}{ideo_colour} = $kolour; + } + foreach $tab (@tabs) { + if ($tab =~ /:/) { + $domcol = (split /:/, $tab)[1]; + $tab = (split /:/, $tab)[0]; + } else { + $domcol = $kolours{'defdom'}; + } + $domfrom = (split /-/, $tab)[0]; + if ($domfrom < 0) { + $domfrom = 0; + } + $domto = (split /-/, $tab)[1]; + if ($domto > $lengths{$label}) { + $domto = $lengths{$label}; + } + if ($domfrom < $domto) { + $annotations{$label}{domains}{$domfrom}{to} = $domto; + $annotations{$label}{domains}{$domfrom}{col} = $domcol; + } + } + } + } + } + close ANNOTATION; + if (keys(%annotations) > 0) { print "(=) annotation loaded for " . keys(%annotations) . " entries\n"; + } else { print "(!) no annotation loaded although you provided a file, please check\n"; } +} + +print "(?) creating ribbons from $hsp{$set2consider} local alignments\n"; +if ($annocolour ne 'scores' && $invertcolour) { print "(!) cannot colour ribbons by both invertion and ideogram/domain/rainbow colours - exiting\n"; exit; +} elsif ($annocolour eq 'query') { print "(?) colouring ribbons by query ideogram/domain colours and $score2colour4report{$score2colour}\n"; +} elsif ($annocolour =~ /query_rainbow/) { print "(?) colouring ribbons by query rainbow colours and $score2colour4report{$score2colour}\n"; +} elsif ($annocolour eq 'database') { print "(?) colouring ribbons by database ideogram/domain colours and $score2colour4report{$score2colour}\n"; +} elsif ($annocolour =~ /database_rainbow/) { print "(?) colouring ribbons by database rainbow colours and $score2colour4report{$score2colour}\n"; +} elsif ($invertcolour) { print "(?) colouring ribbons by invertion and $score2colour4report{$score2colour}\n"; +} else { print "(?) colouring ribbons by $score2colour4report{$score2colour}\n"; } +if ($z_by eq 'score') { print "(?) depth-ordering ribbons by score, highest-scoring at the top\n"; +} elsif ($z_by eq 'score_rev') { print "(?) depth-ordering ribbons by reverse score, lowest-scoring at the top\n"; +} elsif ($z_by eq 'alnlen') { print "(?) depth-ordering ribbons by alignment length, longest at the top\n"; +} else { print "(?) depth-ordering ribbons by reverse alignment length, shortest at the top\n"; } +if ($abscolour && $score2colour ne 'id') { print "(!) absolute colouring currently only allowed with % identity - disabling\n"; $abscolour = 0; } +if ($abscolour) { print "(?) using absolute colouring with blue<=$maxB1, green<=$maxG2, orange<=$maxO3, red>$maxO3\n"; +} else { print "(?) using '$scoreratio2colour4report{$scoreratio2colour}' ratio colouring with blue<=0.25, green<=0.50, orange<=0.75, red>0.75\n"; } + +foreach $entry (sort {$b<=>$a} keys %{$alnlens{$set2consider}}) { $maxalnlen = $entry; last; } +foreach $score (sort {$b<=>$a} keys %{$scores{$set2consider}}) { $maxscore = $score; last; } +foreach $score (sort {$a<=>$b} keys %{$scores{$set2consider}}) { $minscore = $score; last; } +print "(=) min and max $score2colour4report{$score2colour}: ".(sprintf "%.2f", $minscore)." and ".(sprintf "%.2f", $maxscore)."\n"; + +$cold = 0; $warm = 0; $hot = 0; +foreach $score (keys %{$scores{$set2consider}}) { + if ($abscolour && $score2colour eq 'id') { + if ( $score <= $maxB1) { $cold += $scores{$set2consider}{$score}; + } else { + if ( $score > $maxO3) { $hot += $scores{$set2consider}{$score}; } + $warm += $scores{$set2consider}{$score}; } + } else { + if ($scoreratio2colour eq 'minmax') { + $scoreratio = ($score-$minscore) / ($maxscore-$minscore); + } else { $scoreratio = $score / $maxscore; } # max + if ( $scoreratio <= 0.5) { $cold += $scores{$set2consider}{$score}; + } else { + if ( $scoreratio > 0.75) { $hot += $scores{$set2consider}{$score}; } + $warm += $scores{$set2consider}{$score}; } + } +} + +$hiscolours2allow = "(blue|green|orange|red)"; print "(?) checking histogram data\n"; +if ($cold > $max_his_data) { + if ($warm > $max_his_data) { + if ($hot > $max_his_data) { print "(!) too much histogram data - disabling\n"; $hiscolours2allow = 'black'; + } else { print "(!) too much histogram data, will only consider red ribbons\n"; $hiscolours2allow = 'red'; } + } else { print "(!) too much histogram data, will only consider 'warm' ribbons\n"; $hiscolours2allow = '(orange|red)'; } +} +unless ($ribocolours2allow eq "(blue|green|orange|red)") { print "(?) showing only $ribocolours2allow ribbons, histograms are not affected\n"; } + +open (LINKS, ">$blastout.links") || die "Cannot create $blastout.links"; +$uid = 0; +foreach $query (keys %{$mem{$set2consider}}) { + $entries_w_hits{$query} = 1; + $per_query = 0; + %best_hit_entries = (); + foreach $score (sort {$b<=>$a} keys %{$mem{$set2consider}{$query}}) { + if ($abscolour && $score2colour eq 'id') { + if ( $score <= $maxB1) { $colour = $ribocolours{q1}; + } elsif ($score > $maxB1 && $score <= $maxG2) { $colour = $ribocolours{q2}; + } elsif ($score > $maxG2 && $score <= $maxO3) { $colour = $ribocolours{q3}; + } else { $colour = $ribocolours{q4}; } + } else { + if ($scoreratio2colour eq 'minmax') { + $scoreratio = ($score-$minscore) / ($maxscore-$minscore); + } else { $scoreratio = $score / $maxscore; } # max + if ( $scoreratio <= 0.25) { $colour = $ribocolours{q1}; + } elsif ($scoreratio > 0.25 && $scoreratio <= 0.5 ) { $colour = $ribocolours{q2}; + } elsif ($scoreratio > 0.5 && $scoreratio <= 0.75) { $colour = $ribocolours{q3}; + } else { $colour = $ribocolours{q4}; } + } + $best_colour = $out_type eq 'png' ? $colour . "_a1" : "black_a1"; + foreach $database (keys %{$mem{$set2consider}{$query}{$score}}) { + if (($best_hit && $best_hit_type eq 'entry' && defined($best_hit_entries{$database})) || keys(%best_hit_entries)==0 || !$best_hit) { + $best_hit_entries{$database} = 1; + $entries_w_hits{$database} = 1; + foreach $qaln (keys %{$mem{$set2consider}{$query}{$score}{$database}}) { + $a_from = (split / /, $qaln)[0]; + $a_to = (split / /, $qaln)[1]; + if ($per_query == 0) { # i.e. best score + if ($annocolour ne 'scores' || $invertcolour) { $stroker = ",stroke_color=$colour"."_a1".",stroke_thickness=2"; + } else { $stroker = ",stroke_color=$best_colour,stroke_thickness=2"; } + } else { + if ($annocolour ne 'scores' || $invertcolour) { $stroker = ",stroke_color=$colour"."_a2".",stroke_thickness=1"; + } else { $stroker = ""; } + } + foreach $daln (keys %{$mem{$set2consider}{$query}{$score}{$database}{$qaln}}) { + $b_from = (split / /, $daln)[0]; + $b_to = (split / /, $daln)[1]; + if ($z_by =~ /score/) { + if ($z_by eq 'score') { $z = $score; + } else { $z = $maxscore - $score; } + } else { + if ($z_by eq 'alnlen') { $z = $mem{$set2consider}{$query}{$score}{$database}{$qaln}{$daln}; + } else { $z = $maxalnlen - $mem{$set2consider}{$query}{$score}{$database}{$qaln}{$daln}; } + } + use bignum; + $z = $z + 0; + no bignum; + $ribocolour = $colour . "_a3"; + if ($annocolour =~ /query/) { + if (defined($annotations{$query}{ideo_colour})) { $ribocolour = $annotations{$query}{ideo_colour} . "_a3"; + } else { $ribocolour = $kolours{query} . "_a3"; } + foreach $dom_from (sort {$a<=>$b} keys %{$annotations{$query}{domains}}) { + $buffer = (abs($dom_from - $annotations{$query}{domains}{$dom_from}{to}) + 1) * 0.25; + if ($b_from >= ($dom_from - $buffer) && $b_to > $dom_from && $b_from < $annotations{$query}{domains}{$dom_from}{to} && $b_to <= ($annotations{$query}{domains}{$dom_from}{to} + $buffer)) { + $ribocolour = $annotations{$query}{domains}{$dom_from}{col} . "_a3"; + last; + } + } + } elsif ($annocolour =~ /database/) { + if (defined($annotations{$database}{ideo_colour})) { $ribocolour = $annotations{$database}{ideo_colour} . "_a3"; + } else { $ribocolour = $kolours{database} . "_a3"; } + foreach $dom_from (sort {$a<=>$b} keys %{$annotations{$database}{domains}}) { + $buffer = (abs($dom_from - $annotations{$database}{domains}{$dom_from}{to}) + 1) * 0.25; + if ($b_from >= ($dom_from - $buffer) && $b_to > $dom_from && $b_from < $annotations{$database}{domains}{$dom_from}{to} && $b_to <= ($annotations{$database}{domains}{$dom_from}{to} + $buffer)) { + $ribocolour = $annotations{$database}{domains}{$dom_from}{col} . "_a3"; + last; + } + } + } + if ($colour =~ /$hiscolours2allow/) { + if ($a_from > $a_to) { for ($i=$a_to;$i<=$a_from;$i++) { ++$histogram{$query}{$i}{$colour}; } + } else { for ($i=$a_from;$i<=$a_to;$i++) { ++$histogram{$query}{$i}{$colour}; }} + } + if ($b_from > $b_to) { + $inverter = ',twist=1'; + if ($invertcolour) { $ribocolour = 'lime_a3'; } + $dblink = "$database $b_to $b_from"; + if ($colour =~ /$hiscolours2allow/) { for ($i=$b_to;$i<=$b_from;$i++) { ++$histogram{$database}{$i}{$colour}; }} + } else { + $inverter = ',flat=1'; + if ($invertcolour) { $ribocolour = 'black_a3'; } + $dblink = "$database $b_from $b_to"; + if ($colour =~ /$hiscolours2allow/) { for ($i=$b_from;$i<=$b_to;$i++) { ++$histogram{$database}{$i}{$colour}; }} + } + if ($ribocolour =~ /$ribocolours2allow/ || $stroker =~ /$ribocolours2allow/) { + print LINKS "$query $qaln $dblink color=$ribocolour,z=$z,radius=0.98r$stroker$inverter\n"; + ++$uid; + } + ++$per_query; + } + } + } + } + if ($best_hit && $best_hit_type eq 'local') { last; } + } +} +close LINKS; +%mem = (); + +if ($hide_orient_lights) { print "(?) hiding orientation lights\n"; } + +if ($reverse_qorient) { print "(?) reversing orientation of query ideograms\n"; } +open (KARYOTYPE, ">$blastout.karyotype") || die "Cannot create $blastout.karyotype"; +foreach $entry (@{$ordered{query}}) { + if (($w_hits && defined($entries_w_hits{$entry})) || !$w_hits) { + if (defined($lengths{$entry}) && $lengths{$entry} > 0 && $entry =~ /\w/) { + $chr_order .= "$entry,"; + if (defined($annotations{$entry}{ideo_colour})) { print KARYOTYPE "chr - $entry $entry 0 $lengths{$entry} $annotations{$entry}{ideo_colour}\n"; + } else { print KARYOTYPE "chr - $entry $entry 0 $lengths{$entry} $kolours{query}\n"; } + $ultimately_shown{$entry} = 1; + if (defined($annotations{$entry}{domains})) { + $domid = 1; + foreach $from (sort {$a<=>$b} keys %{$annotations{$entry}{domains}}) { + print KARYOTYPE "band $entry dom$domid dom$domid $from $annotations{$entry}{domains}{$from}{to} $annotations{$entry}{domains}{$from}{col}\n"; + ++$domid; + } + } + if ($reverse_qorient) { $chr2rev .= "$entry,"; } + unless ($hide_orient_lights) { + if ($orient_light_width >= $lengths{$entry}/2 || $orient_light_width == 0) { $orient_light_width2use = int($lengths{$entry}/2); + } else { $orient_light_width2use = $orient_light_width; } + print KARYOTYPE "band $entry beg beg 0 $orient_light_width2use $greenlight\n"; + print KARYOTYPE "band $entry end end ".($lengths{$entry}-$orient_light_width2use)." $lengths{$entry} $redlight\n"; + } + } else {print "(!) a query entry has been problematic - ignoring\n"; } + } +} + +if ($reverse_dorient) { print "(?) reversing orientation of database ideograms\n"; } +$chr_radius = 'chromosomes_radius = '; #hs1:0.8r;a:0.9r;d:0.8r +foreach $entry (@{$ordered{database}}) { + if (($w_hits && defined($entries_w_hits{$entry})) || !$w_hits) { + if (defined($lengths{$entry}) && $lengths{$entry} > 0 && $entry =~ /\w/) { + unless (defined($query_entries{$entry})) { + $chr_order .= "$entry,"; + $chr_radius .= "$entry:0.92r;"; + if (defined($annotations{$entry}{ideo_colour})) { print KARYOTYPE "chr - $entry $entry 0 $lengths{$entry} $annotations{$entry}{ideo_colour}\n"; + } else { print KARYOTYPE "chr - $entry $entry 0 $lengths{$entry} $kolours{database}\n"; } + $ultimately_shown{$entry} = 1; + if (defined($annotations{$entry}{domains})) { + $domid = 1; + foreach $from (sort {$a<=>$b} keys %{$annotations{$entry}{domains}}) { + print KARYOTYPE "band $entry dom$domid dom$domid $from $annotations{$entry}{domains}{$from}{to} $annotations{$entry}{domains}{$from}{col}\n"; + ++$domid; + } + } + if ($reverse_dorient) { $chr2rev .= "$entry,"; } + unless ($hide_orient_lights) { + if ($orient_light_width >= $lengths{$entry}/2 || $orient_light_width == 0) { $orient_light_width2use = int($lengths{$entry}/2); + } else { $orient_light_width2use = $orient_light_width; } + print KARYOTYPE "band $entry beg beg 0 $orient_light_width2use $greenlight\n"; + print KARYOTYPE "band $entry end end ".($lengths{$entry}-$orient_light_width2use)." $lengths{$entry} $redlight\n"; + } + } + } else { print "(!) a database entry has been problematic - ignoring\n"; } + } +} +chop $chr_order; +chop $chr_radius; +chop $chr2rev; +close KARYOTYPE; + +if ($w_hits) { + $chr = 'chromosomes = '; + print "(?) only " . keys(%entries_w_hits) . " entries with hits will be shown\n"; + foreach $entry (sort keys %entries_w_hits) { $chr .= "$entry;"; } chop $chr; +} else { $chr = 'chromosomes_display_default = yes'; } + +if ($best_hit) { + if ($best_hit_type eq 'entry') { print "(?) only $uid best local alignments will be shown (= all local alignments of each best hit)\n"; + } else { print "(?) only $uid best local alignments will be shown (= single best local alignment for each best hit)\n"; } +} + +open (ORILABELS, ">$blastout.original_labels") || die "Cannot create $blastout.original_labels"; +$orilabels = ''; +foreach $label (sort keys %original_labels) { + if (defined($ultimately_shown{$label})) { + if ($original_labels{$label} ne $label) { $orilabels .= "$original_labels{$label}\t$label\n"; } + } +} +if ($orilabels =~ /\w/) { print ORILABELS "# original and Circoletto, tab-delimited (which might not be apparent if original label has whitespace)\n$orilabels"; } +close ORILABELS; + +print "(?) creating histogram\n" if %histogram; +@sorted_colours = ( +'red', +'orange', +'green', +'blue', +); +$max4his = 0; +foreach $label (keys %histogram) { + foreach $i (keys %{$histogram{$label}}) { + $tmp = ''; + $sum = 0; + foreach $colour (@sorted_colours[0..$#sorted_colours]) { + if (!defined($histogram{$label}{$i}{$colour})) { $histogram{$label}{$i}{$colour} = 0; } + $tmp .= "$histogram{$label}{$i}{$colour}.0,"; + $sum += $histogram{$label}{$i}{$colour}; + } + chop $tmp; + if ($tmp =~ /\d/) { $hismem{$label}{$tmp}{$i} = 1; } + if ($max4his <= $sum) { $max4his = $sum; } + } +} +open (HIS, ">$blastout.his") || die "Cannot create $blastout.his"; +foreach $label (sort keys %hismem) { + foreach $numbers (keys %{$hismem{$label}}) { + $from = 'na'; + $prev = 'na'; + foreach $coord (sort {$a<=>$b} keys %{$hismem{$label}{$numbers}}) { + if ($from eq 'na') { $from = $coord; } + if ($prev ne 'na' && ($coord > ($prev + 1) || $coord < ($prev - 1))) { + print HIS "$label $from $prev $numbers\n"; + $from = $coord; + } + $prev = $coord; + } + print HIS "$label $from $prev $numbers\n"; + } +} +close HIS; +$axis_thickness = 1; +$axis_spacing = int($max4his / 4); +if ($axis_spacing == 0) { + $axis_thickness = 0; + $axis_spacing = 1000; +} + +unless ($untangling_off) { + if ($reverse_qorder || $reverse_dorder) { print "(!) you have selected to reverse ideogram order, skipping untangling the $uid ribbons\n"; + } else { + if (keys(%lengths) <= 2) { print "(!) skipping untangling the $uid ribbons for less than 3 sequences\n"; + } elsif ($uid <= $max_ribbons2untangle) { + print "(?) untangling the $uid ribbons\n"; + `nice perl $path2circostools/tools/orderchr/bin/orderchr -links $blastout.links -karyotype $blastout.karyotype > $blastout.chr_order`; + open (ORDER, "$blastout.chr_order") || die "Cannot read $blastout.chr_order"; + while (<ORDER>) { + if (/chromosomes_order/) { + chomp; + $chr_order = $_; + } + } + close ORDER; + } else { print "(!) $uid ribbons will take too long to untangle (we allow up to $max_ribbons2untangle) - skipping\n"; } + } +} else { print "(?) untangling of ribbons has been switched off\n"; } + + +if ($annocolour =~ /rainbow/) { + if ($annocolour =~ /grey/) { $rainbow_palette = 'grey'; } else { $rainbow_palette = 'colour'; } + if ($annocolour =~ /query/) { $rainbow_on = 'query'; } else { $rainbow_on = 'database'; } + print "(?) drawing a $rainbow_palette rainbow based on the $rainbow_on\n"; + $rainbow_length = 0; + @split_chr = (split /,/, (split / = /,$chr_order)[1]); + foreach $chr (@split_chr) { + if ($rainbow_on eq 'query' && $query_entries{$chr} || $rainbow_on eq 'database' && $database_entries{$chr}) { + $rainbow_transl{$chr} += $rainbow_length; + $rainbow_length += $lengths{$chr}; + } + } + open (LINKS, "$blastout.links") || die "Cannot read $blastout.links"; + while (<LINKS>) { + chomp; + @split_link = (split /\s/); + if ( $rainbow_on eq 'query' && $query_entries{$split_link[0]}) { $rainbow_colour = ceil( (($rainbow_transl{$split_link[0]} + ($split_link[1]+$split_link[2])/2) / $rainbow_length) / (1/7) ); + } elsif ($rainbow_on eq 'database' && $database_entries{$split_link[3]}) { $rainbow_colour = ceil( (($rainbow_transl{$split_link[3]} + ($split_link[4]+$split_link[5])/2) / $rainbow_length) / (1/7) ); } + $rainbow_colour = "$rainbow_palette-rainbow-".$rainbow_colour.'_a2'; + s/color=[^,]+,/color=$rainbow_colour,/; + $rainbow_links .= "$_\n"; + } + close LINKS; + open (LINKS, ">$blastout.links") || die "Cannot create $blastout.links"; + print LINKS $rainbow_links; + close LINKS; +} + +if ($no_labels) { + print "(?) labels have been switched off\n"; + $show_label = "no"; +} else { + $show_label = "yes"; + $label_size = 11; + if ( $out_size eq '500p') { $label_size += -1; + } elsif ( $out_size eq '1000p') { $label_size += 1; + } elsif ( $out_size eq '2000p') { $label_size += 2; } + if ($out_type eq 'svg') { $label_size += 1; } + $label_size .= 'p'; +} + +@blastreport2split = (split '/',$blastout); +#$cleanblastreport = pop(@blastreport2split); +$out_name = defined $out_name ? $out_name : pop(@blastreport2split); +$record_limit = $max_ribbons * 2; +open (CONF, ">$blastout.conf") || die "Cannot create $blastout.conf"; +print CONF " +<<include etc/housekeeping.conf>> +<<include etc/colors_fonts_patterns.conf>> + +<colors> +red = 247, 42, 66 +green = 51, 204, 94 +blue = 54, 116, 217 +orange = 255, 136, 0 +lime = 186, 255, 0 + +#colour-rainbow-1 = 248, 12, 18 +#colour-rainbow-2 = 238, 17, 0 +#colour-rainbow-3 = 255, 51, 17 +#colour-rainbow-4 = 255, 68, 34 +#colour-rainbow-5 = 255, 102, 68 +#colour-rainbow-6 = 255, 153, 51 +#colour-rainbow-7 = 254, 174, 45 +#colour-rainbow-8 = 204, 187, 51 +#colour-rainbow-9 = 208, 195, 16 +#colour-rainbow-10 = 170, 204, 34 +#colour-rainbow-11 = 105, 208, 37 +#colour-rainbow-12 = 34, 204, 170 +#colour-rainbow-13 = 18, 189, 185 +#colour-rainbow-14 = 17, 170, 187 +#colour-rainbow-15 = 68, 68, 221 +#colour-rainbow-16 = 51, 17, 187 +#colour-rainbow-17 = 59, 12, 189 +#colour-rainbow-18 = 68, 34, 153 + +# Red web color Hex#FF0000 +# Orange color wheel Orange Hex#FF7F00 +# Yellow web color Hex#FFFF00 +# Green X11 Electric Green HTML/CSS “Lime” Color wheel green Hex#00FF00 +# Blue web color Hex#0000FF +# Indigo Electric Indigo Hex#4B0082 +# Violet Electric Violet Hex#8B00FF +colour-rainbow-1 = 255, 0, 0 +colour-rainbow-2 = 255, 127, 0 +colour-rainbow-3 = 255, 255, 0 +colour-rainbow-4 = 0, 255, 0 +colour-rainbow-5 = 0, 0, 255 +colour-rainbow-6 = 75, 0, 130 +colour-rainbow-7 = 143, 0, 255 + +grey-rainbow-1 = 230, 230, 230 +grey-rainbow-2 = 200, 200, 200 +grey-rainbow-3 = 170, 170, 170 +grey-rainbow-4 = 140, 140, 140 +grey-rainbow-5 = 110, 110, 110 +grey-rainbow-6 = 80, 80, 80 +grey-rainbow-7 = 50, 50, 50 +</colors> + +<ideogram> +<spacing> +default = 0.006r +break = 10u +axis_break_at_edge = no +axis_break = no +axis_break_style = 1 +</spacing> +thickness = 12p +stroke_thickness = 1 +stroke_color = black +fill = yes +fill_color = lgrey +radius = 0.66r +show_label = $show_label +label_with_tag = yes +label_font = condensed +label_color = grey +label_radius = dims(ideogram,radius) + 0.104r +label_size = $label_size +band_stroke_thickness = 0 +show_bands = yes +fill_bands = yes +</ideogram> + +show_ticks = yes +show_tick_labels = no +<ticks> +radius = dims(ideogram,radius_outer) +multiplier = 1e-6 +<tick> +spacing = 100u +rspacing = 0.1 +spacing_type = relative +size = 5p +thickness = 1p +color = vvvvdgrey +show_label = no +label_size = 10p +label_offset = 5p +format = %d +</tick> +</ticks> + +karyotype = $blastout.karyotype + +<image> +$dir +file = $out_name.$out_type +radius = $out_size +background = white +angle_offset = -90 +24bit = yes +auto_alpha_colors = yes +auto_alpha_steps = 5 +</image> + +chromosomes_units = 1 +$chr +$chr_order +$chr_radius +$chr2rev + +<links> +ribbon = yes +<link> +show = yes +file = $blastout.links +record_limit = $record_limit +</link> +</links> + +<plots> +<plot> +type = histogram +file = $blastout.his +extend_bin = no +color = white +fill_color = red,orange,green,blue +fill_under = yes +thickness = 0,0,0,0 +min = 0 +r0 = 1.015r +r1 = 1.092r +<axes> +<axis> +color = lgrey +thickness = $axis_thickness +spacing = $axis_spacing +</axis> +</axes> +</plot> +</plots> +"; +close CONF; + +print "(?) running Circos\n"; +`nice perl $path2circos/bin/circos -noparanoid -conf $blastout.conf > $blastout.circos.log`; +sleep(1) if $online; +if (-e "$blastout.$out_type") { print "(=) done: $blastout.$out_type $blastout\n"; +} else { print "(!) there was an error running Circos (no output detected), maybe try once more or something different? - exiting\n"; exit; } + + +sub revcomp { + my $seq = reverse $_[0]; + $seq =~ tr/ACGTacgt/TGCAtgca/; + return $seq; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circoletto.xml Tue Mar 13 05:06:56 2018 -0400 @@ -0,0 +1,110 @@ +<tool id="circoletto" name="Circoletto" version="0.1.0"> + <requirements> + <requirement type="package" version="0.69.5">circos</requirement> + <requirement type="package" version="1.6.924">perl-bioperl</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + perl $__tool_directory__/circoletto.pl -bl $input --out_name circoletto + #if $settings.advanced == "advanced" + #if $settings.link_colors_by.select_link_colors_by == "score" + --score2colour bit + #end if + #if $settings.link_colors_by.select_link_colors_by == "eval" + --score2colour eval + #end if + #if $settings.link_colors_by.select_link_colors_by == "identite" + --score2colour id + #end if + #if $settings.best_hit.select_best_hit == "yes" + --best_hit + #end if + #if $settings.query_order.select_query_order == "invert" + --reverse_qorder + #end if + #if $settings.db_order.select_db_order == "invert" + --reverse_dorder + #end if + #if $settings.color_range.select_color_range == "min" + --scoreratio2colour max + #end if + #if $settings.color_range.select_color_range == "sup" + --scoreratio2colour minmax + #end if + #if $settings.select_links_allowed.value + #set links_allowed = '(' + '|'.join( [ str( $link_type ) for $link_type in $settings.select_links_allowed.value ] ) + ')' + --ribocolours2allow "${links_allowed}" + #end if + #end if + ]]></command> + <inputs> + <param type="data" name="input" label="Résultat BLAST"/> + <conditional name="settings"> + <param name="advanced" type="select" label="Paramètres avancés"> + <option value="simple" selected="true">Non, utiliser les paramètres par défaut.</option> + <option value="advanced">Oui, voir la liste des paramètres.</option> + </param> + <when value="simple"> + </when> + <when value="advanced"> + <conditional name="link_colors_by"> + <param name="select_link_colors_by" type="select" label="Coloration des alignements en fonction"> + <option value="score" selected="true">Du bit score</option> + <option value="eval">De l'e-value</option> + <option value="identite">Du % d'identité</option> + </param> + </conditional> + <param name="select_links_allowed" type="select" label="Séléction des alignements à afficher" multiple="true"> + <option value="blue" selected="true">Bleu (0 - 25%)</option> + <option value="green" selected="true">Vert (25 - 50%)</option> + <option value="orange" selected="true">Orange (50 - 75%)</option> + <option value="red" selected="true">Rouge (75 - 100%)</option> + </param> + <conditional name="best_hit"> + <param name="select_best_hit" type="select" label="Afficher seulement le meilleur alignement pour chaque séquence interrogée"> + <option value="no" selected="true">Non</option> + <option value="yes">Oui</option> + </param> + </conditional> + <conditional name="query_order"> + <param name="select_query_order" type="select" label="Ordre des séquences interrogées"> + <option value="default" selected="true">Par défaut</option> + <option value="invert">Inversé</option> + </param> + </conditional> + <conditional name="db_order"> + <param name="select_db_order" type="select" label="Ordre des séquences de références"> + <option value="default" selected="true">Par défaut</option> + <option value="invert">Inversé</option> + </param> + </conditional> + <conditional name="color_range"> + <param name="select_color_range" type="select" label="Gamme de couleurs"> + <option value="min" selected="true">Par défaut</option> + <option value="sup">Supérieure</option> + </param> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name= "output" format="png" label="${tool.name} - ${input.name}" from_work_dir="circoletto.png"/> + </outputs> + <tests> + <test> + <param name="input" value="blast_170144"/> + <output name="output" file="circoletto.png"/> + </test> + </tests> + <help><![CDATA[ + Cet outil utilise un fichier comportant un résultat de BLAST afin de visualiser, via Circos, les similarités entre les séquences interrogées et les séquences de références. + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubseqtk, + title = {Circoletto}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/infspiredBAT/Circoletto}, +}</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast_170144 Tue Mar 13 05:06:56 2018 -0400 @@ -0,0 +1,6962 @@ +BLASTN 2.5.0+ + + +Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb +Miller (2000), "A greedy algorithm for aligning DNA sequences", J +Comput Biol 2000; 7(1-2):203-14. + + + +Database: ref_vbmd_A-Sw-France-53-170144-17ech4_1714ESIV_061.fa + 8 sequences; 13,423 total letters + + + +Query= 170144-17ech4_c1 + +Length=2541 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 3663 0.0 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 3663 bits (1983), Expect = 0.0 + Identities = 2222/2341 (95%), Gaps = 1/2341 (0%) + Strand=Plus/Minus + +Query 55 AGTAGAAACAAGGCATTTTTTCATGAAGGACAAGCTAAACTCACTATTTTTGCCGTCTGA 114 + ||||||||||||||||||||||||||||||||||||||| |||||| ||||||||||||| +Sbjct 2341 AGTAGAAACAAGGCATTTTTTCATGAAGGACAAGCTAAATTCACTACTTTTGCCGTCTGA 2282 + +Query 115 ACTCTTCAATGGTGGAACAGATCTTCATGATCTCAGCAAATTCTTCTTTCTTGATCCTTC 174 + ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| +Sbjct 2281 GCTCTTCAATGGTGGAACAGATCTTCATGATCTCAGCAAATTCTTCTTTCTTAATCCTTC 2222 + +Query 175 CAGATTCGAAATCAATCCGTGCATCAATTCTGGCCCTAGATACCATGGCCTCCACCATGC 234 + |||| |||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 2221 CAGACTCGAAATCAATCCGTGCATCAATTCTGGCCCTGGATACCATGGCCTCCACCATGC 2162 + +Query 235 TTGAAATTCCAACTGGCCTTCTGTATGAACTGCTAGGAAAGAATTTCTCGAATAGATTGC 294 + | ||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||| +Sbjct 2161 TGGAAATTCCAACTGGCCTCCTGTATGAACTGCTAGGGAAGAATTTCTCGAATAGATTGC 2102 + +Query 295 AGCACTTTTGGTACATTTGTTCATCCTCAAGAATTCCCCTTTGGCTGGTATTGAGGATGG 354 + ||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||| +Sbjct 2101 AGCACTTCTGGTACATTTGTTCATCCTCAAGAATTCCCCTTTGGCTGGTATTGAGAATGG 2042 + +Query 355 AACGGTTCCTTTTTGGAATCCACGAATGTGTAGTAGCAACAGCATCATATTCCATGCTTT 414 + |||| ||||||||||||||||| ||||||||||| ||||||||||||||||||||||||| +Sbjct 2041 AACGATTCCTTTTTGGAATCCAAGAATGTGTAGTTGCAACAGCATCATATTCCATGCTTT 1982 + +Query 415 TAGCTGGACCATGGGCTGGCATCACCACGGCACTGTTTACGGACTCAATTCCCTTGTGGT 474 + |||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||| +Sbjct 1981 TAGCTGGACCATGGGCTGGCATTACCACGGCACTGTTTACGGACTCAATTCCCTTATGGT 1922 + +Query 475 TGACAAACGGATTCAGAGGATTACACAATCTCCCTCGATAATCTACATCCATCAGTTCCC 534 + ||||||||||||||||||||||||||||||| || ||||||||||||||||| || |||| +Sbjct 1921 TGACAAACGGATTCAGAGGATTACACAATCTTCCCCGATAATCTACATCCATTAGCTCCC 1862 + +Query 535 ATTTCAAGCAGACTTCAGGAATGTGGAGATTCCGGATATTATACAGATTTGGTCCTCCAT 594 + |||||||||||||||| || |||||||||||||||||||| || |||||||||||||||| +Sbjct 1861 ATTTCAAGCAGACTTCCGGGATGTGGAGATTCCGGATATTGTATAGATTTGGTCCTCCAT 1802 + +Query 595 CTGAAACCAGTAGTCCTGCCTTTGAATGGGTTTGTTCCCATAGCTTTCTTAACTCGAATG 654 + |||||||||||||||||||||||||||||||||| |||||||| ||| ||| |||||||| +Sbjct 1801 CTGAAACCAGTAGTCCTGCCTTTGAATGGGTTTGCTCCCATAGTTTTTTTAGCTCGAATG 1742 + +Query 655 ATCTTTTCGTTTGGATTTGCATGTCGCCTCTGTGGCATCGATATGTGTACCTGTAGTCCT 714 + |||||||||||||||||||| |||| |||||||||||||| ||||| ||||||||||||| +Sbjct 1741 ATCTTTTCGTTTGGATTTGCGTGTCACCTCTGTGGCATCGGTATGTATACCTGTAGTCCT 1682 + +Query 715 TAATGAATAGTTGAAGTGCCATTTGGGCTGTTGCTGGCCCGAGATCATTGTTTATCATGT 774 + |||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1681 TAATGAATAGCTGAAGAGCCATTTGGGCTGTTGCTGGCCCGAGATCATTGTTTATCATGT 1622 + +Query 775 TGTTCTTTATCACTGTCACCCCAATGCTCATGTCAGCCGATTCATTAACTCCAGATACTC 834 + ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| | +Sbjct 1621 TGTTCTTTATCACTGTCACTCCAATGCTCATGTCAGCCGATTCATTAACTCCAGATACCC 1562 + +Query 835 CAAAGCTGGGCAACTCCATGCTGAAGTTGGCTACAAACCCATATCGGTAGAAAAA-CTTG 893 + |||||||||| | |||||| ||||||||||||||||||||||| ||||||||||| |||| +Sbjct 1561 CAAAGCTGGGTAGCTCCATACTGAAGTTGGCTACAAACCCATAGCGGTAGAAAAAGCTTG 1502 + +Query 894 TGAATTCAAATGTCCCTGTCCTATTTATGTAAGATTTCTTTTTGCTCATATTGATTCCAA 953 + |||||||||| || |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1501 TGAATTCAAACGTTCCTGTCCTATTTATGTAAGATTTCTTTTTGCTCATATTGATTCCAA 1442 + +Query 954 CCAGTTTGCAGGTCCTATAGAACCTATCCACTCCTGCTTGTATTCCCTCATGATTGGGTG 1013 + |||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||| +Sbjct 1441 CCAGTTTGCAGGTCCTATAGAACCTATCCACTCCTGCTTGTATTCCTTCATGATTAGGTG 1382 + +Query 1014 CATTCACTATGAGGGCGAAGTCATCAGAGGATTGGAGTCCATCCCACCAATAGGTGGTTT 1073 + |||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||| +Sbjct 1381 CATTCACTATGAGGGCGAAGTCATCAGAAGATTGGAGTCCATCCCACCAGTAGGTGGTTT 1322 + +Query 1074 TAGTGTACTTCCTTTGCCCGAGATTCAGGATTGAGACTCCTAGAACTGTGCTCAGCATGT 1133 + |||||||| || |||||||||| ||||||||||||||||||||||||||||||||||||| +Sbjct 1321 TAGTGTACCTCTTTTGCCCGAGGTTCAGGATTGAGACTCCTAGAACTGTGCTCAGCATGT 1262 + +Query 1134 TGAACATGCCCATCATCATTCCAGGGCTTAGTGAGGCTGATCCATTTATGAGAAGTGGTC 1193 + | ||||||||||||||||||||||||||||||||||| | |||| |||||| ||||| | +Sbjct 1261 TAAACATGCCCATCATCATTCCAGGGCTTAGTGAGGCCGTGCCATCTATGAGGAGTGGCC 1202 + +Query 1194 TTATCTTCTCGATCTTTTCCCTTGTTGATTCATTGAAGTATTTCAAGTCAATATTTGCGA 1253 + |||||||||||||||||| |||||||||||||||||| |||||||||||||||| ||| | +Sbjct 1201 TTATCTTCTCGATCTTTTTCCTTGTTGATTCATTGAAATATTTCAAGTCAATATCTGCTA 