Mercurial > repos > bgruening > rnaz_annotate
diff test-data/unknown.rnaz @ 0:e123d5c6f489 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 04:12:06 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unknown.rnaz Wed Jan 30 04:12:06 2019 -0500 @@ -0,0 +1,720 @@ + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 83.72 + Shannon entropy: 0.30516 + G+C content: 0.50000 + Mean single sequence MFE: -36.97 + Consensus MFE: -15.85 + Energy contribution: -15.72 + Covariance contribution: -0.13 + Combinations/Pair: 1.35 + Mean z-score: -0.44 + Structure conservation index: 0.43 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.76 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/0-120 +UACAGCAGCUGCUAUUGCUUAUGGCCUGGAUAAGAGGGAGGGGGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +.....(((..(((((.....)))))))).......((..((((((((...(((((..((.((((.(((.....))).))))))..))))).))))))))..))...((((....)))).. ( -39.90, z-score = -0.87, R) +>canFam1.chr9/0-120 +UACAGCAGCUGCUAUUGCUUACGGCUUGGAUAAGAGGGAAGGGGAGAAGAAUAUCCUGGUGUUUGACCUGGGUGGUGGAACUUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +..((((....((....)).....)).)).......((..((((((((...(((((.....((((.(((.....))).))))....))))).))))))))..))...((((....)))).. ( -34.00, z-score = -0.16, R) +>mm5.chr2/0-120 +UACAGCAGCUGCUAUUGCAUAUGGCCUGGAUAAGAGAGAGGGAGAGAAGAACAUCCUUGUGUUUGACCUGGGUGGCGGCACCUUCGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +.....(((..(((((.....)))))))).......((((((((((((...(((((...(((((.(.((.....))))))))....))))).))))))))((((((.....)))))))))) ( -34.60, z-score = 0.44, R) +>galGal2.chr17/0-120 +AACUGCUGCUGCAAUUGCAUACGGAUUGGACAAGAGAGAGGGUGAAAAGAACAUCCUUGUAUUUGACCUGGGUGGUGGAACUUUUGAUGUCUCCCUCCUGACAAUUGACAACGGAGUCUU +.(((.(((.((((((((((...(((..(((((.(((((((((((.......))))))....(((.(((.....))).))))))))..)))))...))))).)))))).)).))))))... ( -33.00, z-score = -0.79, R) +>fr1.chrUn/0-120 +AACCGCUGCUGCCAUUGCUUAUGGUCUGGACAAAAAGGACGGCGAGAAGAACAUCCUCGUGUUCGAUCUCGGUGGCGGCACCUUCGACGUGUCUCUGCUCACCAUUGACAACGGUGUGUU +.((((((((..((...(((....((((.........)))))))((((.((((((....))))))..))))))..)))))..........((((..((.....))..))))..)))..... ( -39.10, z-score = -0.61, R) +>danRer1.chr11/0-120 +UACGGCGGCUGCCAUUGCAUACGGUCUGGACAAGAGGGACGGAGAGAAAAACAUCCUGGUGUUCGAUCUGGGUGGUGGCACCUUUGACGUGUCUCUGCUGACCAUCGAUAACGGCGUGUU +((((.(((.((((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))))))).((((.(.(((......)))).))))....).)))).. ( -41.20, z-score = -0.64, R) +>consensus +UACAGCAGCUGCUAUUGCAUACGGCCUGGACAAGAGGGAGGGAGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAACGGUGUCUU +....(((.(..((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))).....((((((((........))).)))))....).)))... (-15.85 = -15.72 + -0.13) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 83.72 + Shannon entropy: 0.30516 + G+C content: 0.50000 + Mean single sequence MFE: -30.48 + Consensus MFE: -16.68 + Energy contribution: -16.27 + Covariance contribution: -0.41 + Combinations/Pair: 1.38 + Mean z-score: -0.85 + Structure conservation index: 0.55 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -2.64 + SVM RNA-class probability: 0.005929 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUUCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA +..((((....)))).((((((((((((...(((((....(((..(((.....)))..))).....)))))))))))).........((.....))))))).....(((((....))))). ( -29.50, z-score = -1.08, R) +>canFam1.chr9/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAAGUUCCACCACCCAGGUCAAACACCAGGAUAUUCUUCUCCCCUUCCCUCUUAUCCAAGCCGUAAGCAAUAGCAGCUGCUGUA +..((((....))))...((.((((((((....(((....(((..(((.....)))..))).....))).)))))))).))...............((.....)).(((((....))))). ( -24.60, z-score = -1.16, R) +>mm5.chr2/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCGAAGGUGCCGCCACCCAGGUCAAACACAAGGAUGUUCUUCUCUCCCUCUCUCUUAUCCAGGCCAUAUGCAAUAGCAGCUGCUGUA +..((((....))))...((.((((..(((.(((((....(((..(((.....)))....)))...))))))))..)))))).............(((....(((....)))...)))... ( -29.50, z-score = 0.11, R) +>galGal2.chr17/0-120 +AAGACUCCGUUGUCAAUUGUCAGGAGGGAGACAUCAAAAGUUCCACCACCCAGGUCAAAUACAAGGAUGUUCUUUUCACCCUCUCUCUUGUCCAAUCCGUAUGCAAUUGCAGCAGCAGUU +..(((((.((((.((((((((((((((((((((((....(((..(((.....)))..))).....)))))..........))))))))))............))))))))))).).)))) ( -31.10, z-score = -1.92, R) +>fr1.chrUn/0-120 +AACACACCGUUGUCAAUGGUGAGCAGAGACACGUCGAAGGUGCCGCCACCGAGAUCGAACACGAGGAUGUUCUUCUCGCCGUCCUUUUUGUCCAGACCAUAAGCAAUGGCAGCAGCGGUU +.....((((((((..((((((((..((((.(((((...((((....))))....(((....))).)))))))))))))))))............(.((((.....))))).)))))))). ( -37.70, z-score = -0.90, R) +>danRer1.chr11/0-120 +AACACGCCGUUAUCGAUGGUCAGCAGAGACACGUCAAAGGUGCCACCACCCAGAUCGAACACCAGGAUGUUUUUCUCUCCGUCCCUCUUGUCCAGACCGUAUGCAAUGGCAGCCGCCGUA +.....((((((....((((((.