Locus 3690

Sequence ID dm3.chr2R
Location 7,130,572 – 7,130,712
Length 140
Max. P 0.947527
window5057 window5058

overview

Window 7

Location 7,130,572 – 7,130,712
Length 140
Sequences 3
Columns 155
Reading direction forward
Mean pairwise identity 84.52
Shannon entropy 0.21328
G+C content 0.35789
Mean single sequence MFE -39.30
Consensus MFE -27.05
Energy contribution -30.50
Covariance contribution 3.45
Combinations/Pair 1.02
Mean z-score -2.75
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947527
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7130572 140 + 21146708
CGUGGCGUAAGAAACAUACUUAAAAGGCACUCCUUCUUAAAUUACAAUAUUUUAUUACAGUCUAACUUG---------------GCAAUAAAUAUUGUAGUUAAAAGUUCCGGCUAGGCCGUGAAAAAUUGACUUAGGGAGUGUGCUUUUCACCA
.((..(....)..)).......((((((((..((((((((..((((((((((.(((...(((......)---------------)))))))))))))))(((((...(((((((...)))).)))...))))))))))))).))))))))..... ( -38.50, z-score =  -3.09, R)
>droSim1.chr2R 5677951 155 + 19596830
CGUGGCGUAAGAAACAUACUUAAAAGGCACUCCCUCUUAAAUUACAAUAAUUUAUUACAGUCUAACUUGUCUUUUACUGCACUGGCAAUAAAUAUUGUAGUUAAAAGUUCCGGCUAGGCCGUGAAAAAUUGACUAAGGGAGUGUGCUUUUAACUA
.((..(....)..))....((((((((((((((((.......(((((((.((((((.(((((................).))))..)))))))))))))(((((...(((((((...)))).)))...)))))..))))))))).)))))))... ( -44.29, z-score =  -3.65, R)
>droSec1.super_1 4699395 141 + 14215200
CGUGGCGUAAGAAACAUACUUAAAAGGCACUCCCUCUUAAAUUACAAUAAUUUAUUACAGUCUAACUUGUCUUUUACUGCACUGGCAAUAAAUAUUGUAGUUAAGAGUUCCGGCUAGGC--------------UAAGGGUGUGUGCUUUUAACUA
.((..(....)..))....(((((((((((.((((..(((((((...)))))))....((((((.((.(.(((((((((((.((........)).))))).))))))..).)).)))))--------------).)))).)))).)))))))... ( -35.10, z-score =  -1.52, R)
>consensus
CGUGGCGUAAGAAACAUACUUAAAAGGCACUCCCUCUUAAAUUACAAUAAUUUAUUACAGUCUAACUUGUCUUUUACUGCACUGGCAAUAAAUAUUGUAGUUAAAAGUUCCGGCUAGGCCGUGAAAAAUUGACUAAGGGAGUGUGCUUUUAACUA
.((..(....)..))....((((((((((((((((....((((((((((.((((((...(((.....................)))))))))))))))))))........((((...))))..............))))))))).)))))))... (-27.05 = -30.50 +   3.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,130,572 – 7,130,712
Length 140
Sequences 3
Columns 155
Reading direction reverse
Mean pairwise identity 84.52
Shannon entropy 0.21328
G+C content 0.35789
Mean single sequence MFE -35.24
Consensus MFE -26.41
Energy contribution -27.64
Covariance contribution 1.23
Combinations/Pair 1.05
Mean z-score -2.36
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.27
SVM RNA-class probability 0.918679
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7130572 140 - 21146708
UGGUGAAAAGCACACUCCCUAAGUCAAUUUUUCACGGCCUAGCCGGAACUUUUAACUACAAUAUUUAUUGC---------------CAAGUUAGACUGUAAUAAAAUAUUGUAAUUUAAGAAGGAGUGCCUUUUAAGUAUGUUUCUUACGCCACG
((((((((((..((((((............(((.((((...))))))).((((((.(((((((((((((((---------------..((.....))))))).))))))))))..)))))).)))))).)))))(((.......))).))))).. ( -35.00, z-score =  -2.84, R)
>droSim1.chr2R 5677951 155 - 19596830
UAGUUAAAAGCACACUCCCUUAGUCAAUUUUUCACGGCCUAGCCGGAACUUUUAACUACAAUAUUUAUUGCCAGUGCAGUAAAAGACAAGUUAGACUGUAAUAAAUUAUUGUAAUUUAAGAGGGAGUGCCUUUUAAGUAUGUUUCUUACGCCACG
((.(((((((..(((((((((((((.....(((.((((...)))))))....(((((......((((((((....)))))))).....)))))))))....(((((((...))))))).))))))))).))))))).))................ ( -41.20, z-score =  -3.41, R)
>droSec1.super_1 4699395 141 - 14215200
UAGUUAAAAGCACACACCCUUA--------------GCCUAGCCGGAACUCUUAACUACAAUAUUUAUUGCCAGUGCAGUAAAAGACAAGUUAGACUGUAAUAAAUUAUUGUAAUUUAAGAGGGAGUGCCUUUUAAGUAUGUUUCUUACGCCACG
((.(((((((..(((.(((...--------------.((.....))...((((((.(((((((((((((((.(((...................))))))))))).)))))))..))))))))).))).))))))).))................ ( -29.51, z-score =  -0.82, R)
>consensus
UAGUUAAAAGCACACUCCCUUAGUCAAUUUUUCACGGCCUAGCCGGAACUUUUAACUACAAUAUUUAUUGCCAGUGCAGUAAAAGACAAGUUAGACUGUAAUAAAUUAUUGUAAUUUAAGAGGGAGUGCCUUUUAAGUAUGUUUCUUACGCCACG
((.(((((((..(((((((...............((((...))))....((((((.(((((((((((((((..........................)))))))).)))))))..))))))))))))).))))))).))................ (-26.41 = -27.64 +   1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:14:53 2011