Locus 4786

Sequence ID dm3.chr2R
Location 15,640,705 – 15,640,830
Length 125
Max. P 0.999027
window6573 window6574

overview

Window 3

Location 15,640,705 – 15,640,830
Length 125
Sequences 3
Columns 127
Reading direction forward
Mean pairwise identity 78.89
Shannon entropy 0.29250
G+C content 0.52523
Mean single sequence MFE -43.66
Consensus MFE -34.70
Energy contribution -34.27
Covariance contribution -0.43
Combinations/Pair 1.24
Mean z-score -1.74
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.876635
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15640705 125 + 21146708
ACGAGGCCAACAACACGCGGUGUUCCCAAGCGGUCCCCCAUCUAAGUACUAA--CCGCGCCCGACGCUGCUUAAUUUCGGUGAUCGGACGAGAACCGAUGUAUUCAGCGUGGUAUGGUCGUUGGCGA
.....((((((.((.((((((((......))((....))............)--))))).((.((((((..((...(((((..((....))..)))))..))..))))))))....)).)))))).. ( -44.30, z-score =  -0.86, R)
>anoGam1.chr2L 13376492 125 + 48795086
AAGAUGCCAACGACACAUGGUUUUCCCAAGUGGUCACCCACCUAAGUACUAG--CCAUGCCCGAUGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACAUGGUAUGGUCGUUGACAA
....((.(((((((.(((((((.......((((....)))).........))--))))).((.((((((...(((.(((((..((....))..))))).)))..))))))))....))))))).)). ( -41.49, z-score =  -2.11, R)
>apiMel3.GroupUn 283677414 127 + 399230636
AAGAAACCAACAACACACGGUGUUCCCAAGCGGUCAACCGAGAAGGGACUAAAACCGUGCCCGACGUAGCUUGACUUUGGUGAUCGAACGAGAACCAGUAGUUCCUACGUGGUAUGGUCGUUGGCGA
......(((((..........(((((....(((....)))....)))))....((((((((..((((((...(((((((((..((....))..))))).)))).)))))))))))))).)))))... ( -45.20, z-score =  -2.24, R)
>consensus
AAGAAGCCAACAACACACGGUGUUCCCAAGCGGUCACCCAACUAAGUACUAA__CCGUGCCCGACGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACGUGGUAUGGUCGUUGGCGA
.....((((((.......((....((.....))....))...............(((((((..((((((...(((.(((((..((....))..))))).)))..)))))))))))))..)))))).. (-34.70 = -34.27 +  -0.43)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,640,705 – 15,640,830
Length 125
Sequences 3
Columns 127
Reading direction reverse
Mean pairwise identity 78.89
Shannon entropy 0.29250
G+C content 0.52523
Mean single sequence MFE -51.51
Consensus MFE -47.41
Energy contribution -44.43
Covariance contribution -2.98
Combinations/Pair 1.31
Mean z-score -3.80
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.60
SVM RNA-class probability 0.999027
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15640705 125 - 21146708
UCGCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGG--UUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGU
..(((((((((....((((((((......(((((..((....))..))))).......)))))).))((((((--(..((.(((((.(((....))).))))).))))))))))))))))))..... ( -55.02, z-score =  -3.57, R)
>anoGam1.chr2L 13376492 125 - 48795086
UUGUCAACGACCAUACCAUGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACAUCGGGCAUGG--CUAGUACUUAGGUGGGUGACCACUUGGGAAAACCAUGUGUCGUUGGCAUCUU
.((((((((((....((((((((..(((..((((..((....))..))))..)))...)))))).))((((((--......(((((((((....)))))))))....)))))))))))))))).... ( -52.80, z-score =  -4.96, R)
>apiMel3.GroupUn 283677414 127 - 399230636
UCGCCAACGACCAUACCACGUAGGAACUACUGGUUCUCGUUCGAUCACCAAAGUCAAGCUACGUCGGGCACGGUUUUAGUCCCUUCUCGGUUGACCGCUUGGGAACACCGUGUGUUGUUGGUUUCUU
..(((((((((....((((((((..(((..((((..((....))..)))).)))....)))))).))(((((((.....((((....(((....)))...))))..))))))))))))))))..... ( -46.70, z-score =  -2.88, R)
>consensus
UCGCCAACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCACGG__UUAGUACUUAGAUGGGUGACCGCUUGGGAACACCGUGUGUUGUUGGCAUCUU
..(((((((((....((((((((.......((((..((....))..))))........)))))).))((((((.....((.(((((.(((....))).))))).)).)))))))))))))))..... (-47.41 = -44.43 +  -2.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:35:57 2011