diff test-data/tRNA.rnaz @ 0:273a961d332f 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 04:13:47 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.rnaz	Wed Jan 30 04:13:47 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)