Locus 11655

Sequence ID dm3.chr3R
Location 22,772,983 – 22,773,065
Length 82
Max. P 0.995595
window16013 window16014

overview

Window 3

Location 22,772,983 – 22,773,065
Length 82
Sequences 12
Columns 83
Reading direction forward
Mean pairwise identity 82.90
Shannon entropy 0.40671
G+C content 0.45173
Mean single sequence MFE -23.47
Consensus MFE -20.16
Energy contribution -20.49
Covariance contribution 0.33
Combinations/Pair 1.22
Mean z-score -2.38
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.82
SVM RNA-class probability 0.995595
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22772983 82 + 27905053
AAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGCGUUGGCA
..((((((((((((-.......)))))....((((((.....))))))...................)))))))((....)). ( -25.80, z-score =  -2.76, R)
>droSim1.chr3R 22603902 82 + 27517382
AAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGCGAUGUCA
..((((((((((((-.......)))))....((((((.....))))))...................)))))))......... ( -24.40, z-score =  -2.65, R)
>droSec1.super_14 1957473 79 + 2068291
CAGGUUCCACCGAG-AUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCUCGCUG---
.(((((((((((((-.......))))).....((.((((((....)))))).)).............)))))))).....--- ( -27.00, z-score =  -2.97, R)
>droYak2.chr3R 5119425 82 - 28832112
AAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGCGUUGUCA
..((((((((((((-.......)))))....((((((.....))))))...................)))))))......... ( -24.40, z-score =  -2.56, R)
>droEre2.scaffold_4820 5203929 82 - 10470090
AAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGCGUCUUCA
..((((((((((((-.......)))))....((((((.....))))))...................)))))))......... ( -24.40, z-score =  -2.77, R)
>droAna3.scaffold_13340 7143042 82 - 23697760
CAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGUGUUGUCU
..((((((((((((-.......)))))....((((((.....))))))...................)))))))......... ( -24.40, z-score =  -2.40, R)
>dp4.chr2 26119366 82 - 30794189
AAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGUGUUGUCA
..((((((((((((-.......)))))....((((((.....))))))...................)))))))......... ( -24.40, z-score =  -2.43, R)
>droPer1.super_19 1495859 82 - 1869541
AAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGUGCUGUCA
..((((((((((((-.......)))))....((((((.....))))))...................)))))))......... ( -24.40, z-score =  -2.41, R)
>droWil1.scaffold_181130 6044058 82 + 16660200
AAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCUUGUUGACA
((((((((((((((-.......)))))....((((((.....))))))...................)))))))))....... ( -25.70, z-score =  -3.32, R)
>droGri2.scaffold_15074 1845805 82 + 7742996
CAGGUUCUACCGAG-AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGUGCUGACA
..((((((((((((-.......)))))....((((((.....))))))...................)))))))......... ( -24.40, z-score =  -2.58, R)
>anoGam1.chr3L 12831886 82 - 41284009
UAGGUUCCACCGAG-AUUUGAACUCGGAUCGUUGGAUUCAGAGUCCAAAGUGCUAACCAUUACACCAUGGAACCCGGUUGACA
..((((((((((((-.......)))))....((((((.....))))))...................)))))))......... ( -23.50, z-score =  -1.49, R)
>triCas2.ChLG2 12682557 71 + 12900155
--------ACCGAAUGGCUCAAAGAAAAAAAUUAGUCUUAUUUUGUAAAUUAAUGUUAAUUAAUUGGUUCACUUUGGUC----
--------(((((((((..(.((((..........))))........(((((((....))))))))..))).)))))).---- (  -8.80, z-score =  -0.26, R)
>consensus
AAGGUUCUACCGAG_AUUUGAACUCGGAUCGCUGGAUUCAAAGUCCAGAGUGCUAACCAUUACACCAUAGAACCGCGUUGUCA
..((((((((((((........)))))....((((((.....))))))...................)))))))......... (-20.16 = -20.49 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,772,983 – 22,773,065
Length 82
Sequences 12
Columns 83
Reading direction reverse
Mean pairwise identity 82.90
Shannon entropy 0.40671
G+C content 0.45173
Mean single sequence MFE -22.90
Consensus MFE -19.45
Energy contribution -19.80
Covariance contribution 0.35
Combinations/Pair 1.27
Mean z-score -1.55
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.72
SVM RNA-class probability 0.963202
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 22772983 82 - 27905053
UGCCAACGCGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUU
.((....))(((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))).. ( -24.10, z-score =  -1.62, R)
>droSim1.chr3R 22603902 82 - 27517382
UGACAUCGCGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUU
.........(((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))).. ( -23.70, z-score =  -1.48, R)
>droSec1.super_14 1957473 79 - 2068291
---CAGCGAGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAU-CUCGGUGGAACCUG
---.....((((((((.(((((........)))))(((((.......)))))....(((((.......-))))))))))))). ( -26.90, z-score =  -1.93, R)
>droYak2.chr3R 5119425 82 + 28832112
UGACAACGCGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUU
.........(((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))).. ( -23.70, z-score =  -1.57, R)
>droEre2.scaffold_4820 5203929 82 + 10470090
UGAAGACGCGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUU
.........(((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))).. ( -23.70, z-score =  -1.37, R)
>droAna3.scaffold_13340 7143042 82 + 23697760
AGACAACACGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUG
.........(((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))).. ( -23.70, z-score =  -1.65, R)
>dp4.chr2 26119366 82 + 30794189
UGACAACACGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUU
.........(((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))).. ( -23.70, z-score =  -1.72, R)
>droPer1.super_19 1495859 82 + 1869541
UGACAGCACGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUU
.........(((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))).. ( -23.70, z-score =  -1.46, R)
>droWil1.scaffold_181130 6044058 82 - 16660200
UGUCAACAAGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUU
.......(((((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))))) ( -25.00, z-score =  -2.35, R)
>droGri2.scaffold_15074 1845805 82 - 7742996
UGUCAGCACGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU-CUCGGUAGAACCUG
.........(((((((.(((((........)))))(((((.......)))))....(((((.......-)))))))))))).. ( -23.70, z-score =  -1.45, R)
>anoGam1.chr3L 12831886 82 + 41284009
UGUCAACCGGGUUCCAUGGUGUAAUGGUUAGCACUUUGGACUCUGAAUCCAACGAUCCGAGUUCAAAU-CUCGGUGGAACCUA
........((((((((((((((........)))))((((((((.((.((....)))).))))))))..-....))))))))). ( -27.80, z-score =  -2.32, R)
>triCas2.ChLG2 12682557 71 - 12900155
----GACCAAAGUGAACCAAUUAAUUAACAUUAAUUUACAAAAUAAGACUAAUUUUUUUCUUUGAGCCAUUCGGU--------
----.(((..((((....(((((((....)))))))..((((..((((......))))..))))...)))).)))-------- (  -5.10, z-score =   0.38, R)
>consensus
UGACAACACGGUUCUAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAU_CUCGGUAGAACCUU
.........(((((((.(((((........)))))(((((.......)))))....(((((........)))))))))))).. (-19.45 = -19.80 +   0.35)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:47:01 2011