Locus 10862

Sequence ID dm3.chr3R
Location 17,110,708 – 17,110,780
Length 72
Max. P 0.980017
window14926 window14927

overview

Window 6

Location 17,110,708 – 17,110,780
Length 72
Sequences 6
Columns 72
Reading direction forward
Mean pairwise identity 86.61
Shannon entropy 0.24820
G+C content 0.37613
Mean single sequence MFE -16.40
Consensus MFE -12.90
Energy contribution -13.04
Covariance contribution 0.14
Combinations/Pair 1.12
Mean z-score -2.55
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.04
SVM RNA-class probability 0.980017
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17110708 72 + 27905053
GACUGCCUAACUUAAUUUGUAUUCCUUUUACUCCAUUUUGUGGCUGGAUGAUGAUGGUAAAUGGAAUACACG
.................((((((((.((((((.((((............))))..)))))).)))))))).. ( -15.40, z-score =  -2.34, R)
>droEre2.scaffold_4770 13196678 68 - 17746568
GACUGCCUAACUUAAUUUGUAUUCCUUUUACUCCAUUUUGUGGCAGGA----GAUGGUAAAUGGAAUACACG
.................((((((((.((((((...(((((...)))))----...)))))).)))))))).. ( -16.30, z-score =  -2.28, R)
>droYak2.chr3R 5911556 68 + 28832112
GACUGCCUAACUUAAUUUGUAUUCCUUUUACUCCAUUUUGUGGCAGGA----GAUGGUAAAUGGAAUACACG
.................((((((((.((((((...(((((...)))))----...)))))).)))))))).. ( -16.30, z-score =  -2.28, R)
>droSec1.super_38 382242 72 - 400794
GACUGCCUAACUUAAUUUGUAUUCCUUUUACUCCAUCUUGUGGCAGGAUGAUGUUGGUAAAUGGAAUACACG
.................((((((((.((((((.(((((((...))))))).....)))))).)))))))).. ( -19.80, z-score =  -3.32, R)
>droSim1.chr3R 23168761 72 - 27517382
GACUGCCUAACUUAAUUUGUAUUCCUUUUACUCCAUCUUGUGGCAGGAUGAUGAUGGUAAAUGGAAUACACG
.................((((((((.((((((.(((((((...))))))).....)))))).)))))))).. ( -19.80, z-score =  -3.48, R)
>droAna3.scaffold_13340 3771039 56 + 23697760
--UUGCCUAAGUUAAUUUGUAUUCCUUUUAUUCCAUUU--------------GAUGGAAGAUGGAAGACACG
--...............(((.((((.....((((((..--------------.))))))...)))).))).. ( -10.80, z-score =  -1.60, R)
>consensus
GACUGCCUAACUUAAUUUGUAUUCCUUUUACUCCAUUUUGUGGCAGGA____GAUGGUAAAUGGAAUACACG
.................((((((((.((((..(((((...............))))))))).)))))))).. (-12.90 = -13.04 +   0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,110,708 – 17,110,780
Length 72
Sequences 6
Columns 72
Reading direction reverse
Mean pairwise identity 86.61
Shannon entropy 0.24820
G+C content 0.37613
Mean single sequence MFE -14.80
Consensus MFE -10.50
Energy contribution -11.16
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.64
SVM RNA-class probability 0.956993
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17110708 72 - 27905053
CGUGUAUUCCAUUUACCAUCAUCAUCCAGCCACAAAAUGGAGUAAAAGGAAUACAAAUUAAGUUAGGCAGUC
..((((((((.(((((........((((.........))))))))).))))))))................. ( -15.30, z-score =  -3.35, R)
>droEre2.scaffold_4770 13196678 68 + 17746568
CGUGUAUUCCAUUUACCAUC----UCCUGCCACAAAAUGGAGUAAAAGGAAUACAAAUUAAGUUAGGCAGUC
..((((((((.(((((....----(((...........)))))))).))))))))................. ( -15.00, z-score =  -2.31, R)
>droYak2.chr3R 5911556 68 - 28832112
CGUGUAUUCCAUUUACCAUC----UCCUGCCACAAAAUGGAGUAAAAGGAAUACAAAUUAAGUUAGGCAGUC
..((((((((.(((((....----(((...........)))))))).))))))))................. ( -15.00, z-score =  -2.31, R)
>droSec1.super_38 382242 72 + 400794
CGUGUAUUCCAUUUACCAACAUCAUCCUGCCACAAGAUGGAGUAAAAGGAAUACAAAUUAAGUUAGGCAGUC
..((((((((.(((((...((((............))))..))))).))))))))................. ( -17.20, z-score =  -3.00, R)
>droSim1.chr3R 23168761 72 + 27517382
CGUGUAUUCCAUUUACCAUCAUCAUCCUGCCACAAGAUGGAGUAAAAGGAAUACAAAUUAAGUUAGGCAGUC
..((((((((.(((((..(((((............))))).))))).))))))))................. ( -17.00, z-score =  -2.93, R)
>droAna3.scaffold_13340 3771039 56 - 23697760
CGUGUCUUCCAUCUUCCAUC--------------AAAUGGAAUAAAAGGAAUACAAAUUAACUUAGGCAA--
..(((.((((...((((((.--------------..)))))).....)))).)))...............-- (  -9.30, z-score =  -1.60, R)
>consensus
CGUGUAUUCCAUUUACCAUC____UCCUGCCACAAAAUGGAGUAAAAGGAAUACAAAUUAAGUUAGGCAGUC
..((((((((.((((((((.................))))..)))).))))))))................. (-10.50 = -11.16 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:31:54 2011