Locus 3543

Sequence ID dm3.chr2R
Location 6,164,148 – 6,164,238
Length 90
Max. P 0.721306
window4860 window4861

overview

Window 0

Location 6,164,148 – 6,164,238
Length 90
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 90.40
Shannon entropy 0.17107
G+C content 0.41712
Mean single sequence MFE -24.64
Consensus MFE -18.12
Energy contribution -19.08
Covariance contribution 0.96
Combinations/Pair 1.04
Mean z-score -2.15
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.721306
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6164148 90 + 21146708
AAGCCAACAAAUCGGCAGGCAGCCAAACACUCGGAAUAC-----------AAAUAAUCACAAAAUGUGAAUGUUCAGUGAAUGGGAAGUGUGGCUAAAAGC
.(((((((.....(((.....))).....((((...(((-----------.((((.((((.....)))).))))..)))..))))..)).)))))...... ( -21.40, z-score =  -1.77, R)
>droSim1.chr2R 4788552 101 + 19596830
AAGCCAACAAAUCGGCAGGCAGCCAAACACUCGGAAUACCCUCAAAAAUCGAAUAAUCACAAAAUGUGAAUGUUCAGUGAAUGGGAAGUGUGGCUAAAAGC
.(((((.((..(((((.....)))...((((.((.....)).........(((((.((((.....)))).))))))))).....))..)))))))...... ( -27.40, z-score =  -2.81, R)
>droSec1.super_1 3771516 101 + 14215200
AAGCCAACAAAUCGGCAGGCAGCCAAACACUCGGUAUACCCUCAAAAAUCGAAUAAUCACAAAAUGUGAAUGUUCAGUGAAUGGGAAGUGUGGCUAAAAGC
.((((........(((.....)))..(((((.((....))((((...((.(((((.((((.....)))).))))).))...)))).)))))))))...... ( -28.10, z-score =  -2.98, R)
>droYak2.chr2L 18790720 101 + 22324452
AAGCCAACAAAUCGGCAGGCAGCCAAACACUUGGAAUACACUCAAAAAUCGAAAAAUAACAAAAUGUGAAUGUUCAGUGAAUGAAGAGUGUGACUAAAAGC
..(((........)))..((..((((....))))..(((((((...............((.....)).....((((.....))))))))))).......)) ( -17.90, z-score =  -0.80, R)
>droEre2.scaffold_4929 18429939 101 - 26641161
AAGCCAACAAAUCGGCAGGCAGCCAAACACUUGGAAUACCCUCAAAAAUCGAAAAUUCACGAAAUGUGAAUGUUCAGUGAAUGGGGAGUGUGGCUAAAAGC
.((((........(((.....)))...........(((((((((...((.(((.((((((.....)))))).))).))...))))).))))))))...... ( -28.40, z-score =  -2.40, R)
>consensus
AAGCCAACAAAUCGGCAGGCAGCCAAACACUCGGAAUACCCUCAAAAAUCGAAUAAUCACAAAAUGUGAAUGUUCAGUGAAUGGGAAGUGUGGCUAAAAGC
.(((((.((..(((((.....)))...((((.(.....)...........(((((.((((.....)))).))))))))).....))..)))))))...... (-18.12 = -19.08 +   0.96)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,164,148 – 6,164,238
Length 90
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 90.40
Shannon entropy 0.17107
G+C content 0.41712
Mean single sequence MFE -24.24
Consensus MFE -17.86
Energy contribution -18.54
Covariance contribution 0.68
Combinations/Pair 1.08
Mean z-score -2.04
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.632742
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6164148 90 - 21146708
GCUUUUAGCCACACUUCCCAUUCACUGAACAUUCACAUUUUGUGAUUAUUU-----------GUAUUCCGAGUGUUUGGCUGCCUGCCGAUUUGUUGGCUU
......(((((((..((.(((((.....(((.((((.....)))).....)-----------)).....)))))...(((.....)))))..)).))))). ( -20.90, z-score =  -2.10, R)
>droSim1.chr2R 4788552 101 - 19596830
GCUUUUAGCCACACUUCCCAUUCACUGAACAUUCACAUUUUGUGAUUAUUCGAUUUUUGAGGGUAUUCCGAGUGUUUGGCUGCCUGCCGAUUUGUUGGCUU
.....((((((((((((((..(((.((((...((((.....))))...)))).....))))))......))))))..)))))...(((((....))))).. ( -24.60, z-score =  -1.56, R)
>droSec1.super_1 3771516 101 - 14215200
GCUUUUAGCCACACUUCCCAUUCACUGAACAUUCACAUUUUGUGAUUAUUCGAUUUUUGAGGGUAUACCGAGUGUUUGGCUGCCUGCCGAUUUGUUGGCUU
......(((((((..((.(((((..((((...((((.....))))...))))........((.....)))))))...(((.....)))))..)).))))). ( -25.60, z-score =  -1.98, R)
>droYak2.chr2L 18790720 101 - 22324452
GCUUUUAGUCACACUCUUCAUUCACUGAACAUUCACAUUUUGUUAUUUUUCGAUUUUUGAGUGUAUUCCAAGUGUUUGGCUGCCUGCCGAUUUGUUGGCUU
(((...(((((((((..(((.....)))(((((((.(..(((........)))..).)))))))......)))))..(((.....)))))))....))).. ( -21.70, z-score =  -1.79, R)
>droEre2.scaffold_4929 18429939 101 + 26641161
GCUUUUAGCCACACUCCCCAUUCACUGAACAUUCACAUUUCGUGAAUUUUCGAUUUUUGAGGGUAUUCCAAGUGUUUGGCUGCCUGCCGAUUUGUUGGCUU
.....(((((((((((((((.....((((.((((((.....)))))).)))).....)).))).......)))))..)))))...(((((....))))).. ( -28.41, z-score =  -2.79, R)
>consensus
GCUUUUAGCCACACUUCCCAUUCACUGAACAUUCACAUUUUGUGAUUAUUCGAUUUUUGAGGGUAUUCCGAGUGUUUGGCUGCCUGCCGAUUUGUUGGCUU
.....(((((((((((..........(((...((((.....))))...)))..........((....))))))))..)))))...(((((....))))).. (-17.86 = -18.54 +   0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:12:09 2011