Locus 7716

Sequence ID dm3.chr3L
Location 16,805,653 – 16,805,780
Length 127
Max. P 0.818957
window10621 window10622

overview

Window 1

Location 16,805,653 – 16,805,763
Length 110
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 94.59
Shannon entropy 0.08830
G+C content 0.43087
Mean single sequence MFE -23.55
Consensus MFE -22.25
Energy contribution -22.31
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.46
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.68
SVM RNA-class probability 0.784834
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16805653 110 - 24543557
UAAAAAGAACAGCCGAAAGAAAG-UUGGCAAAUCACUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCUAAACAUCAAAGCCGGCAACAUAACCAUCAAACAUCAUUGAAA
...........((((........-.((((..(((((((....)))))))...))))((((.....))))............))))..........((((......)))).. ( -23.80, z-score =  -2.01, R)
>droEre2.scaffold_4784 8733664 109 + 25762168
UAAAAAGAACUGCCAAAAGAAAG-UAGGCACAUCGCUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCCAAACUUCAAAGCCGGCAACA-GCCCAUCAAACAUCAUUGAAA
......((..((((.........-..))))..))(.((((((.(((......(((..(((..(.(((....))).)...))))))....-))))))))).).......... ( -23.80, z-score =  -0.90, R)
>droSec1.super_0 8876558 111 - 21120651
UAAAAAGAACAGCCGAAAGAAAGUUUGGCAAAUCACUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCCAAACAUCAAAGCCGGCAACAGACCCAUCAAACAUCAUUGAAA
...........(((..........(((((..(((((((....)))))))...)))))(((...................))))))..........((((......)))).. ( -23.31, z-score =  -1.47, R)
>droSim1.chr3L 16147264 111 - 22553184
UAAAAAGAACAGCCGAAAGAAAGUUUGGCAAAUCACUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCCAAACAUCAAAGCCGGCAACAGACCCAUCAAACAUCAUUGAAA
...........(((..........(((((..(((((((....)))))))...)))))(((...................))))))..........((((......)))).. ( -23.31, z-score =  -1.47, R)
>consensus
UAAAAAGAACAGCCGAAAGAAAG_UUGGCAAAUCACUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCCAAACAUCAAAGCCGGCAACAGACCCAUCAAACAUCAUUGAAA
...........(((..........(((((..(((((((....)))))))...)))))(((...................))))))..........((((......)))).. (-22.25 = -22.31 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 16,805,685 – 16,805,780
Length 95
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 95.13
Shannon entropy 0.07802
G+C content 0.45811
Mean single sequence MFE -25.43
Consensus MFE -22.80
Energy contribution -22.92
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.82
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.818957
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16805685 95 - 24543557
AAAAGGGCGGGCGGCUAUAAAAAGAACAGCCGAAAGAAAG-UUGGCAAAUCACUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCUAAACAUCAAA
....((((..((((((...........)))).........-(((((..(((((((....)))))))...))))).....)).)))).......... ( -24.20, z-score =  -1.72, R)
>droEre2.scaffold_4784 8733695 95 + 25762168
AAAAGGGCGGGAGGCUAUAAAAAGAACUGCCAAAAGAAAG-UAGGCACAUCGCUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCCAAACUUCAAA
....((((.....(((.......((..((((.........-..))))..))(((((((......)))))))...))).....)))).......... ( -22.50, z-score =  -0.45, R)
>droSec1.super_0 8876590 96 - 21120651
AAAAGGGCGGGCGGCUAUAAAAAGAACAGCCGAAAGAAAGUUUGGCAAAUCACUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCCAAACAUCAAA
....((((..((((((...........))))........(((((((..(((((((....)))))))...))))).))..)).)))).......... ( -27.50, z-score =  -2.55, R)
>droSim1.chr3L 16147296 96 - 22553184
AAAAGGGCGGGCGGCUAUAAAAAGAACAGCCGAAAGAAAGUUUGGCAAAUCACUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCCAAACAUCAAA
....((((..((((((...........))))........(((((((..(((((((....)))))))...))))).))..)).)))).......... ( -27.50, z-score =  -2.55, R)
>consensus
AAAAGGGCGGGCGGCUAUAAAAAGAACAGCCGAAAGAAAG_UUGGCAAAUCACUUGAUGAGGUGAUCAAGCCAAGGCGAGCAGUCCAAACAUCAAA
....((((..(((((.............)))..........(((((..(((((((....)))))))...))))).....)).)))).......... (-22.80 = -22.92 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:32:09 2011