Locus 5382

Sequence ID 3R_DroMel_CAF1
Location 14,140,493 – 14,140,613
Length 120
Max. P 0.643735
window8768 window8769

overview

Window 8

Location 14,140,493 – 14,140,583
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 84.90
Mean single sequence MFE -29.78
Consensus MFE -18.62
Energy contribution -20.66
Covariance contribution 2.04
Combinations/Pair 1.23
Mean z-score -2.14
Structure conservation index 0.63
SVM decision value 0.23
SVM RNA-class probability 0.643735
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14140493 90 + 27905053
GCUGGGCGUUUGUUUACAAUCCGGCUGUGGCAGAGGUGAAAGCCAUGCUCGCCAAGCUUUCUCAUUUUCUCACAGGUGUCUUGAAAGCUU
((((((...(((....))))))))).((((((..(((....))).))).))).((((((((.(((((......)))))....)))))))) ( -28.80)
>DroSec_CAF1 12701 89 + 1
GCUGGGCGUUUGUUUACAAUC-GGCGGUGGCAAAAGCGAAAGCCAUGCUCGCCAAGCUUUCUCACUUUCUCACAGGUGUCUUGAAAGCUU
(((((..((......))..))-)))(((((((...((....))..))).))))((((((((.(((((......)))))....)))))))) ( -33.10)
>DroSim_CAF1 13006 89 + 1
GCUGGGCGUUUGUUUACAAUC-GGCGGUGGCAGAGGCGAAAGCCAUGCUCGCCAAGCUUUCUCACUUUCUCACAGGUGUCUUGAAAGCUU
(((((..((......))..))-)))(((((((..(((....))).))).))))((((((((.(((((......)))))....)))))))) ( -37.60)
>DroEre_CAF1 13236 89 + 1
GCUGGGCGUUUGUUUACAAUC-GGCGGUGGAAGAGGUGAAAGCCAUGCUCGCCAAGCUUUCUCACUUUCUCACAGGUGUCUUGAAAGCUU
(((((..((......))..))-)))(((((..(.(((....))).)..)))))((((((((.(((((......)))))....)))))))) ( -29.90)
>DroAna_CAF1 12502 77 + 1
UUUGGGCGUUUGUUUACAU-----CAGAGGCAUAGGUGAAAGCCGCUGUUGCUGAGCUUU--------CUCACAGGUGUUUUAAAAGCUU
...((((.((((...((((-----(((..(((..(((....)))..)))..))(((....--------)))...)))))..)))).)))) ( -19.50)
>consensus
GCUGGGCGUUUGUUUACAAUC_GGCGGUGGCAGAGGUGAAAGCCAUGCUCGCCAAGCUUUCUCACUUUCUCACAGGUGUCUUGAAAGCUU
....((((((((((..............))))))(((....))).....))))((((((((.(((((......)))))....)))))))) (-18.62 = -20.66 +   2.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,140,512 – 14,140,613
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 80.88
Mean single sequence MFE -33.14
Consensus MFE -20.82
Energy contribution -24.54
Covariance contribution 3.72
Combinations/Pair 1.15
Mean z-score -1.73
Structure conservation index 0.63
SVM decision value 0.09
SVM RNA-class probability 0.577145
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14140512 101 + 27905053
UCCGGCUGUGGCAGAGGUGAAAGCCAUGCUCGCCAAGCUUUCUCAUUUUCUCACAGGUGUCUUGAAAGCUUGGGAGUUGUAACGAAGAGAAGCGGCCCACU
...((((((..(...(((....)))..((((.((((((((((.(((((......)))))....))))))))))))))...........)..)))))).... ( -38.10)
>DroSec_CAF1 12720 100 + 1
UC-GGCGGUGGCAAAAGCGAAAGCCAUGCUCGCCAAGCUUUCUCACUUUCUCACAGGUGUCUUGAAAGCUUGGGAGUUGUAACGAAGAGAAGCGGCACACU
..-(((..(.((....)).)..)))..((((.((((((((((.(((((......)))))....))))))))))))))(((..((........))..))).. ( -35.90)
>DroSim_CAF1 13025 100 + 1
UC-GGCGGUGGCAGAGGCGAAAGCCAUGCUCGCCAAGCUUUCUCACUUUCUCACAGGUGUCUUGAAAGCUUGGGAGUUGUAACGAAGAGAAGCGGCACACU
..-.((.((..(...(((....)))..((((.((((((((((.(((((......)))))....))))))))))))))...........)..)).))..... ( -39.00)
>DroEre_CAF1 13255 100 + 1
UC-GGCGGUGGAAGAGGUGAAAGCCAUGCUCGCCAAGCUUUCUCACUUUCUCACAGGUGUCUUGAAAGCUUCGGAGUUGUAACGAAGAGAAACGGACCACU
..-...(((((....(((....)))..((((.(.((((((((.(((((......)))))....)))))))).)))))...................))))) ( -29.10)
>DroAna_CAF1 12521 88 + 1
-----CAGAGGCAUAGGUGAAAGCCGCUGUUGCUGAGCUUU--------CUCACAGGUGUUUUAAAAGCUUCCGAGUUUUAAUACGGAGAGGCAAGUGAAU
-----(((..(((..(((....)))..)))..))).((((.--------(((....(((((...((((((....))))))))))).)))))))........ ( -23.60)
>consensus
UC_GGCGGUGGCAGAGGUGAAAGCCAUGCUCGCCAAGCUUUCUCACUUUCUCACAGGUGUCUUGAAAGCUUGGGAGUUGUAACGAAGAGAAGCGGCACACU
.......((.((...(((....)))..((((.((((((((((.(((((......)))))....))))))))))))))..............)).))..... (-20.82 = -24.54 +   3.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:24 2006