((((((...((((...((((....))))..)).)).......(((((..........)))))))).)))...))))))....)))))).......... ( -30.50, z-score = -0.16, R) +>consensus +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUGCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA +....(((((((...)))))))....((((.(((((....((...(((.....)))...)).....)))))...))))............................(((((....))))). (-16.68 = -16.27 + -0.41) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 83.72 + Shannon entropy: 0.30516 + G+C content: 0.50000 + Mean single sequence MFE: -30.48 + Consensus MFE: -16.68 + Energy contribution: -16.27 + Covariance contribution: -0.41 + Combinations/Pair: 1.38 + Mean z-score: -0.85 + Structure conservation index: 0.55 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -2.64 + SVM RNA-class probability: 0.005929 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUUCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA +..((((....)))).((((((((((((...(((((....(((..(((.....)))..))).....)))))))))))).........((.....))))))).....(((((....))))). ( -29.50, z-score = -1.08, R) +>canFam1.chr9_rev/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAAGUUCCACCACCCAGGUCAAACACCAGGAUAUUCUUCUCCCCUUCCCUCUUAUCCAAGCCGUAAGCAAUAGCAGCUGCUGUA +..((((....))))...((.((((((((....(((....(((..(((.....)))..))).....))).)))))))).))...............((.....)).(((((....))))). ( -24.60, z-score = -1.16, R) +>mm5.chr2_rev/0-120 +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCGAAGGUGCCGCCACCCAGGUCAAACACAAGGAUGUUCUUCUCUCCCUCUCUCUUAUCCAGGCCAUAUGCAAUAGCAGCUGCUGUA +..((((....))))...((.((((..(((.(((((....(((..(((.....)))....)))...))))))))..)))))).............(((....(((....)))...)))... ( -29.50, z-score = 0.11, R) +>galGal2.chr17_rev/0-120 +AAGACUCCGUUGUCAAUUGUCAGGAGGGAGACAUCAAAAGUUCCACCACCCAGGUCAAAUACAAGGAUGUUCUUUUCACCCUCUCUCUUGUCCAAUCCGUAUGCAAUUGCAGCAGCAGUU +..(((((.((((.((((((((((((((((((((((....(((..(((.....)))..))).....)))))..........))))))))))............))))))))))).).)))) ( -31.10, z-score = -1.92, R) +>fr1.chrUn_rev/0-120 +AACACACCGUUGUCAAUGGUGAGCAGAGACACGUCGAAGGUGCCGCCACCGAGAUCGAACACGAGGAUGUUCUUCUCGCCGUCCUUUUUGUCCAGACCAUAAGCAAUGGCAGCAGCGGUU +.....((((((((..((((((((..((((.(((((...((((....))))....(((....))).)))))))))))))))))............(.((((.....))))).)))))))). ( -37.70, z-score = -0.90, R) +>danRer1.chr11_rev/0-120 +AACACGCCGUUAUCGAUGGUCAGCAGAGACACGUCAAAGGUGCCACCACCCAGAUCGAACACCAGGAUGUUUUUCUCUCCGUCCCUCUUGUCCAGACCGUAUGCAAUGGCAGCCGCCGUA +.....((((((....((((((.((((((...((((...((((....))))..)).)).......(((((..........)))))))).)))...))))))....)))))).......... ( -30.50, z-score = -0.16, R) +>consensus +AAGACACCAUUGUCAAUGGUGAGAAGAGACACAUCAAAGGUGCCACCACCCAGGUCAAACACCAGGAUGUUCUUCUCCCCCUCCCUCUUAUCCAGGCCAUAAGCAAUAGCAGCUGCUGUA +....(((((((...)))))))....((((.(((((....((...(((.....)))...)).....)))))...))))............................(((((....))))). (-16.68 = -16.27 + -0.41) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 83.72 + Shannon entropy: 0.30516 + G+C content: 0.50000 + Mean single sequence MFE: -36.97 + Consensus MFE: -15.85 + Energy contribution: -15.72 + Covariance contribution: -0.13 + Combinations/Pair: 1.35 + Mean z-score: -0.44 + Structure conservation index: 0.43 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.76 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/0-120 +UACAGCAGCUGCUAUUGCUUAUGGCCUGGAUAAGAGGGAGGGGGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +.....(((..(((((.....)))))))).......((..((((((((...(((((..((.((((.(((.....))).))))))..))))).))))))))..))...((((....)))).. ( -39.90, z-score = -0.87, R) +>canFam1.chr9_rev/0-120 +UACAGCAGCUGCUAUUGCUUACGGCUUGGAUAAGAGGGAAGGGGAGAAGAAUAUCCUGGUGUUUGACCUGGGUGGUGGAACUUUUGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +..((((....((....)).....)).)).......((..((((((((...(((((.....((((.(((.....))).))))....))))).))))))))..))...((((....)))).. ( -34.00, z-score = -0.16, R) +>mm5.chr2_rev/0-120 +UACAGCAGCUGCUAUUGCAUAUGGCCUGGAUAAGAGAGAGGGAGAGAAGAACAUCCUUGUGUUUGACCUGGGUGGCGGCACCUUCGAUGUGUCUCUUCUCACCAUUGACAAUGGUGUCUU +.....(((..(((((.....)))))))).......((((((((((((...(((((...(((((.(.((.....))))))))....))))).))))))))((((((.....)))))))))) ( -34.60, z-score = 0.44, R) +>galGal2.chr17_rev/0-120 +AACUGCUGCUGCAAUUGCAUACGGAUUGGACAAGAGAGAGGGUGAAAAGAACAUCCUUGUAUUUGACCUGGGUGGUGGAACUUUUGAUGUCUCCCUCCUGACAAUUGACAACGGAGUCUU +.(((.(((.((((((((((...(((..(((((.(((((((((((.......))))))....(((.(((.....))).))))))))..)))))...))))).)))))).)).))))))... ( -33.00, z-score = -0.79, R) +>fr1.chrUn_rev/0-120 +AACCGCUGCUGCCAUUGCUUAUGGUCUGGACAAAAAGGACGGCGAGAAGAACAUCCUCGUGUUCGAUCUCGGUGGCGGCACCUUCGACGUGUCUCUGCUCACCAUUGACAACGGUGUGUU +.((((((((..((...(((....((((.........)))))))((((.((((((....))))))..))))))..)))))..........((((..((.....))..))))..)))