Locus 7976

Sequence ID dm3.chr3L
Location 19,079,589 – 19,079,654
Length 65
Max. P 0.969027
window10979 window10980

overview

Window 9

Location 19,079,589 – 19,079,654
Length 65
Sequences 5
Columns 70
Reading direction forward
Mean pairwise identity 88.15
Shannon entropy 0.20062
G+C content 0.44684
Mean single sequence MFE -14.25
Consensus MFE -10.31
Energy contribution -10.75
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -2.77
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.66
SVM RNA-class probability 0.958669
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19079589 65 + 24543557
-----UUGCUCUCCGACUCUCCAAUUCUCUCCGUCGGAAUUCGAAGAGCGAAACCCAAUAACAAUAUUGU
-----(((((((.(((...(((.............)))..))).)))))))....(((((....))))). ( -14.42, z-score =  -2.56, R)
>droEre2.scaffold_4784 18898298 68 + 25762168
UUGCUCUCCGCUCCGACUCUCCAAUUCUC--CGUCGGAAUUCAAAGAGCGAAACCCAAUAACAAUACUGU
(((((((....((((((............--.))))))......)))))))................... ( -15.42, z-score =  -3.44, R)
>droYak2.chr3L 2694978 63 - 24197627
-----UUGCUCUCCGACUCUCCAAUUCUC--CGUCGGAAUUCGAAGAGCAAACCCCAAUAACAAUAUUGC
-----(((((((.(((...(((.......--....)))..))).)))))))....(((((....))))). ( -14.70, z-score =  -3.59, R)
>droSec1.super_19 1042908 63 + 1257711
-----UUGCUCUCCGACUCUCCAAUUCUC--CGUCGGAAUUUGAAGAGCGAAACUCAAUAACAACAAUGU
-----((((((((((((............--.)))))).......))))))................... ( -13.13, z-score =  -2.06, R)
>droSim1.chr3L 18392893 63 + 22553184
-----UUGCUCUCCGACUCUCCAAUUCUC--CGUCGGAAUUCGAAGAGCGAAACUCAAUAACAAUAAUGU
-----(((((((.(((...(((.......--....)))..))).)))))))................... ( -13.60, z-score =  -2.22, R)
>consensus
_____UUGCUCUCCGACUCUCCAAUUCUC__CGUCGGAAUUCGAAGAGCGAAACCCAAUAACAAUAAUGU
.....((((((((((((...............)))))).......))))))................... (-10.31 = -10.75 +   0.44)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 19,079,589 – 19,079,654
Length 65
Sequences 5
Columns 70
Reading direction reverse
Mean pairwise identity 88.15
Shannon entropy 0.20062
G+C content 0.44684
Mean single sequence MFE -21.18
Consensus MFE -16.80
Energy contribution -17.40
Covariance contribution 0.60
Combinations/Pair 1.15
Mean z-score -2.59
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.81
SVM RNA-class probability 0.969027
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19079589 65 - 24543557
ACAAUAUUGUUAUUGGGUUUCGCUCUUCGAAUUCCGACGGAGAGAAUUGGAGAGUCGGAGAGCAA-----
.(((((....)))))......(((((((((.((((((.........))))))..)))))))))..----- ( -21.90, z-score =  -2.70, R)
>droEre2.scaffold_4784 18898298 68 - 25762168
ACAGUAUUGUUAUUGGGUUUCGCUCUUUGAAUUCCGACG--GAGAAUUGGAGAGUCGGAGCGGAGAGCAA
.(((((....)))))......((((((((...((((((.--............)))))).)))))))).. ( -23.72, z-score =  -3.00, R)
>droYak2.chr3L 2694978 63 + 24197627
GCAAUAUUGUUAUