Locus 5359

Sequence ID	2R_DroMel_CAF1
Location	17,305,127 – 17,305,245
Length	118
Max. P	0.885717

overview

Window 3

Location	17,305,127 – 17,305,220
Length	93
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	86.84
Mean single sequence MFE	-37.66
Consensus MFE	-26.76
Energy contribution	-27.28
Covariance contribution	0.52
Combinations/Pair	1.14
Mean z-score	-2.40
Structure conservation index	0.71
SVM decision value	0.94
SVM RNA-class probability	0.885717
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17305127 93 - 20766785
GGGGGAUGGUGGCUUGUGGGCCGCUGUGCGUGCCGAUCCCAUUGGGAUUGGACCAUAGGACCCAAG------------CCCAGCCCAGACUAAAGUCAGAACAUU
..(((...(.((((((.((..(.(((((.((.((((((((...)))))))))))))))).))))))------------)))..))).(((....)))........ ( -41.10)
>DroSec_CAF1 29063 91 - 1
GGGGGAUGGGGCCUUGUGGUCCGCUGUGCGUGGCGAUCCCAUUGGGAUUGGACCAUAG--CCCAAG------------CCCAGCCCAGACUAAAGUCAGAACAUU
(((((...((((..(((((((((((......)))((((((...)))))))))))))))--)))...------------))...))).(((....)))........ ( -39.70)
>DroSim_CAF1 30981 91 - 1
GGGGGAUGGGGGCUUGUGGUCCGUUGUGCGUGCCGAUCCCAUUGGGAUUGGACCAUAG--CCCAAG------------CCCAGCCCAGACUAAAGUCAGAACAUU
..(((....(((((((.(((....((((.((.((((((((...)))))))))))))))--))))))------------)))..))).(((....)))........ ( -41.10)
>DroEre_CAF1 25258 90 - 1
-UGGGAUGGUGGCUUGUGGUCCGCUGUGCGUGCCGAUCCCAUUGGGAUUGGGCCAUAA--CCCGAA------------CCCGGCCCAGACUAAAGUCAGAACAUU
-((((.((((((.(((((((((((.......)).((((((...)))))))))))))))--.)))..------------.))).))))(((....)))........ ( -35.00)
>DroYak_CAF1 8072 99 - 1
----GAUGGGGGCUUGUGGUCCGCUGUGCCUGCCGAUCCCAUUGGGAUUGGACCAUAA--CCCAAACCCAAACCGAAACCCAGCCCAGACUAAAGUCAGAACAUU
----..((((((.(((((((((((.......)).((((((...)))))))))))))))--.))...)))).................(((....)))........ ( -31.40)
>consensus
GGGGGAUGGGGGCUUGUGGUCCGCUGUGCGUGCCGAUCCCAUUGGGAUUGGACCAUAG__CCCAAG____________CCCAGCCCAGACUAAAGUCAGAACAUU
..(((.((((((.(((((((((((...)).....((((((...)))))))))))))))...))...............)))).))).(((....)))........ (-26.76 = -27.28 +   0.52)

alignment

secondary structure

dotplot

Window 4

Location	17,305,154 – 17,305,245
Length	91
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	81.79
Mean single sequence MFE	-36.28
Consensus MFE	-24.94
Energy contribution	-25.26
Covariance contribution	0.32
Combinations/Pair	1.15
Mean z-score	-1.92
Structure conservation index	0.69
SVM decision value	0.61
SVM RNA-class probability	0.799435
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17305154 91 - 20766785
CUCGAUUUCAGACGUCUCUC------------UGGAUGGGGGAUGGUGGCUUGUGGGCCGCUGUGCGUGCCGAUCCCAUUGGGAUUGGACCAUAGGACCCAAG-
......((((((......))------------))))(((((.(((((((((....))))))))).)(..((((((((...))))))))..)......))))..- ( -37.10)
>DroSec_CAF1 29090 101 - 1
CUCGAUUUCAGACGACUCUGGAUGGGGUAAGGUGGAUGGGGGAUGGGGCCUUGUGGUCCGCUGUGCGUGGCGAUCCCAUUGGGAUUGGACCAUAG--CCCAAG-
(((.(((.((....(((((....)))))....))))).)))....((((..(((((((((((......)))((((((...)))))))))))))))--)))...- ( -38.70)
>DroSim_CAF1 31008 87 - 1
CUCGAUUUCAGACGACUCUGGUU--------------GGGGGAUGGGGGCUUGUGGUCCGUUGUGCGUGCCGAUCCCAUUGGGAUUGGACCAUAG--CCCAAG-
..(.((..(...((((....)))--------------).)..)).)(((((.((((((((.....).....((((((...)))))))))))))))--)))...- ( -35.20)
>DroEre_CAF1 25285 86 - 1
CUCGAUUUCAGACGACUCUGGAA---------------UGGGAUGGUGGCUUGUGGUCCGCUGUGCGUGCCGAUCCCAUUGGGAUUGGGCCAUAA--CCCGAA-
.((.((((((((....)))))))---------------)(((...(((((((..((..(((...)))..))((((((...)))))))))))))..--))))).- ( -35.00)
>DroYak_CAF1 8110 82 - 1
CUCGAUUUCAGACGACUCUGG--------------------GAUGGGGGCUUGUGGUCCGCUGUGCCUGCCGAUCCCAUUGGGAUUGGACCAUAA--CCCAAAC
..(.((..((((....)))).--------------------.)).)(((.(((((((((((.......)).((((((...)))))))))))))))--))).... ( -35.40)
>consensus
CUCGAUUUCAGACGACUCUGG________________GGGGGAUGGGGGCUUGUGGUCCGCUGUGCGUGCCGAUCCCAUUGGGAUUGGACCAUAG__CCCAAG_
.......(((((....)))))......................((((...(((((((((((...)).....((((((...)))))))))))))))..))))... (-24.94 = -25.26 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:03 2006