# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1391109012 21600
# Node ID b0276d1141fef40226d852b325160db66671ff94
# Parent  08439b004404495f8c43ff430ac336088935f0d7
Fix test case

diff -r 08439b004404 -r b0276d1141fe scythe.xml
--- a/scythe.xml	Mon Jan 13 14:57:53 2014 -0500
+++ b/scythe.xml	Thu Jan 30 13:10:12 2014 -0600
@@ -76,9 +76,9 @@
 
         <tests>
                 <test>
-                        <param name="single_or_paired" value="pe"/>
                         <param name="input_fastq" value="reads.fastq" ftype="fastqillumina"/>
                         <param name="adapter_file" value="illumina_adapters.fa" ftype="fasta"/>
+                        <param name="add_tag" value="False"/>
                         <param name="matches_file" value="True"/>
                         <param name="prior" value="0.3"/>
                         <param name="min_match" value="5"/>
diff -r 08439b004404 -r b0276d1141fe test-data/matches.txt
--- a/test-data/matches.txt	Mon Jan 13 14:57:53 2014 -0500
+++ b/test-data/matches.txt	Thu Jan 30 13:10:12 2014 -0600
@@ -1,64 +1,40 @@
-p(c|s): 0.999973; p(!c|s): 0.000027; adapter: solexa-reverse
-SOLEXA2_0414:3:1:12658:1069#0/1
-AGATCGGAAGAGCGGT
-|||||||||||| |||
-AGATCGGAAGAGNGGT
-_______Q__BBBBBB
-[1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
-
-p(c|s): 1.000000; p(!c|s): 0.000000; adapter: solexa-reverse
-SOLEXA2_0414:3:1:3923:1105#0/1
-AGATCGGAAGAGCGGTTCAG
-||||||||||||||||||||
-AGATCGGAAGAGCGGTTCAG
-b____YWWYYVVTVVYYYYY
-[1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
+p(c|s): 0.581352; p(!c|s): 0.418648; adapter: Multiplexing_adapter_2
+SOLEXA2_0414:3:1:17191:1069#0/1
+CACTCTTTCC
+|||   ||  
+CACAAGTTTT
+BBBBBBBBBB
+[0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61]
 
-p(c|s): 1.000000; p(!c|s): 0.000000; adapter: solexa-reverse
-SOLEXA2_0414:3:1:9865:1095#0/1
-AGATCGGAAGAGCGGTTCAGC
-|||||||||||||||||||||
-AGATCGGAAGAGCGGTTCAGC
-______[[[[Y__________
-[1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
-
-p(c|s): 1.000000; p(!c|s): 0.000000; adapter: solexa-forward
-SOLEXA2_0414:3:1:11267:1102#0/1
-AGATCGGAAGAGCG
-||||||||||||||
-AGATCGGAAGAGCG
-BBBBBBBBBBBBBB
-[1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
+p(c|s): 0.534091; p(!c|s): 0.465909; adapter: Multiplexing_adapter_1
+SOLEXA2_0414:3:1:19703:1080#0/1
+GATCGGAAGAGCACA
+||  || |  |   |
+GAAGGGTATGGTTGA
+BBBBBBBBBBBBBBB
+[0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61]
 
