Mercurial > repos > bgruening > rnaz_randomize_aln
diff test-data/tRNA.rnaz @ 0:5d006d19f70a 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 04:12:32 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA.rnaz Wed Jan 30 04:12:32 2019 -0500 @@ -0,0 +1,156 @@ + +############################ 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)