Locus 8727

Sequence ID 3L_DroMel_CAF1
Location 22,733,755 – 22,733,952
Length 197
Max. P 0.955151
window14292 window14293 window14294

overview

Window 2

Location 22,733,755 – 22,733,872
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.62
Mean single sequence MFE -47.38
Consensus MFE -41.43
Energy contribution -41.65
Covariance contribution 0.22
Combinations/Pair 1.03
Mean z-score -1.55
Structure conservation index 0.87
SVM decision value 0.45
SVM RNA-class probability 0.743051
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22733755 117 + 23771897
GUA---AGUUAUCUGUAUCUGUCGCUCGCCUUGGUGGGUGCGCACAUGCUGAUUGAGGAUGGCUUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUG
...---....(((.((((.((((((((((....))))))).))).)))).)))((((((.(.(((((..((....))(((((((.(....).)))))))))))).)))))))........ ( -46.60)
>DroVir_CAF1 13740 114 + 1
UGG---AUGUGU---UAACUGUCGCUCGCCUUGGUGGGUGCGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUG
.((---((((((---.....(.(((((((....))))))))))))))......((((((.(.(((((..((....))(((((((.(....).)))))))))))).))))))).))..... ( -48.70)
>DroGri_CAF1 13731 114 + 1
UGG---AUGUGU---UAACUGUCGCUCGCCUUGGUGGGUGCGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUG
.((---((((((---.....(.(((((((....))))))))))))))......((((((.(.(((((..((....))(((((((.(....).)))))))))))).))))))).))..... ( -48.70)
>DroWil_CAF1 17790 110 + 1
UUA---AGUUGUC-------GUCGCUCGCCUUGGUGGGUGCGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUG
...---(((((((-------(.(((((((....))))))))).))).)))...((((((.(.(((((..((....))(((((((.(....).)))))))))))).)))))))........ ( -48.00)
>DroMoj_CAF1 14517 114 + 1
UGG---AUGUGU---UAACUGUCGCUCGCCUUGGUGGGUGCGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUG
.((---((((((---.....(.(((((((....))))))))))))))......((((((.(.(((((..((....))(((((((.(....).)))))))))))).))))))).))..... ( -48.70)
>DroAna_CAF1 11737 119 + 1
GGAAGAAGUUAUCUAAAUCUGUCGCUCGCCUUGGUGGGUGCGCACAUGCUGAUUGAAGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAAGGCUUCUCACCC-AAUG
((.((((((.........((.((((..(((((((((((((.((((.((((....((((.....)))).))))...)))).)))).))).))))))..)))).))))))))...))-.... ( -43.60)
>consensus
UGA___AGGUGU___UAACUGUCGCUCGCCUUGGUGGGUGCGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUG
....................(.(((((((....))))))))((....))....((((((.(.(((((..((....))(((((((.(....).)))))))))))).)))))))........ (-41.43 = -41.65 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 22,733,792 – 22,733,912
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.28
Mean single sequence MFE -47.00
Consensus MFE -43.99
Energy contribution -44.68
Covariance contribution 0.69
Combinations/Pair 1.06
Mean z-score -1.14
Structure conservation index 0.94
SVM decision value 0.73
SVM RNA-class probability 0.835998
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22733792 120 + 23771897
CGCACAUGCUGAUUGAGGAUGGCUUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGGUUGAGAAUGGCGCGCUGCCGAAAA
.((((((((....((((((.(.(((((..((....))(((((((.(....).)))))))))))).))))))).((....))....))))))))..........((((.....)))).... ( -47.00)
>DroGri_CAF1 13765 120 + 1
CGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGAUUGAGUAUCGCGCGCUGCCGGAAA
.((((((((....((((((.(.(((((..((....))(((((((.(....).)))))))))))).))))))).((....))....))))))))..........(((.((...)))))... ( -47.20)
>DroSim_CAF1 11674 120 + 1
CGCACAUGCUGAUUGAGGAUGGCUUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGAUUGAGAAUGGCGCGCUGCCGAAAG
.((((((((....((((((.(.(((((..((....))(((((((.(....).)))))))))))).))))))).((....))....))))))))..........((((.....)))).... ( -47.00)
