Locus 5257

Sequence ID dm3.chr2R
Location 18,959,538 – 18,959,625
Length 87
Max. P 0.998484
window7206 window7207

overview

Window 6

Location 18,959,538 – 18,959,625
Length 87
Sequences 13
Columns 87
Reading direction forward
Mean pairwise identity 89.68
Shannon entropy 0.24222
G+C content 0.54616
Mean single sequence MFE -31.45
Consensus MFE -30.63
Energy contribution -29.11
Covariance contribution -1.52
Combinations/Pair 1.50
Mean z-score -3.30
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.37
SVM RNA-class probability 0.998484
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18959538 87 + 21146708
UAUCGCUGCGGACAGGACUUGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGCCU
....(((((((...(((((((((.((((..(((.....))).))))..)))))))))..........((....))...))))))).. ( -35.50, z-score =  -4.62, R)
>droSim1.chr2R 17543106 86 + 19596830
-AUCGCUGCGGACAGGACUUGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGCCU
-...(((((((...(((((((((.((((..(((.....))).))))..)))))))))..........((....))...))))))).. ( -35.50, z-score =  -4.51, R)
>droSec1.super_9 2250884 86 + 3197100
-AUCGCUGCGGACAGGACUUGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGCCU
-...(((((((...(((((((((.((((..(((.....))).))))..)))))))))..........((....))...))))))).. ( -35.50, z-score =  -4.51, R)
>droYak2.chr2R 18921864 86 + 21139217
-AUCGCUGCGGACAGGACUUGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGCCU
-...(((((((...(((((((((.((((..(((.....))).))))..)))))))))..........((....))...))))))).. ( -35.50, z-score =  -4.51, R)
>droEre2.scaffold_4845 20322904 86 + 22589142
-AUCGCUGCGGACAGGACUUGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGCCU
-...(((((((...(((((((((.((((..(((.....))).))))..)))))))))..........((....))...))))))).. ( -35.50, z-score =  -4.51, R)
>droAna3.scaffold_13266 15288896 87 + 19884421
UUUCGCUGCGGACAGGAUUCGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCGCUCGGACACCGCAGCUU
....((((((((((((.......)))))(((((.....))).((((((.....))))))..........)).......))))))).. ( -32.80, z-score =  -3.21, R)
>dp4.chr3 16427764 82 - 19779522
---CGCUGCGGACAGGAUUCGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGC--
---.((((((((((((.......)))))..(((.....))).((((((.....))))))........((....))...)))))))-- ( -29.60, z-score =  -2.80, R)
>droPer1.super_2 5491427 82 - 9036312
---CGCUGCGGACAGGAUUCGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGC--
---.((((((((((((.......)))))..(((.....))).((((((.....))))))........((....))...)))))))-- ( -29.60, z-score =  -2.80, R)
>droWil1.scaffold_180699 2076854 85 - 2593675
GUUCGCAGCUGGUAGGAUUCGAACCUACGCUCCCAGAGGGAAUCUGAUUUCAAGUCAGACGCCUUAACCACUCGGCCACAACUGC--
....((((.(((((((.......)))))(((.....((((..((((((.....))))))..))))........)))..)).))))-- ( -24.82, z-score =  -1.39, R)
>droMoj3.scaffold_6496 18131508 87 + 26866924
AUUCGCUGCGGACAGGAUUCGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGCUC
....((((((((((((.......)))))..(((.....))).((((((.....))))))........((....))...))))))).. ( -30.80, z-score =  -2.94, R)
>droVir3.scaffold_12875 11569674 86 - 20611582
-CCCGCUGCGGACAGGAUUCGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGCUU
-...((((((((((((.......)))))..(((.....))).((((((.....))))))........((....))...))))))).. ( -30.80, z-score =  -2.92, R)
>droGri2.scaffold_15245 15949272 85 - 18325388
AUUCGCUGCGGACAGGAUUCGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGC--
....((((((((((((.......)))))..(((.....))).((((((.....))))))........((....))...)))))))-- ( -29.60, z-score =  -2.74, R)
>anoGam1.chr2R 51289722 81 - 62725911
----GCUGUAGACAGGAUUCGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCGCUCGGACACCACAGC--
----(((((.((((((.......)))))(((((.....))).((((((.....))))))..........)).......).)))))-- ( -23.30, z-score =  -1.40, R)
>consensus
_AUCGCUGCGGACAGGAUUCGAACCUGUGCGGGUAGAACCCAAUGGAUUUCAAGUCCAUCUCCUUAACCACUCGGACACCGCAGC_U
....((((((((((((.......)))))..(((.....))).((((((.....)))))).(((..........)))..))))))).. (-30.63 = -29.11 +  -1.52)