1142 + +Query 1254 GCATTTCTGCTGGTATTTGTGTTCGCAGCTTCATGCTCTTACTTTCAAACATATATCCTT 1313 + ||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||||| +Sbjct 1141 GCATTTCTGCTGGTATTTGTGTTCGTAGCTTCATGCTCTTACTTTCGAACATGTATCCTT 1082 + +Query 1314 TCCCTAATCTTGCCATTTTGTTTGAGAACATTATAGGTGCAATGCTTAAAACATTTCTGA 1373 + ||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||| +Sbjct 1081 TCCCTAATCTTGCCATTTTGTTTGAGAACATTATAGGGGCGATGCTTAAAACATTTCTGA 1022 + +Query 1374 ACCATTCAGGTTGGTTTCTTGTGATGTACGTTATCATCGCCAGAAATATCCTGGGGTTTT 1433 + |||||||||| || |||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 1021 ACCATTCAGGCTGATTTCTTGTGATGTACGTTATCATCGCCAGAAACATCCTGGGGTTTT 962 + +Query 1434 GGTTCTCATTCCATTTGGTGTTGTCCCCAGTAATTGTGAATGAAAGCTCTGTATCTTGTG 1493 + | ||||||||||||||||||||||||||||||||||| || |||||||| |||||||||| +Sbjct 961 GATTCTCATTCCATTTGGTGTTGTCCCCAGTAATTGTAAAGGAAAGCTCGGTATCTTGTG 902 + +Query 1494 AGTTGGTCATCATTTTTCTCACAACATTTGCCAATTTGGCTTTCTTCTCATTCCCCCCAA 1553 + |||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 901 AGTTGGTCATCATTTTCCTCACAACATTTGCCAATTTGGCTTTCTTTTCATTCCCCCCAA 842 + +Query 1554 CTGGGAGCCCAGATTGCTCAAGTTTCTCACAGATGCTTCTTGCTAGTGTTTCTACGAAGT 1613 + ||||||||||||||||||||||||||||||||||||| || || |||||||||||||||| +Sbjct 841 CTGGGAGCCCAGATTGCTCAAGTTTCTCACAGATGCTCCTCGCCAGTGTTTCTACGAAGT 782 + +Query 1614 ACACAAATCCTCTGATTTGCATCCCTGGTGTTGCAATTGCACGTCTTTTCAACTTGCCCC 1673 + |||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| | +Sbjct 781 ACACAAATCCTCTGATCTGCATCCCTGGTGTTGCAATTGCACGCCTTTTCAACTTGCCTC 722 + +Query 1674 TTTCTGCGTCCTTTGTCATTGTGTTTAATGTTAATGCTCTTATTAGATAATTCCTCTTGT 1733 + ||||||| || |||||||||||||||||||| |||||||||||||||||| ||||||||| +Sbjct 721 TTTCTGCATCTTTTGTCATTGTGTTTAATGTCAATGCTCTTATTAGATAACTCCTCTTGT 662 + +Query 1734 CCAATTTCTGTTTTTTCTTCCCTATTGTCCTTTGTGTTACCATTTTCTTAGTCATGTTGT 1793 + || |||||| |||||||| ||||||||||||||||||||||||||||| |||||||||| +Sbjct 661 TCAGTTTCTGCTTTTTCTTTCCTATTGTCCTTTGTGTTACCATTTTCTTGGTCATGTTGT 602 + +Query 1794 CCCTTATTCTTCTTTTTCTTTGGAAATGTGTTGTTATTTCCATTTCTTCTTTATCCATTG 1853 + |||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||| +Sbjct 601 CCCTTATTCTTCTTTTCCTTTGGAAATGTGTTGTTATTTCCATCTCTTCTTTATCCATTG 542 + +Query 1854 ATTCCACCACATCCTTAAGGAAATCTATTAATCTTCCCGATTCATTGGCTGTTAGACTGT 1913 + |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 541 ATTCCATCACATCCTTAAGGAAATCTATTAATCTTCCCGATTCATTGGCTGTTAGACTGT 482 + +Query 1914 TCATTCTAAAGACTTCTATTGTGTTGGCCAAAGCAGTTGCAGCCGGTTGGTTTCTATTCA 1973 + |||| || ||||| |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 481 TCATCCTGAAGACCTCTATTGTGTTGGCCAAAGCAGTTGCAGCCGGTTGGTTTCTATTCA 422 + +Query 1974 ATGTCCAGTCATAGGTCTGACGACCTTGGGTCAGTTTGTCCACTCTTGTTTGTTGAACAA 2033 + |||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||| +Sbjct 421 ATGTCCAGTCATAGGTCTGACGACCTTGAGTCAGTTTGTCCACTCTTGTTTGTTGGACAA 362 + +Query 2034 CCTCCATTGTTTCAAGACAAGAATTTTCAAATATCCCTGGATGGGACTCCTCAAGGAAAG 2093 + ||||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||||| +Sbjct 361 CCTCCATCGTTTCAAGACAAGAGTTTTCAAATATCCCTGGATGGGATTCCTCAAGGAAAG 302 + +Query 2094 CCATTGCCTCAAGGACACAGTCTGTTTGGGCATAACCGCTTGGTTCATTGTCCTCAGGTA 2153 + |||||||||| ||||||||||||||||| ||||| |||||||| |||||||||||||||| +Sbjct 301 CCATTGCCTCCAGGACACAGTCTGTTTGAGCATACCCGCTTGGCTCATTGTCCTCAGGTA 242 + +Query 2154 GTGGTCCATCAATCGGGTTAAGCTGGGGTGCTCCAGTCTCTGTGTTTGTTGTCCATCTTC 2213 + |||| |||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 241 GTGGCCCATCAATCGGGTTAAGCTGGGGTGCTCCAGTTTCTGTGTTTGTTGTCCATCTTC 182 + +Query 2214 CTCTTTCTGAATATTGGTGTGTTCTGTTGATCGTGTCCATTGTATATCCTGTTCCTGTTC 2273 + |||||||||||||||| ||||||||||||| ||||||||| || |||||||| ||||||| +Sbjct 181 CTCTTTCTGAATATTGATGTGTTCTGTTGACCGTGTCCATGGTGTATCCTGTCCCTGTTC 122 + +Query 2274 CGTGACTATATGGGGGATCCCCTGTATAGGGGAATGTAGTGCTTATAGCATTTTGTGCTG 2333 + | ||||||||||||||||| || ||||| ||||||||||||||||||||||||||||||| +Sbjct 121 CATGACTATATGGGGGATCTCCAGTATAAGGGAATGTAGTGCTTATAGCATTTTGTGCTG 62 + +Query 2334 TCACTTTTAAGAAAAGTAGAGTCGGGTTGACATCCATTCAAATGGTTTGCCTGCTTTTGC 2393 + |||||||||||||||||||||||||||||||||||||||||| ||||||||||||| || +Sbjct 61 GCACTTTTAAGAAAAGTAGAGTCGGGTTGACATCCATTCAAATAGTTTGCCTGCTTTCGC 2 + +Query 2394 T 2394 + | +Sbjct 1 T 1 + + + Score = 141 bits (76), Expect = 9e-36 + Identities = 84/88 (95%), Gaps = 0/88 (0%) + Strand=Plus/Minus + +Query 2454 CTTCTTTCTTGATCCTTCCAGATTCGAAATCAATCCGTGCATCAATTCTGGCCCTAGATA 2513 + |||||||||| ||||||||||| |||||||||||||||||||||||||||||||| |||| +Sbjct 2239 CTTCTTTCTTAATCCTTCCAGACTCGAAATCAATCCGTGCATCAATTCTGGCCCTGGATA 2180 + +Query 2514 CCATGGCCTCCACCATGCTTGAAATTCC 2541 + ||||||||||||||||||| |||||||| +Sbjct 2179 CCATGGCCTCCACCATGCTGGAAATTCC 2152 + + + Score = 87.9 bits (47), Expect = 1e-19 + Identities = 54/57 (95%), Gaps = 1/57 (2%) + Strand=Plus/Minus + +Query 1 CATCACCACGGCACTGTTTACGGACTCAATTCCCTTGTGGTTGACAA-CGGATTCAG 56 + ||| |||||||||||||||||||||||||||||||| |||||||||| ||||||||| +Sbjct 1962 CATTACCACGGCACTGTTTACGGACTCAATTCCCTTATGGTTGACAAACGGATTCAG 1906 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 33536388 + + +Query= 170144-17ech4_c2 + +Length=1602 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 2350 0.0 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 2350 bits (1272), Expect = 0.0 + Identities = 1397/1459 (96%), Gaps = 1/1459 (0%) + Strand=Plus/Minus + +Query 1 AGTAGAAACAAGGAGTTTTTT-GAACAAATTACTTGTCAATGGTGAATGGCAACTCAGCA 59 + ||||||||||||||||||||| ||| |||||||||||||||||| ||||||||||||||| +Sbjct 1459 AGTAGAAACAAGGAGTTTTTTTGAATAAATTACTTGTCAATGGTAAATGGCAACTCAGCA 1400 + +Query 60 CCGTCTGGCCAAGACCAACCCACAATGTCACTACTAACACCACAAAAGGATATGCTGCTC 119 + |||||||||||||||||||||||| |||||||||| |||||||||||||||||||||||| +Sbjct 1399 CCGTCTGGCCAAGACCAACCCACAGTGTCACTACTTACACCACAAAAGGATATGCTGCTC 1340 + +Query 120 CCGCTAGTCCAGATTGTGTTCTCTTTGGGTCTCCCTCTGATTAGTTCAACCCAAAAACAA 179 + ||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||| +Sbjct 1339 CCGCTAGTCCAGATTGTGTTCTCTTTGGGTCTCCCTCTGATTAGTTCAACCCAGAAGCAA 1280 + +Query 180 GGTCTAATACAATCTAATCCGGTTAATTCTGGATGCTGGACAAAACTCCCACTGTATCCT 239 + |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| +Sbjct 1279 GGTCTAATACAATCTAATCCGGTTAATTCTGGATGCTGGACAAAACTCCCGCTGTATCCT 1220 + +Query 240 GTCCAGTCTGTTATTCCTACAATGTCTTGCTTTAATGAAAAATTATTGTCTGTTCCAGTC 299 + |||||||| ||||||||||| || |||||||||| ||| ||||||||||||||||||||| +Sbjct 1219 GTCCAGTCAGTTATTCCTACGATATCTTGCTTTACTGAGAAATTATTGTCTGTTCCAGTC 1160 + +Query 300 CATCCGTTTGGGTCCCAAATCATCTCAAAACCGCTCCTTGAACTAGTGCTTTTAGTTCTC 359 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1159 CATCCGTTTGGGTCCCAAATCATCTCAAAACCGCTCCTTGAACTAGTGCTTTTAGTTCTC 1100 + +Query 360 CCTATCCAAATACCATCGCCGTATTTAAATGAAAACCCTTTTACCCCATTTGCCCCATAA 419 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| | +Sbjct 1099 CCTATCCAAATACCATCGCCGTATTTAAACGAAAACCCTTTTACCCCATTTGCCCCATGA 1040 + +Query 420 GAAGATACTGGACCACAACTGCCAGTTCCATCATTAGGGCGCGGATTGTCTCCGAAGACC 479 + || |||||||||||||||||||| |||| ||||||||||||||| |||||||||| ||| +Sbjct 1039 GACGATACTGGACCACAACTGCCTGTTCTATCATTAGGGCGCGGGTTGTCTCCGAGAACC 980 + +Query 480 CCACTGCATATGTATCCTATTTGATACTCCAGATTCTGATTGAAAGACACCCATGGTCGA 539 + ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||| +Sbjct 979 CCACTGCATATGTATCCTATTTGATACTCCAGATTCTGATTAAAAGACACCCATGGTCGA 920 + +Query 540 TTCGAGCCATGCCAATTGTCCCTGCACACACATATGATTTCACCAAAATCAGGATAGCAG 599 + |||||||||||||||||||| |||||||||||||||||||||||| |||||||||| ||| +Sbjct 919 TTCGAGCCATGCCAATTGTCTCTGCACACACATATGATTTCACCAGAATCAGGATAACAG 860 + +Query 600 GAGCATTCCTCATAGTGATAATTAGGAGCATTCAACTCGACTGATTTGACTACTTTCCCC 659 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 859 GAGCATTCCTCATAGTGATAATTAGGAGCATTCAACTCAACTGATTTGACTACTTTCCCC 800 + +Query 660 CTTTCTATTTTGAAGATTCTGTACGAGGCCTGCCCATTACTTAGTCCATCGGTCATTACA 719 + ||||||||||||||||| |||| |||||||||||||||||||||||||||||||||||| +Sbjct 799 TTTTCTATTTTGAAGATTTTGTATGAGGCCTGCCCATTACTTAGTCCATCGGTCATTACA 740 + +Query 720 GTAAAGCAAGAGCCATTCAAGCATGCACATTCAGACTCTTGTGTTCTCAATATGTTGTTT 779 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 739 GTAAAGCAAGAGCCATTCAAGCATGCACATTCAGACTCTTGTGTTCTCAATATGTTGTTT 680 + +Query 780 TTCCAACTCTTGATGGTATCTGTTATTATGTCGTTGTATTTCAGCACAGCCACTGCTCCA 839 + |||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||| +Sbjct 679 TTCCAACTCTTGATAGTGTCTGTTATTATGTCATTGTATTTCAGCACAGCCACTGCTCCA 620 + +Query 840 TTATCTGGGCCAGAAATTCCAATTGTCAACCAACTAGTGCCGTCATGGCAAGCACTTGCT 899 + || |||||||||||||||||||||||||||||||| | |||||||||||||||||||||| +Sbjct 619 TTGTCTGGGCCAGAAATTCCAATTGTCAACCAACTGGAGCCGTCATGGCAAGCACTTGCT 560 + +Query 900 GACCAAGCAACTGACTCAAATCTTGAATTGTATGGAGAAGGGACTTCACCAATAGGACAG 959 + |||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||| +Sbjct 559 GACCAAGCAACTGACTCAAATCTTGAGTTGTATGGAGAGGGGACTTCACCAATAGGACAA 500 + +Query 960 CTCATCAGGGTTCGATAGGGGCTTCTGTCTTTAACAGTTCCATTGGAGTGTTTGTCATTC 1019 + |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||| +Sbjct 499 CTCATCAGGGTTCGATAGGGGCTTCTGTCTTTGACAGTCCCATTGGAGTGTTTGTCATTC 440 + +Query 1020 AGCAGGGCCCCTTGGGTTAAGAAGAATGTTCTACATTCCAAGTGGGAGCATGAGATGAAT 1079 + |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 439 AGCAGGGCCCCTTGAGTTAAGAAGAATGTTCTACATTCCAAGTGGGAGCATGAGATGAAT 380 + +Query 1080 GGCTCTCTTATAACAAACACATCCCCTTTGGAACCGATTCTTACACTGTTATCTTTACTG 1139 + ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 379 GGCTCTCTTATGACAAACACATCCCCTTTGGAACCGATTCTTACACTGTTATCTTTACTG 320 + +Query 1140 TATATAGCCCACCCATTAACAGGGCAGAGAGAAGAACTGCCAGCTAATTTCACTGAAACT 1199 + ||||||||||| ||| |||||||||||||||| ||||||||||||||||| ||||||| | +Sbjct 319 TATATAGCCCATCCACTAACAGGGCAGAGAGAGGAACTGCCAGCTAATTTTACTGAAATT 260 + +Query 1200 GCTGTCTGTTCGGCTACAAAATTGTTGTTACTGATGTTGACATATGTCTGATTTACCCAG 1259 + |||||||||| || |||||||||||||||||||||||||||||||||||||||||||| +Sbjct 259 ACTGTCTGTTCAGCAACAAAATTGTTGTTACTGATGTTGACATATGTCTGATTTACCCAA 200 + +Query 1260 GTGTTGTTTTCGTAAATAATGGCGCTTTGAATGCATGCCTCAGTTTGGTTTTGGTTCCTA 1319 + |||||||||||||||||||| |||||||| ||||||| || || ||||||||||||| | +Sbjct 199 GTGTTGTTTTCGTAAATAATAACGCTTTGATTGCATGCTTCGGTCTGGTTTTGGTTCCCA 140 + +Query 1320 GTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGCAATATCAAGCTA 1379 + ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| +Sbjct 139 GTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGTAATATCAAGCTA 80 + +Query 1380 GCAATTCCATTTGCCATACAGATTGAGCCGATGATTATTATCTTTTGATTTGGATTCATT 1439 + ||||||||||||| ||||||||||||||| |||||||||||||| ||||||||||||||| +Sbjct 79 GCAATTCCATTTGTCATACAGATTGAGCCAATGATTATTATCTTCTGATTTGGATTCATT 20 + +Query 1440 TTAAACTCCTGCTTTTGCT 1458 + ||||||||||||||||||| +Sbjct 19 TTAAACTCCTGCTTTTGCT 1 + + + Score = 97.1 bits (52), Expect = 1e-22 + Identities = 62/67 (93%), Gaps = 0/67 (0%) + Strand=Plus/Minus + +Query 1465 CGCTTTGAATGCATGCCTCAGTTTGGTTTTGGTTCCTAGTTTGAATTGAATGGCTAATCC 1524 + |||||||| ||||||| || || ||||||||||||| ||||||||||||||||||||||| +Sbjct 177 CGCTTTGATTGCATGCTTCGGTCTGGTTTTGGTTCCCAGTTTGAATTGAATGGCTAATCC 118 + +Query 1525 ATATTGA 1531 + ||||||| +Sbjct 117 ATATTGA 111 + + + Score = 58.4 bits (31), Expect = 6e-11 + Identities = 31/31 (100%), Gaps = 0/31 (0%) + Strand=Plus/Minus + +Query 1530 GACACCCATGGTCGATTCGAGCCATGCCAAT 1560 + ||||||||||||||||||||||||||||||| +Sbjct 934 GACACCCATGGTCGATTCGAGCCATGCCAAT 904 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 21085870 + + +Query= 170144-17ech4_c3 + +Length=2396 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 3855 0.0 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 3855 bits (2087), Expect = 0.0 + Identities = 2252/2334 (96%), Gaps = 1/2334 (0%) + Strand=Plus/Minus + +Query 1 AGTAGAAACAAGGTCGTTTTTAAACAATTCAACACTAATTGATGGCCAATCGAATTCTTT 60 + ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| +Sbjct 2334 AGTAGAAACAAGGTCGTTTTTAAACAATTCAACACTAATTGATGGCCAACCGAATTCTTT 2275 + +Query 61 TGGTCGCTGTCTGGCTGTCAGTAAGTATGCTAGAGTCCCGTTTCCGTTTCATTACCAACA 120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2274 TGGTCGCTGTCTGGCTGTCAGTAAGTATGCTAGAGTCCCGTTTCCGTTTCATTACCAACA 2215 + +Query 121 CTACATCTCCTTGCCCTATCAAAACGTTGGCTTTCTCCCCTTTTGTAAGATTGCTCAGCT 180 + | ||||||||||||||||||||||||||||||||||||||||||| |||||||||||| | +Sbjct 2214 CCACATCTCCTTGCCCTATCAAAACGTTGGCTTTCTCCCCTTTTGCAAGATTGCTCAGTT 2155 + +Query 181 CATTGATACTCAATGCTGGTCCATATCTTTTGTTTTCCTTTCCTAGAATTAAAAACCCTC 240 + |||||||||||||||||||||||||||||||||||||||| |||||||||| |||||||| +Sbjct 2154 CATTGATACTCAATGCTGGTCCATATCTTTTGTTTTCCTTCCCTAGAATTAGAAACCCTC 2095 + +Query 241 TCAGTACTGCAGATTCCACTCCAGCAGTCCCCTCATCTGGATCTGCTGTTAATGCACCTG 300 + ||||||||||||||||||||||||| || ||||||||||||||| ||||||||||||||| +Sbjct 2094 TCAGTACTGCAGATTCCACTCCAGCCGTTCCCTCATCTGGATCTTCTGTTAATGCACCTG 2035 + +Query 301 CGTCCTTTCCGAGGACCGTCAGTCTTTTTGTTGCCTTATTGTAGTTGAATACTGGGGAGT 360 + ||||||||||||||||||| || ||||||||||||||||||||||| ||||||||||||| +Sbjct 2034 CGTCCTTTCCGAGGACCGTTAGCCTTTTTGTTGCCTTATTGTAGTTAAATACTGGGGAGT 1975 + +Query 361 TACCTCTTATGAGTATCCTCAGTCCTGATCCTCTTACATTCACAGTTAGAGAAGAGAATT 420 + |||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||| +Sbjct 1974 TACCTCTTATGAGTATTCTCAGTCCTGATCCTCTTACATTTACAGTTAGAGAAGAGAATT 1915 + +Query 421 GCATCCTACTCTGCTCTGGTGGAGCAGCTGCAAATGGCAGTAGCTTTATTATTTGGGCAG 480 + ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| +Sbjct 1914 GCATCCTACTCTGCTCTGGTGGAGCTGCTGCAAATGGCAGTAGCTTTATTATTTGGGCAG 1855 + +Query 481 TATCAAATGTCCCCAGTACATCGCGCATTTGCTGGAATAGTGTTCTCACAAACCCGCTGT 540 + | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1854 TGTCAAATGTCCCCAGTACATCGCGCATTTGCTGGAATAGTGTTCTCACAAACCCGCTGT 1795 + +Query 541 ATTGACCTCTAGCCGCTTTAGGTATTAAAGATTGAAATGGTTCAAATTCCATTTTGTTGT 600 + |||||||||| || ||||||||||||| ||| |||||||| ||||||||||||||||||| +Sbjct 1794 ATTGACCTCTGGCTGCTTTAGGTATTAGAGACTGAAATGGCTCAAATTCCATTTTGTTGT 1735 + +Query 601 ATAGCATTGTGGGGTCTTGGGACCACTGGATCTTCACAGTCTCCCAATTTCTAATGATCC 660 + ||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||| +Sbjct 1734 ATAGCATTGTGGGGTCTTGGGACCATTGGATCTTCACAGTTTCCCAATTTCTAATGATCC 1675 + +Query 661 ATTGATACGTGTTAACGAGTACTGACTCAGGTCCATTGATTTCCCACATCATTGATGATG 720 + ||||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||||| +Sbjct 1674 ATTGATACGTGTTAACGAGCACTGATTCAGGTCCATTGATCTCCCACATCATTGATGATG 1615 + +Query 721 AATAGGTTATTGTCAATTTCTCTGTTCCTTGTATTTCGCTAACCTCTTCAGGAGATAGTA 780 + |||||||||||||||||||||||||||||||| ||||||||||||| ||||||||||||| +Sbjct 1614 AATAGGTTATTGTCAATTTCTCTGTTCCTTGTGTTTCGCTAACCTCCTCAGGAGATAGTA 1555 + +Query 781 GTACATTTCCCCGCTGATCTCGAACTCTCAAGAAGCGATCAATACTCACAACCACTCTCT 840 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1554 GTACATTTCCCCGCTGATCTCGAACTCTCAAGAAGCGATCAATACTCACAACCACTCTCT 1495 + +Query 841 CAGTACTGGAATATTCGTCCACTCCTGTTCTACTGATCCTCACTCCTCTTAATGACATTT 900 + | ||||||||||||||||| ||||||||| |||||||||||||||||||||||||||||| +Sbjct 1494 CTGTACTGGAATATTCGTCTACTCCTGTTTTACTGATCCTCACTCCTCTTAATGACATTT 1435 + +Query 901 CTGTGCTTGGAGTCATATCGGGTAATATGCCTATCATTCCCATGATATTATCAATAGGTT 960 + |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| +Sbjct 1434 CTGTGCTTGGAGTCATATCGGGTAATATACCTATCATTCCCATGATATTATCAATAGGTT 1375 + +Query 961 CAATTCCCCAATTTTGAAACAGCACTTTTGCATCCTTCTGGAAGTGTCTCAGTAGTTGAT 1020 + |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| +Sbjct 1374 CAATTCCCCAATTTTGAAACAGCACTTTTGCATCCTTCTGGAAGTGTCTCAGGAGTTGAT 1315 + +Query 1021 GCATGGGATTCAGCCTTTGGTTTGCTCTGTTTACAAAATTTAGATCGCCTCGAACAGCCT 1080 + |||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| | +Sbjct 1314 GCATGGGATTCAGCCTTTGGTTTGCTCTGTTTACAAAATTTAGATCACCTCGGACAGCTT 1255 + +Query 1081 TTATCATACAATCTTCTTGTGAGAACACCATTGCTACTATGATTGCTTCAGCAATTGACT 1140 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1254 TTATCATACAATCTTCTTGTGAGAACACCATTGCTACTATGATTGCTTCAGCAATTGACT 1195 + +Query 1141 GGTCGTCTCTTCCACTTACTATCAGTTGAATCAGTCTTCTAGTTGCTTTCCTTAAAATGG 1200 + | || |||||||||||||||||||| |||||||| |||||||||||||||||||| |||| +Sbjct 1194 GTTCATCTCTTCCACTTACTATCAGCTGAATCAGCCTTCTAGTTGCTTTCCTTAAGATGG 1135 + +Query 1201 CTGTTGCTCTTCTTCCAACCATTGTAAACTCCTCATATCCCTCATGTACCCTTATCTTCA 1260 + |||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||| +Sbjct 1134 CTGTTGCTCTTCTTCCAACCATTGTAAATTCCTCATACCCCTCATGTACCCTTATCTTCA 1075 + +Query 1261 GTGCTTGGAGATTTCCTGTAAGCACTTCTTCTTCTCTTTTAACTGATGATCCATTTGTTC 1320 + ||||||||||||| |||||||||||||||||||| |||||||| ||||||||| |||||| +Sbjct 1074 GTGCTTGGAGATTGCCTGTAAGCACTTCTTCTTCCCTTTTAACAGATGATCCACTTGTTC 1015 + +Query 1321 TTTTGAACGTGAAACCTCCAAAGCTAAAGGAGGAACTGATTCTCAAACCCATTGCTGCTT 1380 + ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1014 TTTTGAAAGTGAAACCTCCAAAGCTAAAGGAGGAACTGATTCTCAAACCCATTGCTGCTT 955 + +Query 1381 TGCATATATCCACGGCTTGCTCCTCAGTTGGATTTTGTTTAAGGATGTCAATCATCCTTA 1440 + ||||||||||||| |||||||| || ||||||||||||||||||||||||| |||||||| +Sbjct 954 TGCATATATCCACTGCTTGCTCTTCCGTTGGATTTTGTTTAAGGATGTCAACCATCCTTA 895 + +Query 1441 TCCCACCAATTTGTGTGCCGTGACACATCTCCAACAGTGATGCCAGTGGATCTGCTGACA 1500 + |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| +Sbjct 894 TCCCACCAATTTGTGTGCCGTGACACATCTCCAATAGTGATGCCAGTGGATCTGCTGACA 835 + +Query 1501 CTATTGCTCTTCTAACAATGTTTCTGGCAGCAATGATCAAACTCTGATCTACATCATCAT 1560 + |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 834 CTATTGCTCTTCTAACAATGTTTCTGGCAGCAATGATCAAACTCTGGTCTACATCATCAT 775 + +Query 1561 TCTTCACCTCTCCACCTGGAGTGTACATCTGTTCCCAGCAGGTTCCTTGGGTCAAGTGCA 1620 + ||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||| +Sbjct 774 TCTTCACCTCTCCACCTGGAGTGTACATCTGTTCCCAGCAGGTTCCTTGAGTTAAGTGCA 715 + +Query 1621 ATACTTCAATATAAACACTGCTTGTTCCACCTGCTACCGGCAGGAATCTGGTTTTGCGGA 1680 + |||||||||| || |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 714 ATACTTCAATGTAGACACTGCTTGTTCCACCTGCTACCGGCAGGAATCTGGTTTTGCGGA 655 + +Query 1681 CCAGTTCTCTCTCCAACATGTATGCCACCATTAAAGGGGCAATCTTACAATCTTGGAGTT 1740 + |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 654 CCAGTTCTCTTTCCAACATGTATGCCACCATTAAAGGGGCAATCTTACAATCTTGGAGTT 595 + +Query 1741 CCTCTTTCTTTTCCTTTGTTATTGTTAATTGCGATTCCGATGTTAATATTCTGGCTCCCA 1800 + |||||||||| || ||||||||||||||||||||||| ||||||| |||||||||||||| +Sbjct 594 CCTCTTTCTTCTCTTTTGTTATTGTTAATTGCGATTCTGATGTTAGTATTCTGGCTCCCA 535 + +Query 1801 CTTCATTTGGGAAAACAACTTCCATGATAACATCTTGTGCTTCTTTGGCATTGAGATCTG 1860 + ||||||||||||| ||||||||||||||||||||||||||||| |||||| |||| |||| +Sbjct 534 CTTCATTTGGGAAGACAACTTCCATGATAACATCTTGTGCTTCCTTGGCACTGAGGTCTG 475 + +Query 1861 CATGGCCTGGGTTTATGTCAACTCTTCGGCGTATTTTAATTTGATTTCGAAAATGGACGG 1920 + |||||||||||||||| ||||| |||||||||||||||| |||||||||||||||||| | +Sbjct 474 CATGGCCTGGGTTTATATCAACCCTTCGGCGTATTTTAACTTGATTTCGAAAATGGACAG 415 + +Query 1921 GACCAAAGGTCCCATGCTTCAACCTTTCAACTTTTTCAAAATATGTCTTGTATACTTTAG 1980 + |||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 414 GACCAAAGGTCCCATGTTTCAACCTTTCAACTTTTTCAAAATATGTTTTGTATACTTTAG 355 + +Query 1981 GATAGTGGACTGTATCTGTTGTCGGTCCATTCCTATTCCACCAAGTTACGGCTAGGGGTG 2040 + ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| +Sbjct 354 GATAGTGGACTGTATCTGTTGTCGGCCCATTCCTATTCCACCAAGTTACGGCTAGGGGTG 295 + +Query 2041 ACACCATCACCCTGTCTGATCCAGCATCATTTGTCTTACTCCAAAGTATTTGTCCTTGTT 2100 + ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 294 ACACCATCACCCTATCTGATCCAGCATCATTTGTCTTACTCCAAAGTATTTGTCCTTGTT 235 + +Query 2101 CGTTTCTTTCAGGAATCATCTCCATTATCCTCCTGTCTGCTGTAATCGGATACTTCATTG 2160 + |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| +Sbjct 234 CGTTTCTTTCAGGAATCATCTCCATTATTCTCCTGTCTGCTGTAATCGGATACTTCATTG 175 + +Query 2161 CCATCATCCATTTCATTCTGAGAGCGGGATTCTTCTCTTGTCTTCCTGATGTGTATTTTT 2220 + |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| +Sbjct 174 CCATCATCCATTTCATTCTGAGAGCGGGGTTCTTCTCTTGTCTTCCTGATGTGTATTTTT 115 + +Query 2221 T-ATTATTGCCATATGGTCCACAGTGGTTTTTGTCAGTATCTCGCGAGTGCGAGACTGAG 2279 + | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| | +Sbjct 114 TTATTATTGCCATATGGTCCACAGTGGTTTTTGTCAGTATCTCGCGAGTGCGAGACTGCG 55 + +Query 2280 ACATCAGATCTCTTAATTCTTTTATTCTCTCCATATTGAGTATATTTGACCTGC 2333 + |||||||||||||||||||||||||||| |||||||||| |||| ||||||||| +Sbjct 54 ACATCAGATCTCTTAATTCTTTTATTCTTTCCATATTGAATATAATTGACCTGC 1 + + + +Lambda K H + 1.34 0.623 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 31609773 + + +Query= 170144-17ech4_c9 + +Length=1517 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 2338 0.0 + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 191 5e-51 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 2338 bits (1266), Expect = 0.0 + Identities = 1344/1383 (97%), Gaps = 0/1383 (0%) + Strand=Plus/Minus + +Query 2 TTTCATTATGTACTCCGTGGCCCTGCAATGAGACACTTCTGCTGTGAAGTAGTTCCTCCT 61 + |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1383 TTTCATTATGTATTCCGTGGCCCTGCAATGAGACACTTCTGCTGTGAAGTAGTTCCTCCT 1324 + +Query 62 CATACTCGCAATATGCTCAATAGGAGCAACATCTTCTCCTATTTCGTCAAGCTCTATCCA 121 + |||||||||||| |||||||| || |||||||| |||||||||||||||||||||||||| +Sbjct 1323 CATACTCGCAATGTGCTCAATTGGGGCAACATCCTCTCCTATTTCGTCAAGCTCTATCCA 1264 + +Query 122 GCTGGAATCCGTCAACTCACATGCCTTGTTGAATTCACTCTGAATCCAACTTGCCAGTGA 181 + |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| +Sbjct 1263 GCTGGAATCCGTCAACTCACATGCCTTGTTGAATTCACTCTGAATCCAGCTTGCCAGTGA 1204 + +Query 182 CCTAATTTTTGGCTCATCACTATTATACTGTTTTAAATCACCGATATCTTTGCAATCTTC 241 + |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| +Sbjct 1203 TCTAATTTTTGGCTCATCACTATCATACTGTTTTAAATCACCGATATCTTTGCAATCTTC 1144 + +Query 242 AAAATCCACCTTTTCTGGTGCCATGTTTTCACCAAGTGCCCATTTTAACTGACTTGtttt 301 + ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1143 AAAATCCACCTTTTCAGGTGCCATGTTTTCACCAAGTGCCCATTTTAACTGACTTGTTTT 1084 + +Query 302 tttCATGTTCTTGGTTTTGGGGATTTTCTCCTCATTTTCAGCGTCCTGTAGCTCAGATAG 361 + ||||||||| || ||||||||||||||||||||||||||| ||||||||| |||| ||| +Sbjct 1083 TTTCATGTTTTTAGTTTTGGGGATTTTCTCCTCATTTTCAATGTCCTGTAGTTCAGCTAG 1024 + +Query 362 CACTTGTTTCCAAGTCAAGAGATAATTTGGATTTATGCCTTTCTCATGCGGCTTGACAAT 421 + |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1023 CACTTGTTTCCAAGCCAAGAGATAATTTGGATTTATGCCTTTCTCATGCGGCTTGACAAT 964 + +Query 422 GTGGGGCTCTTTCCATCCGAAGAATGTCTTCATGCATTTGATTGCATCATATAGTGGTAT 481 + ||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| +Sbjct 963 GTGGGGCTCTTTCCATCCGAAAAATGTCTTCATGCATTTGATTGCATCATATAGCGGTAT 904 + +Query 482 TCCCTCCCCCTCATGGCTCGGATCTTCAATGCTCAATTTTAGGGCATCCATCAACAGGAA 541 + |||||||||||||||||||||||||||||||| ||||||| |||||||||||||||||| +Sbjct 903 CCCCTCCCCCTCATGGCTCGGATCTTCAATGCTTAATTTTAAGGCATCCATCAACAGGAA 844 + +Query 542 TTTTGACCGTTGAGAACAAGGAGGTCCATCAGGTAATCTGAGAGGGCGTGGTGTTTCCCT 601 + |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| +Sbjct 843 TTTTGACCGTTGAGAACAAGGAGGTCCATCAGGTAATCTGAGGGGGCGTGGTGTTTCCCT 784 + +Query 602 CAAGAATGGTTCAATTCTGGCATTCACTTCTTTTGACATTTGAGAAAGCTTGCCCTCAAT 661 + ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| +Sbjct 783 CAAGAATGGTTCAATTCTGGCATTCACTTCTTTGGACATTTGAGAAAGCTTGCCCTCAAT 724 + +Query 662 GCAGCCGTTCGGTTCGAATCCATCCACATAGGCTCTAAAGTTTTCAATGCTGGAGAAGTT 721 + ||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||| +Sbjct 723 GCAGCCGTTCGGTTCAAATCCATCCACATAGGCTCTAAAGTTTTCAAGGCTGGAGAAGTT 664 + +Query 722 AGGCGGGAGACTTTGGTTGGCAAGCCTATGCATGGTCCCTTTGATTTCAAACCTTTCTTC 781 + |||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| +Sbjct 663 AGGCGGGAGACTTTGGTTGGCAAGCCTATGCATGGTTCCTTTGATTTCAAACCTTTCTTC 604 + +Query 782 AATTGTTTCTTCGCCTCTTTCGGACTGACGAAAGGAGTCCCATAGGGCCCTAATGGCCAT 841 + |||||| ||||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 603 AATTGTCTCTTCGCCTCTTTCGGACTGACGAAAGGAGTCCCATAGGCCCCTAATGGCCAT 544 + +Query 842 TTCCTGCCTGATGGTGAATAATCTAGTCTTGATCCTTGCTCTGCTTTCCTCATCAAGAGT 901 + ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| +Sbjct 543 TTCCTGCCTGATGGTGAATAATCTAGTCTTGATTCTTGCTCTGCTTTCCTCATCAAGAGT 484 + +Query 902 GTAATCTGCCTTAGTGGCCATTTCTTCTCCAGTGAATGAGAAAATGTGGATGTGTGTCTT 961 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 483 GTAATCTGCCTTAGTGGCCATTTCTTCTCCAGTGAATGAGAAAATGTGGATGTGTGTCTT 424 + +Query 962 CTCTGATTTTATTTTGTTGGCTTTTTCTAGATAGTATATGTGAACTTCCCTTCTTGTTAC 1021 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 423 CTCTGATTTTATTTTGTTGGCTTTTTCTAGATAGTATAGGTGAACTTCCCTTCTTGTTAC 364 + +Query 1022 GCCGATTTCAATGAATCGGTTCTCCTTATAGTCATACAGATCCGGAAGGAATTTGGGCTT 1081 + |||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| +Sbjct 363 GCCGATTTCAATGAATCGGTTCTCCTTATAGTCATATAGATCCGGAAGGAATTTGGGCTT 304 + +Query 1082 CTCAACTCCTGTGGTATTGCATATGCTGTTTACCACTGTCCAAGCCATTGTGCGATCCCT 1141 + |||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 303 CTCAACTCCTGTAGTATTGCAGATGCTGTTTACCACTGTCCAAGCCATTGTGCGATCCCT 244 + +Query 1142 TCCCTCAATTATTTCAAATCTGTGTTTTAGGAGTGCATTTGGATTATTGGATTCTACTAT 1201 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 243 TCCCTCAATTATTTCAAATCTGTGTTTTAGGAGTGCATTTGGATTATTGGATTCTACTAT 184 + +Query 1202 TGTCGATTCACCTCGTTCATCAATGAAGTGGAAGTCAGAATACATGAAACAGACTTCCAT 1261 + ||||||||||| ||||||||| ||||||||||| |||||||||||||||||||||||||| +Sbjct 183 TGTCGATTCACTTCGTTCATCGATGAAGTGGAAATCAGAATACATGAAACAGACTTCCAT 124 + +Query 1262 GTGTGTGCATATTGCAGCAAATTTGTTCGTTTCAATTTTTGGGTCTTCTCCATGTTCTTT 1321 + ||||||||||||||||||||||||||| ||||||||||||| |||||||||||||||||| +Sbjct 123 GTGTGTGCATATTGCAGCAAATTTGTTTGTTTCAATTTTTGAGTCTTCTCCATGTTCTTT 64 + +Query 1322 CATTGCCTTTTCCGCAAGCTCGACGATCATTGGGTTGAAGCATTGTCGCACAAAGTCTTC 1381 + ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| +Sbjct 63 CATTGCCTTTTCCGCAAGCTCGACGATCATTGGATTGAAGCATTGTCGCACAAAGTCTTC 4 + +Query 1382 CAT 1384 + ||| +Sbjct 3 CAT 1 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 191 bits (103), Expect = 5e-51 + Identities = 107/109 (98%), Gaps = 0/109 (0%) + Strand=Plus/Minus + +Query 1408 TACATTTTGAAAAGGAAGATTGCCTTTCAAGGCCCCGTGAGGAGTTTGGCATTTTGTAGT 1467 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 968 TACATTTTGAAAAGGAAGATTGCCTTTCAAGGCCCCGTGAGGAGTTTGGCATTTTGTAGT 909 + +Query 1468 GCAATTGTGAACGTGTACATCCGACATCATAATTCCAGAATTAGAGCCC 1516 + ||||||||||||||| |||||||||||||| |||||||||||||||||| +Sbjct 908 GCAATTGTGAACGTGAACATCCGACATCATGATTCCAGAATTAGAGCCC 860 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 19955795 + + +Query= 170144-17ech4_c10 + +Length=1738 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 1805 0.0 + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 204 7e-55 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 1805 bits (977), Expect = 0.0 + Identities = 1032/1059 (97%), Gaps = 1/1059 (0%) + Strand=Plus/Minus + +Query 587 ATTGGATAGAGGGAATATTCCTTAATCCTGTTGCCATTCTTAGTTGGGTGCTTTTAACAT 646 + ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1059 ATTGGATAGAGGGGATATTCCTTAATCCTGTTGCCATTCTTAGTTGGGTGCTTTTAACAT 1000 + +Query 647 ATTTGGGGCATTCCCCAATAGTAATGGGATGTACATTTTGAAAAGGAAGATTGCCTTTCA 706 + ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 999 ATTTGGGGCATTCTCCAATAGTAATGGGATGTACATTTTGAAAAGGAAGATTGCCTTTCA 940 + +Query 707 AGGCCCCGTGAGGAGTTTGGCATTTTGTAGTGCAATTGTGAACGTGTACATCCGACATCA 766 + |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 939 AGGCCCCGTGAGGAGTTTGGCATTTTGTAGTGCAATTGTGAACGTGAACATCCGACATCA 880 + +Query 767 TAATTCCAGAATTAGAGCCCCTATTCAATGCAAATGCATGCCATGGCGCTATTAAGTTCC 826 + | |||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| +Sbjct 879 TGATTCCAGAATTAGAGCCCTTATTCAATGCAAATGCATGCCATGGCGCTATTAAGTTCC 820 + +Query 827 CTGTGGCTTCAAAGGTTATGGTGTCCCCTTGATCTAATAGTGTCCAATAATAATTCATTC 886 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 819 CTGTGGCTTCAAAGGTTATGGTGTCCCCTTGATCTAATAGTGTCCAATAATAATTCATTC 760 + +Query 887 TGCCCGCTTGCTCTCTGACTTTAGGTCTAGCTACTATTTCTGGGGTGAATTTCTGATAGT 946 + |||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||| +Sbjct 759 TGCCCGCTTGTTCCCTGACTTTAGGTCTAGCTACTATTTCTGGGGTGAACTTCTGATAGT 700 + +Query 947 ATTTTGATGATCCAACTGAAACATATGTATGATTATTCTGGTAGAGGGTTTGTTGATCAC 1006 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 699 ATTTTGATGATCCAACTGAAACATATGTATGATTATTCTGGTAGAGGGTTTGTTGATCAC 640 + +Query 1007 TGTCAGTGGGGGGATGATGCACTCCCCAGATCACGAGCACTTCTTTTCCTTTGTTGTTTG 1066 + |||||||||||||||||||||||||||||||||| ||||||||| ||||||||||||||| +Sbjct 639 TGTCAGTGGGGGGATGATGCACTCCCCAGATCACAAGCACTTCTCTTCCTTTGTTGTTTG 580 + +Query 1067 TGTATGAATTGCTGAGCTTAGGATAGGAGTTTCCCTTTTTTACTATCCAGAGCAAATTCC 1126 + ||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| |||| +Sbjct 579 TGTATGACTTGCTGAGCTTAGGATAGGAGTTTCCCTTTTTTACTATCCATAGCAAGTTCC 520 + +Query 1127 GATAAAAGCTATTGACTCCAGAGTGAGAGCATGCAACTGTGGTGCCTTTGGTTGTCTCAT 1186 + |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 519 GATAAAAGCTATTGGCTCCAGAGTGAGAGCATGCAACTGTGGTGCCTTTGGTTGTCTCAT 460 + +Query 1187 GGTTTGGCCATGAGGTTGTTTTTGGGAAAATTTCAAATCTTTCAAATGAAGAAACTGTAC 1246 + |||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| +Sbjct 459 GGTTTGGCCATGAGGTTGCTTTTGGGAAAATTTCAAATCTTTCAAATGAAGAAACTGTAC 400 + +Query 1247 TCAGCTGTTCCCTTAATTCCTCATAATCAGCGAATTCTCCAGGATAGCATGCACCATTTT 1306 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 399 TCAGCTGTTCCCTTAATTCCTCATAATCAGCGAATTCTCCAGGATAGCATGCACCATTTT 340 + +Query 1307 T-GAATTTGAGGTCTCTATTATGTAAGACCACGAATTTGCTGTGAGCAGCAAGTCACATT 1365 + | |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||| | +Sbjct 339 TTGAATTTGAAGTCTCTATTATATAAGACCACGAATTTGCTGTGAGCAGCAAGTCACACT 280 + +Query 1366 CTGGGTTGCCAAGGATCCATCCTGCTACGTTGCAGTTTCCCAGTTGTAATGGGGCCTTTC 1425 + ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| +Sbjct 279 CTGGGTTGCCAAGGATCCATCCTGCTACGTTGCAGTTTCCCAGTTGTAAGGGGGCCTTTC 220 + +Query 1426 CATTAAGGCTGCAGAGTTTCTCATTGTGGCTGTTTTCTAGTAAATTAACTGAATGGGTAA 1485 + ||||||||||||| |||||||||||||||||| ||||||||||||||||||||||||||| +Sbjct 219 CATTAAGGCTGCAAAGTTTCTCATTGTGGCTGCTTTCTAGTAAATTAACTGAATGGGTAA 160 + +Query 1486 CGGTCACATTCTTCTCTAGTATCGTGTCGACAGTGTCTGTGGAATTGTTAGCATGATAGC 1545 + ||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||| +Sbjct 159 CGGTCACATTCTTTTCCAGTATCGTGTCGACAGTGTCTGTGGAATTGTTAGCATGATAGC 100 + +Query 1546 CTACACAAATGGTGTCAGCTTCCAGTGCAGTAAATGCACAGAATAGTACAAATAGTTTTG 1605 + ||||||||||||||||||||||||||| ||| |||||||||||||||||||| ||||||| +Sbjct 99 CTACACAAATGGTGTCAGCTTCCAGTGTAGTGAATGCACAGAATAGTACAAACAGTTTTG 40 + +Query 1606 CTTCCATCTTGGTTTCTTTAATTATCCCCTGCTTTTGCT 1644 + ||||||||||||||||||||||||||||||||||||||| +Sbjct 39 CTTCCATCTTGGTTTCTTTAATTATCCCCTGCTTTTGCT 1 + + + Score = 161 bits (87), Expect = 5e-42 + Identities = 95/99 (96%), Gaps = 1/99 (1%) + Strand=Plus/Minus + +Query 1639 TTTGCTADTGAGCAGCAAGTCACATTCTGGGTTGCCAAGGATCCATCCTGCTACGTTGCA 1698 + |||||| |||||||||||||||| ||||||||||||||||||||||||||||||||||| +Sbjct 304 TTTGCT-GTGAGCAGCAAGTCACACTCTGGGTTGCCAAGGATCCATCCTGCTACGTTGCA 246 + +Query 1699 GTTTCCCAGTTGTAATGGGGCCTTTCCATTAAGGCTGCA 1737 + ||||||||||||||| ||||||||||||||||||||||| +Sbjct 245 GTTTCCCAGTTGTAAGGGGGCCTTTCCATTAAGGCTGCA 207 