>DroWil_CAF1 17820 120 + 1
CGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUAUGCUGAUUGAGUAUGGCUCGCUGUCGAAAG
....(((..((..((((((.(.(((((..((....))(((((((.(....).)))))))))))).)))))))..)).)))((((((..((((((.....))))))...))).)))..... ( -45.60)
>DroMoj_CAF1 14551 120 + 1
CGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGAUUGAGUAUGGCUCGCUGCCGGAAG
.((((((((....((((((.(.(((((..((....))(((((((.(....).)))))))))))).))))))).((....))....))))))))..........((((.....)))).... ( -50.60)
>DroAna_CAF1 11777 118 + 1
CGCACAUGCUGAUUGAAGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAAGGCUUCUCACCC-AAUGGGAGCGUA-AUGCUGGUUAAGAAUGGCGCGCUGCCGGAAG
.((.(((.((......)))))))((((((((.....((((((((.(....).))))))))...(((.(((((...-..)))))((((.-...((.....))....))))))))))))))) ( -44.60)
>consensus
CGCACAUGCUGAUUGAGGAUGGCCUUCUGGCGAAAGUGCUUGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGAUUGAGAAUGGCGCGCUGCCGAAAG
.((((((((....((((((.(.(((((..((....))(((((((.(....).)))))))))))).)))))))((.....))....))))))))..........((((.....)))).... (-43.99 = -44.68 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 22,733,832 – 22,733,952
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.50
Mean single sequence MFE -50.91
Consensus MFE -45.97
Energy contribution -46.42
Covariance contribution 0.45
Combinations/Pair 1.15
Mean z-score -1.75
Structure conservation index 0.90
SVM decision value 1.45
SVM RNA-class probability 0.955151
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22733832 120 + 23771897
UGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGGUUGAGAAUGGCGCGCUGCCGAAAACUGCGCGAGCAGUAUGGGCAGGUGAAGGGCUUUUCGUUGG
((((.(....).))))(((((((((((..(((((...............((((((........))))))..((((.(..(((((....))))).).)))))))))..))))))))))).. ( -52.50)
>DroVir_CAF1 13814 120 + 1
UGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGGUUGAGUAUGGCGCGCUGCCGGAAGCUGCGCGAGCAGUACGGGCAGGUGAAUGGCUUUUCGUUUG
.(((.(....).)))((((((((((((..(((((.........((((.((((((.....))))))..))))((((.(..(((((....))))).).)))))))))..)))))))))))). ( -54.90)
>DroGri_CAF1 13805 120 + 1
UGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGAUUGAGUAUCGCGCGCUGCCGGAAACUGCGCGAGCAGUACGGACACGUGAAUGGCUUUUCGUUAG
((((.(....).))))(((((((((((..(((((((..(((..(((..((((((.....)))).))..)))..)))...(((((....))))).)))....))))..))))))))))).. ( -49.50)
>DroWil_CAF1 17860 120 + 1
UGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUAUGCUGAUUGAGUAUGGCUCGCUGUCGAAAGCUGCGCGAACAGUACGGGCAGGUGAAGGGCUUUUCGUUGG
((((.(....).))))(((((((((((..(((((((..((..((((((((((((.....))))))....(((......)))))))))..))...))))....)))..))))))))))).. ( -47.00)
>DroMoj_CAF1 14591 120 + 1
UGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGAUUGAGUAUGGCUCGCUGCCGGAAGCUGCGCGAGCAGUACGGGCAGGUGAAUGGCUUUUCGUUGG
((((.(....).))))(((((((((((..(((((.........(((..((((((.....))))))...)))((((.(..(((((....))))).).)))))))))..))))))))))).. ( -53.40)
>DroAna_CAF1 11817 118 + 1
UGCCGCACUCGGGGCAGGCGAAAGGCUUCUCACCC-AAUGGGAGCGUA-AUGCUGGUUAAGAAUGGCGCGCUGCCGGAAGCUGCGCGAACAGUACGGGCAGGUGAAGGGUUUUUCGUUGG
((((.(....).))))(((((((((((..(((((.-.(((....))).-.((((.((.........(((((.(.(....)).)))))......)).)))))))))..))))))))))).. ( -48.16)
>consensus
UGCCGCACUCGGGGCAGGCGAAGGGCUUCUCACCCGAAUGGAUGCGUAUGUGCUGAUUGAGUAUGGCGCGCUGCCGGAAGCUGCGCGAGCAGUACGGGCAGGUGAAGGGCUUUUCGUUGG
((((.(....).))))(((((((((((..(((((.........(((..((((((.....))))))...)))((((.(..(((((....))))).).)))))))))..))))))))))).. (-45.97 = -46.42 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:12 2006