..... ( -39.10, z-score = -0.61, R) +>danRer1.chr11_rev/0-120 +UACGGCGGCUGCCAUUGCAUACGGUCUGGACAAGAGGGACGGAGAGAAAAACAUCCUGGUGUUCGAUCUGGGUGGUGGCACCUUUGACGUGUCUCUGCUGACCAUCGAUAACGGCGUGUU +((((.(((.((((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))))))).((((.(.(((......)))).))))....).)))).. ( -41.20, z-score = -0.64, R) +>consensus +UACAGCAGCUGCUAUUGCAUACGGCCUGGACAAGAGGGAGGGAGAGAAGAACAUCCUGGUGUUUGACCUGGGUGGUGGAACCUUUGAUGUGUCUCUUCUCACCAUUGACAACGGUGUCUU +....(((.(..((((..(...(((..((((((...((((.(..........).))))..))))))..))).)..)))).....((((((((........))).)))))....).)))... (-15.85 = -15.72 + -0.13) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 85.83 + Shannon entropy: 0.26644 + G+C content: 0.46111 + Mean single sequence MFE: -29.08 + Consensus MFE: -17.18 + Energy contribution: -17.27 + Covariance contribution: 0.09 + Combinations/Pair: 1.38 + Mean z-score: -0.03 + Structure conservation index: 0.59 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.58 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/120-240 +CAAAGUUGUGGCCACUAAUGGAGAUACUUAUCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA +(((((((....(((((...(((........))).)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -29.23, z-score = -0.65, R) +>panTro1.chr1/120-240 +CAAAGUUGUGGUCACUAAUGGAGAUACUCAUCUGGGUGGAAAAGACUUUGACCAGCAUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCGGGAAAGACAA +(((((((....(((((....(((...))).....)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -26.53, z-score = -0.03, R) +>rn3.chr3/120-240 +UGAAGUGGUGGCCACUAAUGGAGACACUCAUCUGGGUGGGGAAGACUUUGAUCAGCGGGUCAUGGAGCACUUCAUCAAGCUGUACAAAAAGAAGACUGGGAAAGAUGUCAGAAAGGACAA +(((((((((((((.....((....))(((((....))))).................))))))....)))))))(((..((...........))..)))......((((......)))). ( -26.70, z-score = 0.92, R) +>galGal2.chr17/120-240 +UGAAGUUGUGGCUACAAAUGGUGACACACACCUGGGUGGAGAAGACUUUGACCAGCGUGUUAUGGAGCACUUCAUCAAACUCUACAAGAAGAAAACAGGAAAAGAUGUCAGGAAGGAUAA +((((((.((..(((....((....)).((((((((..((((....))))..)))).))))..))).))))))))...............................((((......)))). ( -24.20, z-score = 0.87, R) +>fr1.chrUn/120-240 +UGAAGUGGUGGCCACCAAUGGUGACACUCACCUUGGAGGUGAAGACUUUGAUCAGCGCGUCAUGGAACACUUCAUCAAGCUAUACAAGAAGAAGACUGGCAAAGACGUGCGCAAAGACAA +.(((((..(.(((.((((.((((.....)))))))).))).)..))))).....((((((((((((....)))))...((((..(........)..))))...))))))).......... ( -36.70, z-score = -1.77, R) +>danRer1.chr11/120-240 +UGAAGUGGUGGCCACAAACGGAGACACUCACCUGGGCGGAGAAGACUUCGACCAGCGCGUCAUGGAGCACUUCAUCAAGCUGUACAAGAAGAAGACGGGCAAAGAUGUGCGCAAAGACAA +....((((((.((......))...))).))).(((.(((((....))))).)))((((((((((((....)))))....((((.(........))))).....))))))).......... ( -31.10, z-score = 0.50, R) +>consensus +UGAAGUGGUGGCCACUAAUGGAGACACUCACCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA +((((((..(..(((((...((.(.....).))..)))))..)..))))))....((.(((((((((....)))))....((........))..)))).)).....((((......)))). (-17.18 = -17.27 + 0.09) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 85.83 + Shannon entropy: 0.26644 + G+C content: 0.46111 + Mean single sequence MFE: -23.40 + Consensus MFE: -9.31 + Energy contribution: -9.48 + Covariance contribution: 0.17 + Combinations/Pair: 1.36 + Mean z-score: 0.40 + Structure conservation index: 0.40 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -7.30 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/120-240 +UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUAAGUAUCUCCAUUAGUGGCCACAACUUUG +.((((......)))).....((((((............((......))..(((((....)))))))))))((((((.....((((..((((....))))......)))).....)))))) ( -22.90, z-score = -0.12, R) +>panTro1.chr1/120-240 +UUGUCUUUCCCGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACAUGCUGGUCAAAGUCUUUUCCACCCAGAUGAGUAUCUCCAUUAGUGACCACAACUUUG +.((((......)))).((((((((((((((.................))))((((....)))).))))).))))).......(((...((((........)))).)))............ ( -18.53, z-score = 1.10, R) +>rn3.chr3/120-240 +UUGUCCUUUCUGACAUCUUUCCCAGUCUUCUUUUUGUACAGCUUGAUGAAGUGCUCCAUGACCCGCUGAUCAAAGUCUUCCCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACCACUUCA +.((((......))))...............................(((((((..((((((..((((.(((.................))).))))..)).....))))....))))))) ( -19.43, z-score = 0.66, R) +>galGal2.chr17/120-240 +UUAUCCUUCCUGACAUCUUUUCCUGUUUUCUUCUUGUAGAGUUUGAUGAAGUGCUCCAUAACACGCUGGUCAAAGUCUUCUCCACCCAGGUGUGUGUCACCAUUUGUAGCCACAACUUCA +..........((((((.....((((............(((.((((((.(.(((........)))..).)))))).)))........))))...))))))....((((....))))..... ( -20.75, z-score = 0.35, R) +>fr1.chrUn/120-240 +UUGUCUUUGCGCACGUCUUUGCCAGUCUUCUUCUUGUAUAGCUUGAUGAAGUGUUCCAUGACGCGCUGAUCAAAGUCUUCACCUCCAAGGUGAGUGUCACCAUUGGUGGCCACCACUUCA +..(.(((((.((.((((..((.....((((.((..(.....)..)).)))).....)).)))).))....))))).).(((((.....)))))