Locus 8536

Sequence ID dm3.chr3RHet
Location 116,517 – 116,630
Length 113
Max. P 0.999792
window11726 window11727

overview

Window 6

Location 116,517 – 116,630
Length 113
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 53.01
Shannon entropy 0.70519
G+C content 0.43620
Mean single sequence MFE -28.21
Consensus MFE -17.26
Energy contribution -18.32
Covariance contribution 1.06
Combinations/Pair 1.64
Mean z-score -2.49
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.40
SVM RNA-class probability 0.999792
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 116517 113 + 2517507
GUUUUGGCGUAGCUAGAGAUGGUUUUCUCCGAGCCGAUGAUCUUCUUUCCGCGCUUAAUUCACAGUUUAAUGGCCUUACGCUAUUAGAUGAAACUCCAAAGCGCAAACAAGCC
.....(((...(((.((((......))))..)))................((((((........((((((((((.....)))))))))).........))))))......))) ( -29.43, z-score =  -1.19, R)
>dp4.Unknown_group_58 40934 92 + 69560
---------------------GUUUUAAAAAACAAUACCUUCGGCUCCUAGCCAUAGAAGCUCAGUUUAGCGGUUUAAAACUGCUGAAUGAGUCUCCGAGGUGCAAAAAGGUC
---------------------((((....))))..((((((.(((.....)))...((..((((.(((((((((.....)))))))))))))..)).)))))).......... ( -28.30, z-score =  -3.23, R)
>droPer1.super_76 130788 92 - 268861
---------------------GCUUUAAAAAGCAAUACCAUCGGCUCUUAGCCAUGGAGUCUCAAUAUGGCAGUCUGCAACUUCUGAAUGAGUCUCCGAGGCGUAAAAAGGUC
---------------------((((....)))).........(((.(((.(((.(((((.((((...(((.(((.....))).)))..)))).))))).))).....)))))) ( -24.00, z-score =  -1.30, R)
>droWil1.scaffold_181148 1061548 92 + 5435427
---------------------GUUUUAAUAAACUCCAAGCGGAGUUUACUGCGGUGGAGAAUCAGUUCAGAAGUUUAUCGCUUAUGAAUGAGUCUCCGAAACGUAAAAGGACC
---------------------(((((..((((((((....)))))))).((((.((((((.(((.((((.((((.....)))).))))))).))))))...))))..))))). ( -31.10, z-score =  -4.25, R)
>consensus
_____________________GUUUUAAAAAACAAUACCAUCGGCUCUCAGCCAUGGAGUCUCAGUUUAGCAGUCUAAAACUUCUGAAUGAGUCUCCGAAGCGCAAAAAGGCC
..................................................(((.((((((((((.(((((((((.....))))))))))))))))))).)))........... (-17.26 = -18.32 +   1.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 116,517 – 116,630
Length 113
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 53.01
Shannon entropy 0.70519
G+C content 0.43620
Mean single sequence MFE -25.03
Consensus MFE -10.82
Energy contribution -13.70
Covariance contribution 2.88
Combinations/Pair 1.52
Mean z-score -1.56
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.79
SVM RNA-class probability 0.967847
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 116517 113 - 2517507
GGCUUGUUUGCGCUUUGGAGUUUCAUCUAAUAGCGUAAGGCCAUUAAACUGUGAAUUAAGCGCGGAAAGAAGAUCAUCGGCUCGGAGAAAACCAUCUCUAGCUACGCCAAAAC
((((...((((((((((((......))))).)))))))))))......(((((.......))))).............((((.(((((......))))))))).......... ( -31.40, z-score =  -1.22, R)
>dp4.Unknown_group_58 40934 92 - 69560
GACCUUUUUGCACCUCGGAGACUCAUUCAGCAGUUUUAAACCGCUAAACUGAGCUUCUAUGGCUAGGAGCCGAAGGUAUUGUUUUUUAAAAC---------------------
.((((((.........((((.((((((.(((.((.....)).))).)).))))))))...(((.....)))))))))...............--------------------- ( -21.30, z-score =  -0.77, R)
>droPer1.super_76 130788 92 + 268861
GACCUUUUUACGCCUCGGAGACUCAUUCAGAAGUUGCAGACUGCCAUAUUGAGACUCCAUGGCUAAGAGCCGAUGGUAUUGCUUUUUAAAGC---------------------
...........(((((((((.((((......((((...)))).......)))).))))..(((.....))))).)))...((((....))))--------------------- ( -22.12, z-score =  -0.80, R)
>droWil1.scaffold_181148 1061548 92 - 5435427
GGUCCUUUUACGUUUCGGAGACUCAUUCAUAAGCGAUAAACUUCUGAACUGAUUCUCCACCGCAGUAAACUCCGCUUGGAGUUUAUUAAAAC---------------------
................(((((.(((((((.(((.......))).)))).))).))))).....((((((((((....)))))))))).....--------------------- ( -25.30, z-score =  -3.46, R)
>consensus
GACCUUUUUACGCCUCGGAGACUCAUUCAGAAGCGUUAAACCGCUAAACUGAGACUCCAUCGCUAAAAGCCGAUCGUAGUGUUUUUUAAAAC_____________________
...........(((..((((((((((((((((((.....))))))))).)))))))))..))).................................................. (-10.82 = -13.70 +   2.88)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:47:28 2011