Locus 4362

Sequence ID dm3.chr2R
Location 12,503,621 – 12,503,694
Length 73
Max. P 0.959546
window5981 window5982

overview

Window 1

Location 12,503,621 – 12,503,694
Length 73
Sequences 5
Columns 73
Reading direction forward
Mean pairwise identity 84.35
Shannon entropy 0.27853
G+C content 0.52829
Mean single sequence MFE -23.05
Consensus MFE -19.47
Energy contribution -19.63
Covariance contribution 0.16
Combinations/Pair 1.05
Mean z-score -1.46
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.814061
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12503621 73 + 21146708
UGGUCAGCCCCAAAGGGUAGGGUAUGGGGGUAGGGUACAAUUUGUGAAGCGGUCGCUUCCAAAUGUCCGGCAA
..(((.(((((...............)))))..((.(((.((((.(((((....))))))))))))))))).. ( -24.26, z-score =  -1.11, R)
>droSim1.chr2R 11240796 73 + 19596830
UGGUCAGCCCCAAAAGGGGUAGGGUAUGGGUAGGGUACAAUUUGUGAAGCGGUCGCUUCCAAAUGUCCGGCAA
..(((.(((((....))))).............((.(((.((((.(((((....))))))))))))))))).. ( -25.70, z-score =  -1.89, R)
>droSec1.super_1 10001651 73 + 14215200
UGGUCAGCCCAAAAAGGGGUAGGGUAUGGGUAGGGUACAAUUUGUGAAGCGGUCGCUUCCAAAUGUCCGGCAA
..(((.((((......)))).............((.(((.((((.(((((....))))))))))))))))).. ( -22.50, z-score =  -1.31, R)
>droYak2.chr2R 4660941 65 - 21139217
UAGCCAGCCACAA--------GGGUUUGGGUAGGGUACAAUUUGUGAAGCGGUCGCUUCCAAAUGUCCGGCAA
..(((.(((.(((--------....))))))..((.(((.((((.(((((....))))))))))))))))).. ( -22.80, z-score =  -1.99, R)
>droEre2.scaffold_4845 9232867 64 - 22589142
UAGCCAGCCCCUA--------GGGUAUGGGUAAGGUAAAAUU-GUGAAGCGGUCGCUUCCAAAUGUCCGGCAA
..(((.((((...--------......))))..((...(.((-(.(((((....)))))))).)..))))).. ( -20.00, z-score =  -1.02, R)
>consensus
UGGUCAGCCCCAAA_GG____GGGUAUGGGUAGGGUACAAUUUGUGAAGCGGUCGCUUCCAAAUGUCCGGCAA
..(((.((((.................))))..((....(((((.(((((....))))))))))..))))).. (-19.47 = -19.63 +   0.16)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 12,503,621 – 12,503,694
Length 73
Sequences 5
Columns 73
Reading direction reverse
Mean pairwise identity 84.35
Shannon entropy 0.27853
G+C content 0.52829
Mean single sequence MFE -19.79
Consensus MFE -13.35
Energy contribution -14.15
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.60
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959546
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12503621 73 - 21146708
UUGCCGGACAUUUGGAAGCGACCGCUUCACAAAUUGUACCCUACCCCCAUACCCUACCCUUUGGGGCUGACCA
.....((((((((((((((....))))).)))).))).))....(((((............)))))....... ( -20.30, z-score =  -2.61, R)
>droSim1.chr2R 11240796 73 - 19596830
UUGCCGGACAUUUGGAAGCGACCGCUUCACAAAUUGUACCCUACCCAUACCCUACCCCUUUUGGGGCUGACCA
.....((((((((((((((....))))).)))).))).))...........(..((((....))))..).... ( -20.60, z-score =  -2.81, R)
>droSec1.super_1 10001651 73 - 14215200
UUGCCGGACAUUUGGAAGCGACCGCUUCACAAAUUGUACCCUACCCAUACCCUACCCCUUUUUGGGCUGACCA
.....((((((((((((((....))))).)))).))).))(..((((...............))))..).... ( -17.16, z-score =  -2.27, R)
>droYak2.chr2R 4660941 65 + 21139217
UUGCCGGACAUUUGGAAGCGACCGCUUCACAAAUUGUACCCUACCCAAACCC--------UUGUGGCUGGCUA
..(((((((((((((((((....))))).)))).)))......(((((....--------))).))))))).. ( -20.50, z-score =  -2.80, R)
>droEre2.scaffold_4845 9232867 64 + 22589142
UUGCCGGACAUUUGGAAGCGACCGCUUCAC-AAUUUUACCUUACCCAUACCC--------UAGGGGCUGGCUA
..(((((.(..((((((((....))))).)-))..........(((......--------..))))))))).. ( -20.40, z-score =  -2.53, R)
>consensus
UUGCCGGACAUUUGGAAGCGACCGCUUCACAAAUUGUACCCUACCCAUACCC____CC_UUUGGGGCUGACCA
..(((((((((((((((((....))))).)))).))).))....((................)))))...... (-13.35 = -14.15 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:27:45 2011