Mercurial > repos > bgruening > rnaz_randomize_aln

annotate test-data/tRNA.rnaz @ 0:5d006d19f70a draft default tip

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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
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5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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1
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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2 ############################ RNAz 2.1 ##############################
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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3
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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4 Sequences: 4
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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5 Columns: 73
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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6 Reading direction: forward
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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7 Mean pairwise identity: 80.82
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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8 Shannon entropy: 0.31118
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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9 G+C content: 0.54795
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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10 Mean single sequence MFE: -27.20
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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11 Consensus MFE: -26.50
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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12 Energy contribution: -23.63
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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13 Covariance contribution: -2.87
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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14 Combinations/Pair: 1.43
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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15 Mean z-score: -1.82
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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16 Structure conservation index: 0.97
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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17 Background model: dinucleotide
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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18 Decision model: sequence based alignment quality
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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19 SVM decision value: 2.15
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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20 SVM RNA-class probability: 0.984068
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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21 Prediction: RNA
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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22
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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23 ######################################################################
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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24
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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25 >sacCer1.chr4 1352453 73 - 1531914
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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26 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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27 (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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28 >sacBay.contig_465 14962 73 - 57401
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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29 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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30 (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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31 >sacKlu.Contig1694 137 73 + 4878
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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32 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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33 (((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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34 >sacCas.Contig128 258 73 + 663
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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35 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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36 (((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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37 >consensus
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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38 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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39 (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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40
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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41 ############################ RNAz 2.1 ##############################
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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42
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43 Sequences: 4
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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44 Columns: 73
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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45 Reading direction: reverse
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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46 Mean pairwise identity: 80.82
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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47 Shannon entropy: 0.31118
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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48 G+C content: 0.54795
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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49 Mean single sequence MFE: -24.15
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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50 Consensus MFE: -26.66
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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51 Energy contribution: -23.35
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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52 Covariance contribution: -3.31
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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53 Combinations/Pair: 1.48
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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54 Mean z-score: -1.79
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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55 Structure conservation index: 1.10
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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56 Background model: dinucleotide
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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57 Decision model: sequence based alignment quality
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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58 SVM decision value: 2.58
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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59 SVM RNA-class probability: 0.992927
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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60 Prediction: RNA
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61
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62 ######################################################################
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63
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64 >sacCer1.chr4 1352453 73 + 1531914
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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65 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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66 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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67 >sacBay.contig_465 14962 73 + 57401
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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68 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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69 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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70 >sacKlu.Contig1694 137 73 - 4878
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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71 AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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72 .......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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73 >sacCas.Contig128 258 73 - 663
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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74 UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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75 .(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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76 >consensus
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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77 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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78 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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79
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80 ############################ RNAz 2.1 ##############################
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
81
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
82 Sequences: 4
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
83 Columns: 73
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
84 Reading direction: forward
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
85 Mean pairwise identity: 80.82
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
86 Shannon entropy: 0.31118
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
87 G+C content: 0.54795
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
88 Mean single sequence MFE: -24.15
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
89 Consensus MFE: -26.66
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
90 Energy contribution: -23.35
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
91 Covariance contribution: -3.31
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
92 Combinations/Pair: 1.48
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
93 Mean z-score: -1.79
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
94 Structure conservation index: 1.10
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
95 Background model: dinucleotide
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
96 Decision model: sequence based alignment quality
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
97 SVM decision value: 2.58
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
98 SVM RNA-class probability: 0.992927
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
99 Prediction: RNA
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
100
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
101 ######################################################################
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
102
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
103 >sacCer1.chr4 1352453 73 + 1531914
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
104 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
105 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
106 >sacBay.contig_465 14962 73 + 57401
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
107 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
108 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
109 >sacKlu.Contig1694 137 73 - 4878
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
110 AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
111 .......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
112 >sacCas.Contig128 258 73 - 663
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
113 UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
114 .(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
115 >consensus
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
116 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
117 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
118
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
119 ############################ RNAz 2.1 ##############################
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
120
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
121 Sequences: 4
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
122 Columns: 73
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
123 Reading direction: reverse
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
124 Mean pairwise identity: 80.82
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
125 Shannon entropy: 0.31118
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
126 G+C content: 0.54795
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
127 Mean single sequence MFE: -27.20
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
128 Consensus MFE: -26.50
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
129 Energy contribution: -23.63
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
130 Covariance contribution: -2.87
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
131 Combinations/Pair: 1.43
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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132 Mean z-score: -1.82
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
133 Structure conservation index: 0.97
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
134 Background model: dinucleotide
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
135 Decision model: sequence based alignment quality
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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136 SVM decision value: 2.15
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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137 SVM RNA-class probability: 0.984068
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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138 Prediction: RNA
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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139
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
140 ######################################################################
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
141
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
142 >sacCer1.chr4 1352453 73 - 1531914
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
143 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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144 (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
145 >sacBay.contig_465 14962 73 - 57401
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
146 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
147 (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
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148 >sacKlu.Contig1694 137 73 + 4878
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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diff changeset
149 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
150 (((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
151 >sacCas.Contig128 258 73 + 663
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
152 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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153 (((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R)
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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154 >consensus
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
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diff changeset
155 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff changeset
156 (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87)