annotate test-data/unknown.rnaz @ 0:273a961d332f draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty

############################  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)