-p(c|s): 0.999999; p(!c|s): 0.000001; adapter: solexa-forward
-SOLEXA2_0414:3:1:13556:1104#0/1
-AGATCGGAAGAG
-||||||||||||
-AGATCGGAAGAG
-BBBBBBBBBBBB
-[1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
-
-p(c|s): 0.999995; p(!c|s): 0.000005; adapter: solexa-forward
-SOLEXA2_0414:3:1:13625:1097#0/1
-AGATCGGAAGA
-|||||||||||
-AGATCGGAAGA
-Y____BBBBBB
-[1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
+p(c|s): 0.581352; p(!c|s): 0.418648; adapter: Multiplexing_adapter_1
+SOLEXA2_0414:3:1:18860:1082#0/1
+GATCGGAAGA
+|  || | | 
+GGCCGCATGT
+BBBBBBBBBB
+[0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61]
 
-p(c|s): 1.000000; p(!c|s): 0.000000; adapter: solexa-reverse
-SOLEXA2_0414:3:1:10939:1119#0/1
-AGATCGGAAGAGCGGTTCAGCAGGAATGC
-||||||| |||||||||||||||||| ||
-AGATCGGGAGAGCGGTTCAGCAGGAAGGC
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBB
-[1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
+p(c|s): 0.729153; p(!c|s): 0.270847; adapter: Multiplexing_adapter_2
+SOLEXA2_0414:3:1:13556:1104#0/1
+CACTCTTTC
+||  | || 
+CAGACCTTA
+BBBBBBBBB
+[0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61]
 
-p(c|s): 1.000000; p(!c|s): 0.000000; adapter: solexa-reverse
-SOLEXA2_0414:3:1:12110:1126#0/1
-AGATCGGAAGAGCGGTTCAGCAGGAATGCCG
-|||||||||||||||||||||||||||||||
-AGATCGGAAGAGCGGTTCAGCAGGAATGCCG
-____Y______YYYYYQWWWW___S_BBBBB
-[1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
+p(c|s): 0.745940; p(!c|s): 0.254060; adapter: Multiplexing_adapter_2
+SOLEXA2_0414:3:1:7605:1117#0/1
+CACTCTTTCCCTACACGACGCTC
+|| ||    || | | ||   | 
+CAGTCACCACCCAAAAGAAAATA
+BBBBBBBBBBBBBBBBBBBBBBB
+[0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61, 0.61]
 
diff -r 08439b004404 -r b0276d1141fe test-data/trimmed_sequences.fastq
--- a/test-data/trimmed_sequences.fastq	Mon Jan 13 14:57:53 2014 -0500
+++ b/test-data/trimmed_sequences.fastq	Thu Jan 30 13:10:12 2014 -0600
@@ -1,15 +1,15 @@
 @SOLEXA2_0414:3:1:11146:1065#0/1 
-NTGCGATCAAGGGATAAGGGTGGGACACTGCGGGAGATTCAGAGTAACAGTTNTAAGGTCTGGTTTGTCCGGACACTGCGGNAGA
+N
 +
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+B
 @SOLEXA2_0414:3:1:12658:1069#0/1 
-NCTACATACAGTTGTAAGGTCTGGTTTGTCCTAGGCAGAGGACACTGCGGGAGATTCAGAGTATGTAGC
+NCTACATACAGTTGTAAGGTCTGGTTTGTCCTAGGCAGAGGACACTGCGGGAGATTCAGAGTATGTAGCA
 +
-BOIOKPTTTT_________________________________________________TYYYYY____
+BOIOKPTTTT_________________________________________________TYYYYY_____
 @SOLEXA2_0414:3:1:17191:1069#0/1 
