Locus 3422

Sequence ID 2R_DroMel_CAF1
Location 11,574,856 – 11,575,003
Length 147
Max. P 0.902559
window5582 window5583

overview

Window 2

Location 11,574,856 – 11,574,963
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.48
Mean single sequence MFE -48.90
Consensus MFE -33.66
Energy contribution -35.35
Covariance contribution 1.69
Combinations/Pair 1.09
Mean z-score -2.03
Structure conservation index 0.69
SVM decision value 0.99
SVM RNA-class probability 0.895725
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11574856 107 - 20766785
CAGUGGAGGCAUCGGCUUGGGCUUC------GGAUCGGGUUUGGUUAUCGGCCGGAAGGG-------CUGUUUGUCCGUCCGGUUUCGGAGGCGGAGUCCUAAACGAUGAGGCGGCUGGG
((((.(...(((((....(((((((------(..((.((..........(((((((.(((-------(.....)))).))))))))).))..))))))))....)))))...).)))).. ( -47.20)
>DroSec_CAF1 11298 102 - 1
CAGCGCAGGCAUC------------------GGAUCGGGCUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUCCGUUUUCGGAGGCGGAGUCCAAAACGAUGAGGCGGCUGGC
((((((...((((------------------(..(.((((((.((..((((.((((.((((..((....))..)))).))))...))))..)).)))))).)..)))))..)).)))).. ( -44.50)
>DroSim_CAF1 11599 114 - 1
CAGCGGAGGCAUCGGCUUGGGCUUC------GGAUCGGGCUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUCCGGUUUCGGAGGCGGAGUCCUAAACGAUGUGGCGGCUGGC
((((.(..((((((....(..(...------.)..)((((((.((..(((((((((.((((..((....))..)))).))))))..)))..)).))))))....))))))..).)))).. ( -52.50)
>DroEre_CAF1 11528 117 - 1
CAGUGGAGGCAUCGGCUUGGGCUUGGGCUUGGGCUUGGGUUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUCCGGUUGGGAAGGCGGAGUCCUAGGCGAUGAU---GCUUGG
......((((((((..(..(((....)))..)((((((((((.(((.(((((((((.((((..((....))..)))).)))))))))...))).))).)))))))..))))---)))).. ( -51.40)
>consensus
CAGCGGAGGCAUCGGCUUGGGCUUC______GGAUCGGGCUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUCCGGUUUCGGAGGCGGAGUCCUAAACGAUGAGGCGGCUGGC
((((.(...(((((((....))..............((((((.((..(((((((((.((((..((....))..)))).))))))..)))..)).))))))....)))))...).)))).. (-33.66 = -35.35 +   1.69)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,574,896 – 11,575,003
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.18
Mean single sequence MFE -41.18
Consensus MFE -28.58
Energy contribution -28.94
Covariance contribution 0.36
Combinations/Pair 1.13
Mean z-score -2.25
Structure conservation index 0.69
SVM decision value 1.03
SVM RNA-class probability 0.902559
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11574896 107 - 20766785
UAAAGCUAAAGCAAAGAGCUUGGGCAAACAGUAGAAGCAUCAGUGGAGGCAUCGGCUUGGGCUUC------GGAUCGGGUUUGGUUAUCGGCCGGAAGGG-------CUGUUUGUCCGUC
..(((((.........)))))(((((((((((.(((((...(((.((....)).)))...)))))------...((.((((........)))).))...)-------))))))))))... ( -38.80)
>DroSec_CAF1 11338 102 - 1
UAAAGCUAAAGCAAAGAGCUUGGGCAAACAGUAGAAGCAUCAGCGCAGGCAUC------------------GGAUCGGGCUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUC
..(((((.........)))))(((((((((((..((((...(((.(((((.((------------------(...))))))))))).....((....))))))...)))))))))))... ( -39.20)
>DroSim_CAF1 11639 114 - 1
UAAAGCUAAAGCAAAGAGCUUGGGCAAACAGUAGAAGCAUCAGCGGAGGCAUCGGCUUGGGCUUC------GGAUCGGGCUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUC
..(((((.........)))))(((((((((((..((((.....(((..((...((((((..(...------.)..))))))..))..))).((....))))))...)))))))))))... ( -46.00)
>DroEre_CAF1 11565 120 - 1
UAAAGCUAAAGCAAAGAGCUUGGGCAAACAGCAGACGCAUCAGUGGAGGCAUCGGCUUGGGCUUGGGCUUGGGCUUGGGUUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUC
..(((((.........)))))(((((((((((...(((....))).((((.((((.(..((((..(((....)))..))))..)...))))((....))))))...)))))))))))... ( -47.00)
>DroYak_CAF1 11706 105 - 1
UAAAGCUAAAGCAAAGAGCUUGGGCAAACAGUAGAAGCAUCAAUGGAGG---------------AGGCAUCGGCUUGGGUUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUC
..(((((.........)))))(((((((((((..(((((((((......---------------((((....))))....)))))......((....))))))...)))))))))))... ( -34.90)
>consensus
UAAAGCUAAAGCAAAGAGCUUGGGCAAACAGUAGAAGCAUCAGUGGAGGCAUCGGCUUGGGCUUC______GGAUCGGGUUUGGUUAUCGGCCGGAAGGGCUUACGGCUGUUUGUCCGUC
..(((((.........)))))(((((((((((..((((.((.((....))........................((.((((........)))).)).))))))...)))))))))))... (-28.58 = -28.94 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:05 2006