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 204 bits (110), Expect = 7e-55 + Identities = 120/125 (96%), Gaps = 0/125 (0%) + Strand=Plus/Minus + +Query 59 TTATTTCAGTGCATGCATAAGGAAGGAGTTAAACCAAGACGCATTGAGCAAAACCCAGGG 118 + |||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| +Sbjct 2151 TTATTTCAGTGCATGCATAAGGAAGGAGTTGAACCAAGACGCGTTAAGCAAAACCCAGGG 2092 + +Query 119 ATCATTAATCAGGCACTCCTCAATTGCATCATATAACCCCCCAAGATCAAAGGTCCCAGG 178 + ||||||||||| |||||| ||||||||||||||||||||||||||||||||||||||||| +Sbjct 2091 ATCATTAATCAAGCACTCTTCAATTGCATCATATAACCCCCCAAGATCAAAGGTCCCAGG 2032 + +Query 179 TTCCA 183 + ||||| +Sbjct 2031 TTCCA 2027 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 22893990 + + +Query= 170144-17ech4_c14 + +Length=869 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 1109 0.0 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 1109 bits (600), Expect = 0.0 + Identities = 626/639 (98%), Gaps = 0/639 (0%) + Strand=Plus/Minus + +Query 131 TTAAATAAACTGAAACGAAAAAGTCCTTATCTCTTGCTCCACTTCAAGCAGTAGTTGTAA 190 + |||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| +Sbjct 838 TTAAATAAACTGAAACGAGAAAGTCCTTATCTCTTGCTCCACTTCAAGCAGTAGTTGTAA 779 + +Query 191 TGCTTGCATGAATGTTATCTGTTCAAAGCTATTCTCCGTTATTTTTAATCTGTGTCGCAC 250 + ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 778 TGCTTGCATAAATGTTATCTGTTCAAAGCTATTCTCCGTTATTTTTAATCTGTGTCGCAC 719 + +Query 251 TTCTTCAATTAGCCATCTTATTTCTTCAAATTTCTGGCCCAATTGTTCTCGCCATTTTCC 310 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 718 TTCTTCAATTAGCCATCTTATTTCTTCAAATTTCTGGCCCAATTGTTCTCGCCATTTTCC 659 + +Query 311 GTTTCTGTCTTGAAGGGAATGGAGGTCTCCCGTTCTCATTAGTGCTTCTCCAAGCGAATC 370 + |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 658 GTTTCTGTTTTGAAGGGAATGGAGGTCTCCCGTTCTCATTAGTGCTTCTCCAAGCGAATC 599 + +Query 371 TCTGTAGAGCTTCAGAGACTCGAACTGTATTATCATTCCATTCAAGTCCTTTGATGAGGA 430 + ||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||| +Sbjct 598 TCTGTAGAGTTTCAGAGACTCGAACTGCATTATCATTCCATTCAAGTCCTTTGATGAGGA 539 + +Query 431 TCCCAATTGCATTTTTGACATCCTCATCAGTATGTCCTGGAAGAGAAGGTAACGGTGAGA 490 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 538 TCCCAATTGCATTTTTGACATCCTCATCAGTATGTCCTGGAAGAGAAGGTAACGGTGAGA 479 + +Query 491 TTTCACCTACAATTGCCCCTTTCTCTGTGAAAGCTCTAAGGAGTATCAGAGTTTCCAGTC 550 + ||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 478 TTTCACCTATAATTGCCCCTTCCTCTGTGAAAGCTCTAAGGAGTATCAGAGTTTCCAGTC 419 + +Query 551 GGTCAAAAATCACACTGAAGTTTGCTTTCAATGTAATATTTTTATCCATTATTGCTTGGT 610 + ||||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||| +Sbjct 418 GGTCAAAAATCACACTGAAGTTTGCTTTCAATGTAATGTTTTTATCCATTATTGCCTGGT 359 + +Query 611 CCATTCTGATGCAGAAGGGACCTGCCACCTTTTGCTTGGGCATGAGCATGAACCAGTCCC 670 + ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 358 CCATTCTGATGCAAAAGGGACCTGCCACCTTTTGCTTGGGCATGAGCATGAACCAGTCCC 299 + +Query 671 TTGACATCTCTTCAAGAGTCATGTCAGTCAAATAGTGTGAAGCAGGCACAGAAGCATTGG 730 + ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| +Sbjct 298 TTGACATCTCTTCAAGAGTCATGTCAGTCAAATAGCGTGAAGCAGGCACAGAAGCATTGG 239 + +Query 731 TTATTTTAAGTGATTCATTGTATTCTTCTTCCAGAATAC 769 + |||||||||||| ||||| |||||||||||||||||||| +Sbjct 238 TTATTTTAAGTGCTTCATCGTATTCTTCTTCCAGAATAC 200 + + + Score = 185 bits (100), Expect = 1e-49 + Identities = 101/102 (99%), Gaps = 0/102 (0%) + Strand=Plus/Minus + +Query 1 AGCTATTCTCCGTTATTTTTAATCTGTGTCGCACTTCTTCAATTAGCCATCTTATTYCTT 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| +Sbjct 752 AGCTATTCTCCGTTATTTTTAATCTGTGTCGCACTTCTTCAATTAGCCATCTTATTTCTT 693 + +Query 61 CAAATTTCTGGCCCAATTGTTCTCGCCATTTTCCGTTTCTGT 102 + |||||||||||||||||||||||||||||||||||||||||| +Sbjct 692 CAAATTTCTGGCCCAATTGTTCTCGCCATTTTCCGTTTCTGT 651 + + + Score = 172 bits (93), Expect = 1e-45 + Identities = 97/99 (98%), Gaps = 0/99 (0%) + Strand=Plus/Minus + +Query 771 AGGATCCCAATTGCATTTTTGACATCCTCATCAGTATGTCCTGGAAGAGAAGGTAACGGT 830 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 542 AGGATCCCAATTGCATTTTTGACATCCTCATCAGTATGTCCTGGAAGAGAAGGTAACGGT 483 + +Query 831 GAGATTTCACCTACAATTGCCCCTTTCTCTGTGAAAGCT 869 + ||||||||||||| ||||||||||| ||||||||||||| +Sbjct 482 GAGATTTCACCTATAATTGCCCCTTCCTCTGTGAAAGCT 444 + + + +Lambda K H + 1.33 0.621 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 11340635 + + +Query= 170144-17ech4_c15 + +Length=1280 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 2037 0.0 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 2037 bits (1103), Expect = 0.0 + Identities = 1200/1248 (96%), Gaps = 2/1248 (0%) + Strand=Plus/Minus + +Query 1 TGCTCTCTGTTGATTGGTGTTTCCTCCGCTCCTGGTTCTTATAGCCCAGTACTTGCTTCT 60 + ||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| +Sbjct 1248 TGCTCTCTGTTGATTGGTGTTTCCTCCGCTCCTGGTTCTTATAGCCCAGTATTTGCTTCT 1189 + +Query 61 AAGTTCAAGAGTAACGGAGTCCATTGTTTCCATGTTTTCATTTGAAGCAATTTGAACTCC 120 + |||||||||||||| |||||||||||||||||||||||||||||||||||||||||| || +Sbjct 1188 AAGTTCAAGAGTAATGGAGTCCATTGTTTCCATGTTTTCATTTGAAGCAATTTGAACCCC 1129 + +Query 121 TCTGGTGGACAATTGTCCTCTTGGGATCACTTTTGTCCCTCTGATAAA-CTTGACACCCT 179 + |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| +Sbjct 1128 TCTGGTGGACAATTGTCCTCTTGGGATCACTTTTGTCCCTCTGATAAAACTTGACACCCT 1069 + +Query 180 CAGATCTTCAAATGCTGCAGAATGGCATGCCATCCAGACCAGTTGACTCTTATGAACTGG 239 + |||||||||||||||||||||||||||||||||||| | ||| ||||||||||| ||||| +Sbjct 1068 CAGATCTTCAAATGCTGCAGAATGGCATGCCATCCATATCAGCTGACTCTTATGGACTGG 1009 + +Query 240 ATTCTCATTCGGTCTAATAAGGCTGAACACTTGGCTGTTCTGAAGCAGACGAAAAGGATC 299 + |||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| +Sbjct 1008 ATTCTCATTCGGTCTAATGAGGCTGAACACTTGGCTGTTCTGAAGCAGACGAAAAGGATC 949 + +Query 300 TATCCCAACTAGGGAGTACCCTTCTCTTTCAAAGTCATATCCACTCGCCACAATAAGTCC 359 + || ||| |||||||||||||||||||||||||||||||||||||| |||||||||||||| +Sbjct 948 TACCCCGACTAGGGAGTACCCTTCTCTTTCAAAGTCATATCCACTTGCCACAATAAGTCC 889 + +Query 360 ATATACACAAGCAGGTAGGCAGGATTTATGAGCCACTGATCCTCTCAGAATGAGTGCAGA 419 + ||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||| +Sbjct 888 ATATACACAAGCAGGCAGACAGGATTTATGAGCCACTGATCCTCTCAGAATGAGTGCAGA 829 + +Query 420 TCGTGCCAGAAAAATGAGATCTTCAATCTCAGCATTTCCTGGGTTTCTGCTTTCTCGTAC 479 + |||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| || +Sbjct 828 TCGTGCCAGAAAGATGAGATCTTCAATCTCAGCATTTCCTGGATTTCTGCTTTCTCGCAC 769 + +Query 480 CTGGTCCATCATTGCTCGTTGTGCTGCTGTTTGGAATTTCCCTTTGAGGATGTTGCACAT 539 + ||||||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| +Sbjct 768 CTGGTCCATCATTGCTCGTTGCGCTGCTGTCTGGAATTTCCCTTTGAGGATGTTGCACAT 709 + +Query 540 TCTCTCATATGCAATTCTTGTCCTTCGTCCATTCTCACCTCTCCAAAAGTTCCGATCATT 599 + ||||||||||||||||||||| |||||||||||||| |||||||| |||||||||||||| +Sbjct 708 TCTCTCATATGCAATTCTTGTTCTTCGTCCATTCTCGCCTCTCCAGAAGTTCCGATCATT 649 + +Query 600 GATACCCCGCTTTATCATTCTGATCAGCTCCATTACTAGTGTTCCAACTCCCTTTACTGC 659 + |||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| +Sbjct 648 GATACCCCGCTTTATCATTCGAATCAGCTCCATTACTAGTGTCCCAACTCCCTTTACTGC 589 + +Query 660 TGCACCAGCAGCTCCAGATCTCCTTGGTAGAGTTGAACCTTGCATTAGAGAGCACATTCT 719 + ||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| +Sbjct 588 TGCACCAGCAGCTCCAGATCTCCTTGGGAGAGTTGAACCTTGCATCAGAGAGCACATTCT 529 + +Query 720 GGGATCCATCCCAGTACGCACTAAAGCTCTTGTTCTCTGATATGTAGCATCATTCAGATT 779 + |||||||||||||||||||||||||||||||||||||||||| || ||||||||||| || +Sbjct 528 GGGATCCATCCCAGTACGCACTAAAGCTCTTGTTCTCTGATACGTGGCATCATTCAGGTT 469 + +Query 780 GGAGTGCCAAATCATCAGATGAGTGAGACCAGCAGTAGCATCTTCACCATTGTTGGCTTG 839 + ||| |||||||||||||| ||||||||||||||||||||||||||||||||||| ||||| +Sbjct 468 GGAATGCCAAATCATCAGGTGAGTGAGACCAGCAGTAGCATCTTCACCATTGTTTGCTTG 409 + +Query 840 ACGCCAAATTCTCCTGATTTCATCTTTGTCATATAGAATCAGCTCTCTCATCCATTTTCC 899 + |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| +Sbjct 408 GCGCCAAATTCTCCTGATTTCATCTTTGTCATACAGAATCAGCTCTCTCATCCATTTTCC 349 + +Query 900 ATCTCTCTTTTTGTAGATTGGACCTCCAGTTTTCTTTGGATCTTTCCCCGCACTGGGATG 959 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 348 ATCTCTCTTTTTGTAGATTGGACCTCCAGTTTTCTTTGGATCTTTCCCCGCACTGGGATG 289 + +Query 960 TTCTTCCAAGTATTTGTTTCTTCTCTCGTCGAATGCAGAGAGGACCATTCTCTCTATCGT 1019 + ||||||||| ||||||||||| |||||||| ||||||||||||||||||||||||||||| +Sbjct 288 TTCTTCCAAATATTTGTTTCTCCTCTCGTCAAATGCAGAGAGGACCATTCTCTCTATCGT 229 + +Query 1020 TATACTATTT-GGATCAGCCTCCCTTCATAGTCACTGAGTTGGAGTTCAGTACACATCTG 1078 + |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 228 TATACTATTTTGGATCAGCCTCCCTTCATAGTCACTGAGTTGGAGTTCAGTACACATCTG 169 + +Query 1079 TATGTAGAACCGTCCAATTCCTTCAATCATTCTCCCAACAGATGCTCTGATTTCTGTGGT 1138 + ||||||||| |||||||||||||||| ||||||||||||||||||||||||||| || || +Sbjct 168 TATGTAGAATCGTCCAATTCCTTCAACCATTCTCCCAACAGATGCTCTGATTTCAGTAGT 109 + +Query 1139 GTTTTGGCGTTCTCCACCAGTTTCCATTTGTTCATAAGATCGTTTGGTGCCTTGGGACGC 1198 + |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||| +Sbjct 108 ATTTTGGCGTTCTCCACCAGTTTCCATCTGTTCATAAGATCGTTTGGTGCCTTGAGACGC 49 + +Query 1199 CATGGTGTGGATGTCACTCAGTGAGTGATTATCTACCCTGCTTTTGCT 1246 + ||||||||| ||||||||||| |||||||||||||||||||||||||| +Sbjct 48 CATGGTGTGAATGTCACTCAGCGAGTGATTATCTACCCTGCTTTTGCT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 16804880 + + +Query= 170144-17ech4_c16 + +Length=515 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 580 9e-169 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 580 bits (314), Expect = 9e-169 + Identities = 346/362 (96%), Gaps = 0/362 (0%) + Strand=Plus/Minus + +Query 80 TGAAACAGCACTTTTGCATCCTTCTGGAAGTGTCTCAGTAGTTGATGCATGGGATTCAGC 139 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 1360 TGAAACAGCACTTTTGCATCCTTCTGGAAGTGTCTCAGGAGTTGATGCATGGGATTCAGC 1301 + +Query 140 CTTTGGTTTGCTCTGTTTACAAAATTTAGATCGCCTCGAACAGCCTTTATCATACAATCT 199 + |||||||||||||||||||||||||||||||| ||||| ||||| ||||||||||||||| +Sbjct 1300 CTTTGGTTTGCTCTGTTTACAAAATTTAGATCACCTCGGACAGCTTTTATCATACAATCT 1241 + +Query 200 TCTTGTGAGAACACCATTGCTACTATGATTGCTTCAGCAATTGACTGGTCGTCTCTTCCA 259 + ||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||| +Sbjct 1240 TCTTGTGAGAACACCATTGCTACTATGATTGCTTCAGCAATTGACTGTTCATCTCTTCCA 1181 + +Query 260 CTTACTATCAGTTGAATCAGTCTTCTAGTTGCTTTCCTTAAAATGGCTGTTGCTCTTCTT 319 + ||||||||||| |||||||| |||||||||||||||||||| |||||||||||||||||| +Sbjct 1180 CTTACTATCAGCTGAATCAGCCTTCTAGTTGCTTTCCTTAAGATGGCTGTTGCTCTTCTT 1121 + +Query 320 CCAACCATTGTAAACTCCTCATATCCCTCATGTACCCTTATCTTCAGTGCTTGGAGATTT 379 + |||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| +Sbjct 1120 CCAACCATTGTAAATTCCTCATACCCCTCATGTACCCTTATCTTCAGTGCTTGGAGATTG 1061 + +Query 380 CCTGTAAGCACTTCTTCTTCTCTTTTAACTGATGATCCATTTGTTCTTTTGAACGTGAAA 439 + |||||||||||||||||||| |||||||| ||||||||| ||||||||||||| |||||| +Sbjct 1060 CCTGTAAGCACTTCTTCTTCCCTTTTAACAGATGATCCACTTGTTCTTTTGAAAGTGAAA 1001 + +Query 440 CC 441 + || +Sbjct 1000 CC 999 + + + +Lambda K H + 1.35 0.627 1.14 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 6651500 + + +Query= 170144-17ech4_c20 + +Length=801 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 776 0.0 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 776 bits (420), Expect = 0.0 + Identities = 451/466 (97%), Gaps = 1/466 (0%) + Strand=Plus/Minus + +Query 301 CCTTGGCGTTGTTCCTCAGTTGTGATTTGACTTTTTCATACAAACTTTTTACGTTAAAGT 360 + ||||||| ||||| || ||||||||||||||||||||||| ||| ||||||||||||||| +Sbjct 1458 CCTTGGCATTGTTTCTAAGTTGTGATTTGACTTTTTCATATAAATTTTTTACGTTAAAGT 1399 + +Query 361 CATGGAAATCTAGGGTTCTTTCATTCTCGAGCAGGATGAGTAATTCAGCGTTATAAGTCC 420 + |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| +Sbjct 1398 CATGGAAATCTAGGGTTCTTTCATTCTCGAGCAGTATGAGTAATTCAGCGTTATAAGTCC 1339 + +Query 421 ACACATCCACAAAATCCATCATCGACTTTTTTATTCAAATTCTCAACCCTTTTCTCTAGA 480 + | ||||||| |||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 1338 ATACATCCA-AAAATCCATCATCGACTTTTTTATTCAAATTCTCAATCCTTTTCTCTAGA 1280 + +Query 481 TTATTGAATTCTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTATTGAGTTC 540 + |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 1279 TTATTGAATTCTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTACTGAGTTT 1220 + +Query 541 ACTTTGTTGCTGATCCCATCAATTGCGATTTGTGTACTTTTCTGATCTGCTGCGTAACCA 600 + ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| +Sbjct 1219 ACTTTGTTGCTGATCCCATCAATTGCGATTTGTGTACTTTTCTGATCCGCTGCGTAACCA 1160 + +Query 601 GATCCTTGCTCATTTTGATGATGGTATCCATACCATCCATCTATCATTCCTGTCCACCCT 660 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| +Sbjct 1159 GATCCTTGCTCATTTTGATGATGGTATCCATACCATCCATCTATCATTCCTGTCCATCCT 1100 + +Query 661 CCTTCAATGAATCCGGCAATTGCTCCAAAAAGTCCTCTGGATTGGATAGAGGGAATATTC 720 + ||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||| +Sbjct 1099 CCTTCAATGAATCCGGCAATTGCCCCAAAAAGTCCTCTGGATTGGATAGAGGGGATATTC 1040 + +Query 721 CTTAATCCTGTTGCCATTCTTAGTTGGGTGCTTTTAACATATTTGG 766 + |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1039 CTTAATCCTGTTGCCATTCTTAGTTGGGTGCTTTTAACATATTTGG 994 + + + Score = 65.8 bits (35), Expect = 2e-13 + Identities = 35/35 (100%), Gaps = 0/35 (0%) + Strand=Plus/Minus + +Query 767 AATGGGATGTACATTTTGAAAAGGAAGATTGCCTT 801 + ||||||||||||||||||||||||||||||||||| +Sbjct 977 AATGGGATGTACATTTTGAAAAGGAAGATTGCCTT 943 + + + +Lambda K H + 1.33 0.621 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 10436575 + + +Query= 170144-17ech4_c21 + +Length=580 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 917 0.0 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 917 bits (496), Expect = 0.0 + Identities = 510/517 (99%), Gaps = 0/517 (0%) + Strand=Plus/Minus + +Query 64 AGTAGAAACAAGGGTATTTTTCTTTAATTGTCATACTCCTCTGCATTGTCTCCGAAGAAA 123 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1565 AGTAGAAACAAGGGTATTTTTCTTTAATTGTCATACTCCTCTGCATTGTCTCCGAAGAAA 1506 + +Query 124 TAAGATCCCTCATTACTCATGTCAAAGGAAGGCACGATCGGGTTCGTTGCCTTTTCGTCC 183 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1505 TAAGATCCCTCATTACTCATGTCAAAGGAAGGCACGATCGGGTTCGTTGCCTTTTCGTCC 1446 + +Query 184 GAGAGCTCGAAGACTCCCCGCCCCTGGAAGGACACATCTTCTGGTCTGGCACTTTCCATC 243 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1445 GAGAGCTCGAAGACTCCCCGCCCCTGGAAGGACACATCTTCTGGTCTGGCACTTTCCATC 1386 + +Query 244 ATTTTTATAATTTCAGTCCTCATATCAGATGTTCTGCCTTCAGTGTTTCCAGTAAATGCT 303 + ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1385 ATTCTTATAATTTCAGTCCTCATATCAGATGTTCTGCCTTCAGTGTTTCCAGTAAATGCT 1326 + +Query 304 GCCATGATGGTTGCTCTCTCAAAAGGAAGATTTCTCTGTACTGAGAAGGTAGGTTGTACA 363 + ||||||||||| |||||||| |||||||||||||||||||||||||| |||||||||||| +Sbjct 1325 GCCATGATGGTCGCTCTCTCGAAAGGAAGATTTCTCTGTACTGAGAAAGTAGGTTGTACA 1266 + +Query 364 CTGATTTGCCCTGCGGATGCTCTCTGTTGATTGGTGTTTCCTCCGCTCCTGGTTCTTATA 423 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1265 CTGATTTGCCCTGCGGATGCTCTCTGTTGATTGGTGTTTCCTCCGCTCCTGGTTCTTATA 1206 + +Query 424 GCCCAGTACTTGCTTCTAAGTTCAAGAGTAACGGAGTCCATTGTTTCCATGTTTTCATTT 483 + |||||||| |||||||||||||||||||||| |||||||||||||||||||||||||||| +Sbjct 1205 GCCCAGTATTTGCTTCTAAGTTCAAGAGTAATGGAGTCCATTGTTTCCATGTTTTCATTT 1146 + +Query 484 GAAGCAATTTGAACTCCTCTGGTGGACAATTGTCCTCTTGGGATCACTTTTGTCCCTCTG 543 + |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1145 GAAGCAATTTGAACCCCTCTGGTGGACAATTGTCCTCTTGGGATCACTTTTGTCCCTCTG 1086 + +Query 544 ATAAAACTTGACACCCTCAGATCTTCAAATGCTGCAG 580 + ||||||||||||||||||||||||||||||||||||| +Sbjct 1085 ATAAAACTTGACACCCTCAGATCTTCAAATGCTGCAG 1049 + + + Score = 119 bits (64), Expect = 9e-30 + Identities = 64/64 (100%), Gaps = 0/64 (0%) + Strand=Plus/Minus + +Query 1 CACGATCGGGTTCGTTGCCTTTTCGTCCGAGAGCTCGAAGACTCCCCGCCCCTGGAAGGA 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1473 CACGATCGGGTTCGTTGCCTTTTCGTCCGAGAGCTCGAAGACTCCCCGCCCCTGGAAGGA 1414 + +Query 61 CACA 64 + |||| +Sbjct 1413 CACA 1410 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 7516195 + + +Query= 170144-17ech4_c25 + +Length=560 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 822 0.0 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 822 bits (445), Expect = 0.0 + Identities = 472/485 (97%), Gaps = 2/485 (0%) + Strand=Plus/Minus + +Query 77 TACATTTTGAAATTCAAGTCTTAAATGCATATTCTGCATTGTAATGACCCATTAGAGCAC 136 + ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1753 TACATCTTGAAATTCAAGTCTTAAATGCATATTCTGCATTGTAATGACCCATTAGAGCAC 1694 + +Query 137 ATCCAGAAGCTGATTGCCCCCAGGGAGACTAGTAATACCAGGGAACTGGCGACTGTGGAG 196 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| +Sbjct 1693 ATCCAGAAGCTGATTGCCCCCAGGGAGACTAGTAATACCAGGGAACTGGCGACTGCGGAG 1634 + +Query 197 TAGATCGCCAAAATCTGATGAACTCCCACTGATTCTAATTTTATACCATCTATTTTCTCT 256 + |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| +Sbjct 1633 TAGATCGCCAAAATCTGATGAACTCCCACTGATTCTAATTTTATGCCATCTATTTTCTCT 1574 + +Query 257 CTATTCAATTTGGATTCTTCTGAATATCTGGGATAATTATATGTGCCATTCCTTACGCTT 316 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1573 CTATTCAATTTGGATTCTTCTGAATATCTGGGATAATTATATGTGCCATTCCTTACGCTT 1514 + +Query 317 TCCATGCATTCATTATCACATTTGTGATAGAACTCAAAACAGCCATTACCGATTTCCTTG 376 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1513 TCCATGCATTCATTATCACATTTGTGATAGAACTCAAAACAGCCATTACCGATTTCCTTG 1454 + +Query 377 GCGTTGTTCCTCAGTTGTGATTTGACTTTTTCATACAAACTTTTTACGTTAAAGTCATGG 436 + || ||||| || ||||||||||||||||||||||| ||| |||||||||||||||||||| +Sbjct 1453 GCATTGTTTCTAAGTTGTGATTTGACTTTTTCATATAAATTTTTTACGTTAAAGTCATGG 1394 + +Query 437 AAATCTAGGGTTCTTTCATTCTCGAGCAGGATGAGTAATTCAGCGTTATAAGTCCACACA 496 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||| +Sbjct 1393 AAATCTAGGGTTCTTTCATTCTCGAGCAGTATGAGTAATTCAGCGTTATAAGTCCATACA 1334 + +Query 497 TCCAAAAATCCATCATCGACtttttttATTCAAATTCTCAACCCTTT-CTCTAGATTATT 555 + |||||||||||||||||||||||||| |||||||||||||| ||||| |||||||||||| +Sbjct 1333 TCCAAAAATCCATCATCGACTTTTTT-ATTCAAATTCTCAATCCTTTTCTCTAGATTATT 1275 + +Query 556 GAATT 560 + ||||| +Sbjct 1274 GAATT 1270 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 7250135 + + +Query= 170144-17ech4_c34 + +Length=207 + + +***** No hits found ***** + + + +Lambda K H + 1.34 0.622 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2569023 + + +Query= 170144-17ech4_c44 + +Length=441 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 455 5e-131 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 455 bits (246), Expect = 5e-131 + Identities = 262/270 (97%), Gaps = 0/270 (0%) + Strand=Plus/Minus + +Query 23 TCTCCTCTCATCAAAGGCAGAGAGGACCATTCTCTCTACCGTTATACTATTTTGGATCAG 82 + ||||||||| ||||| |||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 270 TCTCCTCTCGTCAAATGCAGAGAGGACCATTCTCTCTATCGTTATACTATTTTGGATCAG 211 + +Query 83 TCTCCCTTCATAGTCACTGAGTTGGAGTTCAGTACACATCTGTATGTAGAATCGTCCAAT 142 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 210 CCTCCCTTCATAGTCACTGAGTTGGAGTTCAGTACACATCTGTATGTAGAATCGTCCAAT 151 + +Query 143 CCCTTCAACCATTCTCCCAACAGATGCTCTGATTTCAGTAGTATTTTGGCGTTCTCCACC 202 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 150 TCCTTCAACCATTCTCCCAACAGATGCTCTGATTTCAGTAGTATTTTGGCGTTCTCCACC 91 + +Query 203 AGTTTCCATCTGTTCATAGGATCGTTTGGTGCCTTGAGACGCCATGGTGTAAATGTCACT 262 + |||||||||||||||||| ||||||||||||||||||||||||||||||| ||||||||| +Sbjct 90 AGTTTCCATCTGTTCATAAGATCGTTTGGTGCCTTGAGACGCCATGGTGTGAATGTCACT 31 + +Query 263 CAGTGAGTGATTATCTACCCTGCTTTTGCT 292 + ||| |||||||||||||||||||||||||| +Sbjct 30 CAGCGAGTGATTATCTACCCTGCTTTTGCT 1 + + + Score = 243 bits (131), Expect = 4e-67 + Identities = 144/150 (96%), Gaps = 1/150 (1%) + Strand=Plus/Minus + +Query 293 AGAGGACCATTCTCTCTATCGTTATACTATTT-GGATCAGCCTCCCTTCATAGTCACTGA 351 + |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| +Sbjct 250 AGAGGACCATTCTCTCTATCGTTATACTATTTTGGATCAGCCTCCCTTCATAGTCACTGA 191 + +Query 352 GTTGGAGTTCAGTACACATCTGTATGTAGAACCGTCCAATTCCTTCAATCATTCTCCCAA 411 + ||||||||||||||||||||||||||||||| |||||||||||||||| ||||||||||| +Sbjct 190 GTTGGAGTTCAGTACACATCTGTATGTAGAATCGTCCAATTCCTTCAACCATTCTCCCAA 131 + +Query 412 CAGATGCTCTGATTTCTGTGGTGTTTTGGC 441 + |||||||||||||||| || || ||||||| +Sbjct 130 CAGATGCTCTGATTTCAGTAGTATTTTGGC 101 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5667078 + + +Query= 170144-17ech4_c76 + +Length=306 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 396 2e-113 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 396 bits (214), Expect = 2e-113 + Identities = 230/238 (97%), Gaps = 0/238 (0%) + Strand=Plus/Minus + +Query 62 TGTTCGTTTCTTTCAGGAATCATCTCCATTATCCTCCTATCTGCTGTAATCGGATACTTC 121 + |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||| +Sbjct 238 TGTTCGTTTCTTTCAGGAATCATCTCCATTATTCTCCTGTCTGCTGTAATCGGATACTTC 179 + +Query 122 ATTGCCATCATCCATTTCATTCTGAGAGCGGGGTTCTTCTCCTGCCTTCCTGATGTGTAt 181 + ||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||| +Sbjct 178 ATTGCCATCATCCATTTCATTCTGAGAGCGGGGTTCTTCTCTTGTCTTCCTGATGTGTAT 119 + +Query 182 ttttttATTATTGCCATATGGTCCACAGTGGTTTTTGTCAGTATCTCGCGAGTGCGAGAC 241 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 118 TTTTTTATTATTGCCATATGGTCCACAGTGGTTTTTGTCAGTATCTCGCGAGTGCGAGAC 59 + +Query 242 TGCGACATCAGATCTCTTAATTCTCTTATTCTCTCCATGTTGAATATATTTGACCTGC 299 + |||||||||||||||||||||||| ||||||| ||||| ||||||||| ||||||||| +Sbjct 58 TGCGACATCAGATCTCTTAATTCTTTTATTCTTTCCATATTGAATATAATTGACCTGC 1 + + + +Lambda K H + 1.34 0.623 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3886812 + + +Query= 170144-17ech4_c89 + +Length=198 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 169 3e-45 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 169 bits (91), Expect = 3e-45 + Identities = 100/104 (96%), Gaps = 1/104 (1%) + Strand=Plus/Minus + +Query 1 GATGTTCTTCCAAGTATTTGTTTCTTCTCTCGTCGAATGCAGAGAGGACCATTCTCTCTA 60 + ||||||||||||| ||||||||||| |||||||| ||||||||||||||||||||||||| +Sbjct 292 GATGTTCTTCCAAATATTTGTTTCTCCTCTCGTCAAATGCAGAGAGGACCATTCTCTCTA 233 + +Query 61 TCGTTATACTATTT-GGATCAGCCTCCCTTCATAGTCACTGAGT 103 + |||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 232 TCGTTATACTATTTTGGATCAGCCTCCCTTCATAGTCACTGAGT 189 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2449224 + + +Query= 170144-17ech4_c90 + +Length=428 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 532 2e-154 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 532 bits (288), Expect = 2e-154 + Identities = 305/313 (97%), Gaps = 1/313 (0%) + Strand=Plus/Plus + +Query 72 AAATAAATCTGAAGTATGGCCCATTGGGGAGTCACCCAAGGGGGTGGAAGAAGGCTCCAT 131 + ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| +Sbjct 1839 AAATAAATCTGAAGTATGGCCCATTGGGGAGTCACCCAAAGGGGTGGAAGAAGGCTCCAT 1898 + +Query 132 TGGAAAAGTATGTAGGGCCTTACTGGCAAAGTCTGTATTCAATAGTCTGTATGCATCTTC 191 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1899 TGGAAAAGTATGTAGGGCCTTACTGGCAAAGTCTGTATTCAATAGTCTGTATGCATCTTC 1958 + +Query 192 ACAACTCGAGGGGTTTTCAGCTGAATCAAGAAAATTACTTCTAATTGTTCAAGCACTTAG 251 + |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| +Sbjct 1959 ACAACTCGAGGGGTTTTCAGCTGAATCAAGAAAATTACTTCTGATTGTTCAAGCACTTAG 2018 + +Query 252 GGACAACCTGGAACCTGGGACCTTTGATCTT-GGGGGTTATATGATGCAATTGAGGAGTG 310 + ||||||||||||||||||||||||||||||| |||||||||||||||||||||| ||||| +Sbjct 2019 GGACAACCTGGAACCTGGGACCTTTGATCTTGGGGGGTTATATGATGCAATTGAAGAGTG 2078 + +Query 311 CCTGATTAATGATCCCTGGGTTTTGCTCAATGCGTCTTGGTTTAACTCCTTCCTTATGCA 370 + | ||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||| +Sbjct 2079 CTTGATTAATGATCCCTGGGTTTTGCTTAACGCGTCTTGGTTCAACTCCTTCCTTATGCA 2138 + +Query 371 TGCACTGAAATAA 383 + ||||||||||||| +Sbjct 2139 TGCACTGAAATAA 2151 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5494139 + + +Query= 170144-17ech4_c96 + +Length=208 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 305 2e-86 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 305 bits (165), Expect = 2e-86 + Identities = 197/212 (93%), Gaps = 5/212 (2%) + Strand=Plus/Minus + +Query 1 CGAGCAGGATGAGTAATTCAGCGTTATAAGTCCACACATCCAAAA-TCCATCATCGACTT 59 + ||||||| |||||||||||||||||||||||||| |||||||||| |||||||||||||| +Sbjct 1371 CGAGCAGTATGAGTAATTCAGCGTTATAAGTCCATACATCCAAAAATCCATCATCGACTT 1312 + +Query 60 TTT-ATTCAAATTCTCAACCCTTTTCTCTAGATTATTGAATTCTTTGCCCACTGAAGTAA 118 + ||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| +Sbjct 1311 TTTTATTCAAATTCTCAATCCTTTTCTCTAGATTATTGAATTCTTTGCCCACTGAAGTAA 1252 + +Query 119 ATTGAATGTTCATCTTTTCAATTATTGAGTTCACTTTGTTGCTGATCCCATCAATTGCGA 178 + |||||||||||||||||||||||| |||||| |||||||||||||||||||||||||||| +Sbjct 1251 ATTGAATGTTCATCTTTTCAATTACTGAGTTTACTTTGTTGCTGATCCCATCAATTGCGA 1192 + +Query 179 TTTAT-T-CAATTYTGATTCTGCTGCGTAACC 208 + ||| | | | || |||| | ||||||||||| +Sbjct 1191 TTTGTGTACTTTTCTGATCC-GCTGCGTAACC 1161 + + + +Lambda K H + 1.34 0.622 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2582334 + + +Query= 170144-17ech4_c98 + +Length=855 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 1411 0.0 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 1411 bits (764), Expect = 0.0 + Identities = 823/852 (97%), Gaps = 2/852 (0%) + Strand=Plus/Minus + +Query 6 TTATTTCAGTGCATGCATAAGGAAGGAGTTGAACCAAGACGCATTAAGCAAAACCCAGGG 65 + |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| +Sbjct 2151 TTATTTCAGTGCATGCATAAGGAAGGAGTTGAACCAAGACGCGTTAAGCAAAACCCAGGG 2092 + +Query 66 ATCATTAATCAGGCACTCCTCAATTGCACCATATAACCCTCCAAGATCAAAGGTTCCAGG 125 + ||||||||||| |||||| ||||||||| |||||||||| |||||||||||||| ||||| +Sbjct 2091 ATCATTAATCAAGCACTCTTCAATTGCATCATATAACCCCCCAAGATCAAAGGTCCCAGG 2032 + +Query 126 TTCCAGGTTGTCCCTAAGTGCCTGAACAATTAGAAGTAATTT-CTTGATTCAGCTGAAAA 184 + ||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||||| +Sbjct 2031 TTCCAGGTTGTCCCTAAGTGCTTGAACAATCAGAAGTAATTTTCTTGATTCAGCTGAAAA 1972 + +Query 185 CCCCTCGAGTTGTGAAGATGCATACAGACTATTGAATACAGACTTTGCCAGTAAGGCCCT 244 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1971 CCCCTCGAGTTGTGAAGATGCATACAGACTATTGAATACAGACTTTGCCAGTAAGGCCCT 1912 + +Query 245 ACATACTTTTCCAATGGAGCCTTCTTCCACCCCCTTGGGTGACTCCCCAATGGGCCATAC 304 + ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| +Sbjct 1911 ACATACTTTTCCAATGGAGCCTTCTTCCACCCCTTTGGGTGACTCCCCAATGGGCCATAC 1852 + +Query 305 TTCAGATTTATTTTCAAAAA-TTCTTTGGTCATGTCCTTTTCTTTAACAGAAGACTCTGC 363 + |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| +Sbjct 1851 TTCAGATTTATTTTCAAAAAATTCTTTGGTCATGTCCTTTTCTTTAACAGAAGACTCTGC 1792 + +Query 364 TTCAATCATGCTCTCAATCTGTTGAAGAGACTGGAGAAGGCAACGCCTCATTTCCATACC 423 + ||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||| +Sbjct 1791 TTCGATCATGCTCTCAATCTGTTGAAGAGACTGAAGAAGGCAACGCCTCATTTCCATACC 1732 + +Query 424 CCATTTCATTTTGATTTTTGAGGTTCCATTGGTTCTCATATACAGAAACATTGGCCTTGA 483 + ||||||||||||||||||||||||||| |||||||||| |||||||||||||||||| || +Sbjct 1731 CCATTTCATTTTGATTTTTGAGGTTCCGTTGGTTCTCACATACAGAAACATTGGCCTCGA 1672 + +Query 484 CACCTGGCCAATTGAACTCCTTAGAATCATGTCCCCTATTTCAAGAACACAATACTTCTC 543 + |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| +Sbjct 1671 CACCTGGCCAATTGAACTCCGTAGAATCATGTCCCCTATTTCAAGAACACAATACTTCTC 1612 + +Query 544 CCACTTGTGTGGCTCTAGCCTAGGATCAGTGAGAGAAAACTCCATACTCACAAAATTTAC 603 + ||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| +Sbjct 1611 CCACTTGTGTGGCTCCAGCCTCGGATCGGTGAGAGAAAATTCCATACTCACAAAATTTAC 1552 + +Query 604 CACGTCTGTGTCATTCCTTAGATGAGATCTTCCTTTTACAATGAACCCATATAAATTTGT 663 + |||||| ||||| |||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 1551 CACGTCAGTGTCGTTCCTTAGATGAGATCTTCCTTTTACAATGAACCCATATAGATTTGT 1492 + +Query 664 CTTCCGCCTTCCTTCTTTCGTTTTGCATTTGCTTATCATTGGGATTAGCTGAAAATCATC 723 + | |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| +Sbjct 1491 CCTCCGCCTTCCTTCTTTCGTTCTGCATTTGCTTATCATTGGGATTAGCTGAAAATCATC 1432 + +Query 724 CATTGCTGCACAAGATGCATTGAGTAAGGCTGTGTTTATATATACTCCTTTCATTATGTA 783 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1431 CATTGCTGCACAAGATGCATTGAGTAAGGCTGTGTTTATATATACTCCTTTCATTATGTA 1372 + +Query 784 CTCCGTGGCCCTGCAATGAGACACTTCTGCTGTGAAGTAGTTCCTCCTCATACTCGCAAT 843 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1371 TTCCGTGGCCCTGCAATGAGACACTTCTGCTGTGAAGTAGTTCCTCCTCATACTCGCAAT 1312 + +Query 844 ATGCTCAATAGG 855 + |||||||| || +Sbjct 1311 GTGCTCAATTGG 1300 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 11154505 + + +Query= 170144-17ech4_c104 + +Length=281 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 219 4e-60 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 219 bits (118), Expect = 4e-60 + Identities = 168/190 (88%), Gaps = 11/190 (6%) + Strand=Plus/Minus + +Query 1 TCGTAAATAATGGCGCTTTGAATGCATGCCTCAGTTTGGTTTTGGTTCCTAGTTTGAATT 60 + ||||||||||| |||||||| ||||||| || || ||||||||||||| |||||||||| +Sbjct 190 TCGTAAATAATAACGCTTTGATTGCATGCTTCGGTCTGGTTTTGGTTCCCAGTTTGAATT 131 + +Query 61 GAATGGCTAATC-----------TATGTTCCCAATTTGCAATATCAAGCTAGCAATTCCA 109 + |||||||||||| ||||||||||||||| ||||||||||||||||||||| +Sbjct 130 GAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGTAATATCAAGCTAGCAATTCCA 71 + +Query 110 TTTGCCATACAGATTGAGCCGATGATTATTATCTTTTGATTTGGATTCATTTTAAACTCC 169 + |||| ||||||||||||||| |||||||||||||| |||||||||||||||||||||||| +Sbjct 70 TTTGTCATACAGATTGAGCCAATGATTATTATCTTCTGATTTGGATTCATTTTAAACTCC 11 + +Query 170 TGCTTTTGCT 179 + |||||||||| +Sbjct 10 TGCTTTTGCT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3554037 + + +Query= 170144-17ech4_c112 + +Length=414 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 488 4e-141 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 488 bits (264), Expect = 4e-141 + Identities = 278/285 (98%), Gaps = 0/285 (0%) + Strand=Plus/Minus + +Query 74 AAGAGTCATGTCAGTCAAATAGTGTGAAGCAGGCACAGAAGCATTGGTTATTTTAAGTGA 133 + |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| +Sbjct 285 AAGAGTCATGTCAGTCAAATAGCGTGAAGCAGGCACAGAAGCATTGGTTATTTTAAGTGC 226 + +Query 134 TTCATTGTATTCTTCTTCCAGAATACACTTAACTATTTGTTTCCCCGCATGAGTAGCTGA 193 + ||||| |||||||||||||||||||| |||||||||||||||||||||| |||||||||| +Sbjct 225 TTCATCGTATTCTTCTTCCAGAATACGCTTAACTATTTGTTTCCCCGCACGAGTAGCTGA 166 + +Query 194 TTCGATTTCCAGACCAAGAGTGCTGCCTCTCCCTCTTAGAGACTTCTGGTCTCGGCGAAG 253 + ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| +Sbjct 165 TTCGATTTCCAGACCAAGAGTGCTGCCTCTCCCTCTTAGGGACTTCTGGTCTCGGCGAAG 106 + +Query 254 CCTATCGAGAAATGGGGCATCGCCAAGCCCCCAGTTTGCAAACTGCTTGCGGATATGCCA 313 + ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||| +Sbjct 105 CCTATCGAGAAATGGGGCATCGCCAAGCCCCCAGTTTGCAAACCGCTTGCGGATATGCCA 46 + +Query 314 AAGAAAGCAATCTACCTGAAAGCTTGACACAGTGTTTGAATCCAT 358 + ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 45 AAGAAAGCAATCTACCTGAAAGCTTGACACAGTGTTTGAATCCAT 1 + + + Score = 87.9 bits (47), Expect = 2e-20 + Identities = 47/47 (100%), Gaps = 0/47 (0%) + Strand=Plus/Minus + +Query 1 CAAAGAAAGCAATCTACCTGAAAGCTTGACACAGTGTTTGAATCCAT 47 + ||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 47 CAAAGAAAGCAATCTACCTGAAAGCTTGACACAGTGTTTGAATCCAT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5307897 + + +Query= 170144-17ech4_c125 + +Length=168 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 165 3e-44 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 