Locus 5460

Sequence ID	2L_DroMel_CAF1
Location	15,556,880 – 15,557,015
Length	135
Max. P	0.756381

overview

Window 7

Location	15,556,880 – 15,556,977
Length	97
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	84.96
Mean single sequence MFE	-28.84
Consensus MFE	-19.76
Energy contribution	-20.04
Covariance contribution	0.28
Combinations/Pair	1.10
Mean z-score	-2.05
Structure conservation index	0.69
SVM decision value	0.49
SVM RNA-class probability	0.756381
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15556880 97 - 22407834
GUUAAAUCAGGCAUCUUGGGUCAACUUUGGGGCUGCGUAAAUUAGCAGCCAGAAGUUUGCCUUAAGCAUAAU-----CUUCAUAU------AAUCUUCAGAGCACGCC
.........(((..(((((((.((((((..((((((........)))))).)))))).))).))))......-----........------..((....))....))) ( -27.40)
>DroSec_CAF1 70729 102 - 1
GUUAAAUCAGGCAUCUUGGGUCAACUUUGGGGCUGCGCAAAUUAGCAGCCAGAAGUUUGCCUUAAGUAGAAACGUGUAUUAAUAU------AAUCUUUAGAGAAGGCA
(((((..((.(..(((.((((.((((((..((((((........)))))).)))))).)))).....)))..).))..)))))..------................. ( -27.60)
>DroSim_CAF1 62622 102 - 1
GUUAAAUCAGGCAUCUUGGGUCAACUUUGGGGCUGCGUAAAUUAGCAGCCAGAAGUUUGUCUUAAGCAGAAACGUGUAUUAAUAU------AAUCUUUAGAGAUGGUC
(((((..((.(...((((((.(((((((..((((((........)))))).)))).))).))))))......).))..)))))..------.((((....)))).... ( -25.50)
>DroEre_CAF1 64686 107 - 1
CAUAAAUCAGGCAUCUAGGGUCAACUUUGGGGCUGCGUAAAUUAGCACCCA-AAGUUUGCCUUAAGCAGUAACGUGCAUUAACAUACUCGUAAUCUUCAGAGUAGGCC
.........(((...((((((.(((((((((((((.......)))).))))-))))).)))))).(((......))).......(((((..........))))).))) ( -34.60)
>DroYak_CAF1 66421 102 - 1
GAUAAAUCAGGCAUCUAGGGUCAACUUUGUCGCUGCGUAAAUUAGCAGCCAGAAGUUUGCCUUAAGCGGAAACUUGGAUUAAUAU------AAUCUUCAGAGUGGGCC
.........(((...((((((.((((((...(((((........)))))..)))))).)))))).......((((((((((...)------)))))...))))..))) ( -29.10)
>consensus
GUUAAAUCAGGCAUCUUGGGUCAACUUUGGGGCUGCGUAAAUUAGCAGCCAGAAGUUUGCCUUAAGCAGAAACGUGUAUUAAUAU______AAUCUUCAGAGAAGGCC
.........(((.....((((.(((((...((((((........))))))..))))).))))...............................((....))....))) (-19.76 = -20.04 +   0.28)

alignment

secondary structure

dotplot

Window 8

Location	15,556,906 – 15,557,015
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	90.36
Mean single sequence MFE	-34.14
Consensus MFE	-24.84
Energy contribution	-25.12
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.98
Structure conservation index	0.73
SVM decision value	0.31
SVM RNA-class probability	0.684048
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15556906 109 - 22407834
CCAAAUGAGGAGCGCGGAAUCACGGCAGGGGAUUACUGGUUAAAUCAGGCAUCUUGGGUCAACUUUGGGGCUGCGUAAAUUAGCAGCCAGAAGUUUGCCUUAAGCAUAA
....(((..(((.(((.......(((..(((((..(((((...)))))..)))))..)))((((((..((((((........)))))).))))))))))))...))).. ( -35.00)
>DroSec_CAF1 70760 109 - 1
CCAAAUGAGCAGCGCGGAAUCUCGGCAAGGGAUUACUGGUUAAAUCAGGCAUCUUGGGUCAACUUUGGGGCUGCGCAAAUUAGCAGCCAGAAGUUUGCCUUAAGUAGAA
.....(((..(((.(((((((((.....)))))).))))))...)))....(((.((((.((((((..((((((........)))))).)))))).)))).....))). ( -36.20)
>DroSim_CAF1 62653 109 - 1
CCAAAUGAGGAGCGCGGAAUCUCGGCAAGGGAUUACUGGUUAAAUCAGGCAUCUUGGGUCAACUUUGGGGCUGCGUAAAUUAGCAGCCAGAAGUUUGUCUUAAGCAGAA
.....(((..(((.(((((((((.....)))))).))))))...))).....((((((.(((((((..((((((........)))))).)))).))).))))))..... ( -36.10)
>DroEre_CAF1 64723 107 - 1
CCAAAUGAGGAACGCACAAUCAAAGC-GGGGAUUACUGCAUAAAUCAGGCAUCUAGGGUCAACUUUGGGGCUGCGUAAAUUAGCACCCA-AAGUUUGCCUUAAGCAGUA
((......))...((.........((-((......))))..............((((((.(((((((((((((.......)))).))))-))))).)))))).)).... ( -33.50)
>DroYak_CAF1 66452 108 - 1
UCAAAUGAGGAGCGCGAAAUCACGGC-GGGGAUUACUGGAUAAAUCAGGCAUCUAGGGUCAACUUUGUCGCUGCGUAAAUUAGCAGCCAGAAGUUUGCCUUAAGCGGAA
............(((...........-..((((..((((.....))))..))))(((((.((((((...(((((........)))))..)))))).)))))..)))... ( -29.90)
>consensus
CCAAAUGAGGAGCGCGGAAUCACGGCAGGGGAUUACUGGUUAAAUCAGGCAUCUUGGGUCAACUUUGGGGCUGCGUAAAUUAGCAGCCAGAAGUUUGCCUUAAGCAGAA
.............((..............((((..((((.....))))..)))).((((.(((((...((((((........))))))..))))).))))...)).... (-24.84 = -25.12 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:43 2006