Locus 3360

Sequence ID	2R_DroMel_CAF1
Location	11,392,566 – 11,392,660
Length	94
Max. P	0.765703

overview

Window 2

Location	11,392,566 – 11,392,660
Length	94
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	84.35
Mean single sequence MFE	-28.03
Consensus MFE	-17.74
Energy contribution	-16.90
Covariance contribution	-0.84
Combinations/Pair	1.28
Mean z-score	-2.25
Structure conservation index	0.63
SVM decision value	0.51
SVM RNA-class probability	0.765703
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11392566 94 + 20766785
UCCUUCAGCUUUCCCUUCCCCUCCGACCACUUUCC--CUGGCCAAUCCAUGCCAGGCACUUUAAUUAUGCGGACCAGGGGCCUUAGGAGCGGAGUA
..((((.(((((.....((((((((.........(--(((((........)))))).............))))...)))).....))))))))).. ( -27.95)
>DroSec_CAF1 5658 85 + 1
UCCUUCAGAUCCCCUUUC---------CACUUUCC--CUGGCCAAUCCAUGCCAGGCACUUUAAUUAUGCGGACCAGGGGCUUUAGGAGCGGAGUA
((((..((..(((((.((---------(.......--(((((........)))))(((.........))))))..)))))))..))))........ ( -25.50)
>DroSim_CAF1 5254 85 + 1
UCCUUUAGCUCCCCUUUC---------CACUUUCC--CUGGCCAAUCCAUGCCAGGCACUUUAAUUAUGCGGACCAGGGGCUUUAGGAGCGGAGUA
((((..((((((....((---------(.......--(((((........)))))(((.........))))))...))))))..))))........ ( -27.70)
>DroEre_CAF1 8168 91 + 1
UCCCUCAGCUUCCU---CAGCGCCCUCCGCAUUCC--CUGGCCAAUCCAUGCCAGGCACUUUAAUUAUGCGGACCAGGGGCUUUAGGAGCGGAGUA
...(((.(((.(((---.(((.((((((((((..(--(((((........))))))..........)))))))...))))))..)))))).))).. ( -37.10)
>DroYak_CAF1 6189 96 + 1
UCCCUCAGCUCCCUUCACCACUCCCUCCAUCUUCCAACUCGCCAAUCCAUGCCAGGCACUUUAAUUAUGCGGACCAGGGGCUUUAGGAGCGGAGUA
.......(((((((((.....(((((......(((..((.((........)).))(((.........))))))..))))).....)))).))))). ( -21.90)
>consensus
UCCUUCAGCUCCCCUUUC__C_CC__CCACUUUCC__CUGGCCAAUCCAUGCCAGGCACUUUAAUUAUGCGGACCAGGGGCUUUAGGAGCGGAGUA
((((((....((((.......................(((((........)))))(((.........)))......))))......))).)))... (-17.74 = -16.90 +  -0.84)

alignment

secondary structure

dotplot

Window 3

Location	11,392,566 – 11,392,660
Length	94
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	84.35
Mean single sequence MFE	-33.70
Consensus MFE	-19.87
Energy contribution	-20.23
Covariance contribution	0.36
Combinations/Pair	1.13
Mean z-score	-2.34
Structure conservation index	0.59
SVM decision value	0.33
SVM RNA-class probability	0.691019
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11392566 94 - 20766785
UACUCCGCUCCUAAGGCCCCUGGUCCGCAUAAUUAAAGUGCCUGGCAUGGAUUGGCCAG--GGAAAGUGGUCGGAGGGGAAGGGAAAGCUGAAGGA
..(((..(((((..((((.((..(((((((.......))))(((((........)))))--))).)).))))..)))))..)))............ ( -34.20)
>DroSec_CAF1 5658 85 - 1
UACUCCGCUCCUAAAGCCCCUGGUCCGCAUAAUUAAAGUGCCUGGCAUGGAUUGGCCAG--GGAAAGUG---------GAAAGGGGAUCUGAAGGA
........((((..(((((((..(((((..........(.((((((........)))))--).)..)))---------)).)))))..))..)))) ( -30.40)
>DroSim_CAF1 5254 85 - 1
UACUCCGCUCCUAAAGCCCCUGGUCCGCAUAAUUAAAGUGCCUGGCAUGGAUUGGCCAG--GGAAAGUG---------GAAAGGGGAGCUAAAGGA
........((((..(((((((..(((((..........(.((((((........)))))--).)..)))---------))..)))).)))..)))) ( -33.10)
>DroEre_CAF1 8168 91 - 1
UACUCCGCUCCUAAAGCCCCUGGUCCGCAUAAUUAAAGUGCCUGGCAUGGAUUGGCCAG--GGAAUGCGGAGGGCGCUG---AGGAAGCUGAGGGA
..(((.((((((..((((((...(((((((........(.((((((........)))))--).))))))))))).))).---))).))).)))... ( -40.10)
>DroYak_CAF1 6189 96 - 1
UACUCCGCUCCUAAAGCCCCUGGUCCGCAUAAUUAAAGUGCCUGGCAUGGAUUGGCGAGUUGGAAGAUGGAGGGAGUGGUGAAGGGAGCUGAGGGA
..(((.((((((...(((.((..(((.(((..((((..((((...........))))..))))...)))..))))).)))...)))))).)))... ( -30.70)
>consensus
UACUCCGCUCCUAAAGCCCCUGGUCCGCAUAAUUAAAGUGCCUGGCAUGGAUUGGCCAG__GGAAAGUGG__GG_G__GAAAGGGGAGCUGAAGGA
........((((..(((((((..(((((((.......))))(((((........)))))..)))..................)))).)))..)))) (-19.87 = -20.23 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:38 2006