Locus 11005

Sequence ID dm3.chr3R
Location 18,047,104 – 18,047,223
Length 119
Max. P 0.943858
window15121 window15122

overview

Window 1

Location 18,047,104 – 18,047,223
Length 119
Sequences 7
Columns 119
Reading direction forward
Mean pairwise identity 79.97
Shannon entropy 0.39621
G+C content 0.50169
Mean single sequence MFE -38.96
Consensus MFE -22.54
Energy contribution -25.83
Covariance contribution 3.29
Combinations/Pair 1.33
Mean z-score -2.23
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.49
SVM RNA-class probability 0.943858
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18047104 119 + 27905053
GGGAAAUGGAAAAUGAGGGGGAGGAGUUGCAAGUGUCAGCUCUGCGGCAGAGUGCAGAGUUCAAGUCGAAGUUGCUGCUGGUUGUCGCUUAACGAUUUCGUGUCAUUUUUUGCAUUUCC
.(((((((((((((((.(.(((((((((((....).)))))))(((((((...((((..(((.....)))....))))...)))))))........))).).))))))))..))))))) ( -42.20, z-score =  -2.78, R)
>droSim1.chr3R 17863309 119 + 27517382
GGGAAAUGGAAAAUGAGGGGGAGGAGUUGCAAGUGUCAGCUCUGCGGCAGAGUGCAGAGUUCAAGUCGAAGUUGCUGCUGGUUGUCGCUUAACGAUUUCGUGUCAUUUUUUGCAUUUCC
.(((((((((((((((.(.(((((((((((....).)))))))(((((((...((((..(((.....)))....))))...)))))))........))).).))))))))..))))))) ( -42.20, z-score =  -2.78, R)
>droSec1.super_0 18416358 119 + 21120651
GGGAAAUGGAAAAUGAGGGGGAGGAGUUGCAAGUGUCAGCUCUGCGGCAGAGUGCAGAGUUCAAGUCGAAGUUGCUGCUGGUUGUCGCUUAACGAUUUCGUGUCAUUUUUUGCAUUUCC
.(((((((((((((((.(.(((((((((((....).)))))))(((((((...((((..(((.....)))....))))...)))))))........))).).))))))))..))))))) ( -42.20, z-score =  -2.78, R)
>droYak2.chr3R 18898307 119 + 28832112
GGGAAAUGGAAAAUGAGGGGGUGGUGCUGCAAGUGUCAGCUCUGCGGCAGAGUGCAGAGUUCAAGUCGAAGUUGCUGCUGGUUGUCGCUUAACGAUUUCGUGUCAUUUUUUGCAUUUCC
.(((((((((((((((((((.(((..(.....)..))).))))(((((((...((((..(((.....)))....))))...)))))))...(((....))).))))))))..))))))) ( -41.50, z-score =  -2.19, R)
>droEre2.scaffold_4820 441208 119 - 10470090
GGGAAAUGGAAAAUGAGGGGGUGGAGUUGCAAGUGUCAGCUCUGCGGCAGAGUGCAGAGUUCAAGUCGAAGUUGCUGCUGGUUGUCGCUUAACGAUUUCGUGUCAUUUUUUGCAUUUCC
.(((((((((((((((.(.((.((((((((....).)))))))(((((((...((((..(((.....)))....))))...))))))).........)).).))))))))..))))))) ( -40.60, z-score =  -2.36, R)
>dp4.chr2 12237807 98 + 30794189
GGGGGGUGUGGGGGCAGGGAGGACUGUUGCAAGUGUCAG-------GCGGAG-GCAGAGUUCAAGUCGAAGU-------------CGCUUAACGAUUCCGUGUCAUUUUUUGCAUUUCC
.((..(((..((((((.((((.(((......)))((.((-------((((.(-((.........)))....)-------------))))).))..)))).))))....))..)))..)) ( -30.40, z-score =  -1.11, R)
>droMoj3.scaffold_6540 27745019 97 + 34148556
UGCAACUGGCAACAGGGGCCGUGGCAUUUCCGUUGCCUG------GGCAC-GCGCUU-GUUAGAAGCGAAGCU--------------CUUAACGAUAUCGUGUCAUUUUUUGCAUUUCC
((((((.((((((.(((((....))...))))))))).)------(((((-(...((-((((..(((...)))--------------..))))))...)))))).....)))))..... ( -33.60, z-score =  -1.62, R)
>consensus
GGGAAAUGGAAAAUGAGGGGGAGGAGUUGCAAGUGUCAGCUCUGCGGCAGAGUGCAGAGUUCAAGUCGAAGUUGCUGCUGGUUGUCGCUUAACGAUUUCGUGUCAUUUUUUGCAUUUCC
