Locus 5557

Sequence ID dm3.chr3LHet
Location 665,542 – 665,673
Length 131
Max. P 0.614182
window7637 window7638

overview

Window 7

Location 665,542 – 665,673
Length 131
Sequences 3
Columns 131
Reading direction forward
Mean pairwise identity 57.51
Shannon entropy 0.61542
G+C content 0.56754
Mean single sequence MFE -46.63
Consensus MFE -16.06
Energy contribution -17.20
Covariance contribution 1.14
Combinations/Pair 1.47
Mean z-score -1.67
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.614182
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 665542 131 + 2555491
CAUCCUUUUCGGAAGUGCAAGAGGUUCCACAAACUGAGCGCUGAAAAGCGCCUUCGGGCAGUACUUAUUAAUAAGUACUGCUCGAACUGCCUCGCCCAUCAGCACUCAGGAGGAGACUGCCGCAGCCAAGA
..........((...(((..(((((............(((((....))))).(((((((((((((((....)))))))))))))))..)))))((......)).....((((....)).))))).)).... ( -50.90, z-score =  -3.65, R)
>droVir3.scaffold_13049 24538204 131 + 25233164
CAAGCGCUGCGUAAGUGCCAGCGGUUUAUGCGGCUGUCUCCAGAGAAGAGACUCCGAGUAGUUCUGGUCAACAAAUACUGCCCAAACUGUCUGCCUCACCAACAUUCCGGGGAGUCCUGUCGCCGCAAGGU
.((.(((((.((....))))))).))..((((((..(((....)))((.((((((((((((((.(((.((........)).)))))))).....))).((........))))))))))...)))))).... ( -41.30, z-score =  -0.28, R)
>droGri2.scaffold_14853 8980702 118 - 10151454
CACGCACUGCGCAGAUGCCAGCGAUUACUUCGCCUGACUGCAGUCAGCCGGUUGAGGGCGGUGCUCCUCAAACAAUACUGCCCGCACUGCCUGGUUCAUCAGCACUCCGGGCGGUGGU-------------
...(((((((.(....(((.((((.....))))(((((....)))))..)))...).)))))))...........(((((((((...(((.(((....))))))...)))))))))..------------- ( -47.70, z-score =  -1.07, R)
>consensus
CAAGCACUGCGCAAGUGCCAGCGGUUACUCCGACUGACUGCAGAAAAGCGACUCCGGGCAGUACUCAUCAAAAAAUACUGCCCGAACUGCCUGGCUCAUCAGCACUCCGGGGGGUACUG_CGC_GC_A_G_
.....(((((......(((((((((((..........((((......))))....((((((((............)))))))))))))).)))))...((........)))))))................ (-16.06 = -17.20 +   1.14)

alignment

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secondary structure

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dotplot

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Window 8

Location 665,542 – 665,673
Length 131
Sequences 3
Columns 131
Reading direction reverse
Mean pairwise identity 57.51
Shannon entropy 0.61542
G+C content 0.56754
Mean single sequence MFE -49.37
Consensus MFE -16.88
Energy contribution -15.33
Covariance contribution -1.54
Combinations/Pair 1.44
Mean z-score -1.64
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.585921
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 665542 131 - 2555491
UCUUGGCUGCGGCAGUCUCCUCCUGAGUGCUGAUGGGCGAGGCAGUUCGAGCAGUACUUAUUAAUAAGUACUGCCCGAAGGCGCUUUUCAGCGCUCAGUUUGUGGAACCUCUUGCACUUCCGAAAAGGAUG
..((((.(((((.((..(((.((((((((((((..(((...((..((((.((((((((((....)))))))))).)))).)))))..)))))))))))...).)))..)).)))))...))))........ ( -56.60, z-score =  -3.84, R)
>droVir3.scaffold_13049 24538204 131 - 25233164
ACCUUGCGGCGACAGGACUCCCCGGAAUGUUGGUGAGGCAGACAGUUUGGGCAGUAUUUGUUGACCAGAACUACUCGGAGUCUCUUCUCUGGAGACAGCCGCAUAAACCGCUGGCACUUACGCAGCGCUUG
....(((((((((((((((.((((((.((((.(.....).)))).)))))).))).))))))..((((.....)).)).((((((.....)))))).)))))).....(((((.(......)))))).... ( -44.40, z-score =  -0.56, R)
>droGri2.scaffold_14853 8980702 118 + 10151454
-------------ACCACCGCCCGGAGUGCUGAUGAACCAGGCAGUGCGGGCAGUAUUGUUUGAGGAGCACCGCCCUCAACCGGCUGACUGCAGUCAGGCGAAGUAAUCGCUGGCAUCUGCGCAGUGCGUG
-------------..(((.(((((.(.((((.........)))).).))))).(((((((((((((.((...))))))))(((((((....))))).(((((.....))))))).......)))))))))) ( -47.10, z-score =  -0.51, R)
>consensus
_C_U_GC_GCG_CAGCACCCCCCGGAGUGCUGAUGAGCCAGGCAGUUCGGGCAGUAUUUAUUGACAAGAACUGCCCGAAGCCGCUUCUCUGCAGUCAGCCGAAGAAACCGCUGGCACUUACGCAGAGCAUG
......................((((.((((.........)))).((((((((((.((.(....).)).))))))))))........)))).................(((((.(......)))))).... (-16.88 = -15.33 +  -1.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:50:48 2011