Locus 3412

Sequence ID X_DroMel_CAF1
Location 9,127,734 – 9,127,862
Length 128
Max. P 0.978580
window5579 window5580

overview

Window 9

Location 9,127,734 – 9,127,829
Length 95
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -26.02
Consensus MFE -24.08
Energy contribution -24.07
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.93
SVM decision value 0.41
SVM RNA-class probability 0.726670
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9127734 95 - 22224390
CAAUUGGGAUUUGUGAUUAGGC-GAAGCGCAGUCUUUUGUCCUGUUCUAAAAAUAGAACUACGCAUUAGGCACAACGCACACAUGAGCGCCCAAAA
...(((((..(((((.((((((-(.((.((((....)))).))((((((....))))))..))).)))).)))))(((........)))))))).. ( -26.50)
>DroSec_CAF1 3562 95 - 1
CAAUUGGGAUUUGUGAUUAGGC-GAAGCGCAGUCUUUUGUCCCGUUCUAAAAAUAGAACUACGCAUUAGGCACAACGCACACAUGAGCGCCCAAAA
...(((((...((((.....((-(...))).((((..(((...((((((....))))))...)))..))))........))))......))))).. ( -25.30)
>DroEre_CAF1 3551 96 - 1
CAAUUGGGAUUUGUGAUUAGGCUGAAGCGCAGUCUUUUGUCCCGUUCUAAAAAUAGAACAGCGCAUUAGGCACAACGCACACAUGAGCGCCCAAAA
...(((((...........(.((((.((((.(.(....).)..((((((....)))))).)))).)))).)....(((........)))))))).. ( -27.00)
>DroYak_CAF1 3629 96 - 1
CAAUUGGGAUUUGUGAUUAGGCUGAAGCGCAGUCUUUUGUACCGUUCUAAAAAUAGAACUACGCAUUAGGCACAACGCACACAUGAGCGCCCAAAA
...(((((..(((((...((((((.....))))))..(((...((((((....))))))...))).....)))))(((........)))))))).. ( -25.30)
>consensus
CAAUUGGGAUUUGUGAUUAGGC_GAAGCGCAGUCUUUUGUCCCGUUCUAAAAAUAGAACUACGCAUUAGGCACAACGCACACAUGAGCGCCCAAAA
...(((((...((((.....((......)).((((..(((...((((((....))))))...)))..))))........))))......))))).. (-24.08 = -24.07 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 9,127,757 – 9,127,862
Length 105
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 88.99
Mean single sequence MFE -34.67
Consensus MFE -28.60
Energy contribution -29.73
Covariance contribution 1.12
Combinations/Pair 1.04
Mean z-score -2.67
Structure conservation index 0.82
SVM decision value 1.82
SVM RNA-class probability 0.978580
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9127757 105 - 22224390
AAUGGGCGUUUUGCCCGU--CCACCCCACCCACUCCAAUUGGGAUUUGUGAUUAGGC-GAAGCGCAGUCUUUUGUCCUGUUCUAAAAAUAGAACUACGCAUUAGGCAC
.....((((((((((.(.--.(((....((((.......))))....)))..).)))-))))))).((((..(((...((((((....))))))...)))..)))).. ( -37.50)
>DroSec_CAF1 3585 107 - 1
AAUGGGCGUUUUGGCCGCCACCACCCCACCCACUCCAAUUGGGAUUUGUGAUUAGGC-GAAGCGCAGUCUUUUGUCCCGUUCUAAAAAUAGAACUACGCAUUAGGCAC
.....((((((((.((.....(((....((((.......))))....)))....)))-))))))).((((..(((...((((((....))))))...)))..)))).. ( -33.00)
>DroEre_CAF1 3574 97 - 1
AAUGGGCCUUUUGGCCGC-----------CCACUCCAAUUGGGAUUUGUGAUUAGGCUGAAGCGCAGUCUUUUGUCCCGUUCUAAAAAUAGAACAGCGCAUUAGGCAC
....((((....))))((-----------(..........(((((........((((((.....))))))...)))))((((((....)))))).........))).. ( -31.80)
>DroYak_CAF1 3652 108 - 1
AAUGGGCGUUUUGGCCGACCCACCCCCCUCCACUCCAAUUGGGAUUUGUGAUUAGGCUGAAGCGCAGUCUUUUGUACCGUUCUAAAAAUAGAACUACGCAUUAGGCAC
.....((((((..(((....(((..(((............)))....)))....)))..)))))).((((..(((...((((((....))))))...)))..)))).. ( -36.40)
>consensus
AAUGGGCGUUUUGGCCGC__CCACCCCACCCACUCCAAUUGGGAUUUGUGAUUAGGC_GAAGCGCAGUCUUUUGUCCCGUUCUAAAAAUAGAACUACGCAUUAGGCAC
.....(((((((((((............((((.......))))...........))))))))))).((((..(((...((((((....))))))...)))..)))).. (-28.60 = -29.73 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:42 2006