Locus 4518

Sequence ID	3L_DroMel_CAF1
Location	13,015,589 – 13,015,793
Length	204
Max. P	0.721628

overview

Window 8

Location	13,015,589 – 13,015,695
Length	106
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	83.33
Mean single sequence MFE	-35.40
Consensus MFE	-26.02
Energy contribution	-25.77
Covariance contribution	-0.25
Combinations/Pair	1.25
Mean z-score	-1.72
Structure conservation index	0.74
SVM decision value	0.40
SVM RNA-class probability	0.721628
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13015589 106 - 23771897
GGAUUGCGGUUACCGCGCAGGGUUACUUUU-GCGAGGAUGCCUUAUUAUCGGGGGUAUUCCUCAGCCCCUGUAUCAAUUAGCUUUUGUCAGCUGUGACGCGAUUUAA---
((((((((.((((.((((((((........-(((((((((((((.......)))))).))))).))))))))..(((.......)))...)).))))))))))))..--- ( -36.40)
>DroSec_CAF1 6658 106 - 1
AGAUUGCGGCCAGCGCGCAGGGUUACUUUU-GCGAGGGUUCCUCAUUAUUGGGGGUAUUCCUCAGCCGCUGUAUCAAUUAGCUUUUGUCAGCUGUGACGCGAUUUAA---
((((((((..((((((((((((....))))-))(((((.((((((....))))))...))))).).)))))..(((..(((((......))))))))))))))))..--- ( -39.40)
>DroSim_CAF1 6676 106 - 1
AGAUUGCGGCCACCGCGCAGGGUUACUUUU-GUGAGGGCGCCUCAUUAUUGGGGGUAUUCCUCAGCCGCUGUAUCAAUUAGCUUUUGUCAGCUGUGACGCGAUUUAU---
((((((((..(((.((((((((((((....-))((((((.(((((....)))))))...)))))))).))))..(((.......)))...)).))).))))))))..--- ( -34.90)
>DroYak_CAF1 6641 110 - 1
AGAUUCGGGGUAACGCGCAGGGUUGCUUUUUGUGUGGGUGCCUUUUUGUUGGGGGUAUUCAAUGGCUGCUGUAUCAAUUAGCUUUUGUCAGCUGUUGCAUAACUUAGACA
......((((((.(((((((((.....)))))))))..))))))..((((..((.(((.((((((((((.((........))....).))))))))).))).))..)))) ( -30.90)
>consensus
AGAUUGCGGCCACCGCGCAGGGUUACUUUU_GCGAGGGUGCCUCAUUAUUGGGGGUAUUCCUCAGCCGCUGUAUCAAUUAGCUUUUGUCAGCUGUGACGCGAUUUAA___
((((((((........((((((((.........(((((((((((.......)))))).))))))))).))))......(((((......)))))...))))))))..... (-26.02 = -25.77 +  -0.25)

alignment

secondary structure

dotplot

Window 9

Location	13,015,695 – 13,015,793
Length	98
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	88.77
Mean single sequence MFE	-31.07
Consensus MFE	-21.98
Energy contribution	-22.70
Covariance contribution	0.72
Combinations/Pair	1.14
Mean z-score	-1.80
Structure conservation index	0.71
SVM decision value	0.05
SVM RNA-class probability	0.560176
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13015695 98 - 23771897
UACACAUACCGUCCGUCGGGCAAUACAACAGGAAAAGGAAAAGGCAGAUUUGC--GGGCGGUGUGGCCAGCGGGCAGUUGGCGUCGAAUAACUAAAUACU
....((((((((((((...((.......(.......)......))......))--))))))))))((((((.....)))))).................. ( -31.02)
>DroSec_CAF1 6764 98 - 1
UACACAUACCGUCCGUCGGGCAAUACAACAGGAAAAGGAAAAGGCAGAUUUGC--GGGCGGUGUGGCCAGCGGGCAGUUGGCGCCGAAUAACUAAAUACU
....((((((((((((...((.......(.......)......))......))--))))))))))((((((.....)))))).................. ( -31.02)
>DroSim_CAF1 6782 100 - 1
UACAACUGCUAGGCCUCGGGCAAUACAACAGGAAAAGGAAAAGGCAGACUUGGAGGGGGGGUGUGGCCAGCGGGCAGUUGGCGUCGAAUAACUAAAUACU
..((((((((..((....(((.((((..(.....(((...........)))......)..)))).))).)).)))))))).................... ( -25.30)
>DroEre_CAF1 9086 98 - 1
UACACAUACCGUCCGUCGGGCAAUACAACAGGAAAAGGAAAAGGCCGAUUUUC--GGACGGUGUGGCCAGCAGGCGGUUGGCGCGAAAUGAUUAAAUACU
....(((((((((((((((.(.....................).))))....)--))))))))))((((((.....)))))).................. ( -34.20)
>DroYak_CAF1 6751 98 - 1
UACACAUACCGUCCGUCGGGCAAUACAACAGGAAAAGGAAAAGGCCGAUUUUC--GGACGGUGUGGCCAGCCGGCAGUUGGCGCGAAAUGAUUAAAUACU
....(((((((((((((((.(.....................).))))....)--))))))))))((((((.....)))))).................. ( -33.80)
>consensus
UACACAUACCGUCCGUCGGGCAAUACAACAGGAAAAGGAAAAGGCAGAUUUGC__GGGCGGUGUGGCCAGCGGGCAGUUGGCGCCGAAUAACUAAAUACU
....(((((((((((((..((.......(.......)......)).)))......))))))))))((((((.....)))))).................. (-21.98 = -22.70 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:33 2006