Locus 7987

Sequence ID	X_DroMel_CAF1
Location	19,881,806 – 19,881,964
Length	158
Max. P	0.569450

overview

Window 2

Location	19,881,806 – 19,881,926
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.78
Mean single sequence MFE	-29.89
Consensus MFE	-20.90
Energy contribution	-21.78
Covariance contribution	0.88
Combinations/Pair	1.16
Mean z-score	-1.45
Structure conservation index	0.70
SVM decision value	-0.05
SVM RNA-class probability	0.506137
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19881806 120 - 22224390
GGCAAUAAAAAUGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUACCGAACGAUGUCCGGCAGGAGUUUUAGAAAUAUGCAAAGUGUUUCAGGACGAACAGAAACCGGAAUCUCUGUAUCG
((((((((.....)))).))))(((....)))((..(((((((.(((.......(((....)))(((((.(((((((.....))))))))))))..........))).)))))))..)). ( -33.90)
>DroSec_CAF1 35563 120 - 1
GGCAAUAAAAAUGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUACCGAACGAUGUCCGGCAGGAAUUUUAGAAAUAUGCAAAGUGUUUCAGGACGAACAGAAGCCGGAAUCUCUGUAUCG
((((((((.....)))).))))(((....)))((..(((((((..(....)...((((((..........(((((((.....))))))).(......)....)))))))))))))..)). ( -32.00)
>DroEre_CAF1 12900 114 - 1
GGCAAUAAAAAGGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUAACGAACGAUGGCCGGCAGGAAUUUUAGAAAAGUGA--AGUGUUUUAGGACCAGCAGAAGCCGGAAUUUCUGG----
...........((((...(((((((....((((................)))).)))))))...((((((......)))--))).......))))..((((((......)))))).---- ( -27.79)
>DroYak_CAF1 11427 120 - 1
GGCAAUAAAAAUGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUAACAAACGAUGUCCGGCAGGAAUUUUAGAGAAAUGCCACGUCUUAAAGCACCAACAGAAGUCAGAAUCUCUGUAUCG
.((........((((((.(((((((....)))))..))...))))))...(((((..((((...............))))))))).....))....(((((..(....)..))))).... ( -25.86)
>consensus
GGCAAUAAAAAUGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUAACGAACGAUGUCCGGCAGGAAUUUUAGAAAAAUGCAAAGUGUUUCAGGACCAACAGAAGCCGGAAUCUCUGUAUCG
((((((((.....)))).))))(((....)))....(((((((...........((((((..........(((((((.....))))))).(......)....)))))))))))))..... (-20.90 = -21.78 +   0.88)

alignment

secondary structure

dotplot

Window 3

Location	19,881,846 – 19,881,964
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.22
Mean single sequence MFE	-26.07
Consensus MFE	-19.59
Energy contribution	-19.90
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.53
Structure conservation index	0.75
SVM decision value	0.07
SVM RNA-class probability	0.569450
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19881846 118 - 22224390
CUAUGGUAUGGGGAAAAGUCUGGACAGCCAAAUA--UAAGGGCAAUAAAAAUGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUACCGAACGAUGUCCGGCAGGAGUUUUAGAAAUAUGCA
.....(((((...((((.(((.....(((.....--....)))...............((((((((....((((..........))))....)).))))))))).)))).....))))). ( -28.80)
>DroSec_CAF1 35603 116 - 1
CAAUGG----GGGAAAAGUCUAGACAGCCAAAUAUAUAAGGGCAAUAAAAAUGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUACCGAACGAUGUCCGGCAGGAAUUUUAGAAAUAUGCA
......----........((((((...((...........((((.......))))...((((((((....((((..........))))....)).))))))))...))))))........ ( -24.20)
>DroEre_CAF1 12935 117 - 1
AAAUGGGAUGGGAAAAAGUCUGGACAUCGAAAUA--UAAAGGCAAUAAAAAGGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUAACGAACGAUGGCCGGCAGGAAUUUUAGAAAAGUGA-
......((((..............))))......--.............((((((...(((((((....((((................)))).)))))))..))))))..........- ( -23.83)
>DroYak_CAF1 11467 118 - 1
CAAUGGGAUGGGUAAAAGUCUGGACAGCCAAAUA--UAAGGGCAAUAAAAAUGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUAACAAACGAUGUCCGGCAGGAAUUUUAGAGAAAUGCC
.....((((........))))((((((((.....--....)))........((((((.(((((((....)))))..))...)))))).....)))))((((...............)))) ( -27.46)
>consensus
CAAUGGGAUGGGGAAAAGUCUGGACAGCCAAAUA__UAAGGGCAAUAAAAAUGUUAUAUGCCGGCAAAAGUCGGACCAGAGAUAACGAACGAUGUCCGGCAGGAAUUUUAGAAAAAUGCA
..................((((((...((...........((((((((.....)))).)))).......(((((((.(..(........)..)))))))).))...))))))........ (-19.59 = -19.90 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:27 2006