165 bits (89), Expect = 3e-44 + Identities = 94/96 (98%), Gaps = 1/96 (1%) + Strand=Plus/Minus + +Query 74 AATGGAGCCTTCTTCCACCCCCTTGGGTGACTCCCCAATGGGCCATACTTCAGATTTATT 133 + ||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 1899 AATGGAGCCTTCTTCCACCCCTTTGGGTGACTCCCCAATGGGCCATACTTCAGATTTATT 1840 + +Query 134 TTCAAAAA-TTCTTTGGTCATGTCCTTTTCTTTAAC 168 + |||||||| ||||||||||||||||||||||||||| +Sbjct 1839 TTCAAAAAATTCTTTGGTCATGTCCTTTTCTTTAAC 1804 + + + Score = 124 bits (67), Expect = 5e-32 + Identities = 71/73 (97%), Gaps = 0/73 (0%) + Strand=Plus/Minus + +Query 1 TGTTGAAGAGACTGGAGAAGGCAACGCCTCATTTCCATACCCCATTTCATTTTGATTTTT 60 + |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1772 TGTTGAAGAGACTGAAGAAGGCAACGCCTCATTTCCATACCCCATTTCATTTTGATTTTT 1713 + +Query 61 GAGGTTCCATTGG 73 + |||||||| |||| +Sbjct 1712 GAGGTTCCGTTGG 1700 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2049894 + + +Query= 170144-17ech4_c130 + +Length=406 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 701 0.0 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 701 bits (379), Expect = 0.0 + Identities = 397/406 (98%), Gaps = 0/406 (0%) + Strand=Plus/Minus + +Query 1 TCAACATCTACAGCACTCTGCTGTTCCTGTCGATATTCTTCCCTCATTGACTCAGGCACT 60 + |||||||| ||||||||||||||||||||| |||||||||||||||| |||||||||||| +Sbjct 948 TCAACATCCACAGCACTCTGCTGTTCCTGTTGATATTCTTCCCTCATGGACTCAGGCACT 889 + +Query 61 CCTTCCGTAGAAGGCCCTCTTTTCAAACCGTATTTAATGCGACGATAAATACATTTGAAG 120 + ||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 888 CCTTCCGTAGAAGGCCCTCTTTTCAAACCGTATTTAAGGCGACGATAAATACATTTGAAG 829 + +Query 121 AAAAGACGATCAAGAATCCACAATATCAGGTGCAAGATCCCAATTATATTTGCTGCAATG 180 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 828 AAAAGACGATCAAGAATCCACAATATCAGGTGCAAGATCCCAATTATATTTGCTGCAATG 769 + +Query 181 ACAAGAGGATCACTTGAATCGCTGTATCTGCACTCCCATCCGTTTCTGGTAGGCCTGCAA 240 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 768 ACAAGAGGATCACTTGAATCGCTGTATCTGCACTCCCATCCGTTTCTGGTAGGCCTGCAA 709 + +Query 241 ATTTTCAAGAAGGTCATCTTTCAGACCGGCGCTGGAACTGGGGTGTGTTCCAACTGTTCT 300 + ||||||||||||||||||||||||||| ||||||||||| || |||||||||| |||||| +Sbjct 708 ATTTTCAAGAAGGTCATCTTTCAGACCTGCGCTGGAACTAGGATGTGTTCCAATTGTTCT 649 + +Query 301 CATTGCATGCACCATCTGCCTAGTCTGATTGGCAACTTCCATGGCCTCTGCTGCCTGCTC 360 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || +Sbjct 648 CATTGCATGCACCATCTGCCTAGTCTGATTGGCAACTTCCATGGCCTCTGCTGCCTGTTC 589 + +Query 361 ACTCGACCCAGCCATCTGTTCCATAGCCTTAGCTGTAGTGCTAGCC 406 + |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 588 ACTCGACCCAGCCATCTGTTCCATAGCCTTAGCTGTAGTGCTAGCC 543 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5201473 + + +Query= 170144-17ech4_c141 + +Length=424 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 514 7e-149 + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 132 9e-34 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 514 bits (278), Expect = 7e-149 + Identities = 319/339 (94%), Gaps = 1/339 (0%) + Strand=Plus/Minus + +Query 1 TCATAGTGATAATTAGGAGCATTCAGCTCGACTGATTTGACTACTTTCCC-TTCTCTATT 59 + ||||||||||||||||||||||||| ||| |||||||||||||||||||| || |||||| +Sbjct 850 TCATAGTGATAATTAGGAGCATTCAACTCAACTGATTTGACTACTTTCCCCTTTTCTATT 791 + +Query 60 TTGAAGACCTTGTATGAGGCCTGCCCATTACTCAGTCCATCGGTCATTACTGTAAAGCAA 119 + ||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||||||| +Sbjct 790 TTGAAGATTTTGTATGAGGCCTGCCCATTACTTAGTCCATCGGTCATTACAGTAAAGCAA 731 + +Query 120 GAGCCATTTAAGCACGCACATTCAGATTCCTGTGTTCTCAATATGTTGTTTTTCCAGCTC 179 + |||||||| ||||| ||||||||||| || |||||||||||||||||||||||||| ||| +Sbjct 730 GAGCCATTCAAGCATGCACATTCAGACTCTTGTGTTCTCAATATGTTGTTTTTCCAACTC 671 + +Query 180 TTTATGGTGTCTGTTATTATGTCATTGTATTTCAGCACAGCCACTGCTCCATTATCTGGG 239 + || || ||||||||||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 670 TTGATAGTGTCTGTTATTATGTCATTGTATTTCAGCACAGCCACTGCTCCATTGTCTGGG 611 + +Query 240 CCAGAAATTCCAATTGTCAACCAACTAGTGCCGTCATGGCAAGCACTTGCTGACCAAGCA 299 + |||||||||||||||||||||||||| | ||||||||||||||||||||||||||||||| +Sbjct 610 CCAGAAATTCCAATTGTCAACCAACTGGAGCCGTCATGGCAAGCACTTGCTGACCAAGCA 551 + +Query 300 ACTGACTCAAATCTTGAATTGTATGGAGAAGGGACTTCA 338 + ||||||||||||||||| ||||||||||| ||||||||| +Sbjct 550 ACTGACTCAAATCTTGAGTTGTATGGAGAGGGGACTTCA 512 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 132 bits (71), Expect = 9e-34 + Identities = 81/86 (94%), Gaps = 0/86 (0%) + Strand=Plus/Minus + +Query 339 GCTCATGTCAGCCGATTCATTAACTCCAGATACTCCAAAGCTGGGCAACTCCATGCTGAA 398 + ||||||||||||||||||||||||||||||||| ||||||||||| | |||||| ||||| +Sbjct 1596 GCTCATGTCAGCCGATTCATTAACTCCAGATACCCCAAAGCTGGGTAGCTCCATACTGAA 1537 + +Query 399 GTTGGCTACAAACCCATATCGGTAGA 424 + |||||||||||||||||| ||||||| +Sbjct 1536 GTTGGCTACAAACCCATAGCGGTAGA 1511 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5440927 + + +Query= 170144-17ech4_c142 + +Length=335 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 427 8e-123 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 427 bits (231), Expect = 8e-123 + Identities = 259/273 (95%), Gaps = 0/273 (0%) + Strand=Plus/Minus + +Query 40 ATGGAACGGTTCCTTTTTGGAATCCACGAATGTGTAGTAGCAACAGCATCATATTCCATG 99 + |||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||||| +Sbjct 2045 ATGGAACGATTCCTTTTTGGAATCCAAGAATGTGTAGTTGCAACAGCATCATATTCCATG 1986 + +Query 100 CTTTTAGCTGGACCATGGGCTGGCATCACCACGGCACTGTTTACGGACTCAATTCCCTTG 159 + |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| +Sbjct 1985 CTTTTAGCTGGACCATGGGCTGGCATTACCACGGCACTGTTTACGGACTCAATTCCCTTA 1926 + +Query 160 TGGTTGACAAACGGATTCAGAGGATTACACAATCTCCCTCGATAATCTACATCCATCAGT 219 + ||||||||||||||||||||||||||||||||||| || ||||||||||||||||| || +Sbjct 1925 TGGTTGACAAACGGATTCAGAGGATTACACAATCTTCCCCGATAATCTACATCCATTAGC 1866 + +Query 220 TCCCATTTCAAGCAGACTTCAGGAATGTGGAGATTCCGGATATTATACAGATTTGGTCCT 279 + |||||||||||||||||||| || |||||||||||||||||||| || |||||||||||| +Sbjct 1865 TCCCATTTCAAGCAGACTTCCGGGATGTGGAGATTCCGGATATTGTATAGATTTGGTCCT 1806 + +Query 280 CCATCTGAAACCAGTAGTCCTGCCTTTGGATGG 312 + |||||||||||||||||||||||||||| |||| +Sbjct 1805 CCATCTGAAACCAGTAGTCCTGCCTTTGAATGG 1773 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4272831 + + +Query= 170144-17ech4_c153 + +Length=139 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 228 3e-63 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 228 bits (123), Expect = 3e-63 + Identities = 133/138 (96%), Gaps = 0/138 (0%) + Strand=Plus/Minus + +Query 1 AGTGTACATCTGTTCCCAGCAGGTTCCTTGGGTCAAGTGCAATACTTCAATATAAACACT 60 + |||||||||||||||||||||||||||||| || ||||||||||||||||| || ||||| +Sbjct 755 AGTGTACATCTGTTCCCAGCAGGTTCCTTGAGTTAAGTGCAATACTTCAATGTAGACACT 696 + +Query 61 GCTTGTTCCACCTGCTACCGGCAGGAATCTGGTTTTGCGGACCAGTTCTCTCTCCAACAT 120 + ||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| +Sbjct 695 GCTTGTTCCACCTGCTACCGGCAGGAATCTGGTTTTGCGGACCAGTTCTCTTTCCAACAT 636 + +Query 121 GTATGCCACCATTAAAGG 138 + |||||||||||||||||| +Sbjct 635 GTATGCCACCATTAAAGG 618 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1678194 + + +Query= 170144-17ech4_c157 + +Length=189 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 189 2e-51 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 189 bits (102), Expect = 2e-51 + Identities = 113/118 (96%), Gaps = 1/118 (1%) + Strand=Plus/Minus + +Query 53 CTCCAGATTCTGATTGAAAGACACCCATGGTCGATTCGAGCCATGCCAATTGTCCCTGCA 112 + ||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 953 CTCCAGATTCTGATTAAAAGACACCCATGGTCGATTCGAGCCATGCCAATTGTCTCTGCA 894 + +Query 113 CACACATATGATTTCACCAAAATCAGGATAGCAGGAGCATTCCTCATAGTGGATAATT 170 + ||||||||||||||||||| |||||||||| |||||||||||||||||||| |||||| +Sbjct 893 CACACATATGATTTCACCAGAATCAGGATAACAGGAGCATTCCTCATAGTG-ATAATT 837 + + + +Lambda K H + 1.35 0.627 1.14 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2329425 + + +Query= 170144-17ech4_c165 + +Length=290 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 420 1e-120 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 420 bits (227), Expect = 1e-120 + Identities = 270/291 (93%), Gaps = 1/291 (0%) + Strand=Plus/Plus + +Query 1 GATAATAGTATAAGGATCGGTT-CAAAGGGGATGTGTTTGTCATAAGAGAGCCATTCATC 59 + ||||| ||| |||| ||||||| ||||||||||||||||||||||||||||||||||||| +Sbjct 327 GATAACAGTGTAAGAATCGGTTCCAAAGGGGATGTGTTTGTCATAAGAGAGCCATTCATC 386 + +Query 60 TCTTGCTCCCACTTGGAATGCAGAACCTTCTTCTTAACTCAAGGGGCCCTGTTAAATGAC 119 + || ||||||||||||||||| ||||| |||||||||||||||||||||||| | |||||| +Sbjct 387 TCATGCTCCCACTTGGAATGTAGAACATTCTTCTTAACTCAAGGGGCCCTGCTGAATGAC 446 + +Query 120 AAACATTCCAATGGAACCATTAAAGACAGAAGCCCCTATCGAACCCTGATGAGTTGTCCT 179 + ||||| |||||||| || | ||||||||||||||||||||||||||||||||||||||| +Sbjct 447 AAACACTCCAATGGGACTGTCAAAGACAGAAGCCCCTATCGAACCCTGATGAGTTGTCCT 506 + +Query 180 ATTGGTGAAGTTCCCTCTCCATATAACTCAAGATTTGAGTCAGTTGCCTGGTCAGCAAGT 239 + ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||| +Sbjct 507 ATTGGTGAAGTCCCCTCTCCATACAACTCAAGATTTGAGTCAGTTGCTTGGTCAGCAAGT 566 + +Query 240 GCCTGCCATGATGGCTCAAGTTGGTTAACAATTGGAATTTCTGGCCCAGAC 290 + || |||||||| ||||| |||||||| |||||||||||||||||||||||| +Sbjct 567 GCTTGCCATGACGGCTCCAGTTGGTTGACAATTGGAATTTCTGGCCCAGAC 617 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3673836 + + +Query= 170144-17ech4_c168 + +Length=208 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 340 6e-97 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 340 bits (184), Expect = 6e-97 + Identities = 200/208 (96%), Gaps = 0/208 (0%) + Strand=Plus/Minus + +Query 1 TCTGATTGAAAGACACCCATGGTCGATTCGAGCCATGCCAATTGTCCCTGCACACACATA 60 + ||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 945 TCTGATTAAAAGACACCCATGGTCGATTCGAGCCATGCCAATTGTCTCTGCACACACATA 886 + +Query 61 TGATTTCACCAAAATCAGGATAGCAGGAGCATTCCTCATAGTGATAATTAGGAGCATTCA 120 + ||||||||||| |||||||||| ||||||||||||||||||||||||||||||||||||| +Sbjct 885 TGATTTCACCAGAATCAGGATAACAGGAGCATTCCTCATAGTGATAATTAGGAGCATTCA 826 + +Query 121 ACTCGACTGATTTGACTACTTTCCCCCTTTCTATTTTGAAGATTCTGTACGAGGCCTGCC 180 + |||| ||||||||||||||||||||| ||||||||||||||||| |||| |||||||||| +Sbjct 825 ACTCAACTGATTTGACTACTTTCCCCTTTTCTATTTTGAAGATTTTGTATGAGGCCTGCC 766 + +Query 181 CATTACTTAGTCCATCGGTCATTACAGT 208 + |||||||||||||||||||||||||||| +Sbjct 765 CATTACTTAGTCCATCGGTCATTACAGT 738 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2582334 + + +Query= 170144-17ech4_c170 + +Length=133 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 230 9e-64 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 230 bits (124), Expect = 9e-64 + Identities = 130/133 (98%), Gaps = 0/133 (0%) + Strand=Plus/Minus + +Query 1 CAACAGATGCTCTGATTTCAGTAGTATTTTGGCGTTCTCCACCAGTTTCCATCTGTTCAT 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 133 CAACAGATGCTCTGATTTCAGTAGTATTTTGGCGTTCTCCACCAGTTTCCATCTGTTCAT 74 + +Query 61 AGGATCGTTTGGTGCCTTGAGACGCCATGGTGTAAATGTCACTCAGTGAGTGATTATCTA 120 + | ||||||||||||||||||||||||||||||| |||||||||||| ||||||||||||| +Sbjct 73 AAGATCGTTTGGTGCCTTGAGACGCCATGGTGTGAATGTCACTCAGCGAGTGATTATCTA 14 + +Query 121 CCCTGCTTTTGCT 133 + ||||||||||||| +Sbjct 13 CCCTGCTTTTGCT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1598280 + + +Query= 170144-17ech4_rep_c177 + +Length=1062 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 1406 0.0 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 1406 bits (761), Expect = 0.0 + Identities = 789/803 (98%), Gaps = 0/803 (0%) + Strand=Plus/Minus + +Query 1 TCAGGTGCAAGATCCCAATTATATTTGCTGCAATGACAAGAGGATCACTTGAATCGCTGT 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 803 TCAGGTGCAAGATCCCAATTATATTTGCTGCAATGACAAGAGGATCACTTGAATCGCTGT 744 + +Query 61 ATCTGCACTCCCATCCGTTTCTGGTAGGCCTGCAAATTTTCAAGAAGGTCATCTTTCAGA 120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 743 ATCTGCACTCCCATCCGTTTCTGGTAGGCCTGCAAATTTTCAAGAAGGTCATCTTTCAGA 684 + +Query 121 CCGGCGCTGGAACTGGGGTGTGTTCCAACTGTTCTCATTGCATGCACCATCTGCCTAGTC 180 + || ||||||||||| || |||||||||| ||||||||||||||||||||||||||||||| +Sbjct 683 CCTGCGCTGGAACTAGGATGTGTTCCAATTGTTCTCATTGCATGCACCATCTGCCTAGTC 624 + +Query 181 TGATTGGCAACTTCCATGGCCTCTGCTGCCTGCTCACTCGACCCAGCCATCTGTTCCATA 240 + |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| +Sbjct 623 TGATTGGCAACTTCCATGGCCTCTGCTGCCTGTTCACTCGACCCAGCCATCTGTTCCATA 564 + +Query 241 GCCTTAGCTGTAGTGCTAGCCAGAACCATTCTGTTTTCATGCCTGATTAATGGGTTGGTG 300 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 563 GCCTTAGCTGTAGTGCTAGCCAGAACCATTCTGTTTTCATGCCTGATTAATGGGTTGGTG 504 + +Query 301 GTAGTAGCCATTTGTCTGTGAGACCGATGCTGTGAATCAGCAATCTGTTCACAAGTGGCG 360 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 503 GTAGTAGCCATTTGTCTGTGAGACCGATGCTGTGAATCAGCAATCTGTTCACAAGTGGCA 444 + +Query 361 CACACTAGACCAAAAGCAGCTTCTGTGGTTACTGTTCCCATTCTGTTGTATATGAGGCCC 420 + |||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||| +Sbjct 443 CACACTAGGCCAAAAGCAGCTTCTGTGGTTACTGTTCCCATTCTGTTGTATATGAGACCC 384 + +Query 421 ATGCAACTGGCGAGTGCCCCAGTTGAGTAGCTTAATGATACCTCTTTAGCCCCATGGAAT 480 + ||||||||||||||||| |||||||||||||||| ||| ||||||||||||||||||||| +Sbjct 383 ATGCAACTGGCGAGTGCACCAGTTGAGTAGCTTAGTGACACCTCTTTAGCCCCATGGAAT 324 + +Query 481 GTTATTTCCCTTTTTAGCTTCTTGTACAATTTGACTGCTCTATCCATATTGTTCGGGTCC 540 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 323 GTTATTTCCCTTTTTAGCTTCTTGTACAATTTGACTGCTCTATCCATATTGTTCGGGTCC 264 + +Query 541 CCATTTCCATTTAGGGCATTTTGGACAAAGCGTCTACGCTGCAGTCCTCGCTCACTGGGC 600 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 263 CCATTTCCATTTAGGGCATTTTGGACAAAGCGTCTACGCTGCAGTCCTCGCTCACTGGGC 204 + +Query 601 ACGGTGAGCGTGAATACGAATCCCAAAATTCCCTTAGTCAGAGGTGACAGGATCGGTCTT 660 + ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 203 ACGGTGAGCGTGAATACGAATCCCAAAATTCCCTTAGTCAGAGGTGACAGGATTGGTCTT 144 + +Query 661 GTCTTTAGCCACTCCATGAGAGCCTCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCT 720 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 143 GTCTTTAGCCACTCCATGAGAGCCTCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCC 84 + +Query 721 AGTCTCTGTGCGATCTCGGCTTTGAGGGGGCCTGACGGGATGATAGAAAGAACGTACGTT 780 + |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 83 AGTCTCTGCGCGATCTCGGCTTTGAGGGGGCCTGACGGGATGATAGAAAGAACGTACGTT 24 + +Query 781 TCGACCTCGGTTAGAAGACTCAT 803 + ||||||||||||||||||||||| +Sbjct 23 TCGACCTCGGTTAGAAGACTCAT 1 + + + Score = 315 bits (170), Expect = 2e-88 + Identities = 176/179 (98%), Gaps = 0/179 (0%) + Strand=Plus/Minus + +Query 832 AAAATTCCCTTAGTCAGAGGTGACAGGATCGGTCTTGTCTTTAGCCACTCCATGAGAGCC 891 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| +Sbjct 179 AAAATTCCCTTAGTCAGAGGTGACAGGATTGGTCTTGTCTTTAGCCACTCCATGAGAGCC 120 + +Query 892 TCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCTAGTCTCTGTGCGATCTCGGCTTTG 951 + ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||| +Sbjct 119 TCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCCAGTCTCTGCGCGATCTCGGCTTTG 60 + +Query 952 AGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 1010 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 59 AGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 13906570 + + +Query= 170144-17ech4_rep_c178 + +Length=413 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 575 3e-167 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 575 bits (311), Expect = 3e-167 + Identities = 327/335 (98%), Gaps = 0/335 (0%) + Strand=Plus/Minus + +Query 79 TTACTTCAGCTCTATGTTGACAAAATGACCATCGTCAACATCCACAGCATTCTGCTGTTC 138 + ||||| |||||||||||||||||||||||||| |||||||||||||||| |||||||||| +Sbjct 982 TTACTCCAGCTCTATGTTGACAAAATGACCATTGTCAACATCCACAGCACTCTGCTGTTC 923 + +Query 139 CTGTTGATATTCTTCCCTCATGGACTCAGGCACTCCTTCCGTAGAAGGCCCTCTTTTCAA 198 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 922 CTGTTGATATTCTTCCCTCATGGACTCAGGCACTCCTTCCGTAGAAGGCCCTCTTTTCAA 863 + +Query 199 ACCGTATTTAATGCGACGATAAATACATTTGAAGAAAAGACGATCAAGAATCCACAATAT 258 + ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 862 ACCGTATTTAAGGCGACGATAAATACATTTGAAGAAAAGACGATCAAGAATCCACAATAT 803 + +Query 259 CAGGTGCAAGATCCCAATTATATTTGCTGCAATGACAAGAGGATCACTTGAATCGCTGTA 318 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 802 CAGGTGCAAGATCCCAATTATATTTGCTGCAATGACAAGAGGATCACTTGAATCGCTGTA 743 + +Query 319 TCTGCACTCCCATCCGTTTCTGGTAGGCCTGCAAATTTTCAAGAAGGTCATCTTTCAGAC 378 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 742 TCTGCACTCCCATCCGTTTCTGGTAGGCCTGCAAATTTTCAAGAAGGTCATCTTTCAGAC 683 + +Query 379 CGGCGCTGGAACTGGGGTGTGTTCCAACTGTTCTC 413 + | ||||||||||| || |||||||||| ||||||| +Sbjct 682 CTGCGCTGGAACTAGGATGTGTTCCAATTGTTCTC 648 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5294594 + + +Query= 170144-17ech4_rep_c186 + +Length=382 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 601 5e-175 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 601 bits (325), Expect = 5e-175 + Identities = 344/353 (97%), Gaps = 1/353 (0%) + Strand=Plus/Minus + +Query 31 AATTATTGAGTTCACTTTGTTGCTGATCCCATCAATTGCGATTTGTGTACTTTTCTGATC 90 + ||||| |||||| ||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1232 AATTACTGAGTTTACTTTGTTGCTGATCCCATCAATTGCGATTTGTGTACTTTTCTGATC 1173 + +Query 91 TGCTGCGTAACCAGATCCTTGCTCATTTTGATGATGGTATCCATACCATCCATCTATCAT 150 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1172 CGCTGCGTAACCAGATCCTTGCTCATTTTGATGATGGTATCCATACCATCCATCTATCAT 1113 + +Query 151 TCCTGTCCACCCTCCTTCAATGAATCCG-CAATTGCTCCAAAAAGTCCTCTGGATTGGAT 209 + ||||||||| |||||||||||||||||| ||||||| ||||||||||||||||||||||| +Sbjct 1112 TCCTGTCCATCCTCCTTCAATGAATCCGGCAATTGCCCCAAAAAGTCCTCTGGATTGGAT 1053 + +Query 210 AGAGGGAATATTCCTTAATCCTGTTGCCATTCTTAGTTGGGTGCTTTTAACATATTTGGG 269 + |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1052 AGAGGGGATATTCCTTAATCCTGTTGCCATTCTTAGTTGGGTGCTTTTAACATATTTGGG 993 + +Query 270 GCATTCCCCAATAGTAATGGGATGTACATTTTGAAAAGGAAGATTGCCTTTCAAGGCCCC 329 + |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 992 GCATTCTCCAATAGTAATGGGATGTACATTTTGAAAAGGAAGATTGCCTTTCAAGGCCCC 933 + +Query 330 GTGAGGAGTTTGGCATTTTGTAGTGCAATTGTGAACGTGTACATCCGACATCA 382 + ||||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 932 GTGAGGAGTTTGGCATTTTGTAGTGCAATTGTGAACGTGAACATCCGACATCA 880 + + + +Lambda K H + 1.34 0.622 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4882201 + + +Query= 170144-17ech4_rep_c188 + +Length=231 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 228 6e-63 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 228 bits (123), Expect = 6e-63 + Identities = 127/129 (98%), Gaps = 0/129 (0%) + Strand=Plus/Minus + +Query 52 TCAGTATGTCCTGGAAGAGAAGGTAACGGTGAGATTTCACCTACAATTGCCCCTTTCTCT 111 + ||||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||| +Sbjct 512 TCAGTATGTCCTGGAAGAGAAGGTAACGGTGAGATTTCACCTATAATTGCCCCTTCCTCT 453 + +Query 112 GTGAAAGCTCTAAGGAGTATCAGAGTTTCCAGTCGGTCAAAAATCACACTGAAGTTTGCT 171 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 452 GTGAAAGCTCTAAGGAGTATCAGAGTTTCCAGTCGGTCAAAAATCACACTGAAGTTTGCT 393 + +Query 172 TTCAATGTA 180 + ||||||||| +Sbjct 392 TTCAATGTA 384 + + + +Lambda K H + 1.34 0.622 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2888487 + + +Query= 170144-17ech4_rep_c190 + +Length=337 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 279 2e-78 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 279 bits (151), Expect = 2e-78 + Identities = 157/160 (98%), Gaps = 0/160 (0%) + Strand=Plus/Minus + +Query 151 CCTTTCTTCAATTGTTTCTTCGCCTCTTTCGGACTGACGAAAGGAGTCCCATAGGGCCCT 210 + ||||||||||||||| ||||||||||||||||||||||||||||||||||||||| |||| +Sbjct 612 CCTTTCTTCAATTGTCTCTTCGCCTCTTTCGGACTGACGAAAGGAGTCCCATAGGCCCCT 553 + +Query 211 AATGGCCATTTCCTGCCTGATGGTGAATAATCTAGTCTTGATCCTTGCTCTGCTTTCCTC 270 + |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| +Sbjct 552 AATGGCCATTTCCTGCCTGATGGTGAATAATCTAGTCTTGATTCTTGCTCTGCTTTCCTC 493 + +Query 271 ATCAAGAGTGTAATCTGCCTTAGTGGCCATTTCTTCTCCA 310 + |||||||||||||||||||||||||||||||||||||||| +Sbjct 492 ATCAAGAGTGTAATCTGCCTTAGTGGCCATTTCTTCTCCA 453 + + + Score = 204 bits (110), Expect = 1e-55 + Identities = 114/116 (98%), Gaps = 0/116 (0%) + Strand=Plus/Minus + +Query 37 GAGTCCCATAGGGCCCTAATGGCCATTTCCTGCCTGATGGTGAATAATCTAGTCTTGATC 96 + |||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 569 GAGTCCCATAGGCCCCTAATGGCCATTTCCTGCCTGATGGTGAATAATCTAGTCTTGATT 510 + +Query 97 CTTGCTCTGCTTTCCTCATCAAGAGTGTAATCTGCCTTAGTGGCCATTTCTTCTCC 152 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 509 CTTGCTCTGCTTTCCTCATCAAGAGTGTAATCTGCCTTAGTGGCCATTTCTTCTCC 454 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4299453 + + +Query= 170144-17ech4_rep_c191 + +Length=313 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 291 1e-81 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 291 bits (157), Expect = 1e-81 + Identities = 167/172 (97%), Gaps = 0/172 (0%) + Strand=Plus/Minus + +Query 35 TCATTCTTCACCTCTCCACCTGGAGTGTACATCTGTTCCCAGCAGGTTCCTTGGGTCAAG 94 + ||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||| +Sbjct 778 TCATTCTTCACCTCTCCACCTGGAGTGTACATCTGTTCCCAGCAGGTTCCTTGAGTTAAG 719 + +Query 95 TGCAATACTTCAATATAAACACTGCTTGTTCCACCTGCTACCGGCAGGAATCTGGTTTTG 154 + |||||||||||||| || |||||||||||||||||||||||||||||||||||||||||| +Sbjct 718 TGCAATACTTCAATGTAGACACTGCTTGTTCCACCTGCTACCGGCAGGAATCTGGTTTTG 659 + +Query 155 CGGACCAGTTCTCTCTCCAACATGTATGCCACCATTAAAGGGGCAATCTTAC 206 + |||||||||||||| ||||||||||||||||||||||||||||||||||||| +Sbjct 658 CGGACCAGTTCTCTTTCCAACATGTATGCCACCATTAAAGGGGCAATCTTAC 607 + + + Score = 161 bits (87), Expect = 8e-43 + Identities = 99/104 (95%), Gaps = 3/104 (3%) + Strand=Plus/Minus + +Query 205 ACCTACATCTCCTTGCCCTAATCAAAACGTTGGCTTTCTCCCCTTTTGTAAGATTGCTCA 264 + ||| |||||||||||||||| ||||||||||||||||||||||||||| ||||||||||| +Sbjct 2215 ACC-ACATCTCCTTGCCCTA-TCAAAACGTTGGCTTTCTCCCCTTTTGCAAGATTGCTCA 2158 + +Query 265 GCTCATTGATACTCAATGCTGGTCCTATATCTTTTGTTTTCCTT 308 + | ||||||||||||||||||||||| |||||||||||||||||| +Sbjct 2157 GTTCATTGATACTCAATGCTGGTCC-ATATCTTTTGTTTTCCTT 2115 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3979989 + + +Query= 170144-17ech4_rep_c192 + +Length=316 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 529 2e-153 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 529 bits (286), Expect = 2e-153 + Identities = 306/316 (97%), Gaps = 0/316 (0%) + Strand=Plus/Minus + +Query 1 TCTGTTGATTGGTGTTTCCTCCGCTCCTGGTTCTTATAGCCCAGTACTTGCTTCTAAGTT 60 + |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 1243 TCTGTTGATTGGTGTTTCCTCCGCTCCTGGTTCTTATAGCCCAGTATTTGCTTCTAAGTT 1184 + +Query 61 CAAGAGTAACGGAGTCCATTGTTTCCATGTTTTCATTTGAAGCAATTTGAACTCCTCTGG 120 + ||||||||| |||||||||||||||||||||||||||||||||||||||||| ||||||| +Sbjct 1183 CAAGAGTAATGGAGTCCATTGTTTCCATGTTTTCATTTGAAGCAATTTGAACCCCTCTGG 1124 + +Query 121 TGGACAATTGTCCTCTTGGGATCACTTTTGTCCCTCTGATAAAACTTGACACCCTCAGAT 180 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1123 TGGACAATTGTCCTCTTGGGATCACTTTTGTCCCTCTGATAAAACTTGACACCCTCAGAT 1064 + +Query 181 CTTCAAATGCTGCAGAATGGCATGCCATCCAGACCAGTTGACTCTTATGAACTGGATTCT 240 + ||||||||||||||||||||||||||||||| | ||| ||||||||||| |||||||||| +Sbjct 1063 CTTCAAATGCTGCAGAATGGCATGCCATCCATATCAGCTGACTCTTATGGACTGGATTCT 1004 + +Query 241 CATTCGGTCTAATAAGGCTGAACACTTGGCTGTTCTGAAGCAGACGAAAAGGATCTATCC 300 + ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| || +Sbjct 1003 CATTCGGTCTAATGAGGCTGAACACTTGGCTGTTCTGAAGCAGACGAAAAGGATCTACCC 944 + +Query 301 CAACTAGGGAGTACCC 316 + | |||||||||||||| +Sbjct 943 CGACTAGGGAGTACCC 928 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4019922 + + +Query= 170144-17ech4_rep_c193 + +Length=320 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 226 3e-62 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 226 bits (122), Expect = 3e-62 + Identities = 126/128 (98%), Gaps = 0/128 (0%) + Strand=Plus/Minus + +Query 96 TACAGTTAGAGAAGAGAATTGCATCCTACTCTGCTCTGGTGGAGCAGCTGCAAATGGCAG 155 + ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| +Sbjct 1934 TACAGTTAGAGAAGAGAATTGCATCCTACTCTGCTCTGGTGGAGCTGCTGCAAATGGCAG 1875 + +Query 156 TAGCTTTATTATTTGGGCAGTATCAAATGTCCCCAGTACATCGCGCATTTGCTGGAATAG 215 + ||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 1874 TAGCTTTATTATTTGGGCAGTGTCAAATGTCCCCAGTACATCGCGCATTTGCTGGAATAG 1815 + +Query 216 TGTTCTCA 223 + |||||||| +Sbjct 1814 TGTTCTCA 1807 + + + Score = 119 bits (64), Expect = 5e-30 + Identities = 70/73 (96%), Gaps = 0/73 (0%) + Strand=Plus/Minus + +Query 24 CACAGACTCAGGTCCATTGATTTCCCACATCATTGATGATGAATAGGTTATTGTCAATTT 83 + ||| || |||||||||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 1655 CACTGATTCAGGTCCATTGATCTCCCACATCATTGATGATGAATAGGTTATTGTCAATTT 1596 + +Query 84 CTCTGTTCCTTGT 96 + ||||||||||||| +Sbjct 1595 CTCTGTTCCTTGT 1583 + + + +Lambda K H + 1.34 0.622 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4073166 + + +Query= 170144-17ech4_rep_c195 + +Length=288 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 488 3e-141 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 488 bits (264), Expect = 3e-141 + Identities = 280/288 (97%), Gaps = 0/288 (0%) + Strand=Plus/Minus + +Query 1 CCTTCCTTCTTTCGTTTTGCATTTGCTTATCATTGGGATTAGCTGAAAATCATCCATTGC 60 + |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1485 CCTTCCTTCTTTCGTTCTGCATTTGCTTATCATTGGGATTAGCTGAAAATCATCCATTGC 1426 + +Query 61 TGCACAAGATGCATTGAGTAAGGCTGTGTTTATATATACTCCTTTCATTATGTACTCCGT 120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 1425 TGCACAAGATGCATTGAGTAAGGCTGTGTTTATATATACTCCTTTCATTATGTATTCCGT 1366 + +Query 121 GGCCCTGCAATGAGACACTTCTGCTGTGAAGTAGTTCCTCCTCATACTCGCAATATGCTC 180 + |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 1365 GGCCCTGCAATGAGACACTTCTGCTGTGAAGTAGTTCCTCCTCATACTCGCAATGTGCTC 1306 + +Query 181 AATAGGAGCAACATCTTCTCCTATTTCGTCAAGCTCTATCCAGCTGGAATCCGTCAACTC 240 + ||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1305 AATTGGGGCAACATCCTCTCCTATTTCGTCAAGCTCTATCCAGCTGGAATCCGTCAACTC 1246 + +Query 241 ACATGCCTTGTTGAATTCACTCTGAATCCAACTTGCCAGTGACCTAAT 288 + |||||||||||||||||||||||||||||| ||||||||||| ||||| +Sbjct 1245 ACATGCCTTGTTGAATTCACTCTGAATCCAGCTTGCCAGTGATCTAAT 1198 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3647214 + + +Query= 170144-17ech4_rep_c199 + +Length=194 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 213 1e-58 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 213 bits (115), Expect = 1e-58 + Identities = 119/121 (98%), Gaps = 0/121 (0%) + Strand=Plus/Minus + +Query 43 TGGTCATGTCCTTTTCTTTAACAGAAGACTCTGCTTCAATCATGCTCTCAATCTGTTGAA 102 + ||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 1825 TGGTCATGTCCTTTTCTTTAACAGAAGACTCTGCTTCGATCATGCTCTCAATCTGTTGAA 1766 + +Query 103 GAGACTGGAGAAGGCAACGCCTCATTTCCATACCCCATTTCATTTTGATTTTTGAGGTTC 162 + ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1765 GAGACTGAAGAAGGCAACGCCTCATTTCCATACCCCATTTCATTTTGATTTTTGAGGTTC 1706 + +Query 163 C 163 + | +Sbjct 1705 C 1705 + + + Score = 58.4 bits (31), Expect = 6e-12 + Identities = 31/31 (100%), Gaps = 0/31 (0%) + Strand=Plus/Minus + +Query 164 AGGTCCCAGGTTCCAGGTTGTCCCTAAGTGC 194 + ||||||||||||||||||||||||||||||| +Sbjct 2041 AGGTCCCAGGTTCCAGGTTGTCCCTAAGTGC 2011 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2395980 + + +Query= 170144-17ech4_rep_c203 + +Length=295 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 357 9e-102 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 357 bits (193), Expect = 9e-102 + Identities = 276/313 (88%), Gaps = 18/313 (6%) + Strand=Plus/Minus + +Query 1 AAACCAGTAGTCCTGCCTTTGAATGGGTTTGTTCCCATAGCTTTCTTAACTCGAATGATC 60 + ||||||||||||||||||||||||||||||| |||||||| ||| ||| ||||||||||| +Sbjct 1798 AAACCAGTAGTCCTGCCTTTGAATGGGTTTGCTCCCATAGTTTTTTTAGCTCGAATGATC 1739 + +Query 61 TTTTCGTTTGGATTTGCATGTCGCCTCTGTGGCATCGATATGTGTACCTGTAGTCCTTAA 120 + ||||||||||||||||| |||| |||||||||||||| ||||| |||||||||||||||| +Sbjct 1738 TTTTCGTTTGGATTTGCGTGTCACCTCTGTGGCATCGGTATGTATACCTGTAGTCCTTAA 1679 + +Query 121 TGAATAGTTGAAGTGCCATTTGGGCTGTTGCTGGCCCGAGAT------------------ 162 + ||||||| ||||| |||||||||||||||||||||||||||| +Sbjct 1678 TGAATAGCTGAAGAGCCATTTGGGCTGTTGCTGGCCCGAGATCATTGTTTATCATGTTGT 1619 + +Query 163 TCTTTATCACTGTCACCCCAATGCTCATGTCAGCCGATTCATTAACTCCAGATACTCCAA 222 + |||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||| +Sbjct 1618 TCTTTATCACTGTCACTCCAATGCTCATGTCAGCCGATTCATTAACTCCAGATACCCCAA 1559 + +Query 223 AGCTGGGCAACTCCATGCTGAAGTTGGCTACAAACCCATATCGGTAGAAAAAACTTGTGA 282 + ||||||| | |||||| ||||||||||||||||||||||| ||||||||||| ||||||| +Sbjct 1558 AGCTGGGTAGCTCCATACTGAAGTTGGCTACAAACCCATAGCGGTAGAAAAAGCTTGTGA 1499 + +Query 283 ATTCAAATGTCCC 295 + ||||||| || || +Sbjct 1498 ATTCAAACGTTCC 1486 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3740391 + + +Query= 170144-17ech4_rep_c204 + +Length=241 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 141 8e-37 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 141 bits (76), Expect = 8e-37 + Identities = 133/157 (85%), Gaps = 18/157 (11%) + Strand=Plus/Minus + +Query 76 TGTCGCCTCTGTGGCATCGATATGTGTACCTGTAGTCCTTAATGAATAGTTGAAGTGCCA 135 + |||| |||||||||||||| ||||| ||||||||||||||||||||||| ||||| |||| +Sbjct 1720 TGTCACCTCTGTGGCATCGGTATGTATACCTGTAGTCCTTAATGAATAGCTGAAGAGCCA 1661 + +Query 136 TTTGGGCTGTTGCTGGCCCGAGAT------------------TCTTTATCACTGTCACCC 177 + |||||||||||||||||||||||| |||||||||||||||| | +Sbjct 1660 TTTGGGCTGTTGCTGGCCCGAGATCATTGTTTATCATGTTGTTCTTTATCACTGTCACTC 1601 + +Query 178 CAATGCTCATGTCAGCCGATTCATTAACTCCAGATAC 214 + ||||||||||||||||||||||||||||||||||||| +Sbjct 1600 CAATGCTCATGTCAGCCGATTCATTAACTCCAGATAC 1564 + + + +Lambda K H + 1.35 0.625 1.14 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3021597 + + +Query= 170144-17ech4_rep_c205 + +Length=316 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 518 4e-150 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 518 bits (280), Expect = 4e-150 + Identities = 304/316 (96%), Gaps = 0/316 (0%) + Strand=Plus/Minus + +Query 1 AGAAGTTTCTATCATTGACACCCCGCTTTATCATTCGAATCAGTTCCATTACTAGTGTCC 60 + ||||||| | |||||||| |||||||||||||||||||||||| |||||||||||||||| +Sbjct 664 AGAAGTTCCGATCATTGATACCCCGCTTTATCATTCGAATCAGCTCCATTACTAGTGTCC 605 + +Query 61 CAACTCCTTTTACTGCTGCACCAGCAGCTCCAGATCTCCTTGGGAGAGTTGAACCTTGCA 120 + ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 604 CAACTCCCTTTACTGCTGCACCAGCAGCTCCAGATCTCCTTGGGAGAGTTGAACCTTGCA 545 + +Query 121 TTAGAGAGCACATTCTGGGGTCCATCCCTGTACGCACTAAAGCTCTTGTTCTCTGATATG 180 + | ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| | +Sbjct 544 TCAGAGAGCACATTCTGGGATCCATCCCAGTACGCACTAAAGCTCTTGTTCTCTGATACG 485 + +Query 181 TAGCATCATTCAGGTTGGAATGCCAAATCATCAGGTGAGTGAGGCCAGCAGTAGCATCTT 240 + | ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||| +Sbjct 484 TGGCATCATTCAGGTTGGAATGCCAAATCATCAGGTGAGTGAGACCAGCAGTAGCATCTT 425 + +Query 241 CACCATTGTTTGCTTGGCGCCAAATTCTCCTGATTTCATCTTTGTCATACAGAATAAGCT 300 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| +Sbjct 