Locus 9690

Sequence ID dm3.chr3R
Location 8,274,112 – 8,274,213
Length 101
Max. P 0.838775
window13293 window13294

overview

Window 3

Location 8,274,112 – 8,274,213
Length 101
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 66.55
Shannon entropy 0.53059
G+C content 0.44159
Mean single sequence MFE -22.36
Consensus MFE -10.40
Energy contribution -11.00
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.32
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.570866
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8274112 101 + 27905053
------------------AUACUAUUCGGAUCACCGGGAUGGACCUAUACCAAACCCAUUCAAAGUACUUUGGUGUUGCCCGAUGCACCAUUAAGAUUGGAUCAAAAAGCGAAUGAUCC
------------------.((((...(((....)))((((((.............))))))..))))(((((((((........))))))..)))...((((((.........)))))) ( -23.52, z-score =  -0.81, R)
>droEre2.scaffold_4770 4399613 113 - 17746568
ACCACAAGUGGUAAGCAAAUAGAAUUCGGAUCACCGGGAUGGAAGUAUACCAUUCCAA------AUACUCCGGCUACGCCCCAAGCCCCAAUGAGCUUGAAUCAAAAGACGAAUGAUCC
((((....))))...............((((((..(((((((.......)))))))..------.......(((...))).(((((........)))))..............)))))) ( -27.80, z-score =  -1.67, R)
>droYak2.chr3R 12597443 119 + 28832112
ACCACAAAUAGUAAGCAAAUACUAUUCGGAUCACCGGGAUGGACGUAUACCAAACCCAUUCAAAGUACUCCGGCUACGCCCAGUGCAACAAUCAAAUUGAAUCAAAAAACGAAUGAUCC
......(((((((......))))))).(((((...(((.(((.......)))..)))((((...(((((..(((...))).)))))..((((...))))...........))))))))) ( -25.50, z-score =  -2.27, R)
>droSec1.super_0 7447392 77 - 21120651
------------------AUACUAUUCGGAUCACCGGGAUGGUCCUAUACCAAACCC------------------------GAUGCACCAUUAAGAUUGGAUCAAAAAGCGAAUGAUCC
------------------.........((((((.((((.((((.....))))..)))------------------------).....(((.......))).............)))))) ( -18.70, z-score =  -1.38, R)
>droSim1.chr3R 14402022 77 - 27517382
------------------AUACUAUUCGGAUCACCGGGAUGGUCCUAUAGCAAACCC------------------------GAUGCACCAUUAAGAUUGGAUCAAAAAGCGAAUGAUCC
------------------.........((((((.((((...((......))...)))------------------------).....(((.......))).............)))))) ( -16.30, z-score =  -0.47, R)
>consensus
__________________AUACUAUUCGGAUCACCGGGAUGGACCUAUACCAAACCCA_______UACU__GG____GCCCGAUGCACCAUUAAGAUUGGAUCAAAAAGCGAAUGAUCC
...........................((((((..((..(((.......)))..))...............................(((.......))).............)))))) (-10.40 = -11.00 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,274,112 – 8,274,213
Length 101
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 66.55
Shannon entropy 0.53059
G+C content 0.44159
Mean single sequence MFE -29.18
Consensus MFE -14.46
Energy contribution -14.90
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -1.53
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.838775
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8274112 101 - 27905053
GGAUCAUUCGCUUUUUGAUCCAAUCUUAAUGGUGCAUCGGGCAACACCAAAGUACUUUGAAUGGGUUUGGUAUAGGUCCAUCCCGGUGAUCCGAAUAGUAU------------------
((((((.........))))))........(((..(((((((......((((....)))).((((..(((...)))..)))))))))))..)))........------------------ ( -26.80, z-score =  -0.58, R)
>droEre2.scaffold_4770 4399613 113 + 17746568
GGAUCAUUCGUCUUUUGAUUCAAGCUCAUUGGGGCUUGGGGCGUAGCCGGAGUAU------UUGGAAUGGUAUACUUCCAUCCCGGUGAUCCGAAUUCUAUUUGCUUACCACUUGUGGU
(((((...(((((.......(((((((....))))))))))))..(((((.(...------.(((((.(.....)))))).)))))))))))...............((((....)))) ( -35.91, z-score =  -1.42, R)
>droYak2.chr3R 12597443 119 - 28832112
GGAUCAUUCGUUUUUUGAUUCAAUUUGAUUGUUGCACUGGGCGUAGCCGGAGUACUUUGAAUGGGUUUGGUAUACGUCCAUCCCGGUGAUCCGAAUAGUAUUUGCUUACUAUUUGUGGU
((((((.........)))))).....(((..(((...((((((((((((((...((......)).)))))).))))))))...)))..)))(((((((((......))))))))).... ( -35.30, z-score =  -2.01, R)
>droSec1.super_0 7447392 77 + 21120651
GGAUCAUUCGCUUUUUGAUCCAAUCUUAAUGGUGCAUC------------------------GGGUUUGGUAUAGGACCAUCCCGGUGAUCCGAAUAGUAU------------------
((((((.........))))))........(((..((((------------------------(((..((((.....)))).)))))))..)))........------------------ ( -26.70, z-score =  -2.60, R)
>droSim1.chr3R 14402022 77 + 27517382
GGAUCAUUCGCUUUUUGAUCCAAUCUUAAUGGUGCAUC------------------------GGGUUUGCUAUAGGACCAUCCCGGUGAUCCGAAUAGUAU------------------
((((((.........))))))........(((..((((------------------------(((....(.....).....)))))))..)))........------------------ ( -21.20, z-score =  -1.03, R)
>consensus
GGAUCAUUCGCUUUUUGAUCCAAUCUUAAUGGUGCAUCGGGC____CC__AGUA_______UGGGUUUGGUAUAGGUCCAUCCCGGUGAUCCGAAUAGUAU__________________
((((((((.((...((((.......))))....))............................((..(((.......)))..))))))))))........................... (-14.46 = -14.90 +   0.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:09:14 2011