-NAGCAATCTATAGTTTGTGTATTGCCAAGTCTGTTGTGAGCCCTTCCACAAGTTTTGTTTAGAGGAGAACGAGCGCCCTCTNGAT
+NAGCAATCTATAGTTTGTGTATTGCCAAGTCTGTTGTGAGCCCTTC
 +
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:6993:1073#0/1 
 NTGGATCTCCCGCAGTGTCCTAAATGGACAAACCAGACCTTACAACTGTTACTCTGAATCTCCCGCAGTGTCCTCTGCCTAGGAC
 +
@@ -23,9 +23,9 @@
 +
 BEKEEJOHHHTTVVV_____[[Y[[WWVXXXVXXWRRPTTWXXXWWQQWXWWWTWKKLLLLLLHRVTVVNTTVVT_____YWYYY
 @SOLEXA2_0414:3:1:12624:1071#0/1 
-NTGCGATAGTGTCCTGTGTGCCCCTGCACATGCCTGTGGCTTCCCGGGCTTCTGACCACATCCCCACCATCTTTGTGCCTCCGGA
+NTGCGATAGTGTCCTGTGTGCCCCTGCACATGCCTGTGGCTTCCCGGGCTTCTGACCACATCCCCACCATCTTTGTGC
 +
-BQLLMTTTTT__________YYYYY________b___________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BQLLMTTTTT__________YYYYY________b___________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:13769:1080#0/1 
 NAGCAATCTAAAACCCAAAGTATATAAGAAGGGTATGGTTGATTATGTTTTTCTACATATTATTTGACATACTTCTATCTTCCCA
 +
@@ -39,21 +39,21 @@
 +
 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:16010:1079#0/1 
-NAGCAATTACTCTGAATCTCCCGCAGTGTCCTCTGCCTAGGACAAACCAGACCTTACAACTGTTACTCTGAATCTCCCGCAGTGT
+NAGCAATTACTCTGAATCTCCCGCAGTGTCCTCTGCCTAGGACAAACCAGACCTTACAACTGTTACTCTGAATCTCCCG
 +
-BKJQQVWVVV_______________WYYYY_______________V____Y[[[[_________________________BBBBB
+BKJQQVWVVV_______________WYYYY_______________V____Y[[[[________________________
 @SOLEXA2_0414:3:1:17165:1075#0/1 
-NTGCGATCTAGGACACTGCGGGAGATTCAGAGTACAGTTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTCAGAGTAACA
+N
 +
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+B
 @SOLEXA2_0414:3:1:19504:1081#0/1 
 NAGCAATACTTCTATCTTCCCATGTTCTTACTATAGTTTGTGTATTGCCAAGTCTGTTGTGAGCCACATAATAAGGTGTCAAAAT
 +
 BJJOJRRQQRYYYYY__b_______[[[[PWWTWWYYYYY[Y[[[YYYYUTTWVVY[YY[_______________VTTTVTVVTV
 @SOLEXA2_0414:3:1:19703:1080#0/1 
-NAGCAATATTGAATTAAATATATGCCAGTGGACTACTAAAACCCAAAGTATATAAGAAGGGTATGGTTGATTATGTTTTTCTACA
+NAGCAATATTGAATTAAATATATGCCAGTGGACTACTAAAACCCAAAGTATATAA
 +
-BIKOIVWVVVY[Y[YVVTVTYYYYY_W___BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BIKOIVWVVVY[Y[YVVTVTYYYYY_W___BBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:6962:1084#0/1 
 NTGCGATCTGAATCTCCCGCAGTGTCCGGGTGGGGTCAGAAAAATGGGCAGCTCAACTGCAGGTACACGTAGTGCGACCAGTGCC
 +
@@ -79,45 +79,45 @@
 +
 BHMOGRTTTTY[[[Y__________TVVVTYVYYY____WYYYYRPRWRR[[Y[[_____WWWTWWTWWWYYYYY[R[[YYYYYY
 @SOLEXA2_0414:3:1:18860:1082#0/1 
-NAGCAATACAGTTGTAAGGTCTGGTTTGTCCTCACTCAAATGTCATCTCGAATTGTAGTTCTCATAATGGCCGCATGTTGTGGGA