424 CACCATTGTTTGCTTGGCGCCAAATTCTCCTGATTTCATCTTTGTCATACAGAATCAGCT 365 + +Query 301 CTCTCATCCATTTTCC 316 + |||||||||||||||| +Sbjct 364 CTCTCATCCATTTTCC 349 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4019922 + + +Query= 170144-17ech4_rep_c209 + +Length=428 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 645 0.0 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 645 bits (349), Expect = 0.0 + Identities = 402/428 (94%), Gaps = 2/428 (0%) + Strand=Plus/Minus + +Query 3 TTGTTCCTCAGTTGTGACTTAACCTTTTCATA-AAGTTTTTCACGTTAAAGTCATGGAAA 61 + ||||| || |||||||| || || |||||||| || ||||| |||||||||||||||||| +Sbjct 1450 TTGTTTCTAAGTTGTGATTTGACTTTTTCATATAAATTTTTTACGTTAAAGTCATGGAAA 1391 + +Query 62 TCTAGGGTTCTTTCGTTCTCGAGCAGGACGAGTAACTCAGCGTTATAAGTCCATACATCC 121 + |||||||||||||| ||||||||||| | |||||| |||||||||||||||||||||||| +Sbjct 1390 TCTAGGGTTCTTTCATTCTCGAGCAGTATGAGTAATTCAGCGTTATAAGTCCATACATCC 1331 + +Query 122 AAAA-TCCATCATCGACCTTTTTATTCAAATTTTCAATCCTTTTTTCTAGATTATTGAAC 180 + |||| |||||||||||| |||||||||||||| ||||||||||| |||||||||||||| +Sbjct 1330 AAAAATCCATCATCGACTTTTTTATTCAAATTCTCAATCCTTTTCTCTAGATTATTGAAT 1271 + +Query 181 TCTTTACCCACTGAAGTAAACTGAATGTTCATTTTTTCAATTACTGAGTTTACTTTGTTG 240 + ||||| |||||||||||||| ||||||||||| ||||||||||||||||||||||||||| +Sbjct 1270 TCTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTACTGAGTTTACTTTGTTG 1211 + +Query 241 CTGATCCCATCAATTGCGATTTGTGTACTTTTCTGATCTGCTGCGTAACCAGATCCCTGC 300 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||| +Sbjct 1210 CTGATCCCATCAATTGCGATTTGTGTACTTTTCTGATCCGCTGCGTAACCAGATCCTTGC 1151 + +Query 301 TCATTTTGATGGTGGTATCCATACCATCCATCTATCATTCCTGTCCATCCTCCTTCAATG 360 + ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1150 TCATTTTGATGATGGTATCCATACCATCCATCTATCATTCCTGTCCATCCTCCTTCAATG 1091 + +Query 361 AATCCAGCAATTGCCCCAAAAAGTCCTCTGGATTGGATAGAAGGGATATTTCTTAATCCT 420 + ||||| ||||||||||||||||||||||||||||||||||| |||||||| ||||||||| +Sbjct 1090 AATCCGGCAATTGCCCCAAAAAGTCCTCTGGATTGGATAGAGGGGATATTCCTTAATCCT 1031 + +Query 421 GTTGCCAT 428 + |||||||| +Sbjct 1030 GTTGCCAT 1023 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5494139 + + +Query= 170144-17ech4_rep_c210 + +Length=119 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 198 2e-54 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 198 bits (107), Expect = 2e-54 + Identities = 115/119 (97%), Gaps = 0/119 (0%) + Strand=Plus/Minus + +Query 1 GATTTGTGTACTTTTCTGATCTGCTGCGTAACCAGATCCCTGCTCATTTTGATGGTGGTA 60 + ||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| +Sbjct 1193 GATTTGTGTACTTTTCTGATCCGCTGCGTAACCAGATCCTTGCTCATTTTGATGATGGTA 1134 + +Query 61 TCCATACCATCCATCTATCATTCCTGTCCATCCTCCTTCAATGAATCCAGCAATTGCCC 119 + |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| +Sbjct 1133 TCCATACCATCCATCTATCATTCCTGTCCATCCTCCTTCAATGAATCCGGCAATTGCCC 1075 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1411814 + + +Query= 170144-17ech4_rep_c212 + +Length=132 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 126 1e-32 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 126 bits (68), Expect = 1e-32 + Identities = 77/81 (95%), Gaps = 1/81 (1%) + Strand=Plus/Minus + +Query 52 TCAAATCAGATCCGGAAGGAATTTGGGCTTCTCAACTCCTGTGGTATTGCATATGCTGTT 111 + ||| || ||||||||||||||||||||||||||||||||||| |||||||| |||||||| +Sbjct 332 TCATAT-AGATCCGGAAGGAATTTGGGCTTCTCAACTCCTGTAGTATTGCAGATGCTGTT 274 + +Query 112 TACCACTGTCCAAGCCATTGT 132 + ||||||||||||||||||||| +Sbjct 273 TACCACTGTCCAAGCCATTGT 253 + + + Score = 108 bits (58), Expect = 4e-27 + Identities = 58/58 (100%), Gaps = 0/58 (0%) + Strand=Plus/Minus + +Query 1 ATGCTGTTTACCACTGTCCAAGCCATTGTGCGATCCCTTCCCTCAATTATTTCAAATC 58 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 281 ATGCTGTTTACCACTGTCCAAGCCATTGTGCGATCCCTTCCCTCAATTATTTCAAATC 224 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1584961 + + +Query= 170144-17ech4_rep_c213 + +Length=153 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 141 5e-37 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 141 bits (76), Expect = 5e-37 + Identities = 78/79 (99%), Gaps = 0/79 (0%) + Strand=Plus/Minus + +Query 75 TGCCTTTCTCATGCGGCTTGACAATGTGGGGCTCTTTCCATCCGAAGAATGTCTTCATGC 134 + |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 988 TGCCTTTCTCATGCGGCTTGACAATGTGGGGCTCTTTCCATCCGAAAAATGTCTTCATGC 929 + +Query 135 ATTTGATTGCATCATATAG 153 + ||||||||||||||||||| +Sbjct 928 ATTTGATTGCATCATATAG 910 + + + Score = 134 bits (72), Expect = 8e-35 + Identities = 74/75 (99%), Gaps = 0/75 (0%) + Strand=Plus/Minus + +Query 1 TCAAGAATGGTTCAATTCTGGCATTCACTTCTTTTGACATTTGAGAAAGCTTGCCCTCAA 60 + |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| +Sbjct 784 TCAAGAATGGTTCAATTCTGGCATTCACTTCTTTGGACATTTGAGAAAGCTTGCCCTCAA 725 + +Query 61 TGCAGCCGTTCGGTT 75 + ||||||||||||||| +Sbjct 724 TGCAGCCGTTCGGTT 710 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1850229 + + +Query= 170144-17ech4_rep_c214 + +Length=126 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 148 2e-39 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 148 bits (80), Expect = 2e-39 + Identities = 83/85 (98%), Gaps = 0/85 (0%) + Strand=Plus/Minus + +Query 42 CATCCATCAACAGGAATTTTGACCGTTGAGAACAAGGAGGTCCATCAGGTAATCTGAGAG 101 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | +Sbjct 859 CATCCATCAACAGGAATTTTGACCGTTGAGAACAAGGAGGTCCATCAGGTAATCTGAGGG 800 + +Query 102 GGCGTGGTGTTTCCCDCAAGAATGG 126 + ||||||||||||||| ||||||||| +Sbjct 799 GGCGTGGTGTTTCCCTCAAGAATGG 775 + + + +Lambda K H + 1.34 0.623 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1505047 + + +Query= 170144-17ech4_rep_c215 + +Length=372 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 571 4e-166 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 571 bits (309), Expect = 4e-166 + Identities = 327/336 (97%), Gaps = 0/336 (0%) + Strand=Plus/Minus + +Query 35 ACTGAAGTTTGCTTTCAATGTAATATTTTTATCCATTATTGCTTGGTCCATTCTGATGCA 94 + |||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||| +Sbjct 405 ACTGAAGTTTGCTTTCAATGTAATGTTTTTATCCATTATTGCCTGGTCCATTCTGATGCA 346 + +Query 95 GAAGGGACCTGCCACCTTTTGCTTGGGCATGAGCATGAACCAGTCCCTTGACATCTCTTC 154 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 345 AAAGGGACCTGCCACCTTTTGCTTGGGCATGAGCATGAACCAGTCCCTTGACATCTCTTC 286 + +Query 155 AAGAGTCATGTCAGTCAAATAGTGTGAAGCAGGCACAGAAGCATTGGTTATTTTAAGTGA 214 + |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| +Sbjct 285 AAGAGTCATGTCAGTCAAATAGCGTGAAGCAGGCACAGAAGCATTGGTTATTTTAAGTGC 226 + +Query 215 TTCATTGTATTCTTCTTCCAGAATACACTTAACTATTTGTTTCCCCGCATGAGTAGCTGA 274 + ||||| |||||||||||||||||||| |||||||||||||||||||||| |||||||||| +Sbjct 225 TTCATCGTATTCTTCTTCCAGAATACGCTTAACTATTTGTTTCCCCGCACGAGTAGCTGA 166 + +Query 275 TTCGATTTCCAGACCAAGAGTGCTGCCTCTCCCTCTTAGAGACTTCTGGTCTCGGCGAAG 334 + ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| +Sbjct 165 TTCGATTTCCAGACCAAGAGTGCTGCCTCTCCCTCTTAGGGACTTCTGGTCTCGGCGAAG 106 + +Query 335 CCTATCGAGAAATGGGGCATCGCCAAGCCCCCAGTT 370 + |||||||||||||||||||||||||||||||||||| +Sbjct 105 CCTATCGAGAAATGGGGCATCGCCAAGCCCCCAGTT 70 + + + Score = 63.9 bits (34), Expect = 3e-13 + Identities = 34/34 (100%), Gaps = 0/34 (0%) + Strand=Plus/Minus + +Query 1 CCTCATCAGTATGTCCTGGAAGAGAAGGTAACGG 34 + |||||||||||||||||||||||||||||||||| +Sbjct 517 CCTCATCAGTATGTCCTGGAAGAGAAGGTAACGG 484 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4749171 + + +Query= 170144-17ech4_rep_c216 + +Length=243 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 222 3e-61 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 222 bits (120), Expect = 3e-61 + Identities = 126/129 (98%), Gaps = 0/129 (0%) + Strand=Plus/Minus + +Query 115 TCCATCAGGTAATCTGAGAGGGCGTGGTGTTTCCCTCAAGAATGGTTCAATTCTGGCATT 174 + |||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| +Sbjct 819 TCCATCAGGTAATCTGAGGGGGCGTGGTGTTTCCCTCAAGAATGGTTCAATTCTGGCATT 760 + +Query 175 CACTTCTTTTGACATTTGAGAAAGCTTGCCCTCAATGCAGCCGTTCGGTTCGAATCCATC 234 + ||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||| +Sbjct 759 CACTTCTTTGGACATTTGAGAAAGCTTGCCCTCAATGCAGCCGTTCGGTTCAAATCCATC 700 + +Query 235 CACATAGGC 243 + ||||||||| +Sbjct 699 CACATAGGC 691 + + + Score = 191 bits (103), Expect = 8e-52 + Identities = 112/116 (97%), Gaps = 1/116 (1%) + Strand=Plus/Minus + +Query 1 GATTTATGCCTTTCTCATGCGGCTTGACAATGTGGGGGCTCTTTCCATCCGAAGAATGTC 60 + ||||||||||||||||||||||||||||||||||||| ||||||||||||||| |||||| +Sbjct 994 GATTTATGCCTTTCTCATGCGGCTTGACAATGTGGGG-CTCTTTCCATCCGAAAAATGTC 936 + +Query 61 TTCATGCATTTGATTGCATCATATAGTGGTATTCCCTCCCCCTCATGGCTCGGATC 116 + |||||||||||||||||||||||||| ||||| ||||||||||||||||||||||| +Sbjct 935 TTCATGCATTTGATTGCATCATATAGCGGTATCCCCTCCCCCTCATGGCTCGGATC 880 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3048219 + + +Query= 170144-17ech4_rep_c217 + +Length=205 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 239 2e-66 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 239 bits (129), Expect = 2e-66 + Identities = 137/141 (97%), Gaps = 0/141 (0%) + Strand=Plus/Minus + +Query 29 AAAATCCATCATCGAtttttttATTCAAATTCTCAACCCTTTTCTCTAGATTATTGAATT 88 + ||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||| +Sbjct 1329 AAAATCCATCATCGACTTTTTTATTCAAATTCTCAATCCTTTTCTCTAGATTATTGAATT 1270 + +Query 89 CTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTATTGAGTTCACTTTGTTGC 148 + |||||||||||||||||||||||||||||||||||||||||| |||||| |||||||||| +Sbjct 1269 CTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTACTGAGTTTACTTTGTTGC 1210 + +Query 149 TGATCCCATCAATTGCGATTT 169 + ||||||||||||||||||||| +Sbjct 1209 TGATCCCATCAATTGCGATTT 1189 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2542401 + + +Query= 170144-17ech4_rep_c218 + +Length=367 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 316 2e-89 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 316 bits (171), Expect = 2e-89 + Identities = 192/202 (95%), Gaps = 2/202 (1%) + Strand=Plus/Minus + +Query 168 AGTACGCACTAAAGCTCTTGTTCTCTGATATGTAGCATCATTCAGATTGGAGTGCCAAAT 227 + |||||||||||||||||||||||||||||| || ||||||||||| ||||| |||||||| +Sbjct 516 AGTACGCACTAAAGCTCTTGTTCTCTGATACGTGGCATCATTCAGGTTGGAATGCCAAAT 457 + +Query 228 CATCAGATGAGTGAGACCAGCAGTAGCATCTTCACCATTGTTGGCTTGACGCCAAATTCT 287 + |||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||||||| +Sbjct 456 CATCAGGTGAGTGAGACCAGCAGTAGCATCTTCACCATTGTTTGCTTGGCGCCAAATTCT 397 + +Query 288 CCTGATT-CATCTTTGTCATATAGAATCAGCTCTCTCATCCATTTTCCATCTCTCTTTT- 345 + ||||||| ||||||||||||| ||||||||||||||||||||||||||||||||||||| +Sbjct 396 CCTGATTTCATCTTTGTCATACAGAATCAGCTCTCTCATCCATTTTCCATCTCTCTTTTT 337 + +Query 346 GTAGATTGGACCTCCAGTTTTC 367 + |||||||||||||||||||||| +Sbjct 336 GTAGATTGGACCTCCAGTTTTC 315 + + + Score = 281 bits (152), Expect = 7e-79 + Identities = 163/168 (97%), Gaps = 1/168 (1%) + Strand=Plus/Minus + +Query 1 AAATCATCAGATGAGTGAGACCAGCAGTAGCATCTTCACCATTGTTGGCTTGACGCCAAA 60 + |||||||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||| +Sbjct 460 AAATCATCAGGTGAGTGAGACCAGCAGTAGCATCTTCACCATTGTTTGCTTGGCGCCAAA 401 + +Query 61 TTCTCCTGATTTCATCTTTGTCATATAGAATCAGCTCTCTCATCCATTTTCCATCTCTCT 120 + ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| +Sbjct 400 TTCTCCTGATTTCATCTTTGTCATACAGAATCAGCTCTCTCATCCATTTTCCATCTCTCT 341 + +Query 121 TTT-GTAGATTGGACCTCCAGTTTTCTTTGGATCTTTCCCCGCACTGG 167 + ||| |||||||||||||||||||||||||||||||||||||||||||| +Sbjct 340 TTTTGTAGATTGGACCTCCAGTTTTCTTTGGATCTTTCCCCGCACTGG 293 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4682656 + + +Query= 170144-17ech4_rep_c219 + +Length=422 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 420 2e-120 + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 185 6e-50 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 420 bits (227), Expect = 2e-120 + Identities = 236/240 (98%), Gaps = 1/240 (0%) + Strand=Plus/Minus + +Query 1 ACAAAGCGTCTACGCTGCAGTCCTCGCTCACTGGGCACGGTGAGCGTGAATACGAATCCC 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 239 ACAAAGCGTCTACGCTGCAGTCCTCGCTCACTGGGCACGGTGAGCGTGAATACGAATCCC 180 + +Query 61 CAAAATTCCCTTAGTCAGAGGTGACAGGATCGGTCTTGTCTTTAGCCACTCCATGAGAGC 120 + ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 179 -AAAATTCCCTTAGTCAGAGGTGACAGGATTGGTCTTGTCTTTAGCCACTCCATGAGAGC 121 + +Query 121 CTCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCTAGTCTCTGTGCGATCTCGGCTTT 180 + |||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||| +Sbjct 120 CTCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCCAGTCTCTGCGCGATCTCGGCTTT 61 + +Query 181 GAGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 240 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 60 GAGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 1 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 185 bits (100), Expect = 6e-50 + Identities = 107/110 (97%), Gaps = 1/110 (1%) + Strand=Plus/Minus + +Query 313 CAAAAATCCATCATCGACtttttttATTCAAATTCTCAACCCTTTTCTCTAGATTATTGA 372 + |||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||| +Sbjct 1331 CAAAAATCCATCATCGACTTTTTT-ATTCAAATTCTCAATCCTTTTCTCTAGATTATTGA 1273 + +Query 373 ATTCTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTATTGAG 422 + ||||||||||||||||||||||||||||||||||||||||||||| |||| +Sbjct 1272 ATTCTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTACTGAG 1223 + + + Score = 80.5 bits (43), Expect = 3e-18 + Identities = 47/49 (96%), Gaps = 0/49 (0%) + Strand=Plus/Minus + +Query 264 ATCTTTTCAATTATTGAGTTCACTTTGTTGCTGATCCCATCAATTGCGA 312 + ||||||||||||| |||||| |||||||||||||||||||||||||||| +Sbjct 1240 ATCTTTTCAATTACTGAGTTTACTTTGTTGCTGATCCCATCAATTGCGA 1192 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5414321 + + +Query= 170144-17ech4_rep_c220 + +Length=233 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 189 3e-51 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 189 bits (102), Expect = 3e-51 + Identities = 107/109 (98%), Gaps = 1/109 (1%) + Strand=Plus/Minus + +Query 124 TCATTGCATGCACCATCTGCCTAGTCTGATTGGCAACTTCCATGGCCTCTGCTGCCTGCT 183 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | +Sbjct 649 TCATTGCATGCACCATCTGCCTAGTCTGATTGGCAACTTCCATGGCCTCTGCTGCCTGTT 590 + +Query 184 CACTCGTACCCAGCCATCTGTTCCATAGCCTTAGCTGTAGTGCTAGCCA 232 + |||||| |||||||||||||||||||||||||||||||||||||||||| +Sbjct 589 CACTCG-ACCCAGCCATCTGTTCCATAGCCTTAGCTGTAGTGCTAGCCA 542 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2915109 + + +Query= 170144-17ech4_rep_c221 + +Length=279 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 243 2e-67 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 243 bits (131), Expect = 2e-67 + Identities = 137/140 (98%), Gaps = 0/140 (0%) + Strand=Plus/Minus + +Query 71 CCGTTTCTGTCTTGAAGGGAATGGAGGTCTCCCGTTCTCATTAGTGCTTCTCCAAGCGAA 130 + |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 660 CCGTTTCTGTTTTGAAGGGAATGGAGGTCTCCCGTTCTCATTAGTGCTTCTCCAAGCGAA 601 + +Query 131 TCTCTGTAGAGCTTCAGAGACTCGAACTGTATTATCATTCCATTCAAGTCCTTTGATGAG 190 + ||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||| +Sbjct 600 TCTCTGTAGAGTTTCAGAGACTCGAACTGCATTATCATTCCATTCAAGTCCTTTGATGAG 541 + +Query 191 GATCCCAATTGCATTTTTGA 210 + |||||||||||||||||||| +Sbjct 540 GATCCCAATTGCATTTTTGA 521 + + + Score = 122 bits (66), Expect = 3e-31 + Identities = 68/69 (99%), Gaps = 0/69 (0%) + Strand=Plus/Minus + +Query 211 TTGACATCTCTTCAAGAGTCATGTCAGTCAAATAGTGTGAAGCAGGCACAGAAGCATTGG 270 + ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| +Sbjct 298 TTGACATCTCTTCAAGAGTCATGTCAGTCAAATAGCGTGAAGCAGGCACAGAAGCATTGG 239 + +Query 271 TTATTTTAA 279 + ||||||||| +Sbjct 238 TTATTTTAA 230 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3527415 + + +Query= 170144-17ech4_rep_c225 + +Length=301 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 329 2e-93 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 329 bits (178), Expect = 2e-93 + Identities = 187/191 (98%), Gaps = 1/191 (1%) + Strand=Plus/Minus + +Query 112 CTTAACTATTTGTTTCCCCGCATGAGTAGCTGATTCGATTTCCAGACCAAGAGTGCTGCC 171 + |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| +Sbjct 198 CTTAACTATTTGTTTCCCCGCACGAGTAGCTGATTCGATTTCCAGACCAAGAGTGCTGCC 139 + +Query 172 TCTCCCTCTTAGAGACTTCTGGTCTCGGCGAAGCCTATCGAGAAATGGGGCATCGCCAAG 231 + |||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 138 TCTCCCTCTTAGGGACTTCTGGTCTCGGCGAAGCCTATCGAGAAATGGGGCATCGCCAAG 79 + +Query 232 CCCC-AGTTTGCAAACTGCTTGCGGATATGCCAAAGAAAGCAATCTACCTGAAAGCTTGA 290 + |||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||||| +Sbjct 78 CCCCCAGTTTGCAAACCGCTTGCGGATATGCCAAAGAAAGCAATCTACCTGAAAGCTTGA 19 + +Query 291 CACAGTGTTTG 301 + ||||||||||| +Sbjct 18 CACAGTGTTTG 8 + + + Score = 56.5 bits (30), Expect = 4e-11 + Identities = 30/30 (100%), Gaps = 0/30 (0%) + Strand=Plus/Minus + +Query 56 CTGAAAGCTTGACACAGTGTTTGAATCCAT 85 + |||||||||||||||||||||||||||||| +Sbjct 30 CTGAAAGCTTGACACAGTGTTTGAATCCAT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3820257 + + +Query= 170144-17ech4_rep_c227 + +Length=181 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 163 1e-43 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 163 bits (88), Expect = 1e-43 + Identities = 92/94 (98%), Gaps = 0/94 (0%) + Strand=Plus/Minus + +Query 70 GAATCTCTGTAGAGCTTCAGAGACTCGAACTGTATTATCATTCCATTCAAGTCCTTTGAT 129 + |||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||| +Sbjct 603 GAATCTCTGTAGAGTTTCAGAGACTCGAACTGCATTATCATTCCATTCAAGTCCTTTGAT 544 + +Query 130 GAGGATCCCAATTGCATTTTTGACATCCTCATCA 163 + |||||||||||||||||||||||||||||||||| +Sbjct 543 GAGGATCCCAATTGCATTTTTGACATCCTCATCA 510 + + + Score = 102 bits (55), Expect = 3e-25 + Identities = 62/65 (95%), Gaps = 1/65 (2%) + Strand=Plus/Minus + +Query 1 TTGCTCCACTTCAAGCAGTAGTTGTAATGCTTGCATGAATGTTATCTGTTCAAAGCTGMT 60 + |||||||||||||||||||||||||||||||||||| |||||||||||||||||||| | +Sbjct 805 TTGCTCCACTTCAAGCAGTAGTTGTAATGCTTGCATAAATGTTATCTGTTCAAAGCTA-T 747 + +Query 61 TCTCC 65 + ||||| +Sbjct 746 TCTCC 742 + + + +Lambda K H + 1.36 0.629 1.15 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2222937 + + +Query= 170144-17ech4_rep_c232 + +Length=331 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 135 5e-35 + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 134 2e-34 + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 117 2e-29 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 135 bits (73), Expect = 5e-35 + Identities = 80/83 (96%), Gaps = 1/83 (1%) + Strand=Plus/Minus + +Query 75 ATTATCCTCCTGTCTGCTGTAATCGGATACTTCATTGCCATCATCCATTTCATTCTGGAG 134 + ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| || +Sbjct 211 ATTATTCTCCTGTCTGCTGTAATCGGATACTTCATTGCCATCATCCATTTCATTCTG-AG 153 + +Query 135 AGCGGGATTCTTCTCTTGTCTTC 157 + |||||| |||||||||||||||| +Sbjct 152 AGCGGGGTTCTTCTCTTGTCTTC 130 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 134 bits (72), Expect = 2e-34 + Identities = 72/72 (100%), Gaps = 0/72 (0%) + Strand=Plus/Minus + +Query 1 TCAGGTGCAAGATCCCAATTATATTTGCTGCAATGACAAGAGGATCACTTGAATCGCTGT 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 803 TCAGGTGCAAGATCCCAATTATATTTGCTGCAATGACAAGAGGATCACTTGAATCGCTGT 744 + +Query 61 ATCTGCACTCCC 72 + |||||||||||| +Sbjct 743 ATCTGCACTCCC 732 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 117 bits (63), Expect = 2e-29 + Identities = 72/76 (95%), Gaps = 1/76 (1%) + Strand=Plus/Minus + +Query 191 TCTG-TGTAGAGACTGGAGAAGGCAACGCCTCATTTCCATACCCCATTTCATTTTGATTT 249 + |||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1774 TCTGTTGAAGAGACTGAAGAAGGCAACGCCTCATTTCCATACCCCATTTCATTTTGATTT 1715 + +Query 250 TTGAGGTTCCATTGGT 265 + |||||||||| ||||| +Sbjct 1714 TTGAGGTTCCGTTGGT 1699 + + + Score = 106 bits (57), Expect = 4e-26 + Identities = 63/66 (95%), Gaps = 0/66 (0%) + Strand=Plus/Minus + +Query 266 AATCATGTCCCCTATTTCAAGAACACAATACTTCTCCCACTTGTGTGGCTCTAGCCTAGG 325 + ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| || +Sbjct 1647 AATCATGTCCCCTATTTCAAGAACACAATACTTCTCCCACTTGTGTGGCTCCAGCCTCGG 1588 + +Query 326 ATCAGT 331 + ||| || +Sbjct 1587 ATCGGT 1582 + + + +Lambda K H + 1.34 0.623 1.13 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4219587 + + +Query= 170144-17ech4_rep_c235 + +Length=321 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 217 2e-59 + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 134 2e-34 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 217 bits (117), Expect = 2e-59 + Identities = 126/130 (97%), Gaps = 1/130 (1%) + Strand=Plus/Minus + +Query 118 GAC-AAATGACCATCGTCAACATCCACAGCATTCTGCTGTTCCTGTTGATATTCTTCCCT 176 + ||| |||||||||| |||||||||||||||| |||||||||||||||||||||||||||| +Sbjct 964 GACAAAATGACCATTGTCAACATCCACAGCACTCTGCTGTTCCTGTTGATATTCTTCCCT 905 + +Query 177 CATGGACTCAGGCACTCCTTCCGTAGAAGGCCCTCTTTTCAAACCGTATTTAATGCGACG 236 + ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 904 CATGGACTCAGGCACTCCTTCCGTAGAAGGCCCTCTTTTCAAACCGTATTTAAGGCGACG 845 + +Query 237 ATAAATACAT 246 + |||||||||| +Sbjct 844 ATAAATACAT 835 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 134 bits (72), Expect = 2e-34 + Identities = 81/85 (95%), Gaps = 2/85 (2%) + Strand=Plus/Plus + +Query 238 TAAATACATAGAGACCTCAAATTC-AAAAATGGTGCATGCTATCCTGGAGAATTCGCTGA 296 + || ||| |||||||| |||||||| ||||||||||||||||||||||||||||||||||| +Sbjct 315 TATATA-ATAGAGACTTCAAATTCAAAAAATGGTGCATGCTATCCTGGAGAATTCGCTGA 373 + +Query 297 TTATGAGGAATTAAGGGAACAGCTG 321 + ||||||||||||||||||||||||| +Sbjct 374 TTATGAGGAATTAAGGGAACAGCTG 398 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4086477 + + +Query= 170144-17ech4_rep_c236 + +Length=176 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 106 2e-26 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 106 bits (57), Expect = 2e-26 + Identities = 57/57 (100%), Gaps = 0/57 (0%) + Strand=Plus/Minus + +Query 61 CATGCATTCATTATCACATTTGTGATAGAACTCAAAACAGCCATTACCGATTTCCTT 117 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1511 CATGCATTCATTATCACATTTGTGATAGAACTCAAAACAGCCATTACCGATTTCCTT 1455 + + + Score = 102 bits (55), Expect = 3e-25 + Identities = 59/61 (97%), Gaps = 0/61 (0%) + Strand=Plus/Minus + +Query 1 AATCTAGGGTTCTTTCATTCTCGAGCAGGATGAGTAATTCAGCGTTATAAGTCCACACAT 60 + |||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||| +Sbjct 1392 AATCTAGGGTTCTTTCATTCTCGAGCAGTATGAGTAATTCAGCGTTATAAGTCCATACAT 1333 + +Query 61 C 61 + | +Sbjct 1332 C 1332 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2156382 + + +Query= 170144-17ech4_rep_c237 + +Length=256 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 202 4e-55 + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 52.8 4e-10 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 202 bits (109), Expect = 4e-55 + Identities = 124/131 (95%), Gaps = 1/131 (1%) + Strand=Plus/Minus + +Query 126 TCAGTTGAATCAGTCTTCTAGTTGCTTTCCTTAAAATGGGCTGTTGCTCTTCTTCCAACC 185 + |||| |||||||| |||||||||||||||||||| |||| |||||||||||||||||||| +Sbjct 1173 TCAGCTGAATCAGCCTTCTAGTTGCTTTCCTTAAGATGG-CTGTTGCTCTTCTTCCAACC 1115 + +Query 186 ATTGTAAACTCCTCATATCCCTCATGTACCCTTATCTTCAGTGCTTGGAGATTTCCTGTA 245 + |||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||| +Sbjct 1114 ATTGTAAATTCCTCATACCCCTCATGTACCCTTATCTTCAGTGCTTGGAGATTGCCTGTA 1055 + +Query 246 AGCACTTCTTC 256 + ||||||||||| +Sbjct 1054 AGCACTTCTTC 1044 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 52.8 bits (28), Expect = 4e-10 + Identities = 28/28 (100%), Gaps = 0/28 (0%) + Strand=Plus/Minus + +Query 1 TCTTCTGAATATCTGGGATAATTATATG 28 + |||||||||||||||||||||||||||| +Sbjct 1558 TCTTCTGAATATCTGGGATAATTATATG 1531 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3221262 + + +Query= 170144-17ech4_rep_c241 + +Length=319 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 556 9e-162 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 556 bits (301), Expect = 9e-162 + Identities = 313/319 (98%), Gaps = 0/319 (0%) + Strand=Plus/Minus + +Query 1 ATTTGAAGAAAAGACGATCAAGAATCCACAATATCAGGTGCAAGATCCCAATTATATTTG 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 836 ATTTGAAGAAAAGACGATCAAGAATCCACAATATCAGGTGCAAGATCCCAATTATATTTG 777 + +Query 61 CTGCAATGACAAGAGGATCACTTGAATCGCTGTATCTGCACTCCCATCCGTTTCTGGTAG 120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 776 CTGCAATGACAAGAGGATCACTTGAATCGCTGTATCTGCACTCCCATCCGTTTCTGGTAG 717 + +Query 121 GCCTGCAAATTTTCAAGAAGGTCATCTTTCAGCCCGGCGCTGGAACTGGGGTGTGTTCCA 180 + |||||||||||||||||||||||||||||||| || ||||||||||| || ||||||||| +Sbjct 716 GCCTGCAAATTTTCAAGAAGGTCATCTTTCAGACCTGCGCTGGAACTAGGATGTGTTCCA 657 + +Query 181 ACTGTTCTCATTGCATGCACCATCTGCCTAGTCTGATTGGCAACTTCCATGGCCTCTGCT 240 + | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 656 ATTGTTCTCATTGCATGCACCATCTGCCTAGTCTGATTGGCAACTTCCATGGCCTCTGCT 597 + +Query 241 GCCTGCTCACTCGACCCAGCCATCTGTTCCATAGCCTTAGCTGTAGTGCTAGCCAGAACC 300 + ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 596 GCCTGTTCACTCGACCCAGCCATCTGTTCCATAGCCTTAGCTGTAGTGCTAGCCAGAACC 537 + +Query 301 ATTCTGTTTTCATGCCTGA 319 + ||||||||||||||||||| +Sbjct 536 ATTCTGTTTTCATGCCTGA 518 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4059855 + + +Query= 170144-17ech4_rep_c242 + +Length=340 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 409 3e-117 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 409 bits (221), Expect = 3e-117 + Identities = 250/264 (95%), Gaps = 2/264 (1%) + Strand=Plus/Minus + +Query 29 TTGGTTCTCATATACAGAAACATTGGCCTTGACACCTGGCCAATTGAACTCCTTAGAATC 88 + |||||||||| |||||||||||||||||| |||||||||||||||||||||| ||||||| +Sbjct 1703 TTGGTTCTCACATACAGAAACATTGGCCTCGACACCTGGCCAATTGAACTCCGTAGAATC 1644 + +Query 89 ATGTCCCCTATTTCAAGAACACAATACTTCTCCCACTTGTGTGGCTCTAGCCTAGGATCA 148 + ||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| +Sbjct 1643 ATGTCCCCTATTTCAAGAACACAATACTTCTCCCACTTGTGTGGCTCCAGCCTCGGATCG 1584 + +Query 149 GTGAGA-AAAC-TCCATACTCACAAAATTTACCACGTCTGTGTCATTCCTTAGATGAGAT 206 + |||||| ||| |||||||||||||||||||||||||| ||||| ||||||||||||||| +Sbjct 1583 GTGAGAGAAAATTCCATACTCACAAAATTTACCACGTCAGTGTCGTTCCTTAGATGAGAT 1524 + +Query 207 CTTCCTTTTACAATGAACCCATATAAATTTGTCTTCCGCCTTCCTTCTTTCGTTTTGCAT 266 + ||||||||||||||||||||||||| ||||||| |||||||||||||||||||| ||||| +Sbjct 1523 CTTCCTTTTACAATGAACCCATATAGATTTGTCCTCCGCCTTCCTTCTTTCGTTCTGCAT 1464 + +Query 267 TTGCTTATCATTGGGATTAGCTGA 290 + |||||||||||||||||||||||| +Sbjct 1463 TTGCTTATCATTGGGATTAGCTGA 1440 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4339386 + + +Query= 170144-17ech4_rep_c245 + +Length=143 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 152 2e-40 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 152 bits (82), Expect = 2e-40 + Identities = 84/85 (99%), Gaps = 0/85 (0%) + Strand=Plus/Minus + +Query 59 GTTCCACCTGCTACCGGCAGGAATCTGGTTTTGCGGACCAGTTCTCTCTCCAACATGTAT 118 + ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| +Sbjct 691 GTTCCACCTGCTACCGGCAGGAATCTGGTTTTGCGGACCAGTTCTCTTTCCAACATGTAT 632 + +Query 119 GCCACCATTAAAGGGGCAATCTTAC 143 + ||||||||||||||||||||||||| +Sbjct 631 GCCACCATTAAAGGGGCAATCTTAC 607 + + + Score = 108 bits (58), Expect = 5e-27 + Identities = 60/61 (98%), Gaps = 0/61 (0%) + Strand=Plus/Minus + +Query 1 ATCATCATTCTTCACCTCTCCACCTGGAGTGTACATCTGTTCCCAGCAGGTTCCTTGGGT 60 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || +Sbjct 782 ATCATCATTCTTCACCTCTCCACCTGGAGTGTACATCTGTTCCCAGCAGGTTCCTTGAGT 723 + +Query 61 T 61 + | +Sbjct 722 T 722 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1731470 + + +Query= 170144-17ech4_rep_c252 + +Length=254 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 261 6e-73 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 261 bits (141), Expect = 6e-73 + Identities = 197/221 (89%), Gaps = 15/221 (7%) + Strand=Plus/Minus + +Query 49 ACCCTCAGATCTTCAAATGCTGCAGAATGGCATGCCATCCAGACCAGTTGACTCTTATGA 108 + ||||||||||||||||||||||||||||||||||||||||| | ||| ||||||||||| +Sbjct 1073 ACCCTCAGATCTTCAAATGCTGCAGAATGGCATGCCATCCATATCAGCTGACTCTTATGG 1014 + +Query 109 ACTGGATTCTCATT---------------GAACACTTGGCTGTTCTGAAGCAGACGAAAA 153 + |||||||||||||| ||||||||||||||||||||||||||||||| +Sbjct 1013 ACTGGATTCTCATTCGGTCTAATGAGGCTGAACACTTGGCTGTTCTGAAGCAGACGAAAA 954 + +Query 154 GGATCTATCCCAACTAGGGAGTACCCTTCTCTTTCAAAGTCATATCCACTCGCCACAATA 213 + ||||||| ||| |||||||||||||||||||||||||||||||||||||| ||||||||| +Sbjct 953 GGATCTACCCCGACTAGGGAGTACCCTTCTCTTTCAAAGTCATATCCACTTGCCACAATA 894 + +Query 214 AGTCCATATACACAAGCAGGTAGGCAGGATTTATGAGCCAC 254 + |||||||||||||||||||| || ||||||||||||||||| +Sbjct 893 AGTCCATATACACAAGCAGGCAGACAGGATTTATGAGCCAC 853 + + + Score = 86.1 bits (46), Expect = 4e-20 + Identities = 46/46 (100%), Gaps = 0/46 (0%) + Strand=Plus/Minus + +Query 3 GTAGGTTGTACACTGATTTGCCCTGCGGATGCTCTCTGTTGATTGG 48 + |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1277 GTAGGTTGTACACTGATTTGCCCTGCGGATGCTCTCTGTTGATTGG 1232 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3194640 + + +Query= 170144-17ech4_rep_c253 + +Length=147 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 209 1e-57 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 209 bits (113), Expect = 1e-57 + Identities = 117/119 (98%), Gaps = 0/119 (0%) + Strand=Plus/Minus + +Query 29 TGTCTTTAGCCACTCCATGAGAGCCTCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTC 88 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 144 TGTCTTTAGCCACTCCATGAGAGCCTCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTC 85 + +Query 89 TAGTCTCTGTGCGATCTCGGCTTTGAGGGGGCCTGACGGGATGATAGAAAGAACGTACG 147 + |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 84 CAGTCTCTGCGCGATCTCGGCTTTGAGGGGGCCTGACGGGATGATAGAAAGAACGTACG 26 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1784746 + + +Query= 170144-17ech4_rep_c254 + +Length=73 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 95.3 2e-23 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 95.3 bits (51), Expect = 2e-23 + Identities = 51/51 (100%), Gaps = 0/51 (0%) + Strand=Plus/Minus + +Query 1 TGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 51 + ||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 51 TGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 799140 + + +Query= 170144-17ech4_rep_c257 + +Length=215 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 315 4e-89 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 315 bits (170), Expect = 4e-89 + Identities = 176/179 (98%), Gaps = 0/179 (0%) + Strand=Plus/Minus + +Query 14 AAAATTCCCTTAGTCAGAGGTGACAGGATCGGTCTTGTCTTTAGCCACTCCATGAGAGCC 73 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| +Sbjct 179 AAAATTCCCTTAGTCAGAGGTGACAGGATTGGTCTTGTCTTTAGCCACTCCATGAGAGCC 120 + +Query 74 TCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCTAGTCTCTGTGCGATCTCGGCTTTG 133 + ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||| +Sbjct 119 TCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCCAGTCTCTGCGCGATCTCGGCTTTG 60 + +Query 134 AGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 192 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 59 AGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2675511 + + +Query= 170144-17ech4_rep_c258 + +Length=220 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 213 1e-58 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 213 bits (115), Expect = 1e-58 + Identities = 122/125 (98%), Gaps = 1/125 (1%) + Strand=Plus/Minus + +Query 1 AGAG-CTCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCTAGTCTCTGTGCGATCTCG 59 + |||| |||||||||||||||||||||||||||||||||||| |||||||| ||||||||| +Sbjct 125 AGAGCCTCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCCAGTCTCTGCGCGATCTCG 66 + +Query 60 GCTTTGAGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGA 119 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 65 GCTTTGAGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGA 6 + +Query 120 CTCAT 124 + ||||| +Sbjct 5 CTCAT 1 + + + Score = 130 bits (70), Expect = 2e-33 + Identities = 74/76 (97%), Gaps = 0/76 (0%) + Strand=Plus/Minus + +Query 145 TTGACAAAATGACCATCGTCAACATCCACAGCATTCTGCTGTTCCTGTTGATATTCTTCC 204 + |||||||||||||||| |||||||||||||||| |||||||||||||||||||||||||| +Sbjct 966 TTGACAAAATGACCATTGTCAACATCCACAGCACTCTGCTGTTCCTGTTGATATTCTTCC 907 + +Query 205 CTCATGGACTCAGGCA 220 + |||||||||||||||| +Sbjct 906 CTCATGGACTCAGGCA 891 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2742066 + + +Query= 170144-17ech4NODE_1 + +Length=2400 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 3849 0.0 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 3849 bits (2084), Expect = 0.0 + Identities = 2251/2334 (96%), Gaps = 2/2334 (0%) + Strand=Plus/Minus + +Query 1 AGTAGAAACAAGGTCGTTTTTAAACAATTCAACACTAATTGATGGCCAATCGAATTCTTT 60 + ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| +Sbjct 2334 AGTAGAAACAAGGTCGTTTTTAAACAATTCAACACTAATTGATGGCCAACCGAATTCTTT 2275 + +Query 61 TGGTCGCTGTCTGGCTGTCAGTAAGTATGCTAGAGTCCCGTTTCCGTTTCATTACCAACA 120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2274 TGGTCGCTGTCTGGCTGTCAGTAAGTATGCTAGAGTCCCGTTTCCGTTTCATTACCAACA 2215 + +Query 121 CTACATCTCCTTGCCCTATCAAAACGTTGGCTTTCTCCCCTTTTGTAAGATTGCTCAGCT 180 + | ||||||||||||||||||||||||||||||||||||||||||| |||||||||||| | +Sbjct 2214 CCACATCTCCTTGCCCTATCAAAACGTTGGCTTTCTCCCCTTTTGCAAGATTGCTCAGTT 2155 + +Query 181 CATTGATACTCAATGCTGGTCCATATCTTTTGTTTTCCTTTCCTAGAATTAAAAACCCTC 240 + |||||||||||||||||||||||||||||||||||||||| |||||||||| |||||||| +Sbjct 2154 CATTGATACTCAATGCTGGTCCATATCTTTTGTTTTCCTTCCCTAGAATTAGAAACCCTC 2095 + +Query 241 TCAGTACTGCAGATTCCACTCCAGCAGTCCCCTCATCTGGATCTGCTGTTAATGCACCTG 300 + ||||||||||||||||||||||||| || ||||||||||||||| ||||||||||||||| +Sbjct 2094 TCAGTACTGCAGATTCCACTCCAGCCGTTCCCTCATCTGGATCTTCTGTTAATGCACCTG 2035 + +Query 301 CGTCCTTTCCGAGGACCGTCAGTCTTTTTGTTGCCTTATTGTAGTTGAATACTGGGGAGT 360 + ||||||||||||||||||| || ||||||||||||||||||||||| ||||||||||||| +Sbjct 2034 CGTCCTTTCCGAGGACCGTTAGCCTTTTTGTTGCCTTATTGTAGTTAAATACTGGGGAGT 1975 + +Query 361 TACCTCTTATGAGTATCCTCAGTCCTGATCCTCTTACATTCACAGTTAGAGAAGAGAATT 420 + |||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||| +Sbjct 1974 TACCTCTTATGAGTATTCTCAGTCCTGATCCTCTTACATTTACAGTTAGAGAAGAGAATT 1915 + +Query 421 GCATCCTACTCTGCTCTGGTGGAGCAGCTGCAAATGGCAGTAGCTTTATTATTTGGGCAG 480 + ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| +Sbjct 1914 GCATCCTACTCTGCTCTGGTGGAGCTGCTGCAAATGGCAGTAGCTTTATTATTTGGGCAG 1855 + +Query 481 TATCAAATGTCCCCAGTACATCGCGCATTTGCTGGAATAGTGTTCTCACAAACCCGCTGT 540 + | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1854 TGTCAAATGTCCCCAGTACATCGCGCATTTGCTGGAATAGTGTTCTCACAAACCCGCTGT 1795 + +Query 541 ATTGACCTCTAGCCGCTTTAGGTATTAAAGATTGAAATGGTTCAAATTCCATTTTGTTGT 600 + |||||||||| || ||||||||||||| ||| |||||||| ||||||||||||||||||| +Sbjct 1794 ATTGACCTCTGGCTGCTTTAGGTATTAGAGACTGAAATGGCTCAAATTCCATTTTGTTGT 1735 + +Query 601 ATAGCATTGTGGGGTCTTGGGACCACTGGATCTTCACAGTCTCCCAATTTCTAATGATCC 660 + ||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||| +Sbjct 1734 ATAGCATTGTGGGGTCTTGGGACCATTGGATCTTCACAGTTTCCCAATTTCTAATGATCC 1675 + +Query 661 ATTGATACGTGTTAACGAGTACTGACTCAGGTCCATTGATTTCCCACATCATTGATGATG 720 + ||||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||||| +Sbjct 1674 ATTGATACGTGTTAACGAGCACTGATTCAGGTCCATTGATCTCCCACATCATTGATGATG 1615 + +Query 721 AATAGGTTATTGTCAATTTCTCTGTTCCTTGTATTTCGCTAACCTCTTCAGGAGATAGTA 780 + |||||||||||||||||||||||||||||||| ||||||||||||| ||||||||||||| +Sbjct 1614 AATAGGTTATTGTCAATTTCTCTGTTCCTTGTGTTTCGCTAACCTCCTCAGGAGATAGTA 1555 + +Query 781 GTACATTTCCCCGCTGATCTCGAACTCTCAAGAAGCGATCAATACTCACAACCACTCTCT 840 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1554 GTACATTTCCCCGCTGATCTCGAACTCTCAAGAAGCGATCAATACTCACAACCACTCTCT 1495 + +Query 841 CAGTACTGGAATATTCGTCCACTCCTGTTCTACTGATCCTCACTCCTCTTAATGACATTT 900 + | ||||||||||||||||| ||||||||| |||||||||||||||||||||||||||||| +Sbjct 1494 CTGTACTGGAATATTCGTCTACTCCTGTTTTACTGATCCTCACTCCTCTTAATGACATTT 1435 + +Query 901 CTGTGCTTGGAGTCATATCGGGTAATATGCCTATCATTCCCATGATATTATCAATAGGTT 960 + |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| +Sbjct 1434 CTGTGCTTGGAGTCATATCGGGTAATATACCTATCATTCCCATGATATTATCAATAGGTT 1375 + +Query 961 CAATTCCCCAATTTTGAAACAGCACTTTTGCATCCTTCTGGAAGTGTCTCAGTAGTTGAT 1020 + |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| +Sbjct 1374 CAATTCCCCAATTTTGAAACAGCACTTTTGCATCCTTCTGGAAGTGTCTCAGGAGTTGAT 1315 + +Query 1021 GCATGGGATTCAGCCTTTGGTTTGCTCTGTTTACAAAATTTAGATCGCCTCGAACAGCCT 1080 + |||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| | +Sbjct 1314 GCATGGGATTCAGCCTTTGGTTTGCTCTGTTTACAAAATTTAGATCACCTCGGACAGCTT 1255 + +Query 1081 TTATCATACAATCTTCTTGTGAGAACACCATTGCTACTATGATTGCTTCAGCAATTGACT 1140 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1254 TTATCATACAATCTTCTTGTGAGAACACCATTGCTACTATGATTGCTTCAGCAATTGACT 1195 + +Query 1141 GGTCGTCTCTTCCACTTACTATCAGTTGAATCAGTCTTCTAGTTGCTTTCCTTAAAATGG 1200 + | || |||||||||||||||||||| |||||||| |||||||||||||||||||| |||| +Sbjct 1194 GTTCATCTCTTCCACTTACTATCAGCTGAATCAGCCTTCTAGTTGCTTTCCTTAAGATGG 1135 + +Query 1201 CTGTTGCTCTTCTTCCAACCATTGTAAACTCCTCATATCCCTCATGTACCCTTATCTTCA 1260 + |||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||| +Sbjct 1134 CTGTTGCTCTTCTTCCAACCATTGTAAATTCCTCATACCCCTCATGTACCCTTATCTTCA 1075 + +Query 1261 GTGCTTGGAGATTTCCTGTAAGCACTTCTTCTTCTCTTTTAACTGATGATCCATTTGTTC 1320 + ||||||||||||| |||||||||||||||||||| |||||||| ||||||||| |||||| +Sbjct 1074 GTGCTTGGAGATTGCCTGTAAGCACTTCTTCTTCCCTTTTAACAGATGATCCACTTGTTC 1015 + +Query 1321 TTTTGAACGTGAAACCTCCAAAGCTAAAGGAGGAACTGATTCTCAAACCCATTGCTGCTT 1380 + ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1014 TTTTGAAAGTGAAACCTCCAAAGCTAAAGGAGGAACTGATTCTCAAACCCATTGCTGCTT 955 + +Query 1381 TGCATATATCCACGGCTTGCTCCTCAGTTGGATTTTGTTTAAGGATGTCAATCATCCTTA 1440 + ||||||||||||| |||||||| || ||||||||||||||||||||||||| |||||||| +Sbjct 954 TGCATATATCCACTGCTTGCTCTTCCGTTGGATTTTGTTTAAGGATGTCAACCATCCTTA 895 + +Query 1441 TCCCACCAATTTGTGTGCCGTGACACATCTCCAACAGTGATGCCAGTGGATCTGCTGACA 1500 + |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| +Sbjct 894 TCCCACCAATTTGTGTGCCGTGACACATCTCCAATAGTGATGCCAGTGGATCTGCTGACA 835 + +Query 1501 CTATTGCTCTTCTAACAATGTTTCTGGCAGCAATGATCAAACTCTGATCTACATCATCAT 1560 + |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 834 CTATTGCTCTTCTAACAATGTTTCTGGCAGCAATGATCAAACTCTGGTCTACATCATCAT 775 + +Query 1561 TCTTCACCTCTCCACCTGGAGTGTACATCTGTTCCCAGCAGGTTCCTTGGGTCAAGTGCA 1620 + ||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||| +Sbjct 774 TCTTCACCTCTCCACCTGGAGTGTACATCTGTTCCCAGCAGGTTCCTTGAGTTAAGTGCA 715 + +Query 1621 ATACTTCAATATAAACACTGCTTGTTCCACCTGCTACCGGCAGGAATCTGGTTTTGCGGA 1680 + |||||||||| || |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 714 ATACTTCAATGTAGACACTGCTTGTTCCACCTGCTACCGGCAGGAATCTGGTTTTGCGGA 655 + +Query 1681 CCAGTTCTCTCTCCAACATGTATGCCACCATTAAAGGGGCAATCTTACAATCTTGGAGTT 1740 + |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 654 CCAGTTCTCTTTCCAACATGTATGCCACCATTAAAGGGGCAATCTTACAATCTTGGAGTT 595 + +Query 1741 CCTCTTTCTTTTCCTTTGTTATTGTTAATTGCGATTCCGATGTTAATATTCTGGCTCCCA 1800 + |||||||||| || ||||||||||||||||||||||| ||||||| |||||||||||||| +Sbjct 594 CCTCTTTCTTCTCTTTTGTTATTGTTAATTGCGATTCTGATGTTAGTATTCTGGCTCCCA 535 + +Query 1801 CTTCATTTGGGAAAACAACTTCCATGATAACATCTTGTGCTTCTTTGGCATTGAGATCTG 1860 + ||||||||||||| ||||||||||||||||||||||||||||| |||||| |||| |||| +Sbjct 534 CTTCATTTGGGAAGACAACTTCCATGATAACATCTTGTGCTTCCTTGGCACTGAGGTCTG 475 + +Query 1861 CATGGCCTGGGTTTATGTCAACTCTTCGGCGTATTTTAATTTGATTTCGAAA-TGGACGG 1919 + |||||||||||||||| ||||| |||||||||||||||| |||||||||||| ||||| | +Sbjct 474 CATGGCCTGGGTTTATATCAACCCTTCGGCGTATTTTAACTTGATTTCGAAAATGGACAG 415 + +Query 1920 GACCAAAGGTCCCATGCTTCAACCTTTCAACTTTTTCAAAATATGTCTTGTATACTTTAG 1979 + |||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 414 GACCAAAGGTCCCATGTTTCAACCTTTCAACTTTTTCAAAATATGTTTTGTATACTTTAG 355 + +Query 1980 GATAGTGGACTGTATCTGTTGTCGGTCCATTCCTATTCCACCAAGTTACGGCTAGGGGTG 2039 + ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| +Sbjct 354 GATAGTGGACTGTATCTGTTGTCGGCCCATTCCTATTCCACCAAGTTACGGCTAGGGGTG 295 + +Query 2040 ACACCATCACCCTGTCTGATCCAGCATCATTTGTCTTACTCCAAAGTATTTGTCCTTGTT 2099 + ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 294 ACACCATCACCCTATCTGATCCAGCATCATTTGTCTTACTCCAAAGTATTTGTCCTTGTT 235 + +Query 2100 CGTTTCTTTCAGGAATCATCTCCATTATCCTCCTGTCTGCTGTAATCGGATACTTCATTG 2159 + |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| +Sbjct 234 CGTTTCTTTCAGGAATCATCTCCATTATTCTCCTGTCTGCTGTAATCGGATACTTCATTG 175 + +Query 2160 CCATCATCCATTTCATTCTGAGAGCGGGATTCTTCTCTTGTCTTCCTGATGTGTATTTTT 2219 + |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| +Sbjct 174 CCATCATCCATTTCATTCTGAGAGCGGGGTTCTTCTCTTGTCTTCCTGATGTGTATTTTT 115 + +Query 2220 T-ATTATTGCCATATGGTCCACAGTGGTTTTTGTCAGTATCTCGCGAGTGCGAGACTGAG 2278 + | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| | +Sbjct 114 TTATTATTGCCATATGGTCCACAGTGGTTTTTGTCAGTATCTCGCGAGTGCGAGACTGCG 55 + +Query 2279 ACATCAGATCTCTTAATTCTTTTATTCTCTCCATATTGAGTATATTTGACCTGC 2332 + |||||||||||||||||||||||||||| |||||||||| |||| ||||||||| +Sbjct 54 ACATCAGATCTCTTAATTCTTTTATTCTTTCCATATTGAATATAATTGACCTGC 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 31662921 + + +Query= 170144-17ech4NODE_2 + +Length=2253 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 3627 0.0 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 3627 bits (1964), Expect = 0.0 + Identities = 2089/2151 (97%), Gaps = 1/2151 (0%) + Strand=Plus/Minus + +Query 27 TTATTTCAGTGCATGCATAAGGAAGGAGTTAAACCAAGACGCATTGAGCAAAACCCAGGG 86 + |||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| +Sbjct 2151 TTATTTCAGTGCATGCATAAGGAAGGAGTTGAACCAAGACGCGTTAAGCAAAACCCAGGG 2092 + +Query 87 ATCATTAATCAGGCACTCCTCAATTGCATCATATAACCCCCCAAGATCAAAGGTCCCAGG 146 + ||||||||||| |||||| ||||||||||||||||||||||||||||||||||||||||| +Sbjct 2091 ATCATTAATCAAGCACTCTTCAATTGCATCATATAACCCCCCAAGATCAAAGGTCCCAGG 2032 + +Query 147 TTCCAGGTTGTCCCTAAGTGCTTGAACAATTAGAAGTAATTTTCTTGATTCAGCTGAAAA 206 + |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 2031 TTCCAGGTTGTCCCTAAGTGCTTGAACAATCAGAAGTAATTTTCTTGATTCAGCTGAAAA 1972 + +Query 207 CCCCTCGAGTTGTGAAGATGCATACAGACTATTGAATACAGACTTTGCCAGTAAGGCCCT 266 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1971 CCCCTCGAGTTGTGAAGATGCATACAGACTATTGAATACAGACTTTGCCAGTAAGGCCCT 1912 + +Query 267 ACATACTTTTCCAATGGAGCCTTCTTCCACCCCCTTGGGTGACTCCCCAATGGGCCATAC 326 + ||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| +Sbjct 1911 ACATACTTTTCCAATGGAGCCTTCTTCCACCCCTTTGGGTGACTCCCCAATGGGCCATAC 1852 + +Query 327 TTCAGATTTATTTTCAAAAA-TTCTTTGGTCATGTCCTTTTCTTTAACAGAAGACTCTGC 385 + |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| +Sbjct 1851 TTCAGATTTATTTTCAAAAAATTCTTTGGTCATGTCCTTTTCTTTAACAGAAGACTCTGC 1792 + +Query 386 TTCAATCATGCTCTCAATCTGTTGAAGAGACTGGAGAAGGCAACGCCTCATTTCCATACC 445 + ||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||| +Sbjct 1791 TTCGATCATGCTCTCAATCTGTTGAAGAGACTGAAGAAGGCAACGCCTCATTTCCATACC 1732 + +Query 446 CCATTTCATTTTGATTTTTGAGGTTCCATTGGTTCTCATATACAGAAACATTGGCCTTGA 505 + ||||||||||||||||||||||||||| |||||||||| |||||||||||||||||| || +Sbjct 1731 CCATTTCATTTTGATTTTTGAGGTTCCGTTGGTTCTCACATACAGAAACATTGGCCTCGA 1672 + +Query 506 CACCTGGCCAATTGAACTCCTTAGAATCATGTCCCCTATTTCAAGAACACAATACTTCTC 565 + |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| +Sbjct 1671 CACCTGGCCAATTGAACTCCGTAGAATCATGTCCCCTATTTCAAGAACACAATACTTCTC 1612 + +Query 566 CCACTTGTGTGGCTCTAGCCTAGGATCAGTGAGAGAAAACTCCATACTCACAAAATTTAC 625 + ||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| +Sbjct 1611 CCACTTGTGTGGCTCCAGCCTCGGATCGGTGAGAGAAAATTCCATACTCACAAAATTTAC 1552 + +Query 626 CACGTCTGTGTCATTCCTTAGATGAGATCTTCCTTTTACAATGAACCCATATAAATTTGT 685 + |||||| ||||| |||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 1551 CACGTCAGTGTCGTTCCTTAGATGAGATCTTCCTTTTACAATGAACCCATATAGATTTGT 1492 + +Query 686 CTTCCGCCTTCCTTCTTTCGTTTTGCATTTGCTTATCATTGGGATTAGCTGAAAATCATC 745 + | |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| +Sbjct 1491 CCTCCGCCTTCCTTCTTTCGTTCTGCATTTGCTTATCATTGGGATTAGCTGAAAATCATC 1432 + +Query 746 CATTGCTGCACAAGATGCATTGAGTAAGGCTGTGTTTATATATACTCCTTTCATTATGTA 805 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1431 CATTGCTGCACAAGATGCATTGAGTAAGGCTGTGTTTATATATACTCCTTTCATTATGTA 1372 + +Query 806 CTCCGTGGCCCTGCAATGAGACACTTCTGCTGTGAAGTAGTTCCTCCTCATACTCGCAAT 865 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1371 TTCCGTGGCCCTGCAATGAGACACTTCTGCTGTGAAGTAGTTCCTCCTCATACTCGCAAT 1312 + +Query 866 ATGCTCAATAGGAGCAACATCTTCTCCTATTTCGTCAAGCTCTATCCAGCTGGAATCCGT 925 + |||||||| || |||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 1311 GTGCTCAATTGGGGCAACATCCTCTCCTATTTCGTCAAGCTCTATCCAGCTGGAATCCGT 1252 + +Query 926 CAACTCACATGCCTTGTTGAATTCACTCTGAATCCAACTTGCCAGTGACCTAATTTTTGG 985 + |||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| +Sbjct 1251 CAACTCACATGCCTTGTTGAATTCACTCTGAATCCAGCTTGCCAGTGATCTAATTTTTGG 1192 + +Query 986 CTCATCACTATTATACTGTTTTAAATCACCGATATCTTTGCAATCTTCAAAATCCACCTT 1045 + ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1191 CTCATCACTATCATACTGTTTTAAATCACCGATATCTTTGCAATCTTCAAAATCCACCTT 1132 + +Query 1046 TTCTGGTGCCATGTTTTCACCAAGTGCCCATTTTAACTGACTTGtttttttCATGTTCTT 1105 + ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| || +Sbjct 1131 TTCAGGTGCCATGTTTTCACCAAGTGCCCATTTTAACTGACTTGTTTTTTTCATGTTTTT 1072 + +Query 1106 GGTTTTGGGGATTTTCTCCTCATTTTCAGCGTCCTGTAGCTCAGATAGCACTTGTTTCCA 1165 + ||||||||||||||||||||||||||| ||||||||| |||| ||||||||||||||| +Sbjct 1071 AGTTTTGGGGATTTTCTCCTCATTTTCAATGTCCTGTAGTTCAGCTAGCACTTGTTTCCA 1012 + +Query 1166 AGTCAAGAGATAATTTGGATTTATGCCTTTCTCATGCGGCTTGACAATGTGGGGCTCTTT 1225 + || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1011 AGCCAAGAGATAATTTGGATTTATGCCTTTCTCATGCGGCTTGACAATGTGGGGCTCTTT 952 + +Query 1226 CCATCCGAAGAATGTCTTCATGCATTTGATTGCATCATATAGTGGTATTCCCTCCCCCTC 1285 + ||||||||| |||||||||||||||||||||||||||||||| ||||| ||||||||||| +Sbjct 951 CCATCCGAAAAATGTCTTCATGCATTTGATTGCATCATATAGCGGTATCCCCTCCCCCTC 892 + +Query 1286 ATGGCTCGGATCTTCAATGCTCAATTTTAGGGCATCCATCAACAGGAATTTTGACCGTTG 1345 + ||||||||||||||||||||| ||||||| |||||||||||||||||||||||||||||| +Sbjct 891 ATGGCTCGGATCTTCAATGCTTAATTTTAAGGCATCCATCAACAGGAATTTTGACCGTTG 832 + +Query 1346 AGAACAAGGAGGTCCATCAGGTAATCTGAGAGGGCGTGGTGTTTCCCTCAAGAATGGTTC 1405 + |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 831 AGAACAAGGAGGTCCATCAGGTAATCTGAGGGGGCGTGGTGTTTCCCTCAAGAATGGTTC 772 + +Query 1406 AATTCTGGCATTCACTTCTTTTGACATTTGAGAAAGCTTGCCCTCAATGCAGCCGTTCGG 1465 + ||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 771 AATTCTGGCATTCACTTCTTTGGACATTTGAGAAAGCTTGCCCTCAATGCAGCCGTTCGG 712 + +Query 1466 TTCGAATCCATCCACATAGGCTCTAAAGTTTTCAATGCTGGAGAAGTTAGGCGGGAGACT 1525 + ||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||| +Sbjct 711 TTCAAATCCATCCACATAGGCTCTAAAGTTTTCAAGGCTGGAGAAGTTAGGCGGGAGACT 652 + +Query 1526 TTGGTTGGCAAGCCTATGCATGGTCCCTTTGATTTCAAACCTTTCTTCAATTGTTTCTTC 1585 + |||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| +Sbjct 651 TTGGTTGGCAAGCCTATGCATGGTTCCTTTGATTTCAAACCTTTCTTCAATTGTCTCTTC 592 + +Query 1586 GCCTCTTTCGGACTGACGAAAGGAGTCCCATAGGGCCCTAATGGCCATTTCCTGCCTGAT 1645 + |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| +Sbjct 591 GCCTCTTTCGGACTGACGAAAGGAGTCCCATAGGCCCCTAATGGCCATTTCCTGCCTGAT 532 + +Query 1646 GGTGAATAATCTAGTCTTGATCCTTGCTCTGCTTTCCTCATCAAGAGTGTAATCTGCCTT 1705 + ||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 531 GGTGAATAATCTAGTCTTGATTCTTGCTCTGCTTTCCTCATCAAGAGTGTAATCTGCCTT 472 + +Query 1706 AGTGGCCATTTCTTCTCCAGTGAATGAGAAAATGTGGATGTGTGTCTTCTCTGATTTTAT 1765 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 471 AGTGGCCATTTCTTCTCCAGTGAATGAGAAAATGTGGATGTGTGTCTTCTCTGATTTTAT 412 + +Query 1766 TTTGTTGGCTTTTTCTAGATAGTATATGTGAACTTCCCTTCTTGTTACGCCGATTTCAAT 1825 + |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| +Sbjct 411 TTTGTTGGCTTTTTCTAGATAGTATAGGTGAACTTCCCTTCTTGTTACGCCGATTTCAAT 352 + +Query 1826 GAATCGGTTCTCCTTATAGTCATACAGATCCGGAAGGAATTTGGGCTTCTCAACTCCTGT 1885 + |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| +Sbjct 351 GAATCGGTTCTCCTTATAGTCATATAGATCCGGAAGGAATTTGGGCTTCTCAACTCCTGT 292 + +Query 1886 GGTATTGCATATGCTGTTTACCACTGTCCAAGCCATTGTGCGATCCCTTCCCTCAATTAT 1945 + |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 291 AGTATTGCAGATGCTGTTTACCACTGTCCAAGCCATTGTGCGATCCCTTCCCTCAATTAT 232 + +Query 1946 TTCAAATCTGTGTTTTAGGAGTGCATTTGGATTATTGGATTCTACTATTGTCGATTCACC 2005 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 231 TTCAAATCTGTGTTTTAGGAGTGCATTTGGATTATTGGATTCTACTATTGTCGATTCACT 172 + +Query 2006 TCGTTCATCAATGAAGTGGAAGTCAGAATACATGAAACAGACTTCCATGTGTGTGCATAT 2065 + ||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 171 TCGTTCATCGATGAAGTGGAAATCAGAATACATGAAACAGACTTCCATGTGTGTGCATAT 112 + +Query 2066 TGCAGCAAATTTGTTCGTTTCAATTTTTGGGTCTTCTCCATGTTCTTTCATTGCCTTTTC 2125 + ||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||| +Sbjct 111 TGCAGCAAATTTGTTTGTTTCAATTTTTGAGTCTTCTCCATGTTCTTTCATTGCCTTTTC 52 + +Query 2126 CGCAAGCTCGACGATCATTGGGTTGAAGCATTGTCGCACAAAGTCTTCCAT 2176 + ||||||||||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 51 CGCAAGCTCGACGATCATTGGATTGAAGCATTGTCGCACAAAGTCTTCCAT 1 + + + Score = 93.5 bits (50), Expect = 2e-21 + Identities = 52/53 (98%), Gaps = 0/53 (0%) + Strand=Plus/Minus + +Query 2201 AGAAGTTAGGCGGGAGACTTTGGTTGGCAAGCCTATGCATGGTCCCTTTGATT 2253 + ||||||||||||||||||||||||||||||||||||||||||| ||||||||| +Sbjct 670 AGAAGTTAGGCGGGAGACTTTGGTTGGCAAGCCTATGCATGGTTCCTTTGATT 618 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 29709732 + + +Query= 170144-17ech4NODE_3 + +Length=1579 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 2350 0.0 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 2350 bits (1272), Expect = 0.0 + Identities = 1397/1459 (96%), Gaps = 1/1459 (0%) + Strand=Plus/Minus + +Query 1 AGTAGAAACAAGGAGTTTTTT-GAACAAATTACTTGTCAATGGTGAATGGCAACTCAGCA 59 + ||||||||||||||||||||| ||| |||||||||||||||||| ||||||||||||||| +Sbjct 1459 AGTAGAAACAAGGAGTTTTTTTGAATAAATTACTTGTCAATGGTAAATGGCAACTCAGCA 1400 + +Query 60 CCGTCTGGCCAAGACCAACCCACAATGTCACTACTAACACCACAAAAGGATATGCTGCTC 119 + |||||||||||||||||||||||| |||||||||| |||||||||||||||||||||||| +Sbjct 1399 CCGTCTGGCCAAGACCAACCCACAGTGTCACTACTTACACCACAAAAGGATATGCTGCTC 1340 + +Query 120 CCGCTAGTCCAGATTGTGTTCTCTTTGGGTCTCCCTCTGATTAGTTCAACCCAAAAACAA 179 + ||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||| +Sbjct 1339 CCGCTAGTCCAGATTGTGTTCTCTTTGGGTCTCCCTCTGATTAGTTCAACCCAGAAGCAA 1280 + +Query 180 GGTCTAATACAATCTAATCCGGTTAATTCTGGATGCTGGACAAAACTCCCACTGTATCCT 239 + |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| +Sbjct 1279 GGTCTAATACAATCTAATCCGGTTAATTCTGGATGCTGGACAAAACTCCCGCTGTATCCT 1220 + +Query 240 GTCCAGTCTGTTATTCCTACAATGTCTTGCTTTAATGAAAAATTATTGTCTGTTCCAGTC 299 + |||||||| ||||||||||| || |||||||||| ||| ||||||||||||||||||||| +Sbjct 1219 GTCCAGTCAGTTATTCCTACGATATCTTGCTTTACTGAGAAATTATTGTCTGTTCCAGTC 1160 + +Query 300 CATCCGTTTGGGTCCCAAATCATCTCAAAACCGCTCCTTGAACTAGTGCTTTTAGTTCTC 359 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1159 CATCCGTTTGGGTCCCAAATCATCTCAAAACCGCTCCTTGAACTAGTGCTTTTAGTTCTC 1100 + +Query 360 CCTATCCAAATACCATCGCCGTATTTAAATGAAAACCCTTTTACCCCATTTGCCCCATAA 419 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| | +Sbjct 1099 CCTATCCAAATACCATCGCCGTATTTAAACGAAAACCCTTTTACCCCATTTGCCCCATGA 1040 + +Query 420 GAAGATACTGGACCACAACTGCCAGTTCCATCATTAGGGCGCGGATTGTCTCCGAAGACC 479 + || |||||||||||||||||||| |||| ||||||||||||||| |||||||||| ||| +Sbjct 1039 GACGATACTGGACCACAACTGCCTGTTCTATCATTAGGGCGCGGGTTGTCTCCGAGAACC 980 + +Query 480 CCACTGCATATGTATCCTATTTGATACTCCAGATTCTGATTGAAAGACACCCATGGTCGA 539 + ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||| +Sbjct 979 CCACTGCATATGTATCCTATTTGATACTCCAGATTCTGATTAAAAGACACCCATGGTCGA 920 + +Query 540 TTCGAGCCATGCCAATTGTCCCTGCACACACATATGATTTCACCAAAATCAGGATAGCAG 599 + |||||||||||||||||||| |||||||||||||||||||||||| |||||||||| ||| +Sbjct 919 TTCGAGCCATGCCAATTGTCTCTGCACACACATATGATTTCACCAGAATCAGGATAACAG 860 + +Query 600 GAGCATTCCTCATAGTGATAATTAGGAGCATTCAACTCGACTGATTTGACTACTTTCCCC 659 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 859 GAGCATTCCTCATAGTGATAATTAGGAGCATTCAACTCAACTGATTTGACTACTTTCCCC 800 + +Query 660 CTTTCTATTTTGAAGATTCTGTACGAGGCCTGCCCATTACTTAGTCCATCGGTCATTACA 719 + ||||||||||||||||| |||| |||||||||||||||||||||||||||||||||||| +Sbjct 799 TTTTCTATTTTGAAGATTTTGTATGAGGCCTGCCCATTACTTAGTCCATCGGTCATTACA 740 + +Query 720 GTAAAGCAAGAGCCATTCAAGCATGCACATTCAGACTCTTGTGTTCTCAATATGTTGTTT 779 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 739 GTAAAGCAAGAGCCATTCAAGCATGCACATTCAGACTCTTGTGTTCTCAATATGTTGTTT 680 + +Query 780 TTCCAACTCTTGATGGTATCTGTTATTATGTCGTTGTATTTCAGCACAGCCACTGCTCCA 839 + |||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||| +Sbjct 679 TTCCAACTCTTGATAGTGTCTGTTATTATGTCATTGTATTTCAGCACAGCCACTGCTCCA 620 + +Query 840 TTATCTGGGCCAGAAATTCCAATTGTCAACCAACTAGTGCCGTCATGGCAAGCACTTGCT 899 + || |||||||||||||||||||||||||||||||| | |||||||||||||||||||||| +Sbjct 619 TTGTCTGGGCCAGAAATTCCAATTGTCAACCAACTGGAGCCGTCATGGCAAGCACTTGCT 560 + +Query 900 GACCAAGCAACTGACTCAAATCTTGAATTGTATGGAGAAGGGACTTCACCAATAGGACAG 959 + |||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||| +Sbjct 559 GACCAAGCAACTGACTCAAATCTTGAGTTGTATGGAGAGGGGACTTCACCAATAGGACAA 500 + +Query 960 CTCATCAGGGTTCGATAGGGGCTTCTGTCTTTAACAGTTCCATTGGAGTGTTTGTCATTC 1019 + |||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||| +Sbjct 499 CTCATCAGGGTTCGATAGGGGCTTCTGTCTTTGACAGTCCCATTGGAGTGTTTGTCATTC 440 + +Query 1020 AGCAGGGCCCCTTGGGTTAAGAAGAATGTTCTACATTCCAAGTGGGAGCATGAGATGAAT 1079 + |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 439 AGCAGGGCCCCTTGAGTTAAGAAGAATGTTCTACATTCCAAGTGGGAGCATGAGATGAAT 380 + +Query 1080 GGCTCTCTTATAACAAACACATCCCCTTTGGAACCGATTCTTACACTGTTATCTTTACTG 1139 + ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 379 GGCTCTCTTATGACAAACACATCCCCTTTGGAACCGATTCTTACACTGTTATCTTTACTG 320 + +Query 1140 TATATAGCCCACCCATTAACAGGGCAGAGAGAAGAACTGCCAGCTAATTTCACTGAAACT 1199 + ||||||||||| ||| |||||||||||||||| ||||||||||||||||| ||||||| | +Sbjct 319 TATATAGCCCATCCACTAACAGGGCAGAGAGAGGAACTGCCAGCTAATTTTACTGAAATT 260 + +Query 1200 GCTGTCTGTTCGGCTACAAAATTGTTGTTACTGATGTTGACATATGTCTGATTTACCCAG 1259 + |||||||||| || |||||||||||||||||||||||||||||||||||||||||||| +Sbjct 259 ACTGTCTGTTCAGCAACAAAATTGTTGTTACTGATGTTGACATATGTCTGATTTACCCAA 200 + +Query 1260 GTGTTGTTTTCGTAAATAATGGCGCTTTGAATGCATGCCTCAGTTTGGTTTTGGTTCCTA 1319 + |||||||||||||||||||| |||||||| ||||||| || || ||||||||||||| | +Sbjct 199 GTGTTGTTTTCGTAAATAATAACGCTTTGATTGCATGCTTCGGTCTGGTTTTGGTTCCCA 140 + +Query 1320 GTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGCAATATCAAGCTA 1379 + ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| +Sbjct 139 GTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGTAATATCAAGCTA 80 + +Query 1380 GCAATTCCATTTGCCATACAGATTGAGCCGATGATTATTATCTTTTGATTTGGATTCATT 1439 + ||||||||||||| ||||||||||||||| |||||||||||||| ||||||||||||||| +Sbjct 79 GCAATTCCATTTGTCATACAGATTGAGCCAATGATTATTATCTTCTGATTTGGATTCATT 20 + +Query 1440 TTAAACTCCTGCTTTTGCT 1458 + ||||||||||||||||||| +Sbjct 19 TTAAACTCCTGCTTTTGCT 1 + + + Score = 172 bits (93), Expect = 2e-45 + Identities = 113/123 (92%), Gaps = 0/123 (0%) + Strand=Plus/Minus + +Query 1457 CTGTTCGGCTACAAAATTGTTGTTACTGATGTTGACATATGTCTGATTTACCCAGGTGTT 1516 + |||||| || |||||||||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 254 CTGTTCAGCAACAAAATTGTTGTTACTGATGTTGACATATGTCTGATTTACCCAAGTGTT 195 + +Query 1517 GTTTTCGTAAATAATGGCGCTTTGAATGCATGCCTCAGTTTGGTTTTGGTTCCTAGTTTG 1576 + ||||||||||||||| |||||||| ||||||| || || ||||||||||||| |||||| +Sbjct 194 GTTTTCGTAAATAATAACGCTTTGATTGCATGCTTCGGTCTGGTTTTGGTTCCCAGTTTG 135 + +Query 1577 AAT 1579 + ||| +Sbjct 134 AAT 132 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 20780085 + + +Query= 170144-17ech4NODE_5 + +Length=1312 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 2191 0.0 + + +> GQ161157.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 5 nucleocapsid protein (NP) gene, complete cds +Length=1565 + + Score = 2191 bits (1186), Expect = 0.0 + Identities = 1271/1313 (97%), Gaps = 1/1313 (0%) + Strand=Plus/Plus + +Query 1 GCATTCGACGAGAGAAGAAACAAATACTTGGAAGAACATCCCAGTGCGGGGAAAGATCCA 60 + ||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||||| +Sbjct 253 GCATTTGACGAGAGGAGAAACAAATATTTGGAAGAACATCCCAGTGCGGGGAAAGATCCA 312 + +Query 61 AAGAAAACTGGAGGTCCAATCTAC-AAAAGAGAGATGGAAAATGGATGAGAGAGCTGATT 119 + |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| +Sbjct 313 AAGAAAACTGGAGGTCCAATCTACAAAAAGAGAGATGGAAAATGGATGAGAGAGCTGATT 372 + +Query 120 CTATATGACAAAGATGAAATCAGGAGAATTTGGCGTCAAGCCAACAATGGTGAAGATGCT 179 + || |||||||||||||||||||||||||||||||| ||||| |||||||||||||||||| +Sbjct 373 CTGTATGACAAAGATGAAATCAGGAGAATTTGGCGCCAAGCAAACAATGGTGAAGATGCT 432 + +Query 180 ACTGCTGGTCTCACTCATCTGATGATTTGGCACTCCAATCTGAATGATGCTACATATCAG 239 + ||||||||||||||||| |||||||||||||| ||||| ||||||||||| || |||||| +Sbjct 433 ACTGCTGGTCTCACTCACCTGATGATTTGGCATTCCAACCTGAATGATGCCACGTATCAG 492 + +Query 240 AGAACAAGAGCTTTAGTGCGTACTGGGATGGATCCCAGAATGTGCTCTCTAATGCAAGGT 299 + |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| +Sbjct 493 AGAACAAGAGCTTTAGTGCGTACTGGGATGGATCCCAGAATGTGCTCTCTGATGCAAGGT 552 + +Query 300 TCAACTCTACCAAGGAGATCTGGAGCTGCTGGTGCAGCAGTAAAGGGAGTTGGAACACTA 359 + |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 553 TCAACTCTCCCAAGGAGATCTGGAGCTGCTGGTGCAGCAGTAAAGGGAGTTGGGACACTA 612 + +Query 360 GTAATGGAGCTGATCAGAATGATAAAGCGGGGTATCAATGATCGGAACTTTTGGAGAGGT 419 + |||||||||||||| |||||||||||||||||||||||||||||||||| |||||||| +Sbjct 613 GTAATGGAGCTGATTCGAATGATAAAGCGGGGTATCAATGATCGGAACTTCTGGAGAGGC 672 + +Query 420 GAGAATGGACGAAGGACAAGAATTGCATATGAGAGAATGTGCAACATCCTCAAAGGGAAA 479 + |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 673 GAGAATGGACGAAGAACAAGAATTGCATATGAGAGAATGTGCAACATCCTCAAAGGGAAA 732 + +Query 480 TTCCAAACAGCAGCACAACGAGCAATGATGGACCAGGTACGAGAAAGCAGAAACCCAGGA 539 + ||||| |||||||| ||||||||||||||||||||||| |||||||||||||| |||||| +Sbjct 733 TTCCAGACAGCAGCGCAACGAGCAATGATGGACCAGGTGCGAGAAAGCAGAAATCCAGGA 792 + +Query 540 AATGCTGAGATTGAAGATCTCATTTTTCTGGCACGATCTGCACTCATTCTGAGAGGATCA 599 + ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| +Sbjct 793 AATGCTGAGATTGAAGATCTCATCTTTCTGGCACGATCTGCACTCATTCTGAGAGGATCA 852 + +Query 600 GTGGCTCATAAATCCTGCCTACCTGCTTGTGTATATGGACTTATTGTGGCGAGTGGATAT 659 + ||||||||||||||||| || ||||||||||||||||||||||||||||| ||||||||| +Sbjct 853 GTGGCTCATAAATCCTGTCTGCCTGCTTGTGTATATGGACTTATTGTGGCAAGTGGATAT 912 + +Query 660 GACTTTGAAAGAGAAGGGTACTCCCTAGTTGGGATAGATCCTTTTCGTCTGCTTCAGAAC 719 + ||||||||||||||||||||||||||||| ||| |||||||||||||||||||||||||| +Sbjct 913 GACTTTGAAAGAGAAGGGTACTCCCTAGTCGGGGTAGATCCTTTTCGTCTGCTTCAGAAC 972 + +Query 720 AGCCAAGTGTTCAGCCTTATTAGACCGAATGAGAATCCAGTTCATAAGAGTCAACTGGTC 779 + ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||| | +Sbjct 973 AGCCAAGTGTTCAGCCTCATTAGACCGAATGAGAATCCAGTCCATAAGAGTCAGCTGATA 1032 + +Query 780 TGGATGGCATGCCATTCTGCAGCATTTGAAGATCTGAGGGTGTCAAGTTTTATCAGAGGG 839 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1033 TGGATGGCATGCCATTCTGCAGCATTTGAAGATCTGAGGGTGTCAAGTTTTATCAGAGGG 1092 + +Query 840 ACAAAAGTGATCCCAAGAGGACAATTGTCCACCAGAGGAGTTCAAATTGCTTCAAATGAA 899 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 1093 ACAAAAGTGATCCCAAGAGGACAATTGTCCACCAGAGGGGTTCAAATTGCTTCAAATGAA 1152 + +Query 900 AACATGGAAACAATGGACTCCGTTACTCTTGAACTTAGAAGCAAGTACTGGGCTATAAGA 959 + ||||||||||||||||||||| |||||||||||||||||||||| ||||||||||||||| +Sbjct 1153 AACATGGAAACAATGGACTCCATTACTCTTGAACTTAGAAGCAAATACTGGGCTATAAGA 1212 + +Query 960 ACCAGGAGCGGAGGAAACACCAATCAACAGAGAGCATCCGCAGGGCAAATCAGTGTACAA 1019 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1213 ACCAGGAGCGGAGGAAACACCAATCAACAGAGAGCATCCGCAGGGCAAATCAGTGTACAA 1272 + +Query 1020 CCTACCTTCTCAGTACAGAGAAATCTTCCTTTTGAGAGAGCAACCATCATGGCAGCATTT 1079 + ||||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||| +Sbjct 1273 CCTACTTTCTCAGTACAGAGAAATCTTCCTTTCGAGAGAGCGACCATCATGGCAGCATTT 1332 + +Query 1080 ACTGGAAACACTGAAGGCAGAACATCTGATATGAGGACTGAAATTATAAAAATGATGGAA 1139 + ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| +Sbjct 1333 ACTGGAAACACTGAAGGCAGAACATCTGATATGAGGACTGAAATTATAAGAATGATGGAA 1392 + +Query 1140 AGTGCCAGACCAGAAGATGTGTCCTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAA 1199 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1393 AGTGCCAGACCAGAAGATGTGTCCTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAA 1452 + +Query 1200 AAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAGGGATCTTATTTCTTC 1259 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1453 AAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAGGGATCTTATTTCTTC 1512 + +Query 1260 GGAGACAATGCAGAGGAGTATGACAATTAAAGAAAAATACCCTTGTTTCTACT 1312 + ||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1513 GGAGACAATGCAGAGGAGTATGACAATTAAAGAAAAATACCCTTGTTTCTACT 1565 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 17230320 + + +Query= 170144-17ech4NODE_7 + +Length=1100 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 1646 0.0 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 1646 bits (891), Expect = 0.0 + Identities = 992/1042 (95%), Gaps = 2/1042 (0%) + Strand=Plus/Minus + +Query 1 AGTAGAAACAAGGCATTTTT-CATGAAGGACAAGCTAAACTCACTATTTTTGCCGTCTGA 59 + |||||||||||||||||||| |||||||||||||||||| |||||| ||||||||||||| +Sbjct 2341 AGTAGAAACAAGGCATTTTTTCATGAAGGACAAGCTAAATTCACTACTTTTGCCGTCTGA 2282 + +Query 60 ACTCTTCAATGGTGGAACAGATCTTCATGATCTCAGCAAATTCTTCTTTCTTGATCCTTC 119 + ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| +Sbjct 2281 GCTCTTCAATGGTGGAACAGATCTTCATGATCTCAGCAAATTCTTCTTTCTTAATCCTTC 2222 + +Query 120 