((((((((...))))).)))....... ( -31.40, z-score = -0.65, R) +>danRer1.chr11/120-240 +UUGUCUUUGCGCACAUCUUUGCCCGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACGCGCUGGUCGAAGUCUUCUCCGCCCAGGUGAGUGUCUCCGUUUGUGGCCACCACUUCA +..(((...(((((......)))..(((........).)).))..)))((((((..(((((((((.((((.((.((....)).)).))))....))))).......))))....)))))). ( -27.41, z-score = 1.03, R) +>consensus +UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACAACUUCA +.((((......))))...........................(((((..(((((........))))).)))))(((.....((((...((((........)))).)))).....)))... ( -9.31 = -9.48 + 0.17) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 85.83 + Shannon entropy: 0.26644 + G+C content: 0.46111 + Mean single sequence MFE: -23.40 + Consensus MFE: -9.31 + Energy contribution: -9.48 + Covariance contribution: 0.17 + Combinations/Pair: 1.36 + Mean z-score: 0.40 + Structure conservation index: 0.40 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -7.30 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/120-240 +UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUAAGUAUCUCCAUUAGUGGCCACAACUUUG +.((((......)))).....((((((............((......))..(((((....)))))))))))((((((.....((((..((((....))))......)))).....)))))) ( -22.90, z-score = -0.12, R) +>panTro1.chr1_rev/120-240 +UUGUCUUUCCCGACAUCUUUGCCAGUCUUCUUUUUGUACAGUUUGAUGAAGUGUUCCAUGACAUGCUGGUCAAAGUCUUUUCCACCCAGAUGAGUAUCUCCAUUAGUGACCACAACUUUG +.((((......)))).((((((((((((((.................))))((((....)))).))))).))))).......(((...((((........)))).)))............ ( -18.53, z-score = 1.10, R) +>rn3.chr3_rev/120-240 +UUGUCCUUUCUGACAUCUUUCCCAGUCUUCUUUUUGUACAGCUUGAUGAAGUGCUCCAUGACCCGCUGAUCAAAGUCUUCCCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACCACUUCA +.((((......))))...............................(((((((..((((((..((((.(((.................))).))))..)).....))))....))))))) ( -19.43, z-score = 0.66, R) +>galGal2.chr17_rev/120-240 +UUAUCCUUCCUGACAUCUUUUCCUGUUUUCUUCUUGUAGAGUUUGAUGAAGUGCUCCAUAACACGCUGGUCAAAGUCUUCUCCACCCAGGUGUGUGUCACCAUUUGUAGCCACAACUUCA +..........((((((.....((((............(((.((((((.(.(((........)))..).)))))).)))........))))...))))))....((((....))))..... ( -20.75, z-score = 0.35, R) +>fr1.chrUn_rev/120-240 +UUGUCUUUGCGCACGUCUUUGCCAGUCUUCUUCUUGUAUAGCUUGAUGAAGUGUUCCAUGACGCGCUGAUCAAAGUCUUCACCUCCAAGGUGAGUGUCACCAUUGGUGGCCACCACUUCA +..(.(((((.((.((((..((.....((((.((..(.....)..)).)))).....)).)))).))....))))).).(((((.....)))))((((((((...))))).)))....... ( -31.40, z-score = -0.65, R) +>danRer1.chr11_rev/120-240 +UUGUCUUUGCGCACAUCUUUGCCCGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACGCGCUGGUCGAAGUCUUCUCCGCCCAGGUGAGUGUCUCCGUUUGUGGCCACCACUUCA +..(((...(((((......)))..(((........).)).))..)))((((((..(((((((((.((((.((.((....)).)).))))....))))).......))))....)))))). ( -27.41, z-score = 1.03, R) +>consensus +UUGUCUUUCCUGACAUCUUUGCCAGUCUUCUUCUUGUACAGCUUGAUGAAGUGCUCCAUGACACGCUGGUCAAAGUCUUCUCCACCCAGAUGAGUGUCUCCAUUAGUGGCCACAACUUCA +.((((......))))...........................(((((..(((((........))))).)))))(((.....((((...((((........)))).)))).....)))... ( -9.31 = -9.48 + 0.17) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 85.83 + Shannon entropy: 0.26644 + G+C content: 0.46111 + Mean single sequence MFE: -29.08 + Consensus MFE: -17.18 + Energy contribution: -17.27 + Covariance contribution: 0.09 + Combinations/Pair: 1.38 + Mean z-score: -0.03 + Structure conservation index: 0.59 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.58 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/120-240 +CAAAGUUGUGGCCACUAAUGGAGAUACUUAUCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA +(((((((....(((((...(((........))).)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -29.23, z-score = -0.65, R) +>panTro1.chr1_rev/120-240 +CAAAGUUGUGGUCACUAAUGGAGAUACUCAUCUGGGUGGAAAAGACUUUGACCAGCAUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCGGGAAAGACAA +(((((((....(((((....(((...))).....)))))....))))))).......((((........((((.................)))).((((((....))))))....)))). ( -26.53, z-score = -0.03, R) +>rn3.chr3_rev/120-240 +UGAAGUGGUGGCCACUAAUGGAGACACUCAUCUGGGUGGGGAAGACUUUGAUCAGCGGGUCAUGGAGCACUUCAUCAAGCUGUACAAAAAGAAGACUGGGAAAGAUGUCAGAAAGGACAA +(((((((((((((.....((....))(((((....))))).................))))))....)))))))(((..((...........))..)))......((((......)))). ( -26.70, z-score = 0.92, R) +>galGal2.chr17_rev/120-240 +UGAAGUUGUGGCUACAAAUGGUGACACACACCUGGGUGGAGAAGACUUUGACCAGCGUGUUAUGGAGCACUUCAUCAAACUCUACAAGAAGAAAACAGGAAAAGAUGUCAGGAAGGAUAA +((((((.((..(((....((....)).((((((((..((((....))))..)))).))))..))).))))))))...............................((((......)))). ( -24.20, z-score = 0.87, R) +>fr1.chrUn_rev/120-240 +UGAAGUGGUGGCCACCAAUGGUGACACUCACCUUGGAGGUGAAGACUUUGAUCAGCGCGUCAUGGAACACUUCAUCAAGCUAUACAAGAAGAAGACUGGCAAAGACGUGCGCAAAGACAA +.