+NAGCAATACAGTTGTAAGGTCTGGTTTGTCCTCACTCAAATGTCATCTCGAATTGTAGTTCTCATAAT
 +
-BHOKHSWTTT____________________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BHOKHSWTTT____________________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:18912:1089#0/1 
-NTGCGATCATCTGAGGAGGACACTGCGGGAGATTCAGAGTAACAGTTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTCA
+N
 +
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+B
 @SOLEXA2_0414:3:1:3923:1105#0/1 
-NAGCAATAGTCCAGGGATACAGAACCCACTGATACAGAGGCCCAGCTGTAGTTCTATTATTGCTC
+NAGCAATAGTCCAGGGATACAGAACCCACTGATACAGAGGCCCAGCTGTAGTTCTATTATTGCTCAGATCGGAAGAGCGGTTCAG
 +
-BNNNQVWVVV__bbb__b_bb____b________b__Z_______[[[[YYYYYY_____b___b
+BNNNQVWVVV__bbb__b_bb____b________b__Z_______[[[[YYYYYY_____b___bb____YWWYYVVTVVYYYYY
 @SOLEXA2_0414:3:1:6494:1099#0/1 
-NTGCGATTGGTTTGTCCTAGGCAGAGGACACTGCGGGAGATTCAGAGTACAGTTGTAAGGTCTGGTTTGTCCTAGGCAGAATCGC
+N
 +
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+B
 @SOLEXA2_0414:3:1:8413:1097#0/1 
 NTGCGATCCATACCCTTCTTATATACTTTGGGTTTTAGTAGTCCACTGGCATATATTTAATTCAATACATACTCATTAAGCAATG
 +
 BGIGEMQLNQ_______________VXXXX_____WWXXX[YY[[_____WYRYY___________V___YLYYYYYYPY_____
 @SOLEXA2_0414:3:1:9865:1095#0/1 
-NCTACATTAATTGTTTTAATTTTTATTTATTTATTTTTTTGAGACGGAGTCTCGCTGATGTAGC
+NCTACATTAATTGTTTTAATTTTTATTTATTTATTTTTTTGAGACGGAGTCTCGCTGATGTAGCAGATCGGAAGAGCGGTTCAGC
 +
-BKKJKRTTST_____QQQ_b[[[[[QQQQ_QQQbQQQQQQQ_________bb____________
+BKKJKRTTST_____QQQ_b[[[[[QQQQ_QQQbQQQQQQQ_________bb__________________[[[[Y__________
 @SOLEXA2_0414:3:1:10606:1102#0/1 
 NTGCGATATTTGGAACTTCATGTGTCTTTTGTATTGCTTGATAGCAGCATAGAATATGTGAGGTATTTTTGGCTACTTTGTGAAT
 +
 BMMMMTUTTRTTVWV_____b___b__b_QQQQ__[Y[[YYYYYY_______________[[[[[YYYQQQ____BBBBBBBBBB
 @SOLEXA2_0414:3:1:11267:1102#0/1 
-NCTACATTACTCTGAATCTCCCGCAGTGTCCGAGATCGCACCACTGCACCCCAGCCTGGGCGACATGTAGC
+NCTACATTACTCTGAATCTCCCGCAGTGTCCGAGATCGCACCACTGCACCCCAGCCTGGGCGACATGTAGCA
 +
-BEGGEJLHIK______________RTWWWWY[Y[[________________QM__YYYYYXWJVX_____B
+BEGGEJLHIK______________RTWWWWY[Y[[________________QM__YYYYYXWJVX_____BB
 @SOLEXA2_0414:3:1:13556:1104#0/1 
-NTGCGATTTACAACCGTTACTCTGAATCTCCCGCAGTGTCCAGGACAAACCAGACCTTACAACTGTATCGCAA
+NTGCGATTTACAACCGTTACTCTGAATCTCCCGCAGTGTCCAGGACAAAC
 +
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:13625:1097#0/1 
-NTGCGATCTTACAACTGTTACTCTGAATCTCCCGCAGTGTCCAGGACAAACCAGACCTTACAACTGTATCGCAA
+NTGCGATCTTACAACTGTTACTCTGAATCTCCCGCAGTGTCCAGGACAAACCAGACCTTACAACTGTATCGCAAA
 +
-BJKJJTUUST___b_b_____b______________________________bW_bb__bb____[[Y[YYYYY
