Mercurial > repos > bgruening > rnaz_select_seqs
view test-data/tRNA.rnaz @ 0:5f31010cdd15 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
| author | bgruening |
|---|---|
| date | Wed, 30 Jan 2019 03:58:28 -0500 |
| parents | |
| children |
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############################ RNAz 2.1 ############################## Sequences: 4 Columns: 73 Reading direction: forward Mean pairwise identity: 80.82 Shannon entropy: 0.31118 G+C content: 0.54795 Mean single sequence MFE: -27.20 Consensus MFE: -26.50 Energy contribution: -23.63 Covariance contribution: -2.87 Combinations/Pair: 1.43 Mean z-score: -1.82 Structure conservation index: 0.97 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.15 SVM RNA-class probability: 0.984068 Prediction: RNA ###################################################################### >sacCer1.chr4 1352453 73 - 1531914 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) >sacBay.contig_465 14962 73 - 57401 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) >sacKlu.Contig1694 137 73 + 4878 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU (((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R) >sacCas.Contig128 258 73 + 663 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA (((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R) >consensus GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87) ############################ RNAz 2.1 ############################## Sequences: 4 Columns: 73 Reading direction: reverse Mean pairwise identity: 80.82 Shannon entropy: 0.31118 G+C content: 0.54795 Mean single sequence MFE: -24.15 Consensus MFE: -26.66 Energy contribution: -23.35 Covariance contribution: -3.31 Combinations/Pair: 1.48 Mean z-score: -1.79 Structure conservation index: 1.10 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.58 SVM RNA-class probability: 0.992927 Prediction: RNA ###################################################################### >sacCer1.chr4 1352453 73 + 1531914 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) >sacBay.contig_465 14962 73 + 57401 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) >sacKlu.Contig1694 137 73 - 4878 AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC .......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R) >sacCas.Contig128 258 73 - 663 UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC .(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R) >consensus AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31) ############################ RNAz 2.1 ############################## Sequences: 4 Columns: 73 Reading direction: forward Mean pairwise identity: 80.82 Shannon entropy: 0.31118 G+C content: 0.54795 Mean single sequence MFE: -24.15 Consensus MFE: -26.66 Energy contribution: -23.35 Covariance contribution: -3.31 Combinations/Pair: 1.48 Mean z-score: -1.79 Structure conservation index: 1.10 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.58 SVM RNA-class probability: 0.992927 Prediction: RNA ###################################################################### >sacCer1.chr4 1352453 73 + 1531914 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) >sacBay.contig_465 14962 73 + 57401 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R) >sacKlu.Contig1694 137 73 - 4878 AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC .......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R) >sacCas.Contig128 258 73 - 663 UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC .(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R) >consensus AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31) ############################ RNAz 2.1 ############################## Sequences: 4 Columns: 73 Reading direction: reverse Mean pairwise identity: 80.82 Shannon entropy: 0.31118 G+C content: 0.54795 Mean single sequence MFE: -27.20 Consensus MFE: -26.50 Energy contribution: -23.63 Covariance contribution: -2.87 Combinations/Pair: 1.43 Mean z-score: -1.82 Structure conservation index: 0.97 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.15 SVM RNA-class probability: 0.984068 Prediction: RNA ###################################################################### >sacCer1.chr4 1352453 73 - 1531914 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) >sacBay.contig_465 14962 73 - 57401 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R) >sacKlu.Contig1694 137 73 + 4878 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU (((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R) >sacCas.Contig128 258 73 + 663 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA (((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R) >consensus GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87)