Locus 9474

Sequence ID	3R_DroMel_CAF1
Location	25,074,350 – 25,074,476
Length	126
Max. P	0.992404

overview

Window 4

Location	25,074,350 – 25,074,459
Length	109
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	91.65
Mean single sequence MFE	-26.45
Consensus MFE	-21.48
Energy contribution	-20.96
Covariance contribution	-0.52
Combinations/Pair	1.07
Mean z-score	-2.53
Structure conservation index	0.81
SVM decision value	2.33
SVM RNA-class probability	0.992404
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25074350 109 - 27905053
AAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAGGCAGCAAAAAGCGCGGUGCGAAUUAUACAGUGGACAUCAGUCAA--CCAUUGUGUUUUGUUCAAAAAAAAA
.((((((.((.....)).)))))).(((((((((((((..((.((.....)))).)))))......(((((((...........--))))))))))))))).......... ( -24.30)
>DroSec_CAF1 3526 111 - 1
AAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAGGCAGCAAAAAGCGCGGUGCGAAUUAUACAGUGGACAUCAGUCAACACCAUUGUGUUUUGUUGAAAAAAUAA
..(((((.((.....)).)))))(((((((((((((((..((.((.....)))).)))))......(((((((.............)))))))))))))))))........ ( -28.72)
>DroSim_CAF1 3534 111 - 1
AAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAGGCAGCAAAAAGCGCGGUGCGAAUUAUACAGUGGACAUCAGUCAACACCAUUGUGUUUUGUUGAAAAAACAA
..(((((.((.....)).)))))(((((((((((((((..((.((.....)))).)))))......(((((((.............)))))))))))))))))........ ( -28.72)
>DroEre_CAF1 3628 106 - 1
AAUUUGCAUUAAUUUGAAGUAAGUCAGCGAAACCGCAUAAACAGCAAAAUGUGCGGUGCGAAUUAUACAGUGGACAGCAGUCUG--CCAAUGUAUUUUGUUAAAAAAA---
(((((((......((((......))))....((((((((..........)))))))))))))))(((((.(((.(((....)))--))).))))).............--- ( -25.50)
>DroYak_CAF1 3636 107 - 1
AAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAAACAGCAAAAAGUGCGGUGCGAAUUAUACAGUGGACAUCAGUCAG--CCAUUGUAUUUUGUUAAAAAAA--U
(((((((......((((......))))....(((((((............))))))))))))))(((((((((.(........)--))))))))).............--. ( -25.00)
>consensus
AAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAGGCAGCAAAAAGCGCGGUGCGAAUUAUACAGUGGACAUCAGUCAA__CCAUUGUGUUUUGUUAAAAAAA_AA
(((((((......((((......))))....(((((....((........))))))))))))))(((((((((.............)))))))))................ (-21.48 = -20.96 +  -0.52)

alignment

secondary structure

dotplot

Window 5

Location	25,074,381 – 25,074,476
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	96.84
Mean single sequence MFE	-16.16
Consensus MFE	-14.16
Energy contribution	-13.68
Covariance contribution	-0.48
Combinations/Pair	1.06
Mean z-score	-1.27
Structure conservation index	0.88
SVM decision value	-0.02
SVM RNA-class probability	0.524174
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25074381 95 - 27905053
AACAUAAUAAAUAAAACAAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAGGCAGCAAAAAGCGCGGUGCGAAUUAUACAGUGGACAUC
.................((((((((((................(((....)))....((.((.....)))))))))))))).............. ( -16.00)
>DroSec_CAF1 3559 95 - 1
AACAUAAUAAAUAAAACAAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAGGCAGCAAAAAGCGCGGUGCGAAUUAUACAGUGGACAUC
.................((((((((((................(((....)))....((.((.....)))))))))))))).............. ( -16.00)
>DroSim_CAF1 3567 95 - 1
AACAUAAUAAAUAAAACAAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAGGCAGCAAAAAGCGCGGUGCGAAUUAUACAGUGGACAUC
.................((((((((((................(((....)))....((.((.....)))))))))))))).............. ( -16.00)
>DroEre_CAF1 3656 95 - 1
AACAUAAUAAAUAAAACAAUUUGCAUUAAUUUGAAGUAAGUCAGCGAAACCGCAUAAACAGCAAAAUGUGCGGUGCGAAUUAUACAGUGGACAGC
.................(((((((......((((......))))....((((((((..........))))))))))))))).............. ( -16.90)
>DroYak_CAF1 3665 95 - 1
AACAUAAUAAAUAAAACAAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAAACAGCAAAAAGUGCGGUGCGAAUUAUACAGUGGACAUC
.................(((((((......((((......))))....(((((((............)))))))))))))).............. ( -15.90)
>consensus
AACAUAAUAAAUAAAACAAUUUGCAUUAAUUUGAAGUAAAUCAGCGAAACCGCAUAGGCAGCAAAAAGCGCGGUGCGAAUUAUACAGUGGACAUC
.................(((((((......((((......))))....(((((....((........)))))))))))))).............. (-14.16 = -13.68 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:35:31 2006