Locus 8641

Sequence ID dm3.chr3R
Location 186,740 – 186,833
Length 93
Max. P 0.987438
window11863 window11864 window11865 window11866

overview

Window 3

Location 186,740 – 186,833
Length 93
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 85.08
Shannon entropy 0.25338
G+C content 0.52560
Mean single sequence MFE -36.76
Consensus MFE -28.20
Energy contribution -28.96
Covariance contribution 0.76
Combinations/Pair 1.11
Mean z-score -2.73
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.22
SVM RNA-class probability 0.986067
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 186740 93 + 27905053
CGCUCUCGCUCUCUCUUAAGAGAGAGGGAGAGGAGAGUCCCGACGCUCGGGAAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGCAGCAACA---
..(((((.(((((((....))))))).)))))(((..(((((.....))))).....)))....(((..((((((........)))))).)))--- ( -38.90, z-score =  -2.87, R)
>droSim1.chr3R 257187 93 + 27517382
CGCUCUCGCUCUCUCCUAAGAGAGUGGGAGAGGAGAGUCCCGUCGCUCGGGCAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGCAGCAAAA---
.(((((((((((((....)))))))))))((((..(((((((.....)))).)))..))))......))((((((........))))))....--- ( -35.70, z-score =  -1.98, R)
>droSec1.super_6 301702 96 + 4358794
CGCUCUCGCUCUCUCCUAAGAGAGUGGGAGAGGAGAGUCCCGUCGCUUGGGCAUUUGAUUUAAGUGUGCGCUGUUAUCACACCAGCAGCAGCAAAA
..((((((((((((....)))))))))))).((......))...(((.(.(((((((...))))))).)((((((........))))))))).... ( -35.50, z-score =  -1.78, R)
>droYak2.chr3R 545715 93 + 28832112
-GCCCUCGUUCUCUCUUCAGAGAGAGGGAGAGGCGAGACCCGUUGCUCGAGAAUUUGAGUUAAAUGUGCGCUGUUAUUACAGCAGCAAAAAACA--
-((((((.(((((((....))))))).))).)))......((((((((((....))))))..))))((((((((....))))).))).......-- ( -35.80, z-score =  -3.64, R)
>droEre2.scaffold_4770 538094 93 + 17746568
CGCUCUCGUUCUCUCUUCAGAGAGAGGGAGAGGAGAGACACGGUCCUCGGGCAUUUGCUUAAAAUGUGCGCUGUUAUCACACCAGCAGCAACA---
..(((((.(((((((....))))))).)))))(((.(((...))))))(.((((((.....)))))).)((((((........))))))....--- ( -37.90, z-score =  -3.39, R)
>consensus
CGCUCUCGCUCUCUCUUAAGAGAGAGGGAGAGGAGAGUCCCGUCGCUCGGGCAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGCAGCAACA___
..(((((.(((((((....))))))).)))))..(((........)))(.((((((.....)))))).)((((((........))))))....... (-28.20 = -28.96 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 186,740 – 186,833
Length 93
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 85.08
Shannon entropy 0.25338
G+C content 0.52560
Mean single sequence MFE -32.26
Consensus MFE -24.74
Energy contribution -26.94
Covariance contribution 2.20
Combinations/Pair 1.11
Mean z-score -2.24
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.48
SVM RNA-class probability 0.941915
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 186740 93 - 27905053
---UGUUGCUGCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUUCCCGAGCGUCGGGACUCUCCUCUCCCUCUCUCUUAAGAGAGAGCGAGAGCG
---..(((((...((((((.........))))))...)))))..(((((.....))))).....(((((.(((((((....))))))).))))).. ( -39.90, z-score =  -4.06, R)
>droSim1.chr3R 257187 93 - 27517382
---UUUUGCUGCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUGCCCGAGCGACGGGACUCUCCUCUCCCACUCUCUUAGGAGAGAGCGAGAGCG
---.((((((...((((((.........))))))...))))))..((((.....)))).((((((((((((.........)).))))).))))).. ( -35.80, z-score =  -2.81, R)
>droSec1.super_6 301702 96 - 4358794
UUUUGCUGCUGCUGGUGUGAUAACAGCGCACACUUAAAUCAAAUGCCCAAGCGACGGGACUCUCCUCUCCCACUCUCUUAGGAGAGAGCGAGAGCG
...((.(((.((((.........))))))))).............(((.......))).((((((((((((.........)).))))).))))).. ( -28.20, z-score =  -0.68, R)
>droYak2.chr3R 545715 93 - 28832112
--UGUUUUUUGCUGCUGUAAUAACAGCGCACAUUUAACUCAAAUUCUCGAGCAACGGGUCUCGCCUCUCCCUCUCUCUGAAGAGAGAACGAGGGC-
--.(((...(((.(((((....)))))))).....))).......((((.....))))....(((.(((..((((((....))))))..))))))- ( -27.70, z-score =  -1.88, R)
>droEre2.scaffold_4770 538094 93 - 17746568
---UGUUGCUGCUGGUGUGAUAACAGCGCACAUUUUAAGCAAAUGCCCGAGGACCGUGUCUCUCCUCUCCCUCUCUCUGAAGAGAGAACGAGAGCG
---..(((((...((((((.........))))))...)))))......((((((...))).)))(((((..((((((....))))))..))))).. ( -29.70, z-score =  -1.78, R)
>consensus
___UGUUGCUGCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUGCCCGAGCGACGGGACUCUCCUCUCCCUCUCUCUUAAGAGAGAGCGAGAGCG
.....(((((...((((((.........))))))...)))))...((((.....))))......(((((.(((((((....))))))).))))).. (-24.74 = -26.94 +   2.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 186,741 – 186,833