(((((..(.(((.((((.((((.....)))))))).))).)..))))).....((((((((((((....)))))...((((..(........)..))))...))))))).......... ( -36.70, z-score = -1.77, R) +>danRer1.chr11_rev/120-240 +UGAAGUGGUGGCCACAAACGGAGACACUCACCUGGGCGGAGAAGACUUCGACCAGCGCGUCAUGGAGCACUUCAUCAAGCUGUACAAGAAGAAGACGGGCAAAGAUGUGCGCAAAGACAA +....((((((.((......))...))).))).(((.(((((....))))).)))((((((((((((....)))))....((((.(........))))).....))))))).......... ( -31.10, z-score = 0.50, R) +>consensus +UGAAGUGGUGGCCACUAAUGGAGACACUCACCUGGGUGGAGAAGACUUUGACCAGCGUGUCAUGGAACACUUCAUCAAACUGUACAAAAAGAAGACUGGCAAAGAUGUCAGGAAAGACAA +((((((..(..(((((...((.(.....).))..)))))..)..))))))....((.(((((((((....)))))....((........))..)))).)).....((((......)))). (-17.18 = -17.27 + 0.09) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 80.00 + Shannon entropy: 0.37687 + G+C content: 0.50603 + Mean single sequence MFE: -34.52 + Consensus MFE: -15.70 + Energy contribution: -14.52 + Covariance contribution: -1.19 + Combinations/Pair: 1.43 + Mean z-score: 0.11 + Structure conservation index: 0.45 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.92 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/240-360 +UAGAGCUGUGCAGAAACUCUGGCGCAAGGUAGAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGA +..........((((((.((((.(....).))))...((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))).))))))... ( -35.40, z-score = -1.05, R) +>mm5.chr2/240-360 +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA +.....((.((.((((.((((.((.(((((.(((.((((((.....)))))).)))))))))).(((((.(((----((((.......)))))))))).)).)))).....)))))).)). ( -37.30, z-score = -0.73, R) +>rn3.chr3/240-360 +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA +.....((.((.((((.(((.(((.(..........).)))..)))......((((((((....(((((.(((----((((.......)))))))))).))..)))))))))))))).)). ( -32.50, z-score = 0.75, R) +>galGal2.chr17/240-360 +CAGAGCUGUACAGAAACUAAGACGGGAAGUAGAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGA +(((((((((..............((((.((((.(...((...))...).))).).))))(((.....)))..----.......))))((((((((((....)))))))))).)))))... ( -27.10, z-score = 0.14, R) +>fr1.chrUn/240-360 +CCGUGCUGUCCAGAAGCUGCGUCGUGAGGUUGAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGA +..((((.........(((...(((......)))...))).....(((((.((..(((...))).))))))))----))).((((((...(((..(.....)..))).))))))....... ( -32.90, z-score = 1.69, R) +>danRer1.chr11/240-360 +CCGCGCCGUGCAGAAGCUGCGCAGAGAGGUGGAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGA +.((.(((((((((...))))))...(.((..((.(.((((.....)))).).))..))).......))).))----((..((((((...((((((...))))))...))))))..))... ( -41.90, z-score = -0.14, R) +>consensus +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGA +....(((((((....(((.(.....).))).((.(.(((.......))).).))......))))..)))...........(((.((...((((((...))))))...)).)))....... (-15.70 = -14.52 + -1.19) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 80.00 + Shannon entropy: 0.37687 + G+C content: 0.50603 + Mean single sequence MFE: -31.38 + Consensus MFE: -17.15 + Energy contribution: -16.27 + Covariance contribution: -0.88 + Combinations/Pair: 1.50 + Mean z-score: 0.17 + Structure conservation index: 0.55 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.07 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/240-360 +UCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUCUACCUUGCGCCAGAGUUUCUGCACAGCUCUA +....((((((((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))..((((.....))))))))))..........((((((.......)))))). ( -33.30, z-score = -1.00, R) +>mm5.chr2/240-360 +UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +....((((..((((((((..((((..(((((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -33.90, z-score = -1.12, R) +>rn3.chr3/240-360 +UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +....((((..((((((((..((((.((.(((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -31.90, z-score = 0.19, R) +>galGal2.chr17/240-360 +UCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUCUACUUCCCGUCUUAGUUUCUGUACAGCUCUG +.......(((((....(((((.....)))))....))))).(((----(((((.....))))))))..((((((..((...(((....(........)....)))....))...)))))) ( -23.50, z-score = 0.63, R) +>fr1.chrUn/240-360 +UCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUCAACCUCACGACGCAGCUUCUGGACAGCACGG +....(((((.....))))).........((.((((.........----)))).)).((((((((((((.((....)).)))))).................(((...)))..)))))).. ( -29.50, z-score = 1.62, R) +>danRer1.chr11/240-360 +UCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUCCACCUCUCUGCGCAGCUUCUGCACGGCGCGG +.....(((...((((((.......)))))).))).....((.((----(.(((..((.((((.(((((.((((((.....)))))).........))))).)))).)).)).).))))). ( -36.20, z-score = 0.69, R) +>consensus +UCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +.....