Locus 10440

Sequence ID dm3.chr3R
Location 13,781,915 – 13,782,009
Length 94
Max. P 0.991928
window14358 window14359

overview

Window 8

Location 13,781,915 – 13,782,009
Length 94
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 93.76
Shannon entropy 0.10514
G+C content 0.51592
Mean single sequence MFE -30.60
Consensus MFE -24.72
Energy contribution -24.88
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.95
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.624695
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13781915 94 + 27905053
UGCUCUAUUUUCCAUUUCCAGGCUUCACUGUAAGCCGGGACACUUUGUCGGCUGUCUGCUGUAUGUGUGUGACUCUGGGCCGGAAAAUUUGGGC
.((((.(((((((...(((((((((......)))))(..((((.....((((.....)))).....))))..)..))))..)))))))..)))) ( -31.10, z-score =  -1.81, R)
>droEre2.scaffold_4770 9901176 87 - 17746568
UGCCCUAUUUUCCAGUUCCAGGCUUCACUGUAAGCCGGGACACUUUGUCGGGUGUCUGCUGUAUGUGC--GGCUCUGGGCCGGAAAAUU-----
......(((((((.(..(((((((.(((....(((..(((((((......))))))))))....))).--))).))))..)))))))).----- ( -34.40, z-score =  -2.52, R)
>droYak2.chr3R 2374431 87 + 28832112
UGCUCUAUUUUCCAUUGCCAGGCUUCACUGUAAGCCGGGACACUUUGUCGGGUGUCUGCUGUAUGUGC--GGCUCUGGGCCGGAAAAUU-----
......(((((((....(((((((.(((....(((..(((((((......))))))))))....))).--))).))))...))))))).----- ( -31.60, z-score =  -1.96, R)
>droSec1.super_12 1749305 87 - 2123299
UGCUCUAUUUUCCAUUUCCAGGCUUCACUGUAAGCCGGGACACUUUGUCGGGUGUCUGCUGUAUGUGC--GACUCUGGGCCGGAAAAUU-----
......(((((((...(((((..(((((....(((..(((((((......))))))))))....))).--))..)))))..))))))).----- ( -27.80, z-score =  -1.60, R)
>droSim1.chr3R 19808208 87 - 27517382
UGCUCUAUUUUCCAUUUCCAGGCUUCACUGUAAGCCGGGACACUUUGUCGGGUGUCUGCUGUAUGUGU--GACUCUGGGCCGGAAAAUU-----
......(((((((...((((((..(((((((((((..(((((((......)))))))))).)))).))--)).))))))..))))))).----- ( -28.10, z-score =  -1.86, R)
>consensus
UGCUCUAUUUUCCAUUUCCAGGCUUCACUGUAAGCCGGGACACUUUGUCGGGUGUCUGCUGUAUGUGC__GACUCUGGGCCGGAAAAUU_____
......(((((((...(((((..(((((....(((..(((((((......))))))))))....)))...))..)))))..)))))))...... (-24.72 = -24.88 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,781,915 – 13,782,009
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 93.76
Shannon entropy 0.10514
G+C content 0.51592
Mean single sequence MFE -27.72
Consensus MFE -25.28
Energy contribution -25.24
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -2.92
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.51
SVM RNA-class probability 0.991928
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13781915 94 - 27905053
GCCCAAAUUUUCCGGCCCAGAGUCACACACAUACAGCAGACAGCCGACAAAGUGUCCCGGCUUACAGUGAAGCCUGGAAAUGGAAAAUAGAGCA
((....((((((((..((((..((((.......(....)..(((((((.....)))..))))....))))...))))...))))))))...)). ( -24.50, z-score =  -1.86, R)
>droEre2.scaffold_4770 9901176 87 + 17746568
-----AAUUUUCCGGCCCAGAGCC--GCACAUACAGCAGACACCCGACAAAGUGUCCCGGCUUACAGUGAAGCCUGGAACUGGAAAAUAGGGCA
-----.(((((((((.((((.((.--.(((....(((.(((((........)))))...)))....)))..))))))..)))))))))...... ( -30.40, z-score =  -2.80, R)
>droYak2.chr3R 2374431 87 - 28832112
-----AAUUUUCCGGCCCAGAGCC--GCACAUACAGCAGACACCCGACAAAGUGUCCCGGCUUACAGUGAAGCCUGGCAAUGGAAAAUAGAGCA
-----.((((((((..((((.((.--.(((....(((.(((((........)))))...)))....)))..))))))...))))))))...... ( -28.70, z-score =  -3.25, R)
>droSec1.super_12 1749305 87 + 2123299
-----AAUUUUCCGGCCCAGAGUC--GCACAUACAGCAGACACCCGACAAAGUGUCCCGGCUUACAGUGAAGCCUGGAAAUGGAAAAUAGAGCA
-----.((((((((..((((.((.--.(((....(((.(((((........)))))...)))....)))..))))))...))))))))...... ( -28.20, z-score =  -3.40, R)
>droSim1.chr3R 19808208 87 + 27517382
-----AAUUUUCCGGCCCAGAGUC--ACACAUACAGCAGACACCCGACAAAGUGUCCCGGCUUACAGUGAAGCCUGGAAAUGGAAAAUAGAGCA
-----.((((((((..((((.((.--.(((....(((.(((((........)))))...)))....)))..))))))...))))))))...... ( -26.80, z-score =  -3.30, R)
>consensus
_____AAUUUUCCGGCCCAGAGUC__GCACAUACAGCAGACACCCGACAAAGUGUCCCGGCUUACAGUGAAGCCUGGAAAUGGAAAAUAGAGCA
......((((((((..((((.((....(((....(((.(((((........)))))...)))....)))..))))))...))))))))...... (-25.28 = -25.24 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:24:00 2011