Locus 4601

Sequence ID X_DroMel_CAF1
Location 12,057,783 – 12,057,899
Length 116
Max. P 0.926107
window7563 window7564

overview

Window 3

Location 12,057,783 – 12,057,876
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 89.07
Mean single sequence MFE -27.90
Consensus MFE -21.26
Energy contribution -20.89
Covariance contribution -0.38
Combinations/Pair 1.21
Mean z-score -2.50
Structure conservation index 0.76
SVM decision value 1.17
SVM RNA-class probability 0.926107
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12057783 93 + 22224390
AUUGAAAUGGAAGGAGCGUAGGCUAAAAGCCCCAGGAGGUGGUGGAUGCCUAUGUUUUGGCAAUGAUAACUUAUCAACGAAGUCUAAGAACCU
.......((((.(((((((((((.....(((((....)).)))....))))))))))).....(((((...)))))......))))....... ( -24.30)
>DroSec_CAF1 89373 90 + 1
AUUGAAUUGGUAGGAGCGGAGGCUAAAAGCCCGAGGAGG---UGGAUGCCUCUGUUUUGGCCAUGAUAACUUAUCAACGAAGUCUAAGAACCU
.(((...((((..((((((((((.....(((......))---)....))))))))))..))))(((((...))))).)))............. ( -27.80)
>DroEre_CAF1 87045 90 + 1
AUUGAAAUGGUUAGAGCGGAGGCUAAAAGCCCCGGGAGU---UGGAUGCCUCUGUUUUGGCCAUGAUAACUUAUCAACAAAGUCUAAGAACCU
.(((..(((((((((((((((((....((((....).))---)....)))))))))))))))))((((...))))..)))............. ( -30.30)
>DroYak_CAF1 89268 88 + 1
AUUGAAAUGGAAGAAGCGGAGGCUAAAAGCCCCUGGAGG---UGGAUGCCUCCGUUUUGGCCAUAAUAACUUAUCAACGAAGUCUA--AACCU
......((((..(((((((((((......((((....))---.))..)))))))))))..))))......................--..... ( -29.20)
>consensus
AUUGAAAUGGAAGGAGCGGAGGCUAAAAGCCCCAGGAGG___UGGAUGCCUCUGUUUUGGCCAUGAUAACUUAUCAACGAAGUCUAAGAACCU
.(((...(((..(((((((((((.......((.....))........)))))))))))..)))(((((...))))).)))............. (-21.26 = -20.89 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,057,797 – 12,057,899
Length 102
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 89.77
Mean single sequence MFE -28.65
Consensus MFE -20.90
Energy contribution -21.21
Covariance contribution 0.31
Combinations/Pair 1.11
Mean z-score -1.94
Structure conservation index 0.73
SVM decision value 0.36
SVM RNA-class probability 0.705704
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12057797 102 + 22224390
AGCGUAGGCUAAAAGCCCCAGGAGGUGGUGGAUGCCUAUGUUUUGGCAAUGAUAACUUAUCAACGAAGUCUAAGAACCUGGCUUCUGACAUUCCAAGAAAA-A
.((((((((.....(((((....)).)))....))))))))(((((.((((........(((..((((((.........))))))))))))))))))....-. ( -29.10)
>DroSec_CAF1 89387 99 + 1
AGCGGAGGCUAAAAGCCCGAGGAGG---UGGAUGCCUCUGUUUUGGCCAUGAUAACUUAUCAACGAAGUCUAAGAACCUGGCUUCUGACAUGCCAAGAAAA-A
.((((((((.....(((......))---)....))))))))((((((..(((((...)))))..((((((.........))))))......))))))....-. ( -31.50)
>DroEre_CAF1 87059 98 + 1
AGCGGAGGCUAAAAGCCCCGGGAGU---UGGAUGCCUCUGUUUUGGCCAUGAUAACUUAUCAACAAAGUCUAAGAACCUGGCUUCUGACAUGCCAAGAAAA--
.((((((((....((((....).))---)....))))))))((((((..(((((...))))).(((((((.........))))).))....))))))....-- ( -27.50)
>DroYak_CAF1 89282 98 + 1
AGCGGAGGCUAAAAGCCCCUGGAGG---UGGAUGCCUCCGUUUUGGCCAUAAUAACUUAUCAACGAAGUCUA--AACCUGGCUUCUGACAUGAAAACAAAAAA
......((((((((.....((((((---(....)))))))))))))))................((((((..--.....)))))).................. ( -26.50)
>consensus
AGCGGAGGCUAAAAGCCCCAGGAGG___UGGAUGCCUCUGUUUUGGCCAUGAUAACUUAUCAACGAAGUCUAAGAACCUGGCUUCUGACAUGCCAAGAAAA_A
(((((((((.......((.....))........)))))))))((((.((((........(((..((((((.........)))))))))))))))))....... (-20.90 = -21.21 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:08 2006