((((((((((((.......)).))))))...))))..................((((....((.((((((.....)))))).))..............((....)).)))).... (-17.15 = -16.27 + -0.88) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 80.00 + Shannon entropy: 0.37687 + G+C content: 0.50603 + Mean single sequence MFE: -31.38 + Consensus MFE: -17.15 + Energy contribution: -16.27 + Covariance contribution: -0.88 + Combinations/Pair: 1.50 + Mean z-score: 0.17 + Structure conservation index: 0.55 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.07 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/240-360 +UCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUCUACCUUGCGCCAGAGUUUCUGCACAGCUCUA +....((((((((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))..((((.....))))))))))..........((((((.......)))))). ( -33.30, z-score = -1.00, R) +>mm5.chr2_rev/240-360 +UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +....((((..((((((((..((((..(((((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -33.90, z-score = -1.12, R) +>rn3.chr3_rev/240-360 +UCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +....((((..((((((((..((((.((.(((...........))----)))..))))....))))))))((((((.....))))))......))))...(((((((.......))))))) ( -31.90, z-score = 0.19, R) +>galGal2.chr17_rev/240-360 +UCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUCUACUUCCCGUCUUAGUUUCUGUACAGCUCUG +.......(((((....(((((.....)))))....))))).(((----(((((.....))))))))..((((((..((...(((....(........)....)))....))...)))))) ( -23.50, z-score = 0.63, R) +>fr1.chrUn_rev/240-360 +UCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUCAACCUCACGACGCAGCUUCUGGACAGCACGG +....(((((.....))))).........((.((((.........----)))).)).((((((((((((.((....)).)))))).................(((...)))..)))))).. ( -29.50, z-score = 1.62, R) +>danRer1.chr11_rev/240-360 +UCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUCCACCUCUCUGCGCAGCUUCUGCACGGCGCGG +.....(((...((((((.......)))))).))).....((.((----(.(((..((.((((.(((((.((((((.....)))))).........))))).)))).)).)).).))))). ( -36.20, z-score = 0.69, R) +>consensus +UCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUCUACCUCACGCCGGAGUUUCUGCACAGCUCUG +.....((((((((((((.......)).))))))...))))..................((((....((.((((((.....)))))).))..............((....)).)))).... (-17.15 = -16.27 + -0.88) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 80.00 + Shannon entropy: 0.37687 + G+C content: 0.50603 + Mean single sequence MFE: -34.52 + Consensus MFE: -15.70 + Energy contribution: -14.52 + Covariance contribution: -1.19 + Combinations/Pair: 1.43 + Mean z-score: 0.11 + Structure conservation index: 0.45 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -4.92 + SVM RNA-class probability: 0.000000 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/240-360 +UAGAGCUGUGCAGAAACUCUGGCGCAAGGUAGAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGA +..........((((((.((((.(....).))))...((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))).))))))... ( -35.40, z-score = -1.05, R) +>mm5.chr2_rev/240-360 +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA +.....((.((.((((.((((.((.(((((.(((.((((((.....)))))).)))))))))).(((((.(((----((((.......)))))))))).)).)))).....)))))).)). ( -37.30, z-score = -0.73, R) +>rn3.chr3_rev/240-360 +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGA +.....((.((.((((.(((.(((.(..........).)))..)))......((((((((....(((((.(((----((((.......)))))))))).))..)))))))))))))).)). ( -32.50, z-score = 0.75, R) +>galGal2.chr17_rev/240-360 +CAGAGCUGUACAGAAACUAAGACGGGAAGUAGAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGA +(((((((((..............((((.((((.(...((...))...).))).).))))(((.....)))..----.......))))((((((((((....)))))))))).)))))... ( -27.10, z-score = 0.14, R) +>fr1.chrUn_rev/240-360 +CCGUGCUGUCCAGAAGCUGCGUCGUGAGGUUGAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGA +..((((.........(((...(((......)))...))).....(((((.((..(((...))).))))))))----))).((((((...(((..(.....)..))).))))))....... ( -32.90, z-score = 1.69, R) +>danRer1.chr11_rev/240-360 +CCGCGCCGUGCAGAAGCUGCGCAGAGAGGUGGAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGA +.((.(((((((((...))))))...(.((..((.(.((((.....)))).).))..))).......))).))----((..((((((...((((((...))))))...))))))..))... ( -41.90, z-score = -0.14, R) +>consensus +CAGAGCUGUGCAGAAACUCCGGCGUGAGGUAGAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGA +....(((((((....(((.(.....).))).((.(.(((.......))).).))......))))..)))...........(((.((...((((((...))))))...)).)))