+BJKJJTUUST___b_b_____b______________________________bW_bb__bb____[[Y[YYYYYY
 @SOLEXA2_0414:3:1:14055:1098#0/1 
 NAGCAATCTCTGAATCTCCCGCAGTGTCCAGGACAAACCAGACCTTACAACTGTTACTCTGAATCTCCCGCAGTGTCCAGGACAA
 +
@@ -155,9 +155,9 @@
 +
 BIKOOPTTTT_____QQQQ_YYYYYYYYYY_____YYYYY___________________________________YQYYY___Y_
 @SOLEXA2_0414:3:1:7605:1117#0/1 
-NAGCAATCCTTTAGTTCTAGTGTCTAGGGATATGCAAAGTCAGAAAAAACCAGTCACCACCCAAAAGAAAATAGTGCAGACAAGG
+NAGCAATCCTTTAGTTCTAGTGTCTAGGGATATGCAAAGTCAGAAAAAAC
 +
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:13482:1108#0/1 
 NCTACATCTGAATCTCCCGCAGTGTCCGAGATCGCACCACTGCACCCCAGCCTGGGCGACAGCGAGACTCCGTCTCAAAAAAATA
 +
@@ -171,9 +171,9 @@
 +
 BJJOHRTRTT[QQQ[___b____b______[V[[[bbbbb_b___b_b_____________________________________
 @SOLEXA2_0414:3:1:17840:1114#0/1 
-NAGCAATCTCTAGATTACTTATCATACCTAATACAATGTAAATAGTTGTTATACTGTATTGTTTAGGAAATAATGACAAGAAAAA
+NAGCAATCTCTAGATTACTTATCATACCTAATACAATGTAAATAGTTGTTATACTGTATTGTTTAGGAAATAAT
 +
-BOIIIVWWVV_____Y[[[[[[[W[TWTWRYYYYYY[YYY____R_____BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+BOIIIVWWVV_____Y[[[[[[[W[TWTWRYYYYYY[YYY____R_____BBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:18083:1109#0/1 
 NAGCAATTACTCTGAATCTCCCGCAGTGTCCAATACTGTACTTTTTTACATAGTCATTGCTTAATGAATATGTATTGAATTAAAT
 +
@@ -183,18 +183,18 @@
 +
 BIIKHQTTSS[[[Y[_____YYYYYTWVVV_____b___^_________________________YYYYY_____BBBBBBBBBB
 @SOLEXA2_0414:3:1:4029:1119#0/1 
-NAGCAATGGGAGAGTGTTGTTTTTGTCACTTGCCCCAGCAGAGCAGGGGTTTTGGAAGGAGAGGTCTTTAATAGCTTTGAAAATT
+N
 +
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+B
 @SOLEXA2_0414:3:1:10939:1119#0/1 
-NCTACATACAGTTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTATGTAGC
+NCTACATACAGTTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTATGTAGCA
 +
-BQKQLVWVWV_____[Y[[[__________BBBBBBBBBBBBBBBBBBBBBBBBBB
+BQKQLVWVWV_____[Y[[[__________BBBBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:11098:1122#0/1 
 NAGCAATGTTGAGTCCAGGGATACAGAACCCACTGATACAGAGGCCCAGCTGTAGTTCTATTACCAAGTTTTGTACCTTTGTAGC
 +
 BEMGGQQORMVVVVTWWWWWOVTVVWRWWW_______________[[T[YTVTTV_____BBBBBBBBBBBBBBBBBBBBBBBBB
 @SOLEXA2_0414:3:1:12110:1126#0/1 
-NTGCGATTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTCAGATCGCAA
+NTGCGATTGTAAGGTCTGGTTTGTCCTGGACACTGCGGGAGATTCAGATCGCAAAGATCGGAAGAGCGGTTCAGCAGGAATGCCG
 +
-BIIIHQRRRQ[[[[[b__bb_b___YYYYY_____UWWWT[T[[Y__bb_____
+BIIIHQRRRQ[[[[[b__bb_b___YYYYY_____UWWWT[T[[Y__bb_________Y______YYYYYQWWWW___S_BBBBB