CAGATTCGAAATCAATCCGTGCATCAATTCTGGCCCTAGATACCATGGCCTCCACCATGC 179 + |||| |||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 2221 CAGACTCGAAATCAATCCGTGCATCAATTCTGGCCCTGGATACCATGGCCTCCACCATGC 2162 + +Query 180 TTGAAATTCCAACTGGCCTTCTGTATGAACTGCTAGGAAAGAATTTCTCGAATAGATTGC 239 + | ||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||| +Sbjct 2161 TGGAAATTCCAACTGGCCTCCTGTATGAACTGCTAGGGAAGAATTTCTCGAATAGATTGC 2102 + +Query 240 AGCACTTTTGGTACATTTGTTCATCCTCAAGAATTCCCCTTTGGCTGGTATTGAGGATGG 299 + ||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||| +Sbjct 2101 AGCACTTCTGGTACATTTGTTCATCCTCAAGAATTCCCCTTTGGCTGGTATTGAGAATGG 2042 + +Query 300 AACGGTTCCTTTTTGGAATCCACGAATGTGTAGTAGCAACAGCATCATATTCCATGCTTT 359 + |||| ||||||||||||||||| ||||||||||| ||||||||||||||||||||||||| +Sbjct 2041 AACGATTCCTTTTTGGAATCCAAGAATGTGTAGTTGCAACAGCATCATATTCCATGCTTT 1982 + +Query 360 TAGCTGGACCATGGGCTGGCATCACCACGGCACTGTTTACGGACTCAATTCCCTTGTGGT 419 + |||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||| +Sbjct 1981 TAGCTGGACCATGGGCTGGCATTACCACGGCACTGTTTACGGACTCAATTCCCTTATGGT 1922 + +Query 420 TGACAAACGGATTCAGAGGATTACACAATCTCCCTCGATAATCTACATCCATCAGTTCCC 479 + ||||||||||||||||||||||||||||||| || ||||||||||||||||| || |||| +Sbjct 1921 TGACAAACGGATTCAGAGGATTACACAATCTTCCCCGATAATCTACATCCATTAGCTCCC 1862 + +Query 480 ATTTCAAGCAGACTTCAGGAATGTGGAGATTCCGGATATTATACAGATTTGGTCCTCCAT 539 + |||||||||||||||| || |||||||||||||||||||| || |||||||||||||||| +Sbjct 1861 ATTTCAAGCAGACTTCCGGGATGTGGAGATTCCGGATATTGTATAGATTTGGTCCTCCAT 1802 + +Query 540 CTGAAACCAGTAGTCCTGCCTTTGAATGGGTTTGTTCCCATAGCTTTCTTAACTCGAATG 599 + |||||||||||||||||||||||||||||||||| |||||||| ||| ||| |||||||| +Sbjct 1801 CTGAAACCAGTAGTCCTGCCTTTGAATGGGTTTGCTCCCATAGTTTTTTTAGCTCGAATG 1742 + +Query 600 ATCTTTTCGTTTGGATTTGCATGTCGCCTCTGTGGCATCGATATGTGTACCTGTAGTCCT 659 + |||||||||||||||||||| |||| |||||||||||||| ||||| ||||||||||||| +Sbjct 1741 ATCTTTTCGTTTGGATTTGCGTGTCACCTCTGTGGCATCGGTATGTATACCTGTAGTCCT 1682 + +Query 660 TAATGAATAGTTGAAGTGCCATTTGGGCTGTTGCTGGCCCGAGATCATTGTTTATCATGT 719 + |||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1681 TAATGAATAGCTGAAGAGCCATTTGGGCTGTTGCTGGCCCGAGATCATTGTTTATCATGT 1622 + +Query 720 TGTTCTTTATCACTGTCACCCCAATGCTCATGTCAGCCGATTCATTAACTCCAGATACTC 779 + ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| | +Sbjct 1621 TGTTCTTTATCACTGTCACTCCAATGCTCATGTCAGCCGATTCATTAACTCCAGATACCC 1562 + +Query 780 CAAAGCTGGGCAACTCCATGCTGAAGTTGGCTACAAACCCATATCGGTAGAAAAA-CTTG 838 + |||||||||| | |||||| ||||||||||||||||||||||| ||||||||||| |||| +Sbjct 1561 CAAAGCTGGGTAGCTCCATACTGAAGTTGGCTACAAACCCATAGCGGTAGAAAAAGCTTG 1502 + +Query 839 TGAATTCAAATGTCCCTGTCCTATTTATGTAAGATTTCTTTTTGCTCATATTGATTCCAA 898 + |||||||||| || |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1501 TGAATTCAAACGTTCCTGTCCTATTTATGTAAGATTTCTTTTTGCTCATATTGATTCCAA 1442 + +Query 899 CCAGTTTGCAGGTCCTATAGAACCTATCCACTCCTGCTTGTATTCCCTCATGATTGGGTG 958 + |||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||| +Sbjct 1441 CCAGTTTGCAGGTCCTATAGAACCTATCCACTCCTGCTTGTATTCCTTCATGATTAGGTG 1382 + +Query 959 CATTCACTATGAGGGCGAAGTCATCAGAGGATTGGAGTCCATCCCACCAATAGGTGGTTT 1018 + |||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||| +Sbjct 1381 CATTCACTATGAGGGCGAAGTCATCAGAAGATTGGAGTCCATCCCACCAGTAGGTGGTTT 1322 + +Query 1019 TAGTGTACTTCCTTTGCCCGAG 1040 + |||||||| || |||||||||| +Sbjct 1321 TAGTGTACCTCTTTTGCCCGAG 1300 + + + Score = 106 bits (57), Expect = 1e-25 + Identities = 57/57 (100%), Gaps = 0/57 (0%) + Strand=Plus/Minus + +Query 1044 CCTGTCCTATTTATGTAAGATTTCTTTTTGCTCATATTGATTCCAACCAGTTTGCAG 1100 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1487 CCTGTCCTATTTATGTAAGATTTCTTTTTGCTCATATTGATTCCAACCAGTTTGCAG 1431 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 14411780 + + +Query= 170144-17ech4NODE_8 + +Length=1076 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 1834 0.0 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 1834 bits (993), Expect = 0.0 + Identities = 1048/1075 (97%), Gaps = 1/1075 (0%) + Strand=Plus/Plus + +Query 1 AGCAAAAGCAGGGGATAATTAAAGAAACCAAGATGGAAGCAAAACTATTTGTACTATTCT 60 + |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 1 AGCAAAAGCAGGGGATAATTAAAGAAACCAAGATGGAAGCAAAACTGTTTGTACTATTCT 60 + +Query 61 GTGCATTTACTGCACTGGAAGCTGACACCATTTGTGTAGGCTATCATGCTAACAATTCCA 120 + ||||||| ||| |||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 61 GTGCATTCACTACACTGGAAGCTGACACCATTTGTGTAGGCTATCATGCTAACAATTCCA 120 + +Query 121 CAGACACTGTCGACACGATACTAGAGAAGAATGTGACCGTTACCCATTCAGTTAATTTAC 180 + |||||||||||||||||||||| || |||||||||||||||||||||||||||||||||| +Sbjct 121 CAGACACTGTCGACACGATACTGGAAAAGAATGTGACCGTTACCCATTCAGTTAATTTAC 180 + +Query 181 TAGAAAACAGCCACAATGAGAAACTCTGCAGCCTTAATGGAAAGGCCCCATTACAACTGG 240 + |||||| |||||||||||||||||| ||||||||||||||||||||||| |||||||||| +Sbjct 181 TAGAAAGCAGCCACAATGAGAAACTTTGCAGCCTTAATGGAAAGGCCCCCTTACAACTGG 240 + +Query 241 GAAACTGCAACGTAGCAGGATGGATCCTTGGCAACCCAGAATGTGACTTGCTGCTCACAG 300 + |||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||| +Sbjct 241 GAAACTGCAACGTAGCAGGATGGATCCTTGGCAACCCAGAGTGTGACTTGCTGCTCACAG 300 + +Query 301 CAAATTCGTGGTCTTACATAATAGAGACCTCAAATTC-AAAAATGGTGCATGCTATCCTG 359 + |||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||||| +Sbjct 301 CAAATTCGTGGTCTTATATAATAGAGACTTCAAATTCAAAAAATGGTGCATGCTATCCTG 360 + +Query 360 GAGAATTCGCTGATTATGAGGAATTAAGGGAACAGCTGAGTACAGTTTCTTCATTTGAAA 419 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 361 GAGAATTCGCTGATTATGAGGAATTAAGGGAACAGCTGAGTACAGTTTCTTCATTTGAAA 420 + +Query 420 GATTTGAAATTTTCCCAAAAACAACCTCATGGCCAAACCATGAGACAACCAAAGGCACCA 479 + |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| +Sbjct 421 GATTTGAAATTTTCCCAAAAGCAACCTCATGGCCAAACCATGAGACAACCAAAGGCACCA 480 + +Query 480 CAGTTGCATGCTCTCACTCTGGAGTCAATAGCTTTTATCGGAATTTGCTCTGGATAGTAA 539 + |||||||||||||||||||||||| |||||||||||||||||| ||||| |||||||||| +Sbjct 481 CAGTTGCATGCTCTCACTCTGGAGCCAATAGCTTTTATCGGAACTTGCTATGGATAGTAA 540 + +Query 540 AAAAGGGAAACTCCTATCCTAAGCTCAGCAATTCATACACAAACAACAAAGGAAAAGAAG 599 + ||||||||||||||||||||||||||||||| |||||||||||||||||||||| ||||| +Sbjct 541 AAAAGGGAAACTCCTATCCTAAGCTCAGCAAGTCATACACAAACAACAAAGGAAGAGAAG 600 + +Query 600 TGCTCGTGATCTGGGGAGTGCATCATCCCCCCACTGACAGTGATCAACAAACCCTCTACC 659 + |||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 601 TGCTTGTGATCTGGGGAGTGCATCATCCCCCCACTGACAGTGATCAACAAACCCTCTACC 660 + +Query 660 AGAATAATCATACATATGTTTCAGTTGGATCATCAAAATACTATCAGAAATTCACCCCAG 719 + ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||| +Sbjct 661 AGAATAATCATACATATGTTTCAGTTGGATCATCAAAATACTATCAGAAGTTCACCCCAG 720 + +Query 720 AAATAGTAGCTAGACCTAAAGTCAGAGAGCAAGCGGGCAGAATGAATTATTATTGGACAC 779 + ||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||| +Sbjct 721 AAATAGTAGCTAGACCTAAAGTCAGGGAACAAGCGGGCAGAATGAATTATTATTGGACAC 780 + +Query 780 TATTAGATCAAGGGGACACCATAACCTTTGAAGCCACAGGGAACTTAATAGCGCCATGGC 839 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 781 TATTAGATCAAGGGGACACCATAACCTTTGAAGCCACAGGGAACTTAATAGCGCCATGGC 840 + +Query 840 ATGCATTTGCATTGAATAGGGGCTCTAATTCTGGAATTATGATGTCGGATGTACACGTTC 899 + |||||||||||||||||| |||||||||||||||||| |||||||||||||| ||||||| +Sbjct 841 ATGCATTTGCATTGAATAAGGGCTCTAATTCTGGAATCATGATGTCGGATGTTCACGTTC 900 + +Query 900 ACAATTGCACTACAAAATGCCAAACTCCTCACGGGGCCTTGAAAGGCAATCTTCCTTTTC 959 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 901 ACAATTGCACTACAAAATGCCAAACTCCTCACGGGGCCTTGAAAGGCAATCTTCCTTTTC 960 + +Query 960 AAAATGTACATCCCATTACTATTGGGGAATGCCCCAAATATGTTAAAAGCACCCAACTAA 1019 + ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| +Sbjct 961 AAAATGTACATCCCATTACTATTGGAGAATGCCCCAAATATGTTAAAAGCACCCAACTAA 1020 + +Query 1020 GAATGGCAACAGGATTAAGGAATATTCCCTCTATCCAATCCAGAGGACTTTTTGG 1074 + ||||||||||||||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 1021 GAATGGCAACAGGATTAAGGAATATCCCCTCTATCCAATCCAGAGGACTTTTTGG 1075 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 14092700 + + +Query= 170144-17ech4NODE_9 + +Length=1039 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 1714 0.0 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 1714 bits (928), Expect = 0.0 + Identities = 964/982 (98%), Gaps = 0/982 (0%) + Strand=Plus/Plus + +Query 39 ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCGTCAGGCCCCCTC 98 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1 ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCGTCAGGCCCCCTC 60 + +Query 99 AAAGCCGAGATCGCACAGAGACTAGAAGGTGTCTTTGCAGGGAAGAACACAGATCTGGAG 158 + |||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||| +Sbjct 61 AAAGCCGAGATCGCGCAGAGACTGGAAGGTGTCTTTGCAGGGAAGAACACAGATCTGGAG 120 + +Query 159 GCTCTCATGGAGTGGCTAAAGACAAGACCGATCCTGTCACCTCTGACTAAGGGAATTTTG 218 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| +Sbjct 121 GCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGAATTTTG 180 + +Query 219 GGATTCGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTC 278 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 181 GGATTCGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTC 240 + +Query 279 CAAAATGCCCTAAATGGAAATGGGGACCCGAACAATATGGATAGAGCAGTCAAATTGTAC 338 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 241 CAAAATGCCCTAAATGGAAATGGGGACCCGAACAATATGGATAGAGCAGTCAAATTGTAC 300 + +Query 339 AAGAAGCTAAAAAGGGAAATAACATTCCATGGGGCTAAAGAGGTATCATTAAGCTACTCA 398 + |||||||||||||||||||||||||||||||||||||||||||| ||| ||||||||||| +Sbjct 301 AAGAAGCTAAAAAGGGAAATAACATTCCATGGGGCTAAAGAGGTGTCACTAAGCTACTCA 360 + +Query 399 ACTGGGGCACTCGCCAGTTGCATGGGCCTCATATACAACAGAATGGGAACAGTAACCACA 458 + ||||| |||||||||||||||||||| ||||||||||||||||||||||||||||||||| +Sbjct 361 ACTGGTGCACTCGCCAGTTGCATGGGTCTCATATACAACAGAATGGGAACAGTAACCACA 420 + +Query 459 GAAGCTGCTTTTGGTCTAGTGTGCGCCACTTGTGAACAGATTGCTGATTCACAGCATCGG 518 + |||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||| +Sbjct 421 GAAGCTGCTTTTGGCCTAGTGTGTGCCACTTGTGAACAGATTGCTGATTCACAGCATCGG 480 + +Query 519 TCTCACAGACAAATGGCTACTACCACCAACCCATTAATCAGGCATGAAAACAGAATGGTT 578 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 481 TCTCACAGACAAATGGCTACTACCACCAACCCATTAATCAGGCATGAAAACAGAATGGTT 540 + +Query 579 CTGGCTAGCACTACAGCTAAGGCTATGGAACAGATGGCTGGGTCGAGTGAGCAGGCAGCA 638 + |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| +Sbjct 541 CTGGCTAGCACTACAGCTAAGGCTATGGAACAGATGGCTGGGTCGAGTGAACAGGCAGCA 600 + +Query 639 GAGGCCATGGAAGTTGCCAATCAGACTAGGCAGATGGTGCATGCAATGAGAACAGTTGGA 698 + |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 601 GAGGCCATGGAAGTTGCCAATCAGACTAGGCAGATGGTGCATGCAATGAGAACAATTGGA 660 + +Query 699 ACACACCCCAGTTCCAGCGCCGGTCTGAAAGATGACCTTCTTGAAAATTTGCAGGCCTAC 758 + ||||| || ||||||||||| ||||||||||||||||||||||||||||||||||||||| +Sbjct 661 ACACATCCTAGTTCCAGCGCAGGTCTGAAAGATGACCTTCTTGAAAATTTGCAGGCCTAC 720 + +Query 759 CAGAAACGGATGGGAGTGCAGATACAGCGATTCAAGTGATCCTCTTGTCATTGCAGCAAA 818 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 721 CAGAAACGGATGGGAGTGCAGATACAGCGATTCAAGTGATCCTCTTGTCATTGCAGCAAA 780 + +Query 819 TATAATTGGGATCTTGCACCTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGTAT 878 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 781 TATAATTGGGATCTTGCACCTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGTAT 840 + +Query 879 TTATCGTCGCATTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTC 938 + |||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 841 TTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTC 900 + +Query 939 CATGAGGGAAGAATATCAACAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTT 998 + |||||||||||||||||||||||||||||||| |||||||||||||||| |||||||||| +Sbjct 901 CATGAGGGAAGAATATCAACAGGAACAGCAGAGTGCTGTGGATGTTGACAATGGTCATTT 960 + +Query 999 TGTCAACATAGAGCTGAAGTAA 1020 + |||||||||||||||| ||||| +Sbjct 961 TGTCAACATAGAGCTGGAGTAA 982 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 13600785 + + +Query= 170144-17ech4NODE_10 + +Length=917 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 1341 0.0 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 1341 bits (726), Expect = 0.0 + Identities = 819/865 (95%), Gaps = 1/865 (0%) + Strand=Plus/Plus + +Query 54 AGCAAAAGCAGGCAAACCATTTGAATGGATGTCAACCCGACTCTACTTTTCTTAAAAGTG 113 + ||| ||||||||||||| |||||||||||||||||||||||||||||||||||||||||| +Sbjct 1 AGCGAAAGCAGGCAAACTATTTGAATGGATGTCAACCCGACTCTACTTTTCTTAAAAGTG 60 + +Query 114 ACAGCACAAAATGCTATAAGCACTACATTCCCCTATACAGGGGATCCCCCATATAGTCAC 173 + ||||||||||||||||||||||||||||||| ||||| || ||||||||||||||||| +Sbjct 61 CCAGCACAAAATGCTATAAGCACTACATTCCCTTATACTGGAGATCCCCCATATAGTCAT 120 + +Query 174 GGAACAGGAACAGGATATACAATGGACACGATCAACAGAACACACCAATATTCAGAAAGA 233 + |||||||| |||||||| || ||||||||| ||||||||||||| ||||||||||||||| +Sbjct 121 GGAACAGGGACAGGATACACCATGGACACGGTCAACAGAACACATCAATATTCAGAAAGA 180 + +Query 234 GGAAGATGGACAACAAACACAGAGACTGGAGCACCCCAGCTTAACCCGATTGATGGACCA 293 + ||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||| +Sbjct 181 GGAAGATGGACAACAAACACAGAAACTGGAGCACCCCAGCTTAACCCGATTGATGGGCCA 240 + +Query 294 CTACCTGAGGACAATGAACCAAGCGGTTATGCCCAAACAGACTGTGTCCTTGAGGCAATG 353 + ||||||||||||||||| |||||||| ||||| ||||||||||||||||| ||||||||| +Sbjct 241 CTACCTGAGGACAATGAGCCAAGCGGGTATGCTCAAACAGACTGTGTCCTGGAGGCAATG 300 + +Query 354 GCTTTCCTTGAGGAGTCCCATCCAGGGATATTTGAAAATTCTTGTCTTGAAACAATGGAG 413 + |||||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||| +Sbjct 301 GCTTTCCTTGAGGAATCCCATCCAGGGATATTTGAAAACTCTTGTCTTGAAACGATGGAG 360 + +Query 414 GTTGTTCAACAAACAAGAGTGGACAAACTGACCCAAGGTCGTCAGACCTATGACTGGACA 473 + ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||| +Sbjct 361 GTTGTCCAACAAACAAGAGTGGACAAACTGACTCAAGGTCGTCAGACCTATGACTGGACA 420 + +Query 474 TTGAATAGAAACCAACCGGCTGCAACTGCTTTGGCCAACACAATAGAAGTCTTTAGAATG 533 + ||||||||||||||||||||||||||||||||||||||||||||||| ||||| || ||| +Sbjct 421 TTGAATAGAAACCAACCGGCTGCAACTGCTTTGGCCAACACAATAGAGGTCTTCAGGATG 480 + +Query 534 AACAGTCTAACAGCCAATGAATCGGGAAGATTAATAGATTTCCTTAAGGATGTGGTGGAA 593 + |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 481 AACAGTCTAACAGCCAATGAATCGGGAAGATTAATAGATTTCCTTAAGGATGTGATGGAA 540 + +Query 594 TCAATGGATAAAGAAGAAATGGAAATAACAACACATTTCCAAAGAAAAAGAAGAATAAGG 653 + ||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||| +Sbjct 541 TCAATGGATAAAGAAGAGATGGAAATAACAACACATTTCCAAAGGAAAAGAAGAATAAGG 600 + +Query 654 GACAACATGACTAAG-AAATGGTAACACAAAGGACAATAGGGAAGAAAAAACAGAAATTG 712 + ||||||||||| ||| ||||||||||||||||||||||||| |||||||| |||||| || +Sbjct 601 GACAACATGACCAAGAAAATGGTAACACAAAGGACAATAGGAAAGAAAAAGCAGAAACTG 660 + +Query 713 GACAAGAGGAATTATCTAATAAGAGCATTAACATTAAACACAATGACAAAGGACGCAGAA 772 + ||||||||| |||||||||||||||||| |||||||||||||||||||| || |||||| +Sbjct 661 AACAAGAGGAGTTATCTAATAAGAGCATTGACATTAAACACAATGACAAAAGATGCAGAA 720 + +Query 773 AGGGGCAAGTTGAAAAGACGTGCAATTGCAACACCAGGGATGCAAATCAGAGGATTTGTG 832 + || |||||||||||||| |||||||||||||||||||||||||| ||||||||||||||| +Sbjct 721 AGAGGCAAGTTGAAAAGGCGTGCAATTGCAACACCAGGGATGCAGATCAGAGGATTTGTG 780 + +Query 833 TACTTCGTAGAAACACTAGCAAGAAGCATCTGTGAGAAACTTGAGCAATCTGGGCTCCCA 892 + ||||||||||||||||| || || |||||||||||||||||||||||||||||||||||| +Sbjct 781 TACTTCGTAGAAACACTGGCGAGGAGCATCTGTGAGAAACTTGAGCAATCTGGGCTCCCA 840 + +Query 893 GTTGGGGGGAATGAGAAGAAAGCCA 917 + |||||||||||||| |||||||||| +Sbjct 841 GTTGGGGGGAATGAAAAGAAAGCCA 865 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 11978795 + + +Query= 170144-17ech4NODE_12 + +Length=863 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 1328 0.0 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 1328 bits (719), Expect = 0.0 + Identities = 751/767 (98%), Gaps = 0/767 (0%) + Strand=Plus/Plus + +Query 1 CTGGGGGCTTGGCGATGCCCCATTTCTCGATAGGCTTCGCCGAGACCAGAAGTCTCTAAG 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 72 CTGGGGGCTTGGCGATGCCCCATTTCTCGATAGGCTTCGCCGAGACCAGAAGTCCCTAAG 131 + +Query 61 AGGGAGAGGCAGCACTCTTGGTCTGGAAATCGAATCAGCTACTCATGCGGGGAAACAAAT 120 + |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| +Sbjct 132 AGGGAGAGGCAGCACTCTTGGTCTGGAAATCGAATCAGCTACTCGTGCGGGGAAACAAAT 191 + +Query 121 AGTTAAGTGTATTCTGGAAGAAGAATACAATGAATCACTTAAAATAACCAATGCTTCTGT 180 + ||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||| +Sbjct 192 AGTTAAGCGTATTCTGGAAGAAGAATACGATGAAGCACTTAAAATAACCAATGCTTCTGT 251 + +Query 181 GCCTGCTTCACACTATTTGACTGACATGACTCTTGAAGAGATGTCAAGGGACTGGTTCAT 240 + ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 252 GCCTGCTTCACGCTATTTGACTGACATGACTCTTGAAGAGATGTCAAGGGACTGGTTCAT 311 + +Query 241 GCTCATGCCCAAGCAAAAGGTGGCAGGTCCCTTCTGCATCAGAATGGACCAAGCAATAAT 300 + ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| +Sbjct 312 GCTCATGCCCAAGCAAAAGGTGGCAGGTCCCTTTTGCATCAGAATGGACCAGGCAATAAT 371 + +Query 301 GGATAAAAATATTACATTGAAAGCAAACTTCAGTGTGATTTTTGACCGACTGGAAACTCT 360 + ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 372 GGATAAAAACATTACATTGAAAGCAAACTTCAGTGTGATTTTTGACCGACTGGAAACTCT 431 + +Query 361 GATACTCCTTAGAGCTTTCACAGAGAAAGGGGCAATTGTAGGTGAAATCTCACCGTTACC 420 + ||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||| +Sbjct 432 GATACTCCTTAGAGCTTTCACAGAGGAAGGGGCAATTATAGGTGAAATCTCACCGTTACC 491 + +Query 421 TTCTCTTCCAGGACATACTGATGAGGATGTCAAAAATGCAATTGGGATCCTCATCAAAGG 480 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 492 TTCTCTTCCAGGACATACTGATGAGGATGTCAAAAATGCAATTGGGATCCTCATCAAAGG 551 + +Query 481 ACTTGAATGGAATGATAATACAGTTCGAGTCTCTGAAGCTCTACAGAGATTCGCTTGGAG 540 + ||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||| +Sbjct 552 ACTTGAATGGAATGATAATGCAGTTCGAGTCTCTGAAACTCTACAGAGATTCGCTTGGAG 611 + +Query 541 AAGCACTAATGAGAACGGGAGACCTCCATTCCCTTCAAGACAGAAACGGAAAATGGCGAG 600 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 612 AAGCACTAATGAGAACGGGAGACCTCCATTCCCTTCAAAACAGAAACGGAAAATGGCGAG 671 + +Query 601 AACAATTGGGCCAGAAATTTGAAGAAATAAGATGGCTAATTGAAGAAGTGCGACACAGAT 660 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 672 AACAATTGGGCCAGAAATTTGAAGAAATAAGATGGCTAATTGAAGAAGTGCGACACAGAT 731 + +Query 661 TAAAAATAACGGAGAATAGCTTTGAACAGATAACATTCATGCAAGCATTACAACTACTGC 720 + ||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 732 TAAAAATAACGGAGAATAGCTTTGAACAGATAACATTTATGCAAGCATTACAACTACTGC 791 + +Query 721 TTGAAGTGGAGCAAGAGATAAGGACTTTTTCGTTTCAGTTTATTTAA 767 + |||||||||||||||||||||||||||| |||||||||||||||||| +Sbjct 792 TTGAAGTGGAGCAAGAGATAAGGACTTTCTCGTTTCAGTTTATTTAA 838 + + + Score = 137 bits (74), Expect = 4e-35 + Identities = 76/77 (99%), Gaps = 0/77 (0%) + Strand=Plus/Plus + +Query 787 CCCTTCAAGACAGAAACGGAAAATGGCGAGAACAATTGGGCCAGAAATTTGAAGAAATAA 846 + |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 642 CCCTTCAAAACAGAAACGGAAAATGGCGAGAACAATTGGGCCAGAAATTTGAAGAAATAA 701 + +Query 847 GATGGCTAATTGAAGAA 863 + ||||||||||||||||| +Sbjct 702 GATGGCTAATTGAAGAA 718 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 11260865 + + +Query= 170144-17ech4NODE_13 + +Length=704 + Score E +Sequences producing significant alignments: (Bits) Value + + HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1))... 830 0.0 + + +> HE603921.1 Influenza A virus (A/swine/Morbihan/0287/2007(H1N1)) +PB2 gene for polymerase PB2, segment 1, genomic RNA +Length=2334 + + Score = 830 bits (449), Expect = 0.0 + Identities = 488/507 (96%), Gaps = 2/507 (0%) + Strand=Plus/Plus + +Query 200 GAAGAAGAGCAACAGCCATCTTAAGGAAAGCAACTAGAAGGCTGATTCAGCTGATAGTAA 259 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1120 GAAGAAGAGCAACAGCCATCTTAAGGAAAGCAACTAGAAGGCTGATTCAGCTGATAGTAA 1179 + +Query 260 GTGGAAAAGACGAGCAGTCAATTGCTGAAGCAATCATAGTAGCAATGGTGTTTTCACAAG 319 + |||||| ||| || |||||||||||||||||||||||||||||||||||||| ||||||| +Sbjct 1180 GTGGAAGAGATGAACAGTCAATTGCTGAAGCAATCATAGTAGCAATGGTGTTCTCACAAG 1239 + +Query 320 AAGATTGTATGATAAAGGCTGTCCGAGGTGATCTAAA-TTTGTAAACAGAGCAAACCAAA 378 + |||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||| +Sbjct 1240 AAGATTGTATGATAAAAGCTGTCCGAGGTGATCTAAATTTTGTAAACAGAGCAAACCAAA 1299 + +Query 379 GGCTGAATCCCATGCATCAACTCCTGAGACACTTCCAGAAGGACGCAAAAGTGCTGTTTC 438 + ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||| +Sbjct 1300 GGCTGAATCCCATGCATCAACTCCTGAGACACTTCCAGAAGGATGCAAAAGTGCTGTTTC 1359 + +Query 439 AAAATTGGGGAACTGAACCTATTGATAACATCATGGG-ATGATAGGTATATTACCCGATA 497 + |||||||||||| ||||||||||||||| |||||||| |||||||||||||||||||||| +Sbjct 1360 AAAATTGGGGAATTGAACCTATTGATAATATCATGGGAATGATAGGTATATTACCCGATA 1419 + +Query 498 TGACCCCAAGCACAGAAATGTCATTAAGAGGGGTGAGGATTAGTAAAACAGGAGTAGATG 557 + |||| |||||||||||||||||||||||||| |||||||| ||||||||||||||||| | +Sbjct 1420 TGACTCCAAGCACAGAAATGTCATTAAGAGGAGTGAGGATCAGTAAAACAGGAGTAGACG 1479 + +Query 558 AATATTCCAGTACTGAGAGAGTGGCTGTGAGTATTGATCGTTTCTTGAGAGTTCGAGATC 617 + ||||||||||||| |||||||||| ||||||||||||||| ||||||||||||||||||| +Sbjct 1480 AATATTCCAGTACAGAGAGAGTGGTTGTGAGTATTGATCGCTTCTTGAGAGTTCGAGATC 1539 + +Query 618 AGCGGGGAAATGTACTACTATCTCCTGAGGAGGTTAGTGAAACACAAGGAACAGAGAAAT 677 + ||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 1540 AGCGGGGAAATGTACTACTATCTCCTGAGGAGGTTAGCGAAACACAAGGAACAGAGAAAT 1599 + +Query 678 TAACAATAACCTATTCATCATCAATGA 704 + | ||||||||||||||||||||||||| +Sbjct 1600 TGACAATAACCTATTCATCATCAATGA 1626 + + + Score = 337 bits (182), Expect = 3e-95 + Identities = 198/206 (96%), Gaps = 0/206 (0%) + Strand=Plus/Plus + +Query 1 TCCACTGGCATCACTATTGGAGATGTGTCACGGCACACAAATTGGTGGGCTAAGAATGGT 60 + ||||||||||||||||||||||||||||||||||||||||||||||||| |||| ||||| +Sbjct 845 TCCACTGGCATCACTATTGGAGATGTGTCACGGCACACAAATTGGTGGGATAAGGATGGT 904 + +Query 61 TGACATCCTCAAACAAAACCCAACGGAAGAGCAAGCCGTGGATATATGCAAAGCAGCAAT 120 + ||||||||| |||||||| ||||||||||||||||| ||||||||||||||||||||||| +Sbjct 905 TGACATCCTTAAACAAAATCCAACGGAAGAGCAAGCAGTGGATATATGCAAAGCAGCAAT 964 + +Query 121 GGGTTTGAGAATCAGTTCCTCCTTTAGCTTTGGAGGTTTCACTTTCAAAAGAACAAGTGG 180 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 965 GGGTTTGAGAATCAGTTCCTCCTTTAGCTTTGGAGGTTTCACTTTCAAAAGAACAAGTGG 1024 + +Query 181 GTCATCTGTCAAAAAGGAAGAAGAAG 206 + |||||||| |||| ||||||||||| +Sbjct 1025 ATCATCTGTTAAAAGGGAAGAAGAAG 1050 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 9165767 + + +Query= 170144-17ech4NODE_16 + +Length=616 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 989 0.0 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 989 bits (535), Expect = 0.0 + Identities = 590/617 (96%), Gaps = 1/617 (0%) + Strand=Plus/Plus + +Query 1 AATCCAAACGAAAAGGTCATTCGAGCT-AAAAAACTATGGGAGCAAACCCATTCAAAGGC 59 + ||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| +Sbjct 1725 AATCCAAACGAAAAGATCATTCGAGCTAAAAAAACTATGGGAGCAAACCCATTCAAAGGC 1784 + +Query 60 AGGACTACTGGTTTCAGATGGAGGACCAAATCTGTACAACATCCGGAATCTCCACATTCC 119 + ||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| || +Sbjct 1785 AGGACTACTGGTTTCAGATGGAGGACCAAATCTATACAATATCCGGAATCTCCACATCCC 1844 + +Query 120 GGAAGTCTGCTTGAAATGGGAACTAATGGATGTAGATTATCGGGGAAGATTGTGTAATCC 179 + ||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| +Sbjct 1845 GGAAGTCTGCTTGAAATGGGAGCTAATGGATGTAGATTATCGGGGAAGATTGTGTAATCC 1904 + +Query 180 TCTAAATCCATTCGTCAACCACAAGGGAATTGAGTCCGTAAATAGTGCCGTGGTAATGCC 239 + ||| ||||| || |||||||| |||||||||||||||||||| ||||||||||||||||| +Sbjct 1905 TCTGAATCCGTTTGTCAACCATAAGGGAATTGAGTCCGTAAACAGTGCCGTGGTAATGCC 1964 + +Query 240 ATCTCATGGTCCAGCTAAAAGCATGGAATATGATGCTGTTGCAACTACACATTCCTGGAT 299 + | | |||||||||||||||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 1965 AGCCCATGGTCCAGCTAAAAGCATGGAATATGATGCTGTTGCAACTACACATTCTTGGAT 2024 + +Query 300 TCCAAAAAGGAATCGTTCCATTCTCAATACCTGCCAAAGGGGAATTCTTGAGGATGAACA 359 + ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| +Sbjct 2025 TCCAAAAAGGAATCGTTCCATTCTCAATACCAGCCAAAGGGGAATTCTTGAGGATGAACA 2084 + +Query 360 GATGTACCAGAAATGCTGCAATCTATTCGAAAAATTCTTCCCCAGCAGTTCATACAGGAG 419 + ||||||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||| +Sbjct 2085 AATGTACCAGAAGTGCTGCAATCTATTCGAGAAATTCTTCCCTAGCAGTTCATACAGGAG 2144 + +Query 420 GCCAGTTGGAATTTCAAGCATGGTGGAGGCCATGATATCTAGGGCCAGAATTGATGCACG 479 + ||||||||||||||| |||||||||||||||||| |||| |||||||||||||||||||| +Sbjct 2145 GCCAGTTGGAATTTCCAGCATGGTGGAGGCCATGGTATCCAGGGCCAGAATTGATGCACG 2204 + +Query 480 GGTTGATTTCGAATCTGGAAGGATTAAGGAAGAGGAATTCGCTGAGATCATGAAGATCTG 539 + | |||||||||| ||||||||||||||| |||| ||||| |||||||||||||||||||| +Sbjct 2205 GATTGATTTCGAGTCTGGAAGGATTAAGAAAGAAGAATTTGCTGAGATCATGAAGATCTG 2264 + +Query 540 TTCCACCATTGAAGAGCTCAGACGGCAAAAGTAGTGAATTTAGCTTGTCCTTCATGAAAA 599 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2265 TTCCACCATTGAAGAGCTCAGACGGCAAAAGTAGTGAATTTAGCTTGTCCTTCATGAAAA 2324 + +Query 600 AATGCCTTGTTTCTACT 616 + ||||||||||||||||| +Sbjct 2325 AATGCCTTGTTTCTACT 2341 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 7995103 + + +Query= 170144-17ech4NODE_17 + +Length=578 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 881 0.0 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 881 bits (477), Expect = 0.0 + Identities = 534/562 (95%), Gaps = 1/562 (0%) + Strand=Plus/Minus + +Query 1 GTGTTGTCTCCAGTAATTGTGAAGGAAAGCTCTGTATCTTGTGAATTGGTCATCATTTTC 60 + |||||||| ||||||||||| ||||||||||| ||||||||||| ||||||||||||||| +Sbjct 944 GTGTTGTCCCCAGTAATTGTAAAGGAAAGCTCGGTATCTTGTGAGTTGGTCATCATTTTC 885 + +Query 61 CTCACAACATTTGCCAACTTAGCTTTCTTTTCATTCCCCCCAACTGGGAGCCCAGATTGC 120 + ||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||| +Sbjct 884 CTCACAACATTTGCCAATTTGGCTTTCTTTTCATTCCCCCCAACTGGGAGCCCAGATTGC 825 + +Query 121 TCAAGTTTTTCACAGATGCTTCTCGCCAGTGTTTCTACGAAGTATACAAATCCTCTGATC 180 + |||||||| ||||||||||| ||||||||||||||||||||||| ||||||||||||||| +Sbjct 824 TCAAGTTTCTCACAGATGCTCCTCGCCAGTGTTTCTACGAAGTACACAAATCCTCTGATC 765 + +Query 181 TGCATCCCTGGTGTTGCAATTGCACGCCTCTTCAACTTGCCTCTTTCTGCATCTTTTGTC 240 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| +Sbjct 764 TGCATCCCTGGTGTTGCAATTGCACGCCTTTTCAACTTGCCTCTTTCTGCATCTTTTGTC 705 + +Query 241 ATTGTGTTTAATGTCAATGCTCTTATTAGATAACTCCTCTTATTCAGCTTCTGTTTTTTC 300 + ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||| +Sbjct 704 ATTGTGTTTAATGTCAATGCTCTTATTAGATAACTCCTCTTGTTCAGTTTCTGCTTTTTC 645 + +Query 301 TTCCCTATTGTCCTTTGTGTTATCATTTTCTTAGTCGTGTTGTCCCTTACTCTTCTTTTC 360 + || ||||||||||||||||||| ||||||||| ||| |||||||||||| |||||||||| +Sbjct 644 TTTCCTATTGTCCTTTGTGTTACCATTTTCTTGGTCATGTTGTCCCTTATTCTTCTTTTC 585 + +Query 361 CTTTGGAAATGTGTTGTTATTTCCACTTCTTCTTTATCCATTGATTCCACCACATCCTTA 420 + ||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||| +Sbjct 584 CTTTGGAAATGTGTTGTTATTTCCATCTCTTCTTTATCCATTGATTCCATCACATCCTTA 525 + +Query 421 AGAAAATCTATTAATCTTCCCGACTCATTGGCAGTTAGATTGTTCATCTTGAAGACCTCT 480 + || |||||||||||||||||||| |||||||| |||||| |||||||| ||||||||||| +Sbjct 524 AGGAAATCTATTAATCTTCCCGATTCATTGGCTGTTAGACTGTTCATCCTGAAGACCTCT 465 + +Query 481 ATTGTATTGGCCAAAGCAGTTGCAGCCGGTTGGTTTCTATTCAATGTCCAGTCATAGGTC 540 + ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 464 ATTGTGTTGGCCAAAGCAGTTGCAGCCGGTTGGTTTCTATTCAATGTCCAGTCATAGGTC 405 + +Query 541 TGACGACCTTGAGTTCAGTTTG 562 + |||||||||||||| ||||||| +Sbjct 404 TGACGACCTTGAGT-CAGTTTG 384 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 7489589 + + +Query= 170144-17ech4NODE_18 + +Length=551 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 893 0.0 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 893 bits (483), Expect = 0.0 + Identities = 513/527 (97%), Gaps = 3/527 (1%) + Strand=Plus/Minus + +Query 26 TACATTTTGAAATTCAAGTCTTAAATGCATATTCTGCATTGTAATGACCCATTAGAGCAC 85 + ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1753 TACATCTTGAAATTCAAGTCTTAAATGCATATTCTGCATTGTAATGACCCATTAGAGCAC 1694 + +Query 86 ATCCAGAAGCTGATTGCCCCCAGGGAGACTAGTAATACCAGGGAACTGGCGACTGTGGAG 145 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| +Sbjct 1693 ATCCAGAAGCTGATTGCCCCCAGGGAGACTAGTAATACCAGGGAACTGGCGACTGCGGAG 1634 + +Query 146 TAGATCGCCAAAATCTGATGAACTCCCACTGATTCTAATTTTATACCATCTATTTTCTCT 205 + |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| +Sbjct 1633 TAGATCGCCAAAATCTGATGAACTCCCACTGATTCTAATTTTATGCCATCTATTTTCTCT 1574 + +Query 206 CTATTCAATTTGGATTCTTCTGAATATCTGGGATAATTATATGTGCCATTCCTTACGCTT 265 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1573 CTATTCAATTTGGATTCTTCTGAATATCTGGGATAATTATATGTGCCATTCCTTACGCTT 1514 + +Query 266 TCCATGCATTCATTATCACATTTGTGATAGAACTCAAAACAGCCATTACCGATTTCCTTG 325 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1513 TCCATGCATTCATTATCACATTTGTGATAGAACTCAAAACAGCCATTACCGATTTCCTTG 1454 + +Query 326 GCGTTGTTCCTCAGTTGTGATTTGACTTTT-CATACAAACTTTTTACGTTAAAGTCATGG 384 + || ||||| || |||||||||||||||||| |||| ||| |||||||||||||||||||| +Sbjct 1453 GCATTGTTTCTAAGTTGTGATTTGACTTTTTCATATAAATTTTTTACGTTAAAGTCATGG 1394 + +Query 385 AAATCTAGGGTTCTTTCATTCTCGAGCAGGATGAGTAATTCAGCGTTATAAGTCCACACA 444 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||| +Sbjct 1393 AAATCTAGGGTTCTTTCATTCTCGAGCAGTATGAGTAATTCAGCGTTATAAGTCCATACA 1334 + +Query 445 TCCAAAA-TCCATCATCGACtttttttATTCAAATTCTCAACCCTTTTCTCTAGATTATT 503 + ||||||| |||||||||||||||||| |||||||||||||| |||||||||||||||||| +Sbjct 1333 TCCAAAAATCCATCATCGACTTTTTT-ATTCAAATTCTCAATCCTTTTCTCTAGATTATT 1275 + +Query 504 GAATTCTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTA 550 + ||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1274 GAATTCTTTGCCCACTGAAGTAAATTGAATGTTCATCTTTTCAATTA 1228 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 7130408 + + +Query= 170144-17ech4NODE_19 + +Length=542 + Score E +Sequences producing significant alignments: (Bits) Value + + GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)... 