Locus 3504

Sequence ID dm3.chr2R
Location 5,865,012 – 5,865,111
Length 99
Max. P 0.989975
window4806 window4807

overview

Window 6

Location 5,865,012 – 5,865,111
Length 99
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 80.78
Shannon entropy 0.31094
G+C content 0.50466
Mean single sequence MFE -31.05
Consensus MFE -20.75
Energy contribution -21.44
Covariance contribution 0.69
Combinations/Pair 1.21
Mean z-score -2.12
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.890244
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5865012 99 + 21146708
UAGGCAAGGUUGUUGCUUGUGGGUAGGGUUUGAGCUAUGAGCUAUGAGC--UGUGAGCUGUUAGCCCUGAACCCCGAACCUCGAGAAUUGAACCUUUCCCG
..((.((((((....((((.((...(((((((.((((..((((......--....))))..)))).).))))))....)).)))).....)))))).)).. ( -31.70, z-score =  -1.91, R)
>droYak2.chr2L 18492061 100 + 22324452
UAGGCAAGGUUGUUGCUUGUGGGUAGGGUUCGAGCUCUGAGCCUCGAAUCUCGCGAACCUCGAACUUCGAAUAUUGUAAAUUCAAUAUUGAACCUUUCCC-
(((((((.....))))))).(((.((((((((((.((((((........)))).))..)))))))(((.(((((((......)))))))))))))..)))- ( -29.30, z-score =  -1.68, R)
>droSec1.super_359 11330 92 + 13297
UAGGCAAGGUUGUUGCUUGUGGGUAGGGUUUGAGCUAUGAGC---------UGUGAGCUGUUAGCCCUGAACCCCGAACCUCGAGAAUUGAACCUUUCCCG
..((.((((((....((((.((...(((((((.((((..(((---------.....)))..)))).).))))))....)).)))).....)))))).)).. ( -31.60, z-score =  -2.45, R)
>droSim1.chr2R 4497200 92 + 19596830
UAGGCAAGGUUGUUGCUUGUGGGUAGGGUUUGAGCUAUGAGC---------UGUGAGCUGUUAGCCCUGAACCCCGAACCUCGAGAAUUGAACCUUUCCCG
..((.((((((....((((.((...(((((((.((((..(((---------.....)))..)))).).))))))....)).)))).....)))))).)).. ( -31.60, z-score =  -2.45, R)
>consensus
UAGGCAAGGUUGUUGCUUGUGGGUAGGGUUUGAGCUAUGAGC_________UGUGAGCUGUUAGCCCUGAACCCCGAACCUCGAGAAUUGAACCUUUCCCG
..((.((((((....((((.((...(((((((.((((..(((..............)))..))))..)))))))....)).)))).....)))))).)).. (-20.75 = -21.44 +   0.69)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 5,865,012 – 5,865,111
Length 99
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 80.78
Shannon entropy 0.31094
G+C content 0.50466
Mean single sequence MFE -29.41
Consensus MFE -22.05
Energy contribution -22.24
Covariance contribution 0.19
Combinations/Pair 1.22
Mean z-score -2.66
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.39
SVM RNA-class probability 0.989975
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5865012 99 - 21146708
CGGGAAAGGUUCAAUUCUCGAGGUUCGGGGUUCAGGGCUAACAGCUCACA--GCUCAUAGCUCAUAGCUCAAACCCUACCCACAAGCAACAACCUUGCCUA
.(((.((((((..........(((..((((((..((((((..((((....--......))))..)))))).)))))))))..........)))))).))). ( -28.95, z-score =  -2.23, R)
>droYak2.chr2L 18492061 100 - 22324452
-GGGAAAGGUUCAAUAUUGAAUUUACAAUAUUCGAAGUUCGAGGUUCGCGAGAUUCGAGGCUCAGAGCUCGAACCCUACCCACAAGCAACAACCUUGCCUA
-(((...((((((((((((......))))))).((.(((((((.((((.......)))).))).)))))))))))...)))....((((.....))))... ( -29.80, z-score =  -2.79, R)
>droSec1.super_359 11330 92 - 13297
CGGGAAAGGUUCAAUUCUCGAGGUUCGGGGUUCAGGGCUAACAGCUCACA---------GCUCAUAGCUCAAACCCUACCCACAAGCAACAACCUUGCCUA
.(((.((((((..........(((..((((((..((((((..(((.....---------)))..)))))).)))))))))..........)))))).))). ( -29.45, z-score =  -2.81, R)
>droSim1.chr2R 4497200 92 - 19596830
CGGGAAAGGUUCAAUUCUCGAGGUUCGGGGUUCAGGGCUAACAGCUCACA---------GCUCAUAGCUCAAACCCUACCCACAAGCAACAACCUUGCCUA
.(((.((((((..........(((..((((((..((((((..(((.....---------)))..)))))).)))))))))..........)))))).))). ( -29.45, z-score =  -2.81, R)
>consensus
CGGGAAAGGUUCAAUUCUCGAGGUUCGGGGUUCAGGGCUAACAGCUCACA_________GCUCAUAGCUCAAACCCUACCCACAAGCAACAACCUUGCCUA
.(((.((((((..........(((..((((((..((((((..(((..............)))..)))))).)))))))))..........)))))).))). (-22.05 = -22.24 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:11:24 2011