Locus 1935

Sequence ID 3R_DroMel_CAF1
Location 5,462,765 – 5,462,874
Length 109
Max. P 0.927672
window3181 window3182

overview

Window 1

Location 5,462,765 – 5,462,874
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 89.05
Mean single sequence MFE -46.17
Consensus MFE -30.85
Energy contribution -32.60
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.67
SVM decision value 0.15
SVM RNA-class probability 0.605530
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5462765 109 + 27905053
AUGUGGAUGUGGAGGAGGCGGAUGCGGAUGCGGAGGAGGUGGCAUUCGUACUGGCCCCUGGCGCAGCAGAAUUGCUCCCGCUACUGGUACUGCUAUCACGUCCGCCCGA
..((((((((((((.((.(((.(((((((((.(......).))))))))))))(((..(((((.(((......)))..)))))..))).)).)).)))))))))).... ( -45.60)
>DroSec_CAF1 2712 103 + 1
AUGUGGAUGUGGAGGAGGCGGA------UGCGGAGGAGGUGGCAUUCGUACUGGCUCCUGCCGCAGCAGAAUUGCUCCCGCUGCUGUUGCUGCUAUCACGUCCGCCUGA
..(((((((((((((((.(((.------((((((.(......).))))))))).)))))((.(((((((....((....))..))))))).))..)))))))))).... ( -48.00)
>DroEre_CAF1 1968 97 + 1
AUGUGGAUGUGGAGGAGGCG------------GAGGAUGUGGCAUUCGUACUGGCUCCUGCCGCAGCAGAAUUGCUCCCGCUGCUGUUGCUGCUAUCACGUCCGCCCGA
..(((((((((((((((.((------------(.(((((...)))))...))).)))))((.(((((((....((....))..))))))).))..)))))))))).... ( -44.80)
>DroYak_CAF1 1413 97 + 1
AUGUGGAUGUGGAGGAGGCG------------GAGGUGGUGGCAUUCGUACUGGCUCCUGCCGCAGCAGAAUUGCUCCCGCUGCUGGUGCUGCUAUCACGUCCGCCGGA
................((((------------((.(((((((((...((((((((....)))(((((.((.....))..))))).)))))))))))))).))))))... ( -46.30)
>consensus
AUGUGGAUGUGGAGGAGGCG____________GAGGAGGUGGCAUUCGUACUGGCUCCUGCCGCAGCAGAAUUGCUCCCGCUGCUGGUGCUGCUAUCACGUCCGCCCGA
..(((((((((((((((.(((.............................))).)))))((.(((((((....((....))..))))))).))..)))))))))).... (-30.85 = -32.60 +   1.75)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,462,765 – 5,462,874
Length 109
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 89.05
Mean single sequence MFE -39.20
Consensus MFE -30.19
Energy contribution -30.62
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -2.44
Structure conservation index 0.77
SVM decision value 1.18
SVM RNA-class probability 0.927672
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5462765 109 - 27905053
UCGGGCGGACGUGAUAGCAGUACCAGUAGCGGGAGCAAUUCUGCUGCGCCAGGGGCCAGUACGAAUGCCACCUCCUCCGCAUCCGCAUCCGCCUCCUCCACAUCCACAU
..(((((((.(((((.((.......(((((((((....)))))))))...((((((..........))).))).....)))).))).)))))))............... ( -38.40)
>DroSec_CAF1 2712 103 - 1
UCAGGCGGACGUGAUAGCAGCAACAGCAGCGGGAGCAAUUCUGCUGCGGCAGGAGCCAGUACGAAUGCCACCUCCUCCGCA------UCCGCCUCCUCCACAUCCACAU
..(((((((.((....)).((....(((((((((....)))))))))((.(((((...(((....)))...))))))))).------)))))))............... ( -40.90)
>DroEre_CAF1 1968 97 - 1
UCGGGCGGACGUGAUAGCAGCAACAGCAGCGGGAGCAAUUCUGCUGCGGCAGGAGCCAGUACGAAUGCCACAUCCUC------------CGCCUCCUCCACAUCCACAU
..(((((((.(.(((.(..(((...(((((((((....)))))))))(((....)))........)))..)))))))------------)))))............... ( -37.70)
>DroYak_CAF1 1413 97 - 1
UCCGGCGGACGUGAUAGCAGCACCAGCAGCGGGAGCAAUUCUGCUGCGGCAGGAGCCAGUACGAAUGCCACCACCUC------------CGCCUCCUCCACAUCCACAU
...((((((.(((...(((......(((((((((....)))))))))(((....)))........)))...))).))------------))))................ ( -39.80)
>consensus
UCGGGCGGACGUGAUAGCAGCAACAGCAGCGGGAGCAAUUCUGCUGCGGCAGGAGCCAGUACGAAUGCCACCUCCUC____________CGCCUCCUCCACAUCCACAU
...((.(((.(((......((....(((((((((....))))))))).))(((((...(((....)))...))))).............))).))).)).......... (-30.19 = -30.62 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:17 2006