Locus 957

Sequence ID	3L_DroMel_CAF1
Location	2,854,267 – 2,854,409
Length	142
Max. P	0.892262

overview

Window 9

Location	2,854,267 – 2,854,369
Length	102
Sequences	3
Columns	105
Reading direction	forward
Mean pairwise identity	87.18
Mean single sequence MFE	-45.30
Consensus MFE	-36.95
Energy contribution	-36.73
Covariance contribution	-0.21
Combinations/Pair	1.17
Mean z-score	-2.56
Structure conservation index	0.82
SVM decision value	0.97
SVM RNA-class probability	0.892262
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2854267 102 + 23771897
---UCCCACGGGUCCUGCUACUGAAUUGGGUCCUACGGAGCCAGGAGGUAUGGAACCUGUUGCAGCUGCUACUGCAGCUGCCGAUCCUGGUGGCACUCCUGCUCC
---......((..((............))..))...(((((.(((((((.....(((.(((((((((((....))))))).))))...))).)).)))))))))) ( -44.10)
>DroSec_CAF1 99074 102 + 1
---UCCCACGGGUCCCACUACUGAAUUGGGACCUACGGAGCCAGGAGGUAUGGAACCUGCAGCAGCUGCUACUGCUGCUGCCGAUCCUGGUGGCACUCCUGCUCC
---......((((((((.........))))))))..(((((.(((((((..(((.(..((((((((.......)))))))).).))).....)).)))))))))) ( -49.20)
>DroYak_CAF1 104183 105 + 1
AGAUCCCACGGAUCCCGUUACUGAGUUUGGUCCCACGGAGCCAGGAGGUAGGACACCUGCAGCAGCUGCGACCGCUGCUGCCGAUCCAGGUGGCACUCCUGCUCC
.(((((...)))))..(..(((......)))..)..(((((.(((((....(.(((((((((((((.......))))))))......))))).).)))))))))) ( -42.60)
>consensus
___UCCCACGGGUCCCGCUACUGAAUUGGGUCCUACGGAGCCAGGAGGUAUGGAACCUGCAGCAGCUGCUACUGCUGCUGCCGAUCCUGGUGGCACUCCUGCUCC
.........(((.((((.........)))).)))..(((((.(((((...........(((((((......)))))))(((((.......))))))))))))))) (-36.95 = -36.73 +  -0.21)

alignment

secondary structure

dotplot

Window 0

Location	2,854,267 – 2,854,369
Length	102
Sequences	3
Columns	105
Reading direction	reverse
Mean pairwise identity	87.18
Mean single sequence MFE	-45.40
Consensus MFE	-37.40
Energy contribution	-37.40
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-2.11
Structure conservation index	0.82
SVM decision value	0.50
SVM RNA-class probability	0.761281
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2854267 102 - 23771897
GGAGCAGGAGUGCCACCAGGAUCGGCAGCUGCAGUAGCAGCUGCAACAGGUUCCAUACCUCCUGGCUCCGUAGGACCCAAUUCAGUAGCAGGACCCGUGGGA---
(((((.((....))..(((((...((((((((....))))))))....(((.....)))))))))))))......((((..((........))....)))).--- ( -41.50)
>DroSec_CAF1 99074 102 - 1
GGAGCAGGAGUGCCACCAGGAUCGGCAGCAGCAGUAGCAGCUGCUGCAGGUUCCAUACCUCCUGGCUCCGUAGGUCCCAAUUCAGUAGUGGGACCCGUGGGA---
((((((((((.(......(((((.((((((((.......)))))))).)))))....)))))).)))))...(((((((.........))))))).......--- ( -48.10)
>DroYak_CAF1 104183 105 - 1
GGAGCAGGAGUGCCACCUGGAUCGGCAGCAGCGGUCGCAGCUGCUGCAGGUGUCCUACCUCCUGGCUCCGUGGGACCAAACUCAGUAACGGGAUCCGUGGGAUCU
((((((((((.(.((((((...(((((((.((....)).))))))))))))).)....))))).))))).((((......))))......((((((...)))))) ( -46.60)
>consensus
GGAGCAGGAGUGCCACCAGGAUCGGCAGCAGCAGUAGCAGCUGCUGCAGGUUCCAUACCUCCUGGCUCCGUAGGACCCAAUUCAGUAGCGGGACCCGUGGGA___
((((((((((((((.........))))((((((((....))))))))...........))))).)))))......((((..((........))....)))).... (-37.40 = -37.40 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	2,854,302 – 2,854,409
Length	107
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	71.34
Mean single sequence MFE	-42.67
Consensus MFE	-18.71
Energy contribution	-23.15
Covariance contribution	4.44
Combinations/Pair	1.18
Mean z-score	-2.11
Structure conservation index	0.44
SVM decision value	0.20
SVM RNA-class probability	0.629217
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2854302 107 - 23771897
GCAAUUACUACCGGAUGGAACACCAAUGCCUGUGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCUGCAGUAGCAGCUGCAACAGGUUCCAUACCUCCUGGCU
(((............(((....)))...(((((.((....)).)))))..)))..((((((...((((((((....))))))))....(((.....))))))))).. ( -40.60)
>DroSec_CAF1 99109 107 - 1
GCAAUUACUACCGGAUGGAACACCCAUGCCUGUGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCAGCAGUAGCAGCUGCUGCAGGUUCCAUACCUCCUGGCU
(((...........((((.....)))).(((((.((....)).)))))..)))..((((((...((((((((.......)))))))).(((.....))))))))).. ( -41.80)
>DroYak_CAF1 104221 107 - 1
GCAAUUACUACCGGAUGGAACACCCAUGCCUGUGCCCAUAGGAGCAGGAGUGCCACCUGGAUCGGCAGCAGCGGUCGCAGCUGCUGCAGGUGUCCUACCUCCUGGCU
.........((.((((((.....)))).)).))(((...(((((.((((....((((((...(((((((.((....)).)))))))))))))))))..)))))))). ( -43.10)
>DroMoj_CAF1 115913 83 - 1
UCAGCUCAUGCCCGACGGCACGCCCAUGCCGCUGCCGAU------UGGAGCC---GCUGCAGCAGCAGCAGCGGCCGCCGCAGGAGCUGGG---------------C
(((((((.((((((((((((.((.......))))))).)------))).(((---(((((.......))))))))....))).))))))).---------------. ( -45.20)
>consensus
GCAAUUACUACCGGAUGGAACACCCAUGCCUGUGCCCAUAGGAGCAGGAGUGCCACCAGGAUCGGCAGCAGCAGUAGCAGCUGCAGCAGGUUCCAUACCUCCUGGCU
............(((((((((.......(((((.((....)).)))))..((((.........))))((((((((....))))))))..))))))).))........ (-18.71 = -23.15 +   4.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:20 2006