Locus 5573

Sequence ID dm3.chr3LHet
Location 1,040,452 – 1,040,505
Length 53
Max. P 0.771490
window7656 window7657

overview

Window 6

Location 1,040,452 – 1,040,505
Length 53
Sequences 3
Columns 53
Reading direction forward
Mean pairwise identity 94.97
Shannon entropy 0.06931
G+C content 0.44025
Mean single sequence MFE -11.43
Consensus MFE -10.03
Energy contribution -10.70
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.508604
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 1040452 53 + 2555491
GCAGAAGAGACUUGUUAUGGCGGGGGUCAUUUGUGUAAAAGGAACUACACAAA
......((..(((((....)))))..)).((((((((........)))))))) ( -12.80, z-score =  -2.17, R)
>droYak2.chrU 1121137 53 + 28119190
GCAGAAGAGACUUGUUAUGGCGGGGGUCGUAUGUAUAAUAGGAACUACACAAA
(((...((..(((((....)))))..))...)))................... (  -8.80, z-score =  -0.63, R)
>droSec1.super_6 116254 53 + 4358794
GCAGAAGAGACUUGUUAUGGCGGGGGUCGUUUGUGUAAAAGGAACUACACAAA
......((..(((((....)))))..)).((((((((........)))))))) ( -12.70, z-score =  -1.78, R)
>consensus
GCAGAAGAGACUUGUUAUGGCGGGGGUCGUUUGUGUAAAAGGAACUACACAAA
......((..(((((....)))))..)).((((((((........)))))))) (-10.03 = -10.70 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 1,040,452 – 1,040,505
Length 53
Sequences 3
Columns 53
Reading direction reverse
Mean pairwise identity 94.97
Shannon entropy 0.06931
G+C content 0.44025
Mean single sequence MFE -7.36
Consensus MFE -6.56
Energy contribution -6.67
Covariance contribution 0.11
Combinations/Pair 1.08
Mean z-score -1.82
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.771490
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 1040452 53 - 2555491
UUUGUGUAGUUCCUUUUACACAAAUGACCCCCGCCAUAACAAGUCUCUUCUGC
(((((((((......)))))))))............................. (  -8.10, z-score =  -2.17, R)
>droYak2.chrU 1121137 53 - 28119190
UUUGUGUAGUUCCUAUUAUACAUACGACCCCCGCCAUAACAAGUCUCUUCUGC
..((((((((....))))))))...(((..............)))........ (  -5.74, z-score =  -1.05, R)
>droSec1.super_6 116254 53 - 4358794
UUUGUGUAGUUCCUUUUACACAAACGACCCCCGCCAUAACAAGUCUCUUCUGC
(((((((((......))))))))).(((..............)))........ (  -8.24, z-score =  -2.24, R)
>consensus
UUUGUGUAGUUCCUUUUACACAAACGACCCCCGCCAUAACAAGUCUCUUCUGC
(((((((((......))))))))).(((..............)))........ ( -6.56 =  -6.67 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:51:04 2011