Locus 4736

Sequence ID dm3.chr2R
Location 15,393,839 – 15,393,923
Length 84
Max. P 0.995261
window6499 window6500

overview

Window 9

Location 15,393,839 – 15,393,923
Length 84
Sequences 14
Columns 87
Reading direction forward
Mean pairwise identity 92.22
Shannon entropy 0.18596
G+C content 0.57143
Mean single sequence MFE -31.71
Consensus MFE -28.08
Energy contribution -28.46
Covariance contribution 0.38
Combinations/Pair 1.05
Mean z-score -3.00
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.78
SVM RNA-class probability 0.995261
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15393839 84 + 21146708
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUAUGAAGG
.(((.((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..))))))).))).... ( -33.90, z-score =  -3.31, R)
>droSim1.chr2R 14092707 84 + 19596830
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUAUGAAGG
.(((.((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..))))))).))).... ( -33.90, z-score =  -3.31, R)
>droSec1.super_1 12912648 84 + 14215200
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUAUGAAGG
.(((.((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..))))))).))).... ( -33.90, z-score =  -3.31, R)
>droYak2.chr2R 7357588 84 - 21139217
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUACGAAGG
.....((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))........ ( -31.70, z-score =  -2.62, R)
>droEre2.scaffold_4845 9593201 84 + 22589142
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUACGAAGG
.....((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))........ ( -31.70, z-score =  -2.62, R)
>droAna3.scaffold_13266 14368661 84 - 19884421
ACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUACGUCGG
.....((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))........ ( -31.70, z-score =  -2.19, R)
>dp4.chr3 12520878 84 + 19779522
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUACGAAGA
.....((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))........ ( -31.70, z-score =  -2.78, R)
>droPer1.super_99 151300 84 - 176816
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUACGAAGA
.....((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))........ ( -31.70, z-score =  -2.78, R)
>droWil1.scaffold_180701 1374974 84 + 3904529
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUAUUGAAG
.((..((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))...))... ( -32.30, z-score =  -3.22, R)
>droVir3.scaffold_12875 16266562 84 - 20611582
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUACCGAAG
.....((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))........ ( -31.70, z-score =  -2.82, R)
>droMoj3.scaffold_6496 20696146 84 + 26866924
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUAUUGAAG
.((..((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))...))... ( -32.30, z-score =  -3.22, R)
>droGri2.scaffold_15112 1906239 84 + 5172618
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGGCUAUUGAAG
.((..((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))...))... ( -32.30, z-score =  -3.22, R)
>anoGam1.chr2L 19552914 84 - 48795086
ACACUGCCGUGACCAGGAUUCGAACCUGGGUUACUACGGCCACAACGUAGGGUCCUAACCACUAG---ACGAUCACGGCUUCAGAUG
.....((((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))))........ ( -29.70, z-score =  -2.96, R)
>triCas2.ChLG7 1603135 72 + 17478683
GCCUAGCCGUGACCAGGAUUCGAACCUGGUUUACUACGGCC-----------UCCUAACCACUAGCCGACGAUCACGGCGAUG----
.....((((((((((((.......))))).......((((.-----------............))))....)))))))....---- ( -25.42, z-score =  -3.66, R)
>consensus
GCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG___ACGAUCACGGCUACGAAGG
.....((((((((((((.......)))))....(((((.......)))))(((....)))............)))))))........ (-28.08 = -28.46 +   0.38)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,393,839 – 15,393,923
Length 84
Sequences 14
Columns 87
Reading direction reverse
Mean pairwise identity 92.22
Shannon entropy 0.18596
G+C content 0.57143
Mean single sequence MFE -30.19
Consensus MFE -29.30
Energy contribution -29.41
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965552
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15393839 84 - 21146708
CCUUCAUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
....(((.(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).))). ( -30.70, z-score =  -1.84, R)
>droSim1.chr2R 14092707 84 - 19596830
CCUUCAUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
....(((.(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).))). ( -30.70, z-score =  -1.84, R)
>droSec1.super_1 12912648 84 - 14215200
CCUUCAUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
....(((.(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).))). ( -30.70, z-score =  -1.84, R)
>droYak2.chr2R 7357588 84 + 21139217
CCUUCGUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
....(((.(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).))). ( -30.30, z-score =  -1.53, R)
>droEre2.scaffold_4845 9593201 84 - 22589142
CCUUCGUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
....(((.(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).))). ( -30.30, z-score =  -1.53, R)
>droAna3.scaffold_13266 14368661 84 + 19884421
CCGACGUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGU
...((((.(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).)))) ( -31.90, z-score =  -1.64, R)
>dp4.chr3 12520878 84 - 19779522
UCUUCGUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
....(((.(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).))). ( -30.30, z-score =  -1.63, R)
>droPer1.super_99 151300 84 + 176816
UCUUCGUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
....(((.(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).))). ( -30.30, z-score =  -1.63, R)
>droWil1.scaffold_180701 1374974 84 - 3904529
CUUCAAUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
........(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))))..... ( -30.00, z-score =  -1.82, R)
>droVir3.scaffold_12875 16266562 84 + 20611582
CUUCGGUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
........(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))))..... ( -30.00, z-score =  -1.14, R)
>droMoj3.scaffold_6496 20696146 84 - 26866924
CUUCAAUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
........(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))))..... ( -30.00, z-score =  -1.82, R)
>droGri2.scaffold_15112 1906239 84 - 5172618
CUUCAAUAGCCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
........(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))))..... ( -30.00, z-score =  -1.82, R)
>anoGam1.chr2L 19552914 84 + 48795086
CAUCUGAAGCCGUGAUCGU---CUAGUGGUUAGGACCCUACGUUGUGGCCGUAGUAACCCAGGUUCGAAUCCUGGUCACGGCAGUGU
........(((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))))..... ( -30.30, z-score =  -2.14, R)
>triCas2.ChLG7 1603135 72 - 17478683
----CAUCGCCGUGAUCGUCGGCUAGUGGUUAGGA-----------GGCCGUAGUAAACCAGGUUCGAAUCCUGGUCACGGCUAGGC
----....(((((((......((((.(((((....-----------)))))))))...(((((.......))))))))))))..... ( -27.20, z-score =  -2.11, R)
>consensus
CCUUCAUAGCCGUGAUCGU___CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGC
........(((((((.......(((.((((((.(((.....))).)))))))))....(((((.......))))))))))))..... (-29.30 = -29.41 +   0.11)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:34:58 2011