Locus 4777

Sequence ID dm3.chr2R
Location 15,618,921 – 15,619,050
Length 129
Max. P 0.998388
window6561 window6562

overview

Window 1

Location 15,618,921 – 15,619,050
Length 129
Sequences 3
Columns 129
Reading direction forward
Mean pairwise identity 79.43
Shannon entropy 0.28279
G+C content 0.52065
Mean single sequence MFE -42.06
Consensus MFE -36.41
Energy contribution -36.20
Covariance contribution -0.21
Combinations/Pair 1.28
Mean z-score -1.36
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.830411
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15618921 129 + 21146708
GUGGACGAGGCCAACAACACGCGGUGUUCCCAAGCGGUCCCUCAUCUAAGUACUAACCGCGCCCGACGCUGCUUAAUUUCGGUGAUCGGACGAGAACCGAUGUAUUCAGCGUGGUAUGGUCGUUGGCGA
.........(((((((((((...))))).(((.(((((....(......).....)))))(((..((((((..((...(((((..((....))..)))))..))..))))))))).)))..)))))).. ( -43.70, z-score =  -0.16, R)
>anoGam1.chr2L 13355661 126 + 48795086
---GAAGAUGCCAACGACACAUGGUUUUCCCAAGUGGUCACCCACCUAAGUACUAGCCAUGCCCGAUGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACAUGGUAUGGUCGUUGACAA
---.....((.(((((((.(((((((.......((((....)))).........))))))).((.((((((...(((.(((((..((....))..))))).)))..))))))))....))))))).)). ( -41.49, z-score =  -1.98, R)
>apiMel3.GroupUn 327590583 125 - 399230636
----AAGAAACCAACAACACACGGUGUUCCCAAGCGGUCACCCAUUCAAGUAUUAACCGUGCCCGACGUAGCUUGACUUUGGUGAUCGAACGAGAACCAGUAGUUCCUACGUGGUAUGGUCGUUGGCGA
----......(((((.......((((..((.....)).)))).............((((((((..((((((...(((((((((..((....))..))))).)))).)))))))))))))).)))))... ( -41.00, z-score =  -1.94, R)
>consensus
___GAAGAAGCCAACAACACACGGUGUUCCCAAGCGGUCACCCAUCUAAGUACUAACCGUGCCCGACGUUGCUUAACUUCGGUGAUCGGACGAGAACCGGUGUUUUCAACGUGGUAUGGUCGUUGGCGA
.........((((((.......((((...((....)).)))).............((((((((..((((((...(((.(((((..((....))..))))).)))..)))))))))))))).)))))).. (-36.41 = -36.20 +  -0.21)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 15,618,921 – 15,619,050
Length 129
Sequences 3
Columns 129
Reading direction reverse
Mean pairwise identity 79.43
Shannon entropy 0.28279
G+C content 0.52065
Mean single sequence MFE -49.11
Consensus MFE -46.21
Energy contribution -42.89
Covariance contribution -3.31
Combinations/Pair 1.32
Mean z-score -3.25
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.34
SVM RNA-class probability 0.998388
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15618921 129 - 21146708
UCGCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGAGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGUCCAC
..((((((((((...((((((((......(((((..((....))..))))).......)))))).))((((((((....(((....))).))))))..((.....))))).)))))))))......... ( -49.02, z-score =  -2.23, R)
>anoGam1.chr2L 13355661 126 - 48795086
UUGUCAACGACCAUACCAUGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACAUCGGGCAUGGCUAGUACUUAGGUGGGUGACCACUUGGGAAAACCAUGUGUCGUUGGCAUCUUC---
.((((((((((....((((((((..(((..((((..((....))..))))..)))...)))))).))((((((......(((((((((....)))))))))....)))))))))))))))).....--- ( -52.80, z-score =  -4.96, R)
>apiMel3.GroupUn 327590583 125 + 399230636
UCGCCAACGACCAUACCACGUAGGAACUACUGGUUCUCGUUCGAUCACCAAAGUCAAGCUACGUCGGGCACGGUUAAUACUUGAAUGGGUGACCGCUUGGGAACACCGUGUGUUGUUGGUUUCUU----
..(((((((((....((((((((..(((..((((..((....))..)))).)))....)))))).))(((((((.....((..(.(((....))).)..))...)))))))))))))))).....---- ( -45.50, z-score =  -2.56, R)
>consensus
UCGCCAACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCACGGUUAGUACUUAGAUGGGUGACCGCUUGGGAACACCGUGUGUUGUUGGCAUCUUC___
..(((((((((....((((((((.......((((..((....))..))))........)))))).))(((((((.....(((((.(((....))).)))))...))))))))))))))))......... (-46.21 = -42.89 +  -3.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:35:48 2011