Locus 1439

Sequence ID	2R_DroMel_CAF1
Location	5,516,535 – 5,516,627
Length	92
Max. P	0.999788

overview

Window 8

Location	5,516,535 – 5,516,627
Length	92
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	90.44
Mean single sequence MFE	-31.21
Consensus MFE	-24.32
Energy contribution	-24.36
Covariance contribution	0.04
Combinations/Pair	1.13
Mean z-score	-4.49
Structure conservation index	0.78
SVM decision value	3.01
SVM RNA-class probability	0.998116
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5516535 92 + 20766785
GCCAAAUAAAUCUUGAUUUCCCCCGACCUAUUCAUGGCCAAAAAAAUUGGCCAGAAUUGUCGGGGGAAUUACACCAGCAGAUUGUCUAUAUG---
........(((((((..((((((((((..((((.(((((((.....))))))))))).))))))))))...)).....))))).........--- ( -35.70)
>DroSec_CAF1 40986 92 + 1
GCCAAAUAAAUCUUGAUUUCCCCCGACCUAUUCACGGCCAAAAAAAUUGGCAGGAAUUGUUGGGGGAAUUACACCAGCAGAUUGUCUAUAUG---
........(((((((..((((((((((..((((...(((((.....)))))..)))).))))))))))...)).....))))).........--- ( -29.80)
>DroSim_CAF1 18196 92 + 1
GCCAAAUAAAUCUUGAUUUCCCCCGACCUAUUCACGGCCAAAAAAAUUGGCCAGAAUUGUUGGGGGAAUUACACCAGCAGAUUGUCUAUAUG---
........(((((((..((((((((((..((((..((((((.....)))))).)))).))))))))))...)).....))))).........--- ( -31.00)
>DroEre_CAF1 17847 94 + 1
ACCGAAUAAAUCUUGAUUUCC-CCGACCUAUUCACGGCCAAAAAAGUUGGCCAAAAAUGUCGGGGGAAUUACACCAGCAGAUUGUCCAUAUACAU
...((...(((((((((((((-(((((........((((((.....))))))......))))))))))))).......))))).))......... ( -30.35)
>DroYak_CAF1 18404 90 + 1
GCCGAAUAAAUCUUGAUUUCC-CCGAUCUAUUCACGGCCAAAAAA-UUGGCCUCAAAUGUCGGGGGGAUUACACCAGCAGAUUGUCUAUUUG---
..(((((((((((((((..((-(((((..(((...((((((....-))))))...))))))))))..)))).......)))))...))))))--- ( -29.21)
>consensus
GCCAAAUAAAUCUUGAUUUCCCCCGACCUAUUCACGGCCAAAAAAAUUGGCCAGAAUUGUCGGGGGAAUUACACCAGCAGAUUGUCUAUAUG___
........(((((((..((((((((((........((((((.....))))))......))))))))))...)).....)))))............ (-24.32 = -24.36 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	5,516,535 – 5,516,627
Length	92
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	90.44
Mean single sequence MFE	-30.30
Consensus MFE	-26.20
Energy contribution	-27.64
Covariance contribution	1.44
Combinations/Pair	1.10
Mean z-score	-3.20
Structure conservation index	0.86
SVM decision value	4.08
SVM RNA-class probability	0.999788
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5516535 92 - 20766785
---CAUAUAGACAAUCUGCUGGUGUAAUUCCCCCGACAAUUCUGGCCAAUUUUUUUGGCCAUGAAUAGGUCGGGGGAAAUCAAGAUUUAUUUGGC
---((.(((...(((((..((((....((((((((((.(((((((((((.....))))))).))))..)))))))))))))))))))))).)).. ( -37.60)
>DroSec_CAF1 40986 92 - 1
---CAUAUAGACAAUCUGCUGGUGUAAUUCCCCCAACAAUUCCUGCCAAUUUUUUUGGCCGUGAAUAGGUCGGGGGAAAUCAAGAUUUAUUUGGC
---((.(((...(((((..((((....(((((((.((.(((((.(((((.....))))).).))))..)).))))))))))))))))))).)).. ( -27.10)
>DroSim_CAF1 18196 92 - 1
---CAUAUAGACAAUCUGCUGGUGUAAUUCCCCCAACAAUUCUGGCCAAUUUUUUUGGCCGUGAAUAGGUCGGGGGAAAUCAAGAUUUAUUUGGC
---((.(((...(((((..((((....(((((((.((.(((((((((((.....))))))).))))..)).))))))))))))))))))).)).. ( -31.00)
>DroEre_CAF1 17847 94 - 1
AUGUAUAUGGACAAUCUGCUGGUGUAAUUCCCCCGACAUUUUUGGCCAACUUUUUUGGCCGUGAAUAGGUCGG-GGAAAUCAAGAUUUAUUCGGU
.(((......)))....(((((.((((.(((((((((((((.(((((((.....))))))).))))..)))))-)).......)).))))))))) ( -28.41)
>DroYak_CAF1 18404 90 - 1
---CAAAUAGACAAUCUGCUGGUGUAAUCCCCCCGACAUUUGAGGCCAA-UUUUUUGGCCGUGAAUAGAUCGG-GGAAAUCAAGAUUUAUUCGGC
---..............(((((...((((.(((((((((((..((((((-....))))))..)))).).))))-)).......))))...))))) ( -27.40)
>consensus
___CAUAUAGACAAUCUGCUGGUGUAAUUCCCCCGACAAUUCUGGCCAAUUUUUUUGGCCGUGAAUAGGUCGGGGGAAAUCAAGAUUUAUUUGGC
............(((((..((((....((((((((((..((((((((((.....))))))).)))...)))))))))))))))))))........ (-26.20 = -27.64 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:53 2006