Locus 3012

Sequence ID 2L_DroMel_CAF1
Location 8,606,250 – 8,606,360
Length 110
Max. P 0.927065
window4793 window4794

overview

Window 3

Location 8,606,250 – 8,606,360
Length 110
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 84.30
Mean single sequence MFE -29.08
Consensus MFE -24.26
Energy contribution -25.30
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -2.02
Structure conservation index 0.83
SVM decision value 1.18
SVM RNA-class probability 0.927065
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8606250 110 + 22407834
UUGCCACUGAUAGUGCUCCGGCUUCCAUUGCACUUGG-UUGGAUUUCCAUUUUUU------GUUCGUAGUGUUUUUUGGUGGCGAAACUUAUUCGCAGCUGUGCAAAUUUGUGCAGC
(((((((..(.((..((.(((...(((.......)))-.(((....)))......------..))).))..))..)..)))))))............((((..((....))..)))) ( -32.40)
>DroSec_CAF1 34605 108 + 1
UUGCCACUGAUAGUGCUCCGGCUUCCAUUGCACUUAG-UUGGAUUUCCAUUUUUU-------UUCGUCCUGUUU-UUGGUGGCGAAACUUUUUCGCAGCUGUGCAAAUUUGUGCAGC
(((((((..(.(((((...((...))...)))))...-.(((....)))......-------............-)..)))))))............((((..((....))..)))) ( -30.80)
>DroSim_CAF1 40296 109 + 1
UUGCCACUGAUAGUGCUCCGGCUUCCAUUGCACUUGG-UUGGAUUUCCAUUUUUU------GUUCGUCCUGUUU-UUGGUGGCGAAACUUUUUCGCAGCUGUGCAAAUUUGUGCAGC
(((((((..(.(((((...((...))...)))))...-..((((...((.....)------)...)))).....-)..)))))))............((((..((....))..)))) ( -31.80)
>DroYak_CAF1 36988 115 + 1
UUGCCAGUGAUAGUGCUCGGGCUUCCAUUGCACUUGC-UUGGAUUUCCAUUUUUUAUUUUUUUUCAUCCUGUUU-UUGGUGGCGAAACUUUUUUGCAGCUGUGCAAAUUUGUGCAGC
..(((((.(((((.....(((..((((..((....))-.))))..)))((.....))...........))))).-))))).(((((.....))))).((((..((....))..)))) ( -29.20)
>DroAna_CAF1 35784 115 + 1
UUGCCCCUGAUAGCGCACGGGUUUCCAUUCCUCCUAUAUUUUUUUUCUAUUUUCCAUUUUUUUUGUUUUUACGU-UUGGUGGCAAAACUU-UUCGCAGCUGUGCAAAUUUGUGCAGC
(((((((....((((...(((.......))).......................((.......))......)))-).)).))))).....-......((((..((....))..)))) ( -21.20)
>consensus
UUGCCACUGAUAGUGCUCCGGCUUCCAUUGCACUUGG_UUGGAUUUCCAUUUUUU______GUUCGUCCUGUUU_UUGGUGGCGAAACUUUUUCGCAGCUGUGCAAAUUUGUGCAGC
((((((((((..((((...((...))...))))......(((....)))..........................))))))))))............((((..((....))..)))) (-24.26 = -25.30 +   1.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,606,250 – 8,606,360
Length 110
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 84.30
Mean single sequence MFE -23.62
Consensus MFE -17.26
Energy contribution -18.70
Covariance contribution 1.44
Combinations/Pair 1.05
Mean z-score -1.83
Structure conservation index 0.73
SVM decision value 0.42
SVM RNA-class probability 0.730885
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8606250 110 - 22407834
GCUGCACAAAUUUGCACAGCUGCGAAUAAGUUUCGCCACCAAAAAACACUACGAAC------AAAAAAUGGAAAUCCAA-CCAAGUGCAAUGGAAGCCGGAGCACUAUCAGUGGCAA
((((..((....))..))))...(((.....)))(((((.................------......(((....))).-...(((((..(((...)))..)))))....))))).. ( -25.80)
>DroSec_CAF1 34605 108 - 1
GCUGCACAAAUUUGCACAGCUGCGAAAAAGUUUCGCCACCAA-AAACAGGACGAA-------AAAAAAUGGAAAUCCAA-CUAAGUGCAAUGGAAGCCGGAGCACUAUCAGUGGCAA
((..(.....((((((....))))))....(((((((.....-.....)).))))-------).....(((....))).-...(((((..(((...)))..)))))....)..)).. ( -26.30)
>DroSim_CAF1 40296 109 - 1
GCUGCACAAAUUUGCACAGCUGCGAAAAAGUUUCGCCACCAA-AAACAGGACGAAC------AAAAAAUGGAAAUCCAA-CCAAGUGCAAUGGAAGCCGGAGCACUAUCAGUGGCAA
((..(.....((((((....))))))...(((.((((.....-.....)).)))))------......(((....))).-...(((((..(((...)))..)))))....)..)).. ( -25.20)
>DroYak_CAF1 36988 115 - 1
GCUGCACAAAUUUGCACAGCUGCAAAAAAGUUUCGCCACCAA-AAACAGGAUGAAAAAAAAUAAAAAAUGGAAAUCCAA-GCAAGUGCAAUGGAAGCCCGAGCACUAUCACUGGCAA
((((((......))))(((.(((.......(((((((.....-.....)).)))))............(((....))).-)))(((((..(((....))).)))))....))))).. ( -23.00)
>DroAna_CAF1 35784 115 - 1
GCUGCACAAAUUUGCACAGCUGCGAA-AAGUUUUGCCACCAA-ACGUAAAAACAAAAAAAAUGGAAAAUAGAAAAAAAAUAUAGGAGGAAUGGAAACCCGUGCGCUAUCAGGGGCAA
((((..((....))..))))......-.....(((((.((..-..((....))..............................((.((.((((....))))...)).)).))))))) ( -17.80)
>consensus
GCUGCACAAAUUUGCACAGCUGCGAAAAAGUUUCGCCACCAA_AAACAGGACGAAA______AAAAAAUGGAAAUCCAA_CCAAGUGCAAUGGAAGCCGGAGCACUAUCAGUGGCAA
((((..((....))..))))..............(((((.............................(((....))).....(((((..(((...)))..)))))....))))).. (-17.26 = -18.70 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:09 2006