Length 92
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 85.35
Shannon entropy 0.24844
G+C content 0.52160
Mean single sequence MFE -36.70
Consensus MFE -28.20
Energy contribution -28.96
Covariance contribution 0.76
Combinations/Pair 1.11
Mean z-score -2.79
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.28
SVM RNA-class probability 0.987438
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 186741 92 + 27905053
GCUCUCGCUCUCUCUUAAGAGAGAGGGAGAGGAGAGUCCCGACGCUCGGGAAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGCAGCAACA---
.(((((.(((((((....))))))).)))))(((..(((((.....))))).....)))....(((..((((((........)))))).)))--- ( -38.90, z-score =  -2.98, R)
>droSim1.chr3R 257188 92 + 27517382
GCUCUCGCUCUCUCCUAAGAGAGUGGGAGAGGAGAGUCCCGUCGCUCGGGCAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGCAGCAAAA---
(((((((((((((....)))))))))))((((..(((((((.....)))).)))..))))......))((((((........))))))....--- ( -35.40, z-score =  -1.98, R)
>droSec1.super_6 301703 95 + 4358794
GCUCUCGCUCUCUCCUAAGAGAGUGGGAGAGGAGAGUCCCGUCGCUUGGGCAUUUGAUUUAAGUGUGCGCUGUUAUCACACCAGCAGCAGCAAAA
.((((((((((((....)))))))))))).((......))...(((.(.(((((((...))))))).)((((((........))))))))).... ( -35.50, z-score =  -1.86, R)
>droYak2.chr3R 545715 93 + 28832112
GCCCUCGUUCUCUCUUCAGAGAGAGGGAGAGGCGAGACCCGUUGCUCGAGAAUUUGAGUUAAAUGUGCGCUGUUAUUACAGCAGCAAAAAACA--
((((((.(((((((....))))))).))).)))......((((((((((....))))))..))))((((((((....))))).))).......-- ( -35.80, z-score =  -3.64, R)
>droEre2.scaffold_4770 538095 92 + 17746568
GCUCUCGUUCUCUCUUCAGAGAGAGGGAGAGGAGAGACACGGUCCUCGGGCAUUUGCUUAAAAUGUGCGCUGUUAUCACACCAGCAGCAACA---
.(((((.(((((((....))))))).)))))(((.(((...))))))(.((((((.....)))))).)((((((........))))))....--- ( -37.90, z-score =  -3.47, R)
>consensus
GCUCUCGCUCUCUCUUAAGAGAGAGGGAGAGGAGAGUCCCGUCGCUCGGGCAUUUGCUUUAAGUGUGCGCUGUUAUCACACCAGCAGCAACA___
.(((((.(((((((....))))))).)))))..(((........)))(.((((((.....)))))).)((((((........))))))....... (-28.20 = -28.96 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 186,741 – 186,833
Length 92
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 85.35
Shannon entropy 0.24844
G+C content 0.52160
Mean single sequence MFE -32.26
Consensus MFE -24.74
Energy contribution -26.94
Covariance contribution 2.20
Combinations/Pair 1.11
Mean z-score -2.31
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.56
SVM RNA-class probability 0.950078
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 186741 92 - 27905053
---UGUUGCUGCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUUCCCGAGCGUCGGGACUCUCCUCUCCCUCUCUCUUAAGAGAGAGCGAGAGC
---..(((((...((((((.........))))))...)))))..(((((.....))))).....(((((.(((((((....))))))).))))). ( -39.90, z-score =  -4.16, R)
>droSim1.chr3R 257188 92 - 27517382
---UUUUGCUGCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUGCCCGAGCGACGGGACUCUCCUCUCCCACUCUCUUAGGAGAGAGCGAGAGC
---.((((((...((((((.........))))))...))))))..((((.....)))).((((((((((((.........)).))))).))))). ( -35.80, z-score =  -2.91, R)
>droSec1.super_6 301703 95 - 4358794
UUUUGCUGCUGCUGGUGUGAUAACAGCGCACACUUAAAUCAAAUGCCCAAGCGACGGGACUCUCCUCUCCCACUCUCUUAGGAGAGAGCGAGAGC
...((.(((.((((.........))))))))).............(((.......))).((((((((((((.........)).))))).))))). ( -28.20, z-score =  -0.74, R)
>droYak2.chr3R 545715 93 - 28832112
--UGUUUUUUGCUGCUGUAAUAACAGCGCACAUUUAACUCAAAUUCUCGAGCAACGGGUCUCGCCUCUCCCUCUCUCUGAAGAGAGAACGAGGGC
--.(((...(((.(((((....)))))))).....))).......((((.....))))....(((.(((..((((((....))))))..)))))) ( -27.70, z-score =  -1.88, R)
>droEre2.scaffold_4770 538095 92 - 17746568
---UGUUGCUGCUGGUGUGAUAACAGCGCACAUUUUAAGCAAAUGCCCGAGGACCGUGUCUCUCCUCUCCCUCUCUCUGAAGAGAGAACGAGAGC
---..(((((...((((((.........))))))...)))))......((((((...))).)))(((((..((((((....))))))..))))). ( -29.70, z-score =  -1.87, R)
>consensus
___UGUUGCUGCUGGUGUGAUAACAGCGCACACUUAAAGCAAAUGCCCGAGCGACGGGACUCUCCUCUCCCUCUCUCUUAAGAGAGAGCGAGAGC
.....(((((...((((((.........))))))...)))))...((((.....))))......(((((.(((((((....))))))).))))). (-24.74 = -26.94 +   2.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:49:24 2011