....... (-15.70 = -14.52 + -1.19) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 82.22 + Shannon entropy: 0.33146 + G+C content: 0.47735 + Mean single sequence MFE: -32.55 + Consensus MFE: -18.57 + Energy contribution: -18.10 + Covariance contribution: -0.47 + Combinations/Pair: 1.42 + Mean z-score: -0.11 + Structure conservation index: 0.57 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -3.82 + SVM RNA-class probability: 0.000001 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/271-391 +GAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGACCCUGACUCAGGCCAAAUUUGAAGAGCUCAA +(((((((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))))))))((((..((((...)))).((....)).....)))). ( -30.50, z-score = -0.31, R) +>mm5.chr2/271-391 +GAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +((.((((((.....)))))).))...(((((........((----((((.......))))))((((((((.((((.....))))...(.(((......))).)...))))))))))))). ( -36.20, z-score = -0.98, R) +>rn3.chr3/271-391 +GAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +.....((((..(((((....((((((((....(((((.(((----((((.......)))))))))).))..))))))))))))).(((.......))).))))................. ( -35.10, z-score = -0.51, R) +>galGal2.chr17/271-391 +GAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGACGCUUACUCGUGCCAAAUUUGAAGAACUGAA +(((.(((((.(((.((..(((......)))..))..)))..----..........(((((((((((....)))))))))))........))))).)))...................... ( -27.00, z-score = 0.10, R) +>fr1.chrUn/271-391 +GAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGACACUGACCCGUGCCAAAUUUGAAGAGCUUAA +.....((((....((((..((((((((........))).((----....((((((...(((..(.....)..))).))))))..)))))))..).))).))))................. ( -33.20, z-score = -0.02, R) +>danRer1.chr11/271-391 +GAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGACUCUCACCAGAGCCAAGUUUGAAGAGCUCAA +((((.((((.....))))..(((((((........)))...----((..((((((...((((((...))))))...))))))..))))))))))....(((((.........).)))).. ( -33.30, z-score = 1.06, R) +>consensus +GAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +.....((((....(((....((((((...((.....))....................((((((...))))))))))))..))).(((.......))).))))................. (-18.57 = -18.10 + -0.47) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 82.22 + Shannon entropy: 0.33146 + G+C content: 0.47735 + Mean single sequence MFE: -33.18 + Consensus MFE: -22.01 + Energy contribution: -20.72 + Covariance contribution: -1.30 + Combinations/Pair: 1.48 + Mean z-score: 0.17 + Structure conservation index: 0.66 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -3.58 + SVM RNA-class probability: 0.000003 + Prediction: OTHER + +###################################################################### + +>hg17.chr1/271-391 +UUGAGCUCUUCAAAUUUGGCCUGAGUCAGGGUCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUC +((((((((((((.........)))...)))).)))))....((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))((((((.....))))))... ( -34.00, z-score = -0.30, R) +>mm5.chr2/271-391 +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUC +....(.(((((....(..((.(((((((((((...((((...(((((......)))))....))))......)))----))))))))..))..)))))))((((((.....))))))... ( -35.10, z-score = -0.81, R) +>rn3.chr3/271-391 +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUC +((((((...((((....(((((......))))).....(((((....((((((...))))))....)))))....----.....)))).))))))..((.((((((.....)))))).)) ( -34.40, z-score = 0.10, R) +>galGal2.chr17/271-391 +UUCAGUUCUUCAAAUUUGGCACGAGUAAGCGUCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUC +....((.((........)).))(((((((((.(((...(((((....(((((.....)))))....))))).(((----(((((.....))))))))....)))..))))).)))).... ( -27.00, z-score = 0.33, R) +>fr1.chrUn/271-391 +UUAAGCUCUUCAAAUUUGGCACGGGUCAGUGUCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUC +.................((((((((((....(((.(((((.....))))).....)))..)))))).........----.((((((.((.((....)))).))))))....))))..... ( -34.20, z-score = 0.29, R) +>danRer1.chr11/271-391 +UUGAGCUCUUCAAACUUGGCUCUGGUGAGAGUCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUC +..(((((..........))))).(((((((((((.(((....)))((((((....(..(((.((((((....)).----)))))))..)...))).)))..))))))))...)))..... ( -34.40, z-score = 1.40, R) +>consensus +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUC +...(((...(((.....(((((......)))))...((((((((((((.......)).))))))...))))..............))).))).....((.((((((.....)))))).)) (-22.01 = -20.72 + -1.30) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: forward + Mean pairwise identity: 82.22 + Shannon entropy: 0.33146 + G+C content: 0.47735 + Mean single sequence MFE: -33.18 + Consensus MFE: -22.01 + Energy contribution: -20.72 + Covariance contribution: -1.30 + Combinations/Pair: 1.48 + Mean z-score: 0.17 + Structure conservation index: 0.66 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -3.58 + SVM RNA-class probability: 0.000003 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/271-391 +UUGAGCUCUUCAAAUUUGGCCUGAGUCAGGGUCUCAGAAAAGUCUUCUCCUUCAUAGAAGGACUCAAUUUCAAUUACUGCUUGCUUGAUGUUGAGAAGACAGGGCCCGUUUGGCCUUUUC +((((((((((((.........)))