Mercurial > repos > bgruening > rnaz_randomize_aln

comparison 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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comparison
equal deleted inserted replaced
-1:000000000000 0:5d006d19f70a
1
2 ############################ RNAz 2.1 ##############################
3
4 Sequences: 4
5 Columns: 73
6 Reading direction: forward
7 Mean pairwise identity: 80.82
8 Shannon entropy: 0.31118
9 G+C content: 0.54795
10 Mean single sequence MFE: -27.20
11 Consensus MFE: -26.50
12 Energy contribution: -23.63
13 Covariance contribution: -2.87
14 Combinations/Pair: 1.43
15 Mean z-score: -1.82
16 Structure conservation index: 0.97
17 Background model: dinucleotide
18 Decision model: sequence based alignment quality
19 SVM decision value: 2.15
20 SVM RNA-class probability: 0.984068
21 Prediction: RNA
22
23 ######################################################################
24
25 >sacCer1.chr4 1352453 73 - 1531914
26 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
27 (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R)
28 >sacBay.contig_465 14962 73 - 57401
29 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
30 (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R)
31 >sacKlu.Contig1694 137 73 + 4878
32 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU
33 (((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R)
34 >sacCas.Contig128 258 73 + 663
35 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA
36 (((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R)
37 >consensus
38 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
39 (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87)
40
41 ############################ RNAz 2.1 ##############################
42
43 Sequences: 4
44 Columns: 73
45 Reading direction: reverse
46 Mean pairwise identity: 80.82
47 Shannon entropy: 0.31118
48 G+C content: 0.54795
49 Mean single sequence MFE: -24.15
50 Consensus MFE: -26.66
51 Energy contribution: -23.35
52 Covariance contribution: -3.31
53 Combinations/Pair: 1.48
54 Mean z-score: -1.79
55 Structure conservation index: 1.10
56 Background model: dinucleotide
57 Decision model: sequence based alignment quality
58 SVM decision value: 2.58
59 SVM RNA-class probability: 0.992927
60 Prediction: RNA
61
62 ######################################################################
63
64 >sacCer1.chr4 1352453 73 + 1531914
65 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
66 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R)
67 >sacBay.contig_465 14962 73 + 57401
68 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
69 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R)
70 >sacKlu.Contig1694 137 73 - 4878
71 AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
72 .......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R)
73 >sacCas.Contig128 258 73 - 663
74 UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC
75 .(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R)
76 >consensus
77 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
78 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31)
79
80 ############################ RNAz 2.1 ##############################
81
82 Sequences: 4
83 Columns: 73
84 Reading direction: forward
85 Mean pairwise identity: 80.82
86 Shannon entropy: 0.31118
87 G+C content: 0.54795
88 Mean single sequence MFE: -24.15
89 Consensus MFE: -26.66
90 Energy contribution: -23.35
91 Covariance contribution: -3.31
92 Combinations/Pair: 1.48
93 Mean z-score: -1.79
94 Structure conservation index: 1.10
95 Background model: dinucleotide
96 Decision model: sequence based alignment quality
97 SVM decision value: 2.58
98 SVM RNA-class probability: 0.992927
99 Prediction: RNA
100
101 ######################################################################
102
103 >sacCer1.chr4 1352453 73 + 1531914
104 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
105 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R)
106 >sacBay.contig_465 14962 73 + 57401
107 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
108 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score = -2.22, R)
109 >sacKlu.Contig1694 137 73 - 4878
110 AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
111 .......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score = -1.87, R)
112 >sacCas.Contig128 258 73 - 663
113 UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC
114 .(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score = -0.83, R)
115 >consensus
116 AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
117 .(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 + -3.31)
118
119 ############################ RNAz 2.1 ##############################
120
121 Sequences: 4
122 Columns: 73
123 Reading direction: reverse
124 Mean pairwise identity: 80.82
125 Shannon entropy: 0.31118
126 G+C content: 0.54795
127 Mean single sequence MFE: -27.20
128 Consensus MFE: -26.50
129 Energy contribution: -23.63
130 Covariance contribution: -2.87
131 Combinations/Pair: 1.43
132 Mean z-score: -1.82
133 Structure conservation index: 0.97
134 Background model: dinucleotide
135 Decision model: sequence based alignment quality
136 SVM decision value: 2.15
137 SVM RNA-class probability: 0.984068
138 Prediction: RNA
139
140 ######################################################################
141
142 >sacCer1.chr4 1352453 73 - 1531914
143 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
144 (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R)
145 >sacBay.contig_465 14962 73 - 57401
146 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
147 (((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score = -2.35, R)
148 >sacKlu.Contig1694 137 73 + 4878
149 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU
150 (((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score = -1.34, R)
151 >sacCas.Contig128 258 73 + 663
152 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA
153 (((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score = -1.22, R)
154 >consensus
155 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
156 (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 + -2.87)