Locus 2235

Sequence ID dm3.chr2L
Location 17,225,168 – 17,225,231
Length 63
Max. P 0.843925
window3083 window3084

overview

Window 3

Location 17,225,168 – 17,225,231
Length 63
Sequences 6
Columns 70
Reading direction forward
Mean pairwise identity 76.35
Shannon entropy 0.45660
G+C content 0.42715
Mean single sequence MFE -14.85
Consensus MFE -6.07
Energy contribution -6.77
Covariance contribution 0.69
Combinations/Pair 1.29
Mean z-score -1.99
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.586323
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17225168 63 + 23011544
ACUGACUUUGAGUACGGAAAUUCCAUGCUAAAAUGGAAAUGGGAAUGGUGGUUUUCAGAGUUG-------
...(((((((((.((.(..(((((...((.....)).....)))))..).)).))))))))).------- ( -17.60, z-score =  -2.96, R)
>droSim1.chr2L 16922826 69 + 22036055
ACUGACUUUGAGUACGGAAAUUCCGUGCUAAAAUGGAAAUGG-AAUGCUGGGAGCGAGUAAAGAGAGUUG
...((((((.(((((((.....))))))).............-..(((((....).))))...)))))). ( -16.30, z-score =  -2.41, R)
>droSec1.super_7 851619 69 + 3727775
ACUGACUUUGAGUACGGAAAUUCCGUGCUAAAAUGGAAAUGG-AAUGCUGGGAGCGAGUAAAGAGAGUUG
...((((((.(((((((.....))))))).............-..(((((....).))))...)))))). ( -16.30, z-score =  -2.41, R)
>droYak2.chr2R 17259919 69 - 21139217
ACUGACUUUGAUUACGGAAAUUCCGUGCUAAAAUGGAAAUGG-AAUGGUGGGAACGAAUAAAGAAAGUUG
(((..(((((.((.(.(..(((((((............))))-)))..).)....)).)))))..))).. ( -10.10, z-score =  -0.76, R)
>droEre2.scaffold_4845 15567546 68 - 22589142
ACUGACUUUGAUUACGGAAAUUCCGUGCUAAAAUGGAAAUGG-AAUGGUGGGAGCGA-UGAAGAAAGUUG
...((((((....((((.....))))(((...((.(......-..).))...)))..-.....)))))). ( -10.60, z-score =  -0.64, R)
>droAna3.scaffold_12916 12553945 63 - 16180835
------ACUGACUGCGGAAAUUCCAGAGGAAGGACGAAAUGG-AAUGCUGGGGUCUGAUGGCGAAAGUUG
------...((((.(((..((((((..(......)....)))-))).))).))))....(((....))). ( -18.20, z-score =  -2.78, R)
>consensus
ACUGACUUUGAGUACGGAAAUUCCGUGCUAAAAUGGAAAUGG_AAUGCUGGGAGCGAGUAAAGAAAGUUG
..........(((((((.....)))))))......................................... ( -6.07 =  -6.77 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 17,225,168 – 17,225,231
Length 63
Sequences 6
Columns 70
Reading direction reverse
Mean pairwise identity 76.35
Shannon entropy 0.45660
G+C content 0.42715
Mean single sequence MFE -7.14
Consensus MFE -3.95
Energy contribution -3.90
Covariance contribution -0.05
Combinations/Pair 1.25
Mean z-score -1.71
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.88
SVM RNA-class probability 0.843925
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17225168 63 - 23011544
-------CAACUCUGAAAACCACCAUUCCCAUUUCCAUUUUAGCAUGGAAUUUCCGUACUCAAAGUCAGU
-------.....((((..............(.((((((......)))))).).............)))). (  -6.23, z-score =  -0.61, R)
>droSim1.chr2L 16922826 69 - 22036055
CAACUCUCUUUACUCGCUCCCAGCAUU-CCAUUUCCAUUUUAGCACGGAAUUUCCGUACUCAAAGUCAGU
..(((..((((....((.....))...-.............((.((((.....)))).)).))))..))) (  -9.50, z-score =  -2.96, R)
>droSec1.super_7 851619 69 - 3727775
CAACUCUCUUUACUCGCUCCCAGCAUU-CCAUUUCCAUUUUAGCACGGAAUUUCCGUACUCAAAGUCAGU
..(((..((((....((.....))...-.............((.((((.....)))).)).))))..))) (  -9.50, z-score =  -2.96, R)
>droYak2.chr2R 17259919 69 + 21139217
CAACUUUCUUUAUUCGUUCCCACCAUU-CCAUUUCCAUUUUAGCACGGAAUUUCCGUAAUCAAAGUCAGU
..(((..((((....((....))....-................((((.....))))....))))..))) (  -5.50, z-score =  -1.65, R)
>droEre2.scaffold_4845 15567546 68 + 22589142
CAACUUUCUUCA-UCGCUCCCACCAUU-CCAUUUCCAUUUUAGCACGGAAUUUCCGUAAUCAAAGUCAGU
..(((((.....-..(((.........-.............)))((((.....))))....))))).... (  -6.35, z-score =  -2.16, R)
>droAna3.scaffold_12916 12553945 63 + 16180835
CAACUUUCGCCAUCAGACCCCAGCAUU-CCAUUUCGUCCUUCCUCUGGAAUUUCCGCAGUCAGU------
...............(((......(((-(((..............)))))).......)))...------ (  -5.76, z-score =   0.08, R)
>consensus
CAACUUUCUUCACUCGCUCCCACCAUU_CCAUUUCCAUUUUAGCACGGAAUUUCCGUACUCAAAGUCAGU
............................................((((.....))))............. ( -3.95 =  -3.90 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:47:27 2011