.(((((((((((((((.(.((((..((((..((((.(((((..(((((((..((............))...))))))).))))).))))))))..)))).).))))))))..))))))) (-22.54 = -25.83 +   3.29)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 18,047,104 – 18,047,223
Length 119
Sequences 7
Columns 119
Reading direction reverse
Mean pairwise identity 79.97
Shannon entropy 0.39621
G+C content 0.50169
Mean single sequence MFE -26.63
Consensus MFE -9.89
Energy contribution -15.14
Covariance contribution 5.25
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.777349
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18047104 119 - 27905053
GGAAAUGCAAAAAAUGACACGAAAUCGUUAAGCGACAACCAGCAGCAACUUCGACUUGAACUCUGCACUCUGCCGCAGAGCUGACACUUGCAACUCCUCCCCCUCAUUUUCCAUUUCCC
(((((((...(((((((.(((....)))...((((....((((......(((.....))).(((((........)))))))))....))))............))))))).))))))). ( -28.00, z-score =  -3.41, R)
>droSim1.chr3R 17863309 119 - 27517382
GGAAAUGCAAAAAAUGACACGAAAUCGUUAAGCGACAACCAGCAGCAACUUCGACUUGAACUCUGCACUCUGCCGCAGAGCUGACACUUGCAACUCCUCCCCCUCAUUUUCCAUUUCCC
(((((((...(((((((.(((....)))...((((....((((......(((.....))).(((((........)))))))))....))))............))))))).))))))). ( -28.00, z-score =  -3.41, R)
>droSec1.super_0 18416358 119 - 21120651
GGAAAUGCAAAAAAUGACACGAAAUCGUUAAGCGACAACCAGCAGCAACUUCGACUUGAACUCUGCACUCUGCCGCAGAGCUGACACUUGCAACUCCUCCCCCUCAUUUUCCAUUUCCC
(((((((...(((((((.(((....)))...((((....((((......(((.....))).(((((........)))))))))....))))............))))))).))))))). ( -28.00, z-score =  -3.41, R)
>droYak2.chr3R 18898307 119 - 28832112
GGAAAUGCAAAAAAUGACACGAAAUCGUUAAGCGACAACCAGCAGCAACUUCGACUUGAACUCUGCACUCUGCCGCAGAGCUGACACUUGCAGCACCACCCCCUCAUUUUCCAUUUCCC
(((((((...(((((((.(((....)))...((..(((....((((...(((.....))).(((((........)))))))))....)))..)).........))))))).))))))). ( -29.80, z-score =  -3.57, R)
>droEre2.scaffold_4820 441208 119 + 10470090
GGAAAUGCAAAAAAUGACACGAAAUCGUUAAGCGACAACCAGCAGCAACUUCGACUUGAACUCUGCACUCUGCCGCAGAGCUGACACUUGCAACUCCACCCCCUCAUUUUCCAUUUCCC
(((((((...(((((((.(((....)))...((((....((((......(((.....))).(((((........)))))))))....))))............))))))).))))))). ( -28.00, z-score =  -3.56, R)
>dp4.chr2 12237807 98 - 30794189
GGAAAUGCAAAAAAUGACACGGAAUCGUUAAGCG-------------ACUUCGACUUGAACUCUGC-CUCCGC-------CUGACACUUGCAACAGUCCUCCCUGCCCCCACACCCCCC
(((..(((((.........((((..(((((((((-------------....)).)))))....)).-.)))).-------.......)))))....))).................... ( -14.73, z-score =  -0.31, R)
>droMoj3.scaffold_6540 27745019 97 - 34148556
GGAAAUGCAAAAAAUGACACGAUAUCGUUAAG--------------AGCUUCGCUUCUAAC-AAGCGC-GUGCC------CAGGCAACGGAAAUGCCACGGCCCCUGUUGCCAGUUGCA
.....(((((....((.((((.....((((..--------------(((...)))..))))-.....)-)))..------))((((((((....((....))..))))))))..))))) ( -29.90, z-score =  -1.31, R)
>consensus
GGAAAUGCAAAAAAUGACACGAAAUCGUUAAGCGACAACCAGCAGCAACUUCGACUUGAACUCUGCACUCUGCCGCAGAGCUGACACUUGCAACUCCACCCCCUCAUUUUCCAUUUCCC
(((((((...(((((((.(((....)))...((((....((((......(((.....))).(((((........)))))))))....))))............))))))).))))))). ( -9.89 = -15.14 +   5.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:34:35 2011