...)))).)))))....((((((((((((...)))))).(((((.((((.((.....)).)))).)))))))))))((((((.....))))))... ( -34.00, z-score = -0.30, R) +>mm5.chr2_rev/271-391 +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUUGCUUGAUGCUGAGAAGACAAGGCUCUCUUAGCCUUUUC +....(.(((((....(..((.(((((((((((...((((...(((((......)))))....))))......)))----))))))))..))..)))))))((((((.....))))))... ( -35.10, z-score = -0.81, R) +>rn3.chr3_rev/271-391 +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCUGAGAAGUCUUCUCCUUCGAAGAAGGACUCAAUUUCAAUC----CUCGCUUGAUGCUGAGAAGACAGGGCUCUCUUGGCCUUUUC +((((((...((((....(((((......))))).....(((((....((((((...))))))....)))))....----.....)))).))))))..((.((((((.....)))))).)) ( -34.40, z-score = 0.10, R) +>galGal2.chr17_rev/271-391 +UUCAGUUCUUCAAAUUUGGCACGAGUAAGCGUCUCAGAGAAAUCCUCUCCUUCAAAAAAGGAUUCUAUUUCAAUU----CUAGCUUGGUGCUGGGAUGACAGGGCCCGCUUCGCUUUCUC +....((.((........)).))(((((((((.(((...(((((....(((((.....)))))....))))).(((----(((((.....))))))))....)))..))))).)))).... ( -27.00, z-score = 0.33, R) +>fr1.chrUn_rev/271-391 +UUAAGCUCUUCAAAUUUGGCACGGGUCAGUGUCUCGGAGAAAUCUUCUCCCUCAAAGAAAGACUCGAUCUCAAUG----CGGGCCUGGUGCUGGGCAGACAGGGCCCUCUUUGCCUUCUC +.................((((((((((....(((.(((((.....))))).....)))..)))))).........----.((((((.((.((....)))).))))))....))))..... ( -34.20, z-score = 0.29, R) +>danRer1.chr11_rev/271-391 +UUGAGCUCUUCAAACUUGGCUCUGGUGAGAGUCUCAGAGAAAUCUUCUCCCUCAAAGAAGGACUCGAUCUCGAUG----CGGGCCUGAUGCUGGGCAGACAGGGCUCUCUUAGCCUUCUC +..(((((..........))))).(((((((((((.(((....)))((((((....(..(((.((((((....)).----)))))))..)...))).)))..))))))))...)))..... ( -34.40, z-score = 1.40, R) +>consensus +UUCAGCUCUUCAAAUUUGGCCCGAGUAAGGGUCUCAGAGAAAUCUUCUCCUUCAAAGAAGGACUCAAUUUCAAUC____CUGGCUUGAUGCUGAGAAGACAGGGCCCUCUUAGCCUUCUC +...(((...(((.....(((((......)))))...((((((((((((.......)).))))))...))))..............))).))).....((.((((((.....)))))).)) (-22.01 = -20.72 + -1.30) + +############################ RNAz 2.1 ############################## + + Sequences: 6 + Columns: 120 + Reading direction: reverse + Mean pairwise identity: 82.22 + Shannon entropy: 0.33146 + G+C content: 0.47735 + Mean single sequence MFE: -32.55 + Consensus MFE: -18.57 + Energy contribution: -18.10 + Covariance contribution: -0.47 + Combinations/Pair: 1.42 + Mean z-score: -0.11 + Structure conservation index: 0.57 + Background model: dinucleotide + Decision model: sequence based alignment quality + SVM decision value: -3.82 + SVM RNA-class probability: 0.000001 + Prediction: OTHER + +###################################################################### + +>hg17.chr1_rev/271-391 +GAAAAGGCCAAACGGGCCCUGUCUUCUCAACAUCAAGCAAGCAGUAAUUGAAAUUGAGUCCUUCUAUGAAGGAGAAGACUUUUCUGAGACCCUGACUCAGGCCAAAUUUGAAGAGCUCAA +(((((((((.....))))..((((((((((..((((((.....))..))))..)))).((((((...)))))))))))))))))((((..((((...)))).((....)).....)))). ( -30.50, z-score = -0.31, R) +>mm5.chr2_rev/271-391 +GAAAAGGCUAAGAGAGCCUUGUCUUCUCAGCAUCAAGCAAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +((.((((((.....)))))).))...(((((........((----((((.......))))))((((((((.((((.....))))...(.(((......))).)...))))))))))))). ( -36.20, z-score = -0.98, R) +>rn3.chr3_rev/271-391 +GAAAAGGCCAAGAGAGCCCUGUCUUCUCAGCAUCAAGCGAG----GAUUGAAAUUGAGUCCUUCUUCGAAGGAGAAGACUUCUCAGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +.....((((..(((((....((((((((....(((((.(((----((((.......)))))))))).))..))))))))))))).(((.......))).))))................. ( -35.10, z-score = -0.51, R) +>galGal2.chr17_rev/271-391 +GAGAAAGCGAAGCGGGCCCUGUCAUCCCAGCACCAAGCUAG----AAUUGAAAUAGAAUCCUUUUUUGAAGGAGAGGAUUUCUCUGAGACGCUUACUCGUGCCAAAUUUGAAGAACUGAA +(((.(((((.(((.((..(((......)))..))..)))..----..........(((((((((((....)))))))))))........))))).)))...................... ( -27.00, z-score = 0.10, R) +>fr1.chrUn_rev/271-391 +GAGAAGGCAAAGAGGGCCCUGUCUGCCCAGCACCAGGCCCG----CAUUGAGAUCGAGUCUUUCUUUGAGGGAGAAGAUUUCUCCGAGACACUGACCCGUGCCAAAUUUGAAGAGCUUAA +.....((((....((((..((((((((........))).((----....((((((...(((..(.....)..))).))))))..)))))))..).))).))))................. ( -33.20, z-score = -0.02, R) +>danRer1.chr11_rev/271-391 +GAGAAGGCUAAGAGAGCCCUGUCUGCCCAGCAUCAGGCCCG----CAUCGAGAUCGAGUCCUUCUUUGAGGGAGAAGAUUUCUCUGAGACUCUCACCAGAGCCAAGUUUGAAGAGCUCAA +((((.((((.....))))..(((((((........)))...----((..((((((...((((((...))))))...))))))..))))))))))....(((((.........).)))).. ( -33.30, z-score = 1.06, R) +>consensus +GAAAAGGCCAAGAGAGCCCUGUCUUCCCAGCAUCAAGCAAG____AAUUGAAAUUGAGUCCUUCUUUGAAGGAGAAGACUUCUCUGAGACCCUUACUCGGGCCAAAUUUGAAGAGCUGAA +.....((((....(((....((((((...((.....))....................((((((...))))))))))))..))).(((.......))).))))................. (-18.57 = -18.10 + -0.47)