832 0.0 + + +> GQ161154.1 Influenza A virus (A/swine/Greven/IDT2889/2004(H1N1)) +segment 2 polymerase PB1 (PB1) and PB1-F2 protein (PB1-F2) +genes, complete cds +Length=2341 + + Score = 832 bits (450), Expect = 0.0 + Identities = 509/538 (95%), Gaps = 2/538 (0%) + Strand=Plus/Minus + +Query 2 TTCAGGATTGAGACTCCTAGAACTGTGCTCAGCATGTTGAACATGCCCATCATCATTCCA 61 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 1298 TTCAGGATTGAGACTCCTAGAACTGTGCTCAGCATGTTAAACATGCCCATCATCATTCCA 1239 + +Query 62 GGGCTTAGTGAGGCTGATCCATTTATGAGAAGTGGTCTTATCTTCTCGATCTTTTCCCTT 121 + |||||||||||||| | |||| |||||| ||||| ||||||||||||||||||| |||| +Sbjct 1238 GGGCTTAGTGAGGCCGTGCCATCTATGAGGAGTGGCCTTATCTTCTCGATCTTTTTCCTT 1179 + +Query 122 GTTGATTCATTGAAGTATTTCAAGTCAATATTTGCGAGCATTTCTGCTGGTATTTGTGTT 181 + |||||||||||||| |||||||||||||||| ||| |||||||||||||||||||||||| +Sbjct 1178 GTTGATTCATTGAAATATTTCAAGTCAATATCTGCTAGCATTTCTGCTGGTATTTGTGTT 1119 + +Query 182 CGCAGCTTCATGCTCTTACTTTCAAACATATATCCTTTCCCTAATCTTGCCATTTTGTTT 241 + || |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||| +Sbjct 1118 CGTAGCTTCATGCTCTTACTTTCGAACATGTATCCTTTCCCTAATCTTGCCATTTTGTTT 1059 + +Query 242 GAGAACATTATAGGTGCAATGCTTAAAACATTTCTGAACCATTCAGGTTGGTTTCTTGTG 301 + |||||||||||||| || ||||||||||||||||||||||||||||| || ||||||||| +Sbjct 1058 GAGAACATTATAGGGGCGATGCTTAAAACATTTCTGAACCATTCAGGCTGATTTCTTGTG 999 + +Query 302 ATGTACGTTATCATCGCCAGAAATATCCTGGGGTTTTGGTTCTCATTCCATTTGGTGTTG 361 + ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||| +Sbjct 998 ATGTACGTTATCATCGCCAGAAACATCCTGGGGTTTTGATTCTCATTCCATTTGGTGTTG 939 + +Query 362 TCCCCAGTAATTGTGAATGAAAGCTCTGTATCTTGTGAGTTGGTCATCATTTTC-TCACA 420 + |||||||||||||| || |||||||| ||||||||||||||||||||||||||| ||||| +Sbjct 938 TCCCCAGTAATTGTAAAGGAAAGCTCGGTATCTTGTGAGTTGGTCATCATTTTCCTCACA 879 + +Query 421 ACATTTGCCAATTTGGCTTTCTTCTCATTCCCCCCAACTGGGAGCCCAGATTGCTCAAGT 480 + ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| +Sbjct 878 ACATTTGCCAATTTGGCTTTCTTTTCATTCCCCCCAACTGGGAGCCCAGATTGCTCAAGT 819 + +Query 481 TTCTCACAGATGCTTCTTGCTAGTGTTTCTACGAAGTACACAAATCCTCTGAT-TGCA 537 + |||||||||||||| || || |||||||||||||||||||||||||||||||| |||| +Sbjct 818 TTCTCACAGATGCTCCTCGCCAGTGTTTCTACGAAGTACACAAATCCTCTGATCTGCA 761 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 7010681 + + +Query= 170144-17ech4NODE_20 + +Length=536 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 811 0.0 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 811 bits (439), Expect = 0.0 + Identities = 488/512 (95%), Gaps = 2/512 (0%) + Strand=Plus/Plus + +Query 27 ATGGATTCAAACACTGTGTCAAGCTTTCAGGTAGATTGCTTTCTTTGGCATATTCGCAAG 86 + ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 1 ATGGATTCAAACACTGTGTCAAGCTTTCAGGTAGATTGCTTTCTTTGGCATATCCGCAAG 60 + +Query 87 CGGCTTGCAAACT-GGGGCTTGGCGATGCCCCATTTCTCGATAGGCTTCGTCGAGATCAG 145 + ||| ||||||||| |||||||||||||||||||||||||||||||||||| ||||| ||| +Sbjct 61 CGGTTTGCAAACTGGGGGCTTGGCGATGCCCCATTTCTCGATAGGCTTCGCCGAGACCAG 120 + +Query 146 AAGTCCCTAAGGGGAAGAGGTAGCACTCTCGGTCTGGAAATTGAATCAGCTACTCGTGCG 205 + ||||||||||| || ||||| |||||||| ||||||||||| |||||||||||||||||| +Sbjct 121 AAGTCCCTAAGAGGGAGAGGCAGCACTCTTGGTCTGGAAATCGAATCAGCTACTCGTGCG 180 + +Query 206 GGGAAACAAATAGTTAATCGTATTCTGGAAGAGGAATACGATGAAGAACTTAAAATAACC 265 + ||||||||||||||||| |||||||||||||| ||||||||||||| ||||||||||||| +Sbjct 181 GGGAAACAAATAGTTAAGCGTATTCTGGAAGAAGAATACGATGAAGCACTTAAAATAACC 240 + +Query 266 ATTGCTTCTGTGCCTGTTTCACGCTATTTGACTGACATGACTCTTGAAGAGATGTCAAGG 325 + | |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| +Sbjct 241 AATGCTTCTGTGCCTGCTTCACGCTATTTGACTGACATGACTCTTGAAGAGATGTCAAGG 300 + +Query 326 GACTGGTTCATGCTCATGCCCAAGCAAAAAGTGGCAGGTCCC-TTTGCATCAGAATGGAC 384 + ||||||||||||||||||||||||||||| |||||||||||| ||||||||||||||||| +Sbjct 301 GACTGGTTCATGCTCATGCCCAAGCAAAAGGTGGCAGGTCCCTTTTGCATCAGAATGGAC 360 + +Query 385 CAGGCAATAATGGATAAAACCATCACATTGAAAGCAAATTTTAGTGTGATTTTTGACCGA 444 + ||||||||||||||||||| ||| |||||||||||||| || |||||||||||||||||| +Sbjct 361 CAGGCAATAATGGATAAAAACATTACATTGAAAGCAAACTTCAGTGTGATTTTTGACCGA 420 + +Query 445 CTGGAAACCCTGATACTCCTTAGAGCTTTCACAGAGGAAGGGGCAATTGTGGGTGAAATC 504 + |||||||| ||||||||||||||||||||||||||||||||||||||| | ||||||||| +Sbjct 421 CTGGAAACTCTGATACTCCTTAGAGCTTTCACAGAGGAAGGGGCAATTATAGGTGAAATC 480 + +Query 505 TCACCGTTACCTTCTCTTCCAGGACATACTGA 536 + |||||||||||||||||||||||||||||||| +Sbjct 481 TCACCGTTACCTTCTCTTCCAGGACATACTGA 512 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 6930863 + + +Query= 170144-17ech4NODE_23 + +Length=456 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 773 0.0 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 773 bits (418), Expect = 0.0 + Identities = 443/455 (97%), Gaps = 1/455 (0%) + Strand=Plus/Minus + +Query 1 AGTTGTGATTTGACTTTTTCATACAAACTTTTTACGTTAAAGTCATGGAAATCTAGGGTT 60 + ||||||||||||||||||||||| ||| |||||||||||||||||||||||||||||||| +Sbjct 1441 AGTTGTGATTTGACTTTTTCATATAAATTTTTTACGTTAAAGTCATGGAAATCTAGGGTT 1382 + +Query 61 CTTTCATTCTCGAGCAGGATGAGTAATTCAGCGTTATAAGTCCACACATCCAAAA-TCCA 119 + ||||||||||||||||| |||||||||||||||||||||||||| |||||||||| |||| +Sbjct 1381 CTTTCATTCTCGAGCAGTATGAGTAATTCAGCGTTATAAGTCCATACATCCAAAAATCCA 1322 + +Query 120 TCATCGACTTTTTTATTCAAATTCTCAACCCTTTTCTCTAGATTATTGAATTCTTTGCCC 179 + |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| +Sbjct 1321 TCATCGACTTTTTTATTCAAATTCTCAATCCTTTTCTCTAGATTATTGAATTCTTTGCCC 1262 + +Query 180 ACTGAAGTAAATTGAATGTTCATCTTTTCAATTATTGAGTTCACTTTGTTGCTGATCCCA 239 + |||||||||||||||||||||||||||||||||| |||||| |||||||||||||||||| +Sbjct 1261 ACTGAAGTAAATTGAATGTTCATCTTTTCAATTACTGAGTTTACTTTGTTGCTGATCCCA 1202 + +Query 240 TCAATTGCGATTTGTGTACTTTTCTGATCTGCTGCGTAACCAGATCCTTGCTCATTTTGA 299 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| +Sbjct 1201 TCAATTGCGATTTGTGTACTTTTCTGATCCGCTGCGTAACCAGATCCTTGCTCATTTTGA 1142 + +Query 300 TGATGGTATCCATACCATCCATCTATCATTCCTGTCCACCCTCCTTCAATGAATCCGGCA 359 + |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| +Sbjct 1141 TGATGGTATCCATACCATCCATCTATCATTCCTGTCCATCCTCCTTCAATGAATCCGGCA 1082 + +Query 360 ATTGCTCCAAAAAGTCCTCTGGATTGGATAGAGGGAATATTCCTTAATCCTGTTGCCATT 419 + ||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||| +Sbjct 1081 ATTGCCCCAAAAAGTCCTCTGGATTGGATAGAGGGGATATTCCTTAATCCTGTTGCCATT 1022 + +Query 420 CTTAGTTGGGTGCTTTTAACATATTTGGGGCATTC 454 + ||||||||||||||||||||||||||||||||||| +Sbjct 1021 CTTAGTTGGGTGCTTTTAACATATTTGGGGCATTC 987 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 5866623 + + +Query= 170144-17ech4NODE_26 + +Length=351 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 350 2e-99 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 350 bits (189), Expect = 2e-99 + Identities = 195/198 (98%), Gaps = 0/198 (0%) + Strand=Plus/Plus + +Query 154 ATGGATTCAAACACTGTGTCAAGCTTTCAGGTAGATTGCTTTCTTTGGCATATCCGCAAG 213 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1 ATGGATTCAAACACTGTGTCAAGCTTTCAGGTAGATTGCTTTCTTTGGCATATCCGCAAG 60 + +Query 214 CAGTTTGCAAACTGGGGGCTTGGCGATGCCCCATTTCTCGATAGGCTTCGCCGAGACCAG 273 + | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 61 CGGTTTGCAAACTGGGGGCTTGGCGATGCCCCATTTCTCGATAGGCTTCGCCGAGACCAG 120 + +Query 274 AAGTCTCTAAGAGGGAGAGGCAGCACTCTTGGTCTGGAAATCGAATCAGCTACTCATGCG 333 + ||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||| +Sbjct 121 AAGTCCCTAAGAGGGAGAGGCAGCACTCTTGGTCTGGAAATCGAATCAGCTACTCGTGCG 180 + +Query 334 GGGAAACAAATAGTTAAG 351 + |||||||||||||||||| +Sbjct 181 GGGAAACAAATAGTTAAG 198 + + + Score = 224 bits (121), Expect = 1e-61 + Identities = 125/127 (98%), Gaps = 0/127 (0%) + Strand=Plus/Plus + +Query 1 CTGGGGGCTTGGCGATGCCCCATTTCTCGATAGGCTTCGCCGAGACCAGAAGTCTCTAAG 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| +Sbjct 72 CTGGGGGCTTGGCGATGCCCCATTTCTCGATAGGCTTCGCCGAGACCAGAAGTCCCTAAG 131 + +Query 61 AGGGAGAGGCAGCACTCTTGGTCTGGAAATCGAATCAGCTACTCATGCGGGGAAACAAAT 120 + |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| +Sbjct 132 AGGGAGAGGCAGCACTCTTGGTCTGGAAATCGAATCAGCTACTCGTGCGGGGAAACAAAT 191 + +Query 121 AGTTAAG 127 + ||||||| +Sbjct 192 AGTTAAG 198 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 4469808 + + +Query= 170144-17ech4NODE_28 + +Length=311 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 464 5e-134 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 464 bits (251), Expect = 5e-134 + Identities = 273/283 (96%), Gaps = 3/283 (1%) + Strand=Plus/Plus + +Query 30 TGAACTCAAAAAAGTCGATGATGGATTTTTGGATGTGTGGACTTATAACGCTGAATTACT 89 + |||| | ||||||||||||||||||||||||||||| ||||||||||||||||||||||| +Sbjct 1303 TGAA-T-AAAAAAGTCGATGATGGATTTTTGGATGTATGGACTTATAACGCTGAATTACT 1360 + +Query 90 CATCCTGCTCGAGAATGAAAGAACCCTAGATTTCCATGACTTTAACGTAAAAAGTTTGTA 149 + ||| ||||||||||||||||||||||||||||||||||||||||||||||||| ||| || +Sbjct 1361 CATACTGCTCGAGAATGAAAGAACCCTAGATTTCCATGACTTTAACGTAAAAAATTTATA 1420 + +Query 150 TGAAAAAGTCAAATCACAACTGAGGAACAACGCCAAGGAAATCGGTAATGGCTG-TTTGA 208 + ||||||||||||||||||||| || ||||| ||||||||||||||||||||||| ||||| +Sbjct 1421 TGAAAAAGTCAAATCACAACTTAGAAACAATGCCAAGGAAATCGGTAATGGCTGTTTTGA 1480 + +Query 209 GTTCTATCACAAATGTGATAATGAATGCATGGAAAGCGTAAGGAATGGCACATATAATTA 268 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1481 GTTCTATCACAAATGTGATAATGAATGCATGGAAAGCGTAAGGAATGGCACATATAATTA 1540 + +Query 269 TCCCAGATATTCAGAAGAATCCAAATTGAATAGAGAGAAAATA 311 + ||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1541 TCCCAGATATTCAGAAGAATCCAAATTGAATAGAGAGAAAATA 1583 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3953367 + + +Query= 170144-17ech4NODE_29 + +Length=282 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 435 4e-125 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 435 bits (235), Expect = 4e-125 + Identities = 250/257 (97%), Gaps = 1/257 (0%) + Strand=Plus/Minus + +Query 27 TTATTTCAGTGCATGCATAAGGAAGGAGTTAAACCAAGACGCATTGAGCAAAACCCAGGG 86 + |||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| +Sbjct 2151 TTATTTCAGTGCATGCATAAGGAAGGAGTTGAACCAAGACGCGTTAAGCAAAACCCAGGG 2092 + +Query 87 ATCATTAATCAGGCACTCCTCAATTGCATCATATAACCCCCCAAGATCAAAGGTCCCAGG 146 + ||||||||||| |||||| ||||||||||||||||||||||||||||||||||||||||| +Sbjct 2091 ATCATTAATCAAGCACTCTTCAATTGCATCATATAACCCCCCAAGATCAAAGGTCCCAGG 2032 + +Query 147 TTCCAGGTTGTCCCTAAGTGCTTGAACAATTAGAAGTAATTTTCTTGATTCAGCTGAAAA 206 + |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 2031 TTCCAGGTTGTCCCTAAGTGCTTGAACAATCAGAAGTAATTTTCTTGATTCAGCTGAAAA 1972 + +Query 207 CCC-TCGAGTTGTGAAGATGCATACAGACTATTGAATACAGACTTTGCCAGTAAGGCCCT 265 + ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1971 CCCCTCGAGTTGTGAAGATGCATACAGACTATTGAATACAGACTTTGCCAGTAAGGCCCT 1912 + +Query 266 ACATACTTTTCCAATGG 282 + ||||||||||||||||| +Sbjct 1911 ACATACTTTTCCAATGG 1895 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3567348 + + +Query= 170144-17ech4NODE_30 + +Length=281 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 429 2e-123 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 429 bits (232), Expect = 2e-123 + Identities = 249/257 (97%), Gaps = 2/257 (1%) + Strand=Plus/Plus + +Query 1 CCATTGGAAAAGTATGTAGGGCCTTACTGGCAAAGTCTGTATTCAATAGTCTGTATGCAT 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1895 CCATTGGAAAAGTATGTAGGGCCTTACTGGCAAAGTCTGTATTCAATAGTCTGTATGCAT 1954 + +Query 61 CTTCACAACTCGA-GGGTTTTCAGCTGAATCAAGAAAATTACTTCTAATTGTTCAAGCAC 119 + ||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||| +Sbjct 1955 CTTCACAACTCGAGGGGTTTTCAGCTGAATCAAGAAAATTACTTCTGATTGTTCAAGCAC 2014 + +Query 120 TTAGGGACAACCTGGAACCTGGGACCTTTGATCTT-GGGGGTTATATGATGCAATTGAGG 178 + ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| | +Sbjct 2015 TTAGGGACAACCTGGAACCTGGGACCTTTGATCTTGGGGGGTTATATGATGCAATTGAAG 2074 + +Query 179 AGTGCCTGATTAATGATCCCTGGGTTTTGCTCAATGCGTCTTGGTTTAACTCCTTCCTTA 238 + ||||| ||||||||||||||||||||||||| || ||||||||||| ||||||||||||| +Sbjct 2075 AGTGCTTGATTAATGATCCCTGGGTTTTGCTTAACGCGTCTTGGTTCAACTCCTTCCTTA 2134 + +Query 239 TGCATGCACTGAAATAA 255 + ||||||||||||||||| +Sbjct 2135 TGCATGCACTGAAATAA 2151 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3554037 + + +Query= 170144-17ech4NODE_31 + +Length=279 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 411 6e-118 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 411 bits (222), Expect = 6e-118 + Identities = 241/250 (96%), Gaps = 2/250 (1%) + Strand=Plus/Plus + +Query 30 TGAACTCAAAAAAGTCGATGATGGATTTTTGGATGTGTGGACTTATAACGCTGAATTACT 89 + |||| | ||||||||||||||||||||||||||||| ||||||||||||||||||||||| +Sbjct 1303 TGAA-T-AAAAAAGTCGATGATGGATTTTTGGATGTATGGACTTATAACGCTGAATTACT 1360 + +Query 90 CATCCTGCTCGAGAATGAAAGAACCCTAGATTTCCATGACTTTAACGTAAAAAGTTTGTA 149 + ||| ||||||||||||||||||||||||||||||||||||||||||||||||| ||| || +Sbjct 1361 CATACTGCTCGAGAATGAAAGAACCCTAGATTTCCATGACTTTAACGTAAAAAATTTATA 1420 + +Query 150 TGAAAAAGTCAAATCACAACTGAGGAACAACGCCAAGGAAATCGGTAATGGCTGTTTTGA 209 + ||||||||||||||||||||| || ||||| ||||||||||||||||||||||||||||| +Sbjct 1421 TGAAAAAGTCAAATCACAACTTAGAAACAATGCCAAGGAAATCGGTAATGGCTGTTTTGA 1480 + +Query 210 GTTCTATCACAAATGTGATAATGAATGCATGGAAAGCGTAAGGAATGGCACATATAATTA 269 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1481 GTTCTATCACAAATGTGATAATGAATGCATGGAAAGCGTAAGGAATGGCACATATAATTA 1540 + +Query 270 TCCCAGATAT 279 + |||||||||| +Sbjct 1541 TCCCAGATAT 1550 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3527415 + + +Query= 170144-17ech4NODE_32 + +Length=256 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 315 5e-89 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 315 bits (170), Expect = 5e-89 + Identities = 176/179 (98%), Gaps = 0/179 (0%) + Strand=Plus/Minus + +Query 40 AAAATTCCCTTAGTCAGAGGTGACAGGATCGGTCTTGTCTTTAGCCACTCCATGAGAGCC 99 + ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| +Sbjct 179 AAAATTCCCTTAGTCAGAGGTGACAGGATTGGTCTTGTCTTTAGCCACTCCATGAGAGCC 120 + +Query 100 TCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCTAGTCTCTGTGCGATCTCGGCTTTG 159 + ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||| +Sbjct 119 TCCAGATCTGTGTTCTTCCCTGCAAAGACACCTTCCAGTCTCTGCGCGATCTCGGCTTTG 60 + +Query 160 AGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 218 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 59 AGGGGGCCTGACGGGATGATAGAAAGAACGTACGTTTCGACCTCGGTTAGAAGACTCAT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3221262 + + +Query= 170144-17ech4NODE_33 + +Length=248 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 374 7e-107 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 374 bits (202), Expect = 7e-107 + Identities = 217/224 (97%), Gaps = 1/224 (0%) + Strand=Plus/Minus + +Query 26 TTATTTCAGTGCATGCATAAGGAAGGAGTTAAACCAAGACGCATTGAGCAAAACCCAGGG 85 + |||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| +Sbjct 2151 TTATTTCAGTGCATGCATAAGGAAGGAGTTGAACCAAGACGCGTTAAGCAAAACCCAGGG 2092 + +Query 86 ATCATTAATCAGGCACTCCTCAATTGCATCATATAACCCCC-AAGATCAAAGGTCCCAGG 144 + ||||||||||| |||||| |||||||||||||||||||||| |||||||||||||||||| +Sbjct 2091 ATCATTAATCAAGCACTCTTCAATTGCATCATATAACCCCCCAAGATCAAAGGTCCCAGG 2032 + +Query 145 TTCCAGGTTGTCCCTAAGTGCTTGAACAATTAGAAGTAATTTTCTTGATTCAGCTGAAAA 204 + |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 2031 TTCCAGGTTGTCCCTAAGTGCTTGAACAATCAGAAGTAATTTTCTTGATTCAGCTGAAAA 1972 + +Query 205 CCCCTCGAGTTGTGAAGATGCATACAGACTATTGAATACAGACT 248 + |||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1971 CCCCTCGAGTTGTGAAGATGCATACAGACTATTGAATACAGACT 1928 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 3114774 + + +Query= 170144-17ech4NODE_36 + +Length=232 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 387 9e-111 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 387 bits (209), Expect = 9e-111 + Identities = 226/234 (97%), Gaps = 2/234 (1%) + Strand=Plus/Plus + +Query 1 GCTGAATTACTCATCCTGCTCGAGAATGAAAGAACCCTAGATTTCCATGACTTTAACGTA 60 + |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1350 GCTGAATTACTCATACTGCTCGAGAATGAAAGAACCCTAGATTTCCATGACTTTAACGTA 1409 + +Query 61 AAAAGTTTGTATG-AAAAGTCAAATCACAACTGAGGAACAACGCCAAGGAAATCGGTAAT 119 + |||| ||| |||| |||||||||||||||||| || ||||| |||||||||||||||||| +Sbjct 1410 AAAAATTTATATGAAAAAGTCAAATCACAACTTAGAAACAATGCCAAGGAAATCGGTAAT 1469 + +Query 120 GGCTG-TTTGAGTTCTATCACAAATGTGATAATGAATGCATGGAAAGCGTAAGGAATGGC 178 + ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1470 GGCTGTTTTGAGTTCTATCACAAATGTGATAATGAATGCATGGAAAGCGTAAGGAATGGC 1529 + +Query 179 ACATATAATTATCCCAGATATTCAGAAGAATCCAAATTGAATAGAGAGAAAATA 232 + |||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1530 ACATATAATTATCCCAGATATTCAGAAGAATCCAAATTGAATAGAGAGAAAATA 1583 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2901798 + + +Query= 170144-17ech4NODE_40 + +Length=213 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 363 1e-103 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 363 bits (196), Expect = 1e-103 + Identities = 209/215 (97%), Gaps = 2/215 (1%) + Strand=Plus/Minus + +Query 1 CATTCAAGTCCTTTGATGAGGATCCCAATTGCATTTT-GACATCCTCATCAGTATGTCCT 59 + ||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 560 CATTCAAGTCCTTTGATGAGGATCCCAATTGCATTTTTGACATCCTCATCAGTATGTCCT 501 + +Query 60 GGAAGAGAAGGTAACGGTGAGATTTCACCTACAATTGCCCCTTTCTCTGTGAAAGCTCTA 119 + ||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||| +Sbjct 500 GGAAGAGAAGGTAACGGTGAGATTTCACCTATAATTGCCCCTTCCTCTGTGAAAGCTCTA 441 + +Query 120 AGGAGTATCAGAGTTTCCAGTCGGTCAAAA-TCACACTGAAGTTTGCTTTCAATGTAATA 178 + |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| +Sbjct 440 AGGAGTATCAGAGTTTCCAGTCGGTCAAAAATCACACTGAAGTTTGCTTTCAATGTAATG 381 + +Query 179 TTTTTATCCATTATTGCTTGGTCCATTCTGATGCA 213 + ||||||||||||||||| ||||||||||||||||| +Sbjct 380 TTTTTATCCATTATTGCCTGGTCCATTCTGATGCA 346 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2648889 + + +Query= 170144-17ech4NODE_43 + +Length=209 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 305 2e-86 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 305 bits (165), Expect = 2e-86 + Identities = 177/183 (97%), Gaps = 0/183 (0%) + Strand=Plus/Plus + +Query 1 GGGTTTTCAGCTGAATCAAGAAAATTACTTCTAATTGTTCAAGCACTTAGGGACAACCTG 60 + |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| +Sbjct 1969 GGGTTTTCAGCTGAATCAAGAAAATTACTTCTGATTGTTCAAGCACTTAGGGACAACCTG 2028 + +Query 61 GAACCTGGGACCTTTGATCTTGGGGGGTTATATGATGCAATTGAGGAGTGCCTGATTAAT 120 + |||||||||||||||||||||||||||||||||||||||||||| |||||| |||||||| +Sbjct 2029 GAACCTGGGACCTTTGATCTTGGGGGGTTATATGATGCAATTGAAGAGTGCTTGATTAAT 2088 + +Query 121 GATCCCTGGGTTTTGCTCAATGCGTCTTGGTTTAACTCCTTCCTTATGCATGCACTGAAA 180 + ||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||| +Sbjct 2089 GATCCCTGGGTTTTGCTTAACGCGTCTTGGTTCAACTCCTTCCTTATGCATGCACTGAAA 2148 + +Query 181 TAA 183 + ||| +Sbjct 2149 TAA 2151 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2595645 + + +Query= 170144-17ech4NODE_44 + +Length=208 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 298 4e-84 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 298 bits (161), Expect = 4e-84 + Identities = 176/183 (96%), Gaps = 1/183 (1%) + Strand=Plus/Plus + +Query 1 GGGTTTTCAGCTGAATCAAGAAAATTACTTCTAATTGTTCAAGCACTTAGGGACAACCTG 60 + |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| +Sbjct 1969 GGGTTTTCAGCTGAATCAAGAAAATTACTTCTGATTGTTCAAGCACTTAGGGACAACCTG 2028 + +Query 61 GAACCTGGGACCTTTGATCTT-GGGGGTTATATGATGCAATTGAGGAGTGCCTGATTAAT 119 + ||||||||||||||||||||| |||||||||||||||||||||| |||||| |||||||| +Sbjct 2029 GAACCTGGGACCTTTGATCTTGGGGGGTTATATGATGCAATTGAAGAGTGCTTGATTAAT 2088 + +Query 120 GATCCCTGGGTTTTGCTCAATGCGTCTTGGTTTAACTCCTTCCTTATGCATGCACTGAAA 179 + ||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||| +Sbjct 2089 GATCCCTGGGTTTTGCTTAACGCGTCTTGGTTCAACTCCTTCCTTATGCATGCACTGAAA 2148 + +Query 180 TAA 182 + ||| +Sbjct 2149 TAA 2151 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2582334 + + +Query= 170144-17ech4NODE_45 + +Length=206 + Score E +Sequences producing significant alignments: (Bits) Value + + KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N... 276 2e-77 + + +> KP822960.1 Influenza A virus (A/swine/France/22-140428/2014(H1N1)) +segment 4 hemagglutinin (HA) gene, complete cds +Length=1753 + + Score = 276 bits (149), Expect = 2e-77 + Identities = 168/177 (95%), Gaps = 2/177 (1%) + Strand=Plus/Minus + +Query 1 AAACAGCCATTACCGATTTCCTTGGCGTTGTTCCTCAGTTGTGATTTGACTTTTTCATAC 60 + |||||||||||||||||||||||||| ||||| || ||||||||||||||||||||||| +Sbjct 1477 AAACAGCCATTACCGATTTCCTTGGCATTGTTTCTAAGTTGTGATTTGACTTTTTCATAT 1418 + +Query 61 AAACTTTTTACGTTAAAGTCATGGAAATCTAGGGTTCTTTCATTCTCGAGCAGGATGAGT 120 + ||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 1417 AAATTTTTTACGTTAAAGTCATGGAAATCTAGGGTTCTTTCATTCTCGAGCAGTATGAGT 1358 + +Query 121 AATTCAGCGTTATAAGTCCACACATCCAAAAATCCATCATCGACTTTTTTGAGTTCA 177 + |||||||||||||||||||| ||||||||||||||||||||||||||||| | |||| +Sbjct 1357 AATTCAGCGTTATAAGTCCATACATCCAAAAATCCATCATCGACTTTTTT-A-TTCA 1303 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2555712 + + +Query= 170144-17ech4NODE_46 + +Length=205 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404... 307 6e-87 + + +> KR700282.1 Influenza A virus (A/swine/France/IIIeetVilaine-0404/2011(H1N2)) +segment 7 matrix protein 2 (M2) and matrix protein +1 (M1) genes, complete cds +Length=982 + + Score = 307 bits (166), Expect = 6e-87 + Identities = 175/179 (98%), Gaps = 1/179 (1%) + Strand=Plus/Plus + +Query 26 ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCGTCAGG-CCCCTC 84 + ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||| +Sbjct 1 ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCGTCAGGCCCCCTC 60 + +Query 85 AAAGCCGAGATCGCACAGAGACTAGAAGGTGTCTTTGCAGGGAAGAACACAGATCTGGAG 144 + |||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||| +Sbjct 61 AAAGCCGAGATCGCGCAGAGACTGGAAGGTGTCTTTGCAGGGAAGAACACAGATCTGGAG 120 + +Query 145 GCTCTCATGGAGTGGCTAAAGACAAGACCGATCCTGTCACCTCTGACTAAGGGAATTTT 203 + ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| +Sbjct 121 GCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGAATTTT 179 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2542401 + + +Query= 170144-17ech4NODE_48 + +Length=199 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 300 1e-84 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 300 bits (162), Expect = 1e-84 + Identities = 187/199 (94%), Gaps = 2/199 (1%) + Strand=Plus/Minus + +Query 3 GTGTTGTTTTCGTAAATAATGGCGCTTTGAATGCATGCCTCAGTTTGGTTT-GGTTCCTA 61 + |||||||||||||||||||| |||||||| ||||||| || || |||||| |||||| | +Sbjct 199 GTGTTGTTTTCGTAAATAATAACGCTTTGATTGCATGCTTCGGTCTGGTTTTGGTTCCCA 140 + +Query 62 GTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGCAATATCAAGCTA 121 + ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| +Sbjct 139 GTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGTAATATCAAGCTA 80 + +Query 122 GCAATTCCATTTGCCATACAGATTGAGCCGATGATTATTATCTT-TGATTTGGATTCATT 180 + ||||||||||||| ||||||||||||||| |||||||||||||| ||||||||||||||| +Sbjct 79 GCAATTCCATTTGTCATACAGATTGAGCCAATGATTATTATCTTCTGATTTGGATTCATT 20 + +Query 181 TTAAACTCCTGCTTTTGCT 199 + ||||||||||||||||||| +Sbjct 19 TTAAACTCCTGCTTTTGCT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2462535 + + +Query= 170144-17ech4NODE_49 + +Length=191 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 326 2e-92 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 326 bits (176), Expect = 2e-92 + Identities = 187/192 (97%), Gaps = 1/192 (1%) + Strand=Plus/Plus + +Query 1 TGCATCAGAATGGACCAAGCAATAATGGATAAAAATATTACATTGAAAGCAAACTTCAGT 60 + ||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||| +Sbjct 346 TGCATCAGAATGGACCAGGCAATAATGGATAAAAACATTACATTGAAAGCAAACTTCAGT 405 + +Query 61 GTGA-TTTTGACCGACTGGAAACTCTGATACTCCTTAGAGCTTTCACAGAGAAAGGGGCA 119 + |||| |||||||||||||||||||||||||||||||||||||||||||||| |||||||| +Sbjct 406 GTGATTTTTGACCGACTGGAAACTCTGATACTCCTTAGAGCTTTCACAGAGGAAGGGGCA 465 + +Query 120 ATTGTAGGTGAAATCTCACCGTTACCTTCTCTTCCAGGACATACTGATGAGGATGTCAAA 179 + ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 466 ATTATAGGTGAAATCTCACCGTTACCTTCTCTTCCAGGACATACTGATGAGGATGTCAAA 525 + +Query 180 AATGCAATTGGG 191 + |||||||||||| +Sbjct 526 AATGCAATTGGG 537 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2356047 + + +Query= 170144-17ech4NODE_50 + +Length=180 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 305 2e-86 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 305 bits (165), Expect = 2e-86 + Identities = 176/181 (97%), Gaps = 1/181 (1%) + Strand=Plus/Minus + +Query 1 TTTTGACATCCTCATCAGTATGTCCTGGAAGAGAAGGTAACGGTGAGATTTCACCTACAA 60 + ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || +Sbjct 526 TTTTGACATCCTCATCAGTATGTCCTGGAAGAGAAGGTAACGGTGAGATTTCACCTATAA 467 + +Query 61 TTGCCCCTTTCTCTGTGAAAGCTCTAAGGAGTATCAGAGTTTCCAGTCGGTCAAAA-TCA 119 + ||||||||| |||||||||||||||||||||||||||||||||||||||||||||| ||| +Sbjct 466 TTGCCCCTTCCTCTGTGAAAGCTCTAAGGAGTATCAGAGTTTCCAGTCGGTCAAAAATCA 407 + +Query 120 CACTGAAGTTTGCTTTCAATGTAATATTTTTATCCATTATTGCTTGGTCCATTCTGATGC 179 + ||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||| +Sbjct 406 CACTGAAGTTTGCTTTCAATGTAATGTTTTTATCCATTATTGCCTGGTCCATTCTGATGC 347 + +Query 180 A 180 + | +Sbjct 346 A 346 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2209626 + + +Query= 170144-17ech4NODE_55 + +Length=166 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 241 5e-67 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 241 bits (130), Expect = 5e-67 + Identities = 153/164 (93%), Gaps = 1/164 (1%) + Strand=Plus/Minus + +Query 3 GTGTTGTTTTCGTAAATAATGGCGCTTTGAATGCATGCCTCAGTTTGGTTT-GGTTCCTA 61 + |||||||||||||||||||| |||||||| ||||||| || || |||||| |||||| | +Sbjct 199 GTGTTGTTTTCGTAAATAATAACGCTTTGATTGCATGCTTCGGTCTGGTTTTGGTTCCCA 140 + +Query 62 GTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGCAATATCAAGCTA 121 + ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| +Sbjct 139 GTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATTTGTAATATCAAGCTA 80 + +Query 122 GCAATTCCATTTGCCATACAGATTGAGCCGATGATTATTATCTT 165 + ||||||||||||| ||||||||||||||| |||||||||||||| +Sbjct 79 GCAATTCCATTTGTCATACAGATTGAGCCAATGATTATTATCTT 36 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 2023272 + + +Query= 170144-17ech4NODE_56 + +Length=160 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 255 2e-71 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 255 bits (138), Expect = 2e-71 + Identities = 149/154 (97%), Gaps = 1/154 (1%) + Strand=Plus/Minus + +Query 8 TGGTTTTGGTTCCTAGTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATT 67 + ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 154 TGGTTTTGGTTCCCAGTTTGAATTGAATGGCTAATCCATATTGAGATTATGTTCCCAATT 95 + +Query 68 TGCAATATCAAGCTAGCAATTCCATTTGCCATACAGATTGAGCCGATGATTATTATCTT- 126 + || ||||||||||||||||||||||||| ||||||||||||||| |||||||||||||| +Sbjct 94 TGTAATATCAAGCTAGCAATTCCATTTGTCATACAGATTGAGCCAATGATTATTATCTTC 35 + +Query 127 TGATTTGGATTCATTTTAAACTCCTGCTTTTGCT 160 + |||||||||||||||||||||||||||||||||| +Sbjct 34 TGATTTGGATTCATTTTAAACTCCTGCTTTTGCT 1 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1943406 + + +Query= 170144-17ech4NODE_57 + +Length=160 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 279 1e-78 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 279 bits (151), Expect = 1e-78 + Identities = 158/161 (98%), Gaps = 1/161 (1%) + Strand=Plus/Minus + +Query 1 CATTCAAGTCCTTTGATGAGGATCCCAATTGCATTTT-GACATCCTCATCAGTATGTCCT 59 + ||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| +Sbjct 560 CATTCAAGTCCTTTGATGAGGATCCCAATTGCATTTTTGACATCCTCATCAGTATGTCCT 501 + +Query 60 GGAAGAGAAGGTAACGGTGAGATTTCACCTACAATTGCCCCTTTCTCTGTGAAAGCTCTA 119 + ||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||| +Sbjct 500 GGAAGAGAAGGTAACGGTGAGATTTCACCTATAATTGCCCCTTCCTCTGTGAAAGCTCTA 441 + +Query 120 AGGAGTATCAGAGTTTCCAGTCGGTCAAAAATCACACTGAA 160 + ||||||||||||||||||||||||||||||||||||||||| +Sbjct 440 AGGAGTATCAGAGTTTCCAGTCGGTCAAAAATCACACTGAA 400 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1943406 + + +Query= 170144-17ech4NODE_58 + +Length=159 + Score E +Sequences producing significant alignments: (Bits) Value + + KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N... 159 1e-42 + + +> KR700921.1 Influenza A virus (A/swine/France/50-120350/2012(H1N1)) +segment 3 polymerase PA (PA) and PA-X protein (PA-X) genes, +complete cds +Length=2151 + + Score = 159 bits (86), Expect = 1e-42 + Identities = 96/101 (95%), Gaps = 0/101 (0%) + Strand=Plus/Minus + +Query 59 TTATTTCAGTGCATGCATAAGGAAGGAGTTAAACCAAGACGCATTGAGCAAAACCCAGGG 118 + |||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| +Sbjct 2151 TTATTTCAGTGCATGCATAAGGAAGGAGTTGAACCAAGACGCGTTAAGCAAAACCCAGGG 2092 + +Query 119 ATCATTAATCAGGCACTCCTCAATTGCATCATATAACCCCC 159 + ||||||||||| |||||| |||||||||||||||||||||| +Sbjct 2091 ATCATTAATCAAGCACTCTTCAATTGCATCATATAACCCCC 2051 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1930095 + + +Query= 170144-17ech4NODE_61 + +Length=149 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 248 3e-69 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 248 bits (134), Expect = 3e-69 + Identities = 145/150 (97%), Gaps = 1/150 (1%) + Strand=Plus/Plus + +Query 1 AGCAAAAGCAGGAGTTTAAAATGAATCCAAATCA-AAGATAATAATCATCGGCTCAATCT 59 + |||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||| +Sbjct 1 AGCAAAAGCAGGAGTTTAAAATGAATCCAAATCAGAAGATAATAATCATTGGCTCAATCT 60 + +Query 60 GTATGGCAAATGGAATTGCTAGCTTGATATTGCAAATTGGGAACATAATCTCAATATGGA 119 + ||||| ||||||||||||||||||||||||| |||||||||||||||||||||||||||| +Sbjct 61 GTATGACAAATGGAATTGCTAGCTTGATATTACAAATTGGGAACATAATCTCAATATGGA 120 + +Query 120 TTAGCCATTCAATTCAAACTAGGAACCAAA 149 + |||||||||||||||||||| ||||||||| +Sbjct 121 TTAGCCATTCAATTCAAACTGGGAACCAAA 150 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1811384 + + +Query= 170144-17ech4NODE_62 + +Length=149 + Score E +Sequences producing significant alignments: (Bits) Value + + KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H... 259 1e-72 + + +> KR701500.1 Influenza A virus (A/swine/Cotes d'Armor/0388/2009(H1N1)) +nuclear export protein (NEP) and nonstructural protein +1 (NS1) genes, complete cds +Length=838 + + Score = 259 bits (140), Expect = 1e-72 + Identities = 147/150 (98%), Gaps = 1/150 (1%) + Strand=Plus/Plus + +Query 1 TTTTGACCGACTGGAAACTCTGATACTCCTTAGAGCTTTCACAGAGAAAGGGGCAATTGT 60 + |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| | +Sbjct 411 TTTTGACCGACTGGAAACTCTGATACTCCTTAGAGCTTTCACAGAGGAAGGGGCAATTAT 470 + +Query 61 AGGTGAAATCTCACCGTTACCTTCTCTTCCAGGACATACTGATGAGGATGTC-AAAATGC 119 + |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| +Sbjct 471 AGGTGAAATCTCACCGTTACCTTCTCTTCCAGGACATACTGATGAGGATGTCAAAAATGC 530 + +Query 120 AATTGGGATCCTCATCAAAGGACTTGAATG 149 + |||||||||||||||||||||||||||||| +Sbjct 531 AATTGGGATCCTCATCAAAGGACTTGAATG 560 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1811384 + + +Query= 170144-17ech4NODE_63 + +Length=138 + Score E +Sequences producing significant alignments: (Bits) Value + + CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) ne... 207 4e-57 + + +> CY110765.1 Influenza A virus (A/swine/Aisne/0054/2010(H1N1)) +neuraminidase (NA) gene, complete cds +Length=1459 + + Score = 207 bits (112), Expect = 4e-57 + Identities = 125/131 (95%), Gaps = 1/131 (1%) + Strand=Plus/Plus + +Query 1 AATCCAAATCAAAAGATAATAATCATCGGCTCAATCTGTATGGCAAATGGAATTGCTAGC 60 + ||||||||||| |||||||||||||| ||||||||||||||| ||||||||||||||||| +Sbjct 24 AATCCAAATCAGAAGATAATAATCATTGGCTCAATCTGTATGACAAATGGAATTGCTAGC 83 + +Query 61 TTGATATTGCAAATTGGGAACATAATCTCAATATGGATTAGCCATTCAATTCAAACTAGG 120 + |||||||| |||||||||||||||||||||||||||||||||||||||||||||||| || +Sbjct 84 TTGATATTACAAATTGGGAACATAATCTCAATATGGATTAGCCATTCAATTCAAACTGGG 143 + +Query 121 AACCAAA-CCA 130 + ||||||| ||| +Sbjct 144 AACCAAAACCA 154 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 1664875 + + + Database: ref_vbmd_A-Sw-France-53-170144-17ech4_1714ESIV_061.fa + Posted date: Oct 16, 2017 2:59 PM + Number of letters in database: 13,423 + Number of sequences in database: 8 + + + +Matrix: blastn matrix 1 -2 +Gap Penalties: Existence: 0, Extension: 2.5