Locus 1939

Sequence ID 2R_DroMel_CAF1
Location 7,317,519 – 7,317,610
Length 91
Max. P 0.980420
window3204 window3205

overview

Window 4

Location 7,317,519 – 7,317,610
Length 91
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 93.92
Mean single sequence MFE -27.30
Consensus MFE -20.50
Energy contribution -20.90
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.75
SVM decision value 0.82
SVM RNA-class probability 0.859484
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7317519 91 + 20766785
UGUUGCAACUGCAAGCUGCAACUG-------CAAAUGCCACAGGCGAGUGUUAACGUAUACCCAUUAAAUGGGAUACCGAAAGGCGUAAACAAGUGAC
..(((((..(((.....)))..))-------))).((((...))))..((((.(((....(((((...)))))...((....))))).))))...... ( -25.00)
>DroSec_CAF1 113098 91 + 1
UGUUGCAACUGCAAGCUGCAACUG-------CAAAUGCCACAGACGAGUGUUAACGUAUACCCAUUAAAUGGGAUACCGAAAGGCGUAAACAAGUGAC
..(((((..(((.....)))..))-------)))..........((..((((.(((....(((((...)))))...((....))))).))))..)).. ( -24.20)
>DroSim_CAF1 117561 91 + 1
UGUUGCAACUGCAAGCUGCAACUG-------CAAAUGCCACAGUCGAGUGUUAACGUAUACCCAUUAAAUGGGAUACCGAAAGGCGUAAACAAGUGAC
..(((((..(((.....)))..))-------)))........((((..((((.(((....(((((...)))))...((....))))).))))..)))) ( -27.40)
>DroEre_CAF1 113141 98 + 1
UGUUGCAACUGCAAGCUGCAACUGCAAGCUGCAACUGCCGCAGAGGAGUGUUAACGUAUACCCAUUAAAUGGUAUACCGAAAGGCGUAAACAAGUGAC
.((..(..((((.((((((....)).))))((....)).)))).....((((.(((((((((........))))))((....))))).)))).)..)) ( -29.60)
>DroYak_CAF1 116089 91 + 1
UGUUGCAACUGCAAGCUGCAACUG-------CAACUGCCUCAGUCGAGUGUUAACGUAUACCCAUUAAAUGGGAUACCGAAAGGCGUAAACAAGUGAC
.((((((..(((.....)))..))-------)))).......((((..((((.(((....(((((...)))))...((....))))).))))..)))) ( -30.30)
>consensus
UGUUGCAACUGCAAGCUGCAACUG_______CAAAUGCCACAGACGAGUGUUAACGUAUACCCAUUAAAUGGGAUACCGAAAGGCGUAAACAAGUGAC
.((((((.(.....).))))))......................((..((((.(((....(((((...)))))...((....))))).))))..)).. (-20.50 = -20.90 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,317,519 – 7,317,610
Length 91
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 93.92
Mean single sequence MFE -28.28
Consensus MFE -22.68
Energy contribution -23.28
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.80
SVM decision value 1.86
SVM RNA-class probability 0.980420
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7317519 91 - 20766785
GUCACUUGUUUACGCCUUUCGGUAUCCCAUUUAAUGGGUAUACGUUAACACUCGCCUGUGGCAUUUG-------CAGUUGCAGCUUGCAGUUGCAACA
(((((..((...((.....))(((((((((...))))).))))..........))..))))).....-------..((((((((.....)))))))). ( -26.70)
>DroSec_CAF1 113098 91 - 1
GUCACUUGUUUACGCCUUUCGGUAUCCCAUUUAAUGGGUAUACGUUAACACUCGUCUGUGGCAUUUG-------CAGUUGCAGCUUGCAGUUGCAACA
......(((..(.(((.....(((((((((...))))).))))....(((......)))))).)..)-------))((((((((.....)))))))). ( -26.10)
>DroSim_CAF1 117561 91 - 1
GUCACUUGUUUACGCCUUUCGGUAUCCCAUUUAAUGGGUAUACGUUAACACUCGACUGUGGCAUUUG-------CAGUUGCAGCUUGCAGUUGCAACA
(((((..(((..((.....))(((((((((...))))).))))..........))).))))).....-------..((((((((.....)))))))). ( -27.00)
>DroEre_CAF1 113141 98 - 1
GUCACUUGUUUACGCCUUUCGGUAUACCAUUUAAUGGGUAUACGUUAACACUCCUCUGCGGCAGUUGCAGCUUGCAGUUGCAGCUUGCAGUUGCAACA
.............(((.....(((((((........)))))))((............))))).(((((((((.(((((....)).)))))))))))). ( -30.50)
>DroYak_CAF1 116089 91 - 1
GUCACUUGUUUACGCCUUUCGGUAUCCCAUUUAAUGGGUAUACGUUAACACUCGACUGAGGCAGUUG-------CAGUUGCAGCUUGCAGUUGCAACA
.............(((((((((((((((((...))))).))))(....)...)))..))))).((((-------((..(((.....)))..)))))). ( -31.10)
>consensus
GUCACUUGUUUACGCCUUUCGGUAUCCCAUUUAAUGGGUAUACGUUAACACUCGACUGUGGCAUUUG_______CAGUUGCAGCUUGCAGUUGCAACA
(((((.((((.(((((....)))..(((((...))))).....)).)))).......)))))..............((((((((.....)))))))). (-22.68 = -23.28 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:49 2006