alignment

Postscript

secondary structure

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dotplot

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Window 7

Location 18,959,538 – 18,959,625
Length 87
Sequences 13
Columns 87
Reading direction reverse
Mean pairwise identity 89.68
Shannon entropy 0.24222
G+C content 0.54616
Mean single sequence MFE -32.91
Consensus MFE -32.25
Energy contribution -30.88
Covariance contribution -1.37
Combinations/Pair 1.52
Mean z-score -2.33
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.65
SVM RNA-class probability 0.993871
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18959538 87 - 21146708
AGGCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCAAGUCCUGUCCGCAGCGAUA
..((((((((.(((..........))).).(((((((((......((((.....))))......)))))))))...))))))).... ( -35.40, z-score =  -2.81, R)
>droSim1.chr2R 17543106 86 - 19596830
AGGCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCAAGUCCUGUCCGCAGCGAU-
..((((((((.(((..........))).).(((((((((......((((.....))))......)))))))))...)))))))...- ( -35.40, z-score =  -2.84, R)
>droSec1.super_9 2250884 86 - 3197100
AGGCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCAAGUCCUGUCCGCAGCGAU-
..((((((((.(((..........))).).(((((((((......((((.....))))......)))))))))...)))))))...- ( -35.40, z-score =  -2.84, R)
>droYak2.chr2R 18921864 86 - 21139217
AGGCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCAAGUCCUGUCCGCAGCGAU-
..((((((((.(((..........))).).(((((((((......((((.....))))......)))))))))...)))))))...- ( -35.40, z-score =  -2.84, R)
>droEre2.scaffold_4845 20322904 86 - 22589142
AGGCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCAAGUCCUGUCCGCAGCGAU-
..((((((((.(((..........))).).(((((((((......((((.....))))......)))))))))...)))))))...- ( -35.40, z-score =  -2.84, R)
>droAna3.scaffold_13266 15288896 87 - 19884421
AAGCUGCGGUGUCCGAGCGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCGAAUCCUGUCCGCAGCGAAA
..(((((((.......((((.((..(.((((((.......))))))...)..)).))))(((((.......)))))))))))).... ( -33.80, z-score =  -2.43, R)
>dp4.chr3 16427764 82 + 19779522
--GCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCGAAUCCUGUCCGCAGCG---
--(((((((.......((((.((..(.((((((.......))))))...)..)).))))(((((.......)))))))))))).--- ( -31.70, z-score =  -2.29, R)
>droPer1.super_2 5491427 82 + 9036312
--GCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCGAAUCCUGUCCGCAGCG---
--(((((((.......((((.((..(.((((((.......))))))...)..)).))))(((((.......)))))))))))).--- ( -31.70, z-score =  -2.29, R)
>droWil1.scaffold_180699 2076854 85 + 2593675
--GCAGUUGUGGCCGAGUGGUUAAGGCGUCUGACUUGAAAUCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCAGCUGCGAAC
--((((((((((((....)))))..((((((((.......))))))((((...))))))(((((.......)))))))))))).... ( -30.00, z-score =  -1.75, R)
>droMoj3.scaffold_6496 18131508 87 - 26866924
GAGCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCGAAUCCUGUCCGCAGCGAAU
..(((((((.......((((.((..(.((((((.......))))))...)..)).))))(((((.......)))))))))))).... ( -31.90, z-score =  -1.94, R)
>droVir3.scaffold_12875 11569674 86 + 20611582
AAGCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCGAAUCCUGUCCGCAGCGGG-
..(((((((.......((((.((..(.((((((.......))))))...)..)).))))(((((.......))))))))))))...- ( -31.90, z-score =  -1.62, R)
>droGri2.scaffold_15245 15949272 85 + 18325388
--GCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCGAAUCCUGUCCGCAGCGAAU
--(((((((.......((((.((..(.((((((.......))))))...)..)).))))(((((.......)))))))))))).... ( -31.70, z-score =  -2.12, R)
>anoGam1.chr2R 51289722 81 + 62725911
--GCUGUGGUGUCCGAGCGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCGAAUCCUGUCUACAGC----
--(((((((.......((((.((..(.((((((.......))))))...)..)).))))(((((.......))))))))))))---- ( -28.10, z-score =  -1.69, R)
>consensus
A_GCUGCGGUGUCCGAGUGGUUAAGGAGAUGGACUUGAAAUCCAUUGGGUUCUACCCGCACAGGUUCGAAUCCUGUCCGCAGCGAU_
..(((((((.......((((.((..(.((((((.......))))))...)..)).))))(((((.......)))))))))))).... (-32.25 = -30.88 +  -1.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:44:47 2011