Locus 4500

Sequence ID X_DroMel_CAF1
Location 11,886,612 – 11,886,724
Length 112
Max. P 0.915933
window7402 window7403

overview

Window 2

Location 11,886,612 – 11,886,724
Length 112
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 89.88
Mean single sequence MFE -40.87
Consensus MFE -32.33
Energy contribution -33.33
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.79
SVM decision value 0.34
SVM RNA-class probability 0.696527
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11886612 112 + 22224390
-----UCGACAUCACCGGCGGCUGACGGACCAGAAAAUAAGCAUCCUGGCUCAUUCCACGACGCUCCUGGCCACUCCACCUGGCUUGUCCGACUGUUCACCGCCGCUGAUGUUGAUG
-----(((((((((.((((((.((((((((.........(((.((.(((......))).)).)))...(((((.......))))).))))).....))))))))).))))))))).. ( -44.80)
>DroSec_CAF1 18504 114 + 1
ACCACUCGACAUCACCGGCGGCUGACGGACCAGAAAAUAAGCAUCCUGGCUCAUUACGCGACGCUCCGGCACACUCCACCUGGCUUGUCGGACUGUUCACCGCCGCUGAUAGUG---
..((((....((((.((((((.(((.(..((((............))))..)........(((.(((((((....((....))..))))))).)))))))))))).))))))))--- ( -37.60)
>DroYak_CAF1 22591 112 + 1
-----UCGACAUCACCGGCGGCUGACGGACCAGAAAAUAAGCAUCCUGGCUCAUUCCACGACGCUCCUGGCCACUCCACCUGGCUUGUCCGACUGCUCACCGCCGCUGAUGCUGAUG
-----(((.(((((.((((((.((((((((.........(((.((.(((......))).)).)))...(((((.......))))).))))).....))))))))).))))).))).. ( -40.20)
>consensus
_____UCGACAUCACCGGCGGCUGACGGACCAGAAAAUAAGCAUCCUGGCUCAUUCCACGACGCUCCUGGCCACUCCACCUGGCUUGUCCGACUGUUCACCGCCGCUGAUGCUGAUG
.....(((.(((((.((((((.((((((.((((............))))..........((((..((.((........)).))..))))...))).))))))))).))))).))).. (-32.33 = -33.33 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,886,612 – 11,886,724
Length 112
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 89.88
Mean single sequence MFE -50.57
Consensus MFE -43.25
Energy contribution -44.03
Covariance contribution 0.78
Combinations/Pair 1.08
Mean z-score -2.65
Structure conservation index 0.86
SVM decision value 1.10
SVM RNA-class probability 0.915933
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11886612 112 - 22224390
CAUCAACAUCAGCGGCGGUGAACAGUCGGACAAGCCAGGUGGAGUGGCCAGGAGCGUCGUGGAAUGAGCCAGGAUGCUUAUUUUCUGGUCCGUCAGCCGCCGGUGAUGUCGA-----
..((.((((((.(((((((.....(.(((((..((((.......))))((((((((((.(((......))).))))))).....)))))))).).))))))).)))))).))----- ( -53.50)
>DroSec_CAF1 18504 114 - 1
---CACUAUCAGCGGCGGUGAACAGUCCGACAAGCCAGGUGGAGUGUGCCGGAGCGUCGCGUAAUGAGCCAGGAUGCUUAUUUUCUGGUCCGUCAGCCGCCGGUGAUGUCGAGUGGU
---((((((((.(((((((..((..(((((((..((....))..)))..))))............(..((((((........))))))..)))..))))))).))))....)))).. ( -44.40)
>DroYak_CAF1 22591 112 - 1
CAUCAGCAUCAGCGGCGGUGAGCAGUCGGACAAGCCAGGUGGAGUGGCCAGGAGCGUCGUGGAAUGAGCCAGGAUGCUUAUUUUCUGGUCCGUCAGCCGCCGGUGAUGUCGA-----
..((.((((((.(((((((.....(.(((((..((((.......))))((((((((((.(((......))).))))))).....)))))))).).))))))).)))))).))----- ( -53.80)
>consensus
CAUCAACAUCAGCGGCGGUGAACAGUCGGACAAGCCAGGUGGAGUGGCCAGGAGCGUCGUGGAAUGAGCCAGGAUGCUUAUUUUCUGGUCCGUCAGCCGCCGGUGAUGUCGA_____
...(.((((((.(((((((..((.((((((((..((....))..)).....(((((((.(((......))).)))))))....))))).).))..))))))).)))))).)...... (-43.25 = -44.03 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:41 2006