Locus 10197

Sequence ID dm3.chr3R
Location 12,073,753 – 12,073,804
Length 51
Max. P 0.932742
window14024 window14025

overview

Window 4

Location 12,073,753 – 12,073,804
Length 51
Sequences 6
Columns 62
Reading direction forward
Mean pairwise identity 78.17
Shannon entropy 0.37665
G+C content 0.45408
Mean single sequence MFE -8.35
Consensus MFE -6.37
Energy contribution -6.87
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.04
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.592773
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12073753 51 + 27905053
UGGAGUGGUUUGAAACAUUCCAUCUCUCUUUCUCUCUUCCGCACUCCCUUU-----------
(((((((........))))))).............................----------- (  -8.80, z-score =  -1.38, R)
>droEre2.scaffold_4770 11598114 51 + 17746568
UGGAGUGGUUUGAAACAUUCCAUCUCUCUUUCUCUCUUCCGCACUCCCUUU-----------
(((((((........))))))).............................----------- (  -8.80, z-score =  -1.38, R)
>droYak2.chr3R 14475775 51 - 28832112
UGGAGUGGUUUGAAACAUUCCAUCUCUCUUUCUCUCUUCCGCACUCCCUUU-----------
(((((((........))))))).............................----------- (  -8.80, z-score =  -1.38, R)
>droSec1.super_12 49257 51 - 2123299
UGGAGUGGUUUGAAACAUUCCAUCUCUCUUUCUCCCUUCCGCACUCCCUUU-----------
(((((((........))))))).............................----------- (  -8.80, z-score =  -1.27, R)
>droSim1.chr3R 18125630 51 - 27517382
UGGAGUGGUUUGAAACAUUCCAUCUCUCUUUCUCUCUUCCGCACUCCCUUU-----------
(((((((........))))))).............................----------- (  -8.80, z-score =  -1.38, R)
>droGri2.scaffold_14906 13671059 60 - 14172833
UGAAGCUGUCCAAGCUCUUCCAUUUUCAUUUCUCAC--CCGCUUGACAAUCAACGAGAACGU
(((...((((.((((.....................--..)))))))).))).......... (  -6.10, z-score =   0.54, R)
>consensus
UGGAGUGGUUUGAAACAUUCCAUCUCUCUUUCUCUCUUCCGCACUCCCUUU___________
(((((((........)))))))........................................ ( -6.37 =  -6.87 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 12,073,753 – 12,073,804
Length 51
Sequences 6
Columns 62
Reading direction reverse
Mean pairwise identity 78.17
Shannon entropy 0.37665
G+C content 0.45408
Mean single sequence MFE -13.37
Consensus MFE -8.75
Energy contribution -9.50
Covariance contribution 0.75
Combinations/Pair 1.17
Mean z-score -2.02
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932742
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12073753 51 - 27905053
-----------AAAGGGAGUGCGGAAGAGAGAAAGAGAGAUGGAAUGUUUCAAACCACUCCA
-----------....(((((((....).........(((((.....)))))....)))))). ( -13.50, z-score =  -2.55, R)
>droEre2.scaffold_4770 11598114 51 - 17746568
-----------AAAGGGAGUGCGGAAGAGAGAAAGAGAGAUGGAAUGUUUCAAACCACUCCA
-----------....(((((((....).........(((((.....)))))....)))))). ( -13.50, z-score =  -2.55, R)
>droYak2.chr3R 14475775 51 + 28832112
-----------AAAGGGAGUGCGGAAGAGAGAAAGAGAGAUGGAAUGUUUCAAACCACUCCA
-----------....(((((((....).........(((((.....)))))....)))))). ( -13.50, z-score =  -2.55, R)
>droSec1.super_12 49257 51 + 2123299
-----------AAAGGGAGUGCGGAAGGGAGAAAGAGAGAUGGAAUGUUUCAAACCACUCCA
-----------....(((((((....).........(((((.....)))))....)))))). ( -13.70, z-score =  -2.13, R)
>droSim1.chr3R 18125630 51 + 27517382
-----------AAAGGGAGUGCGGAAGAGAGAAAGAGAGAUGGAAUGUUUCAAACCACUCCA
-----------....(((((((....).........(((((.....)))))....)))))). ( -13.50, z-score =  -2.55, R)
>droGri2.scaffold_14906 13671059 60 + 14172833
ACGUUCUCGUUGAUUGUCAAGCGG--GUGAGAAAUGAAAAUGGAAGAGCUUGGACAGCUUCA
.((((.(((((..(..((.....)--)..)..))))).))))...(((((.....))))).. ( -12.50, z-score =   0.21, R)
>consensus
___________AAAGGGAGUGCGGAAGAGAGAAAGAGAGAUGGAAUGUUUCAAACCACUCCA
...............(((((((....).........(((((.....)))))....)))))). ( -8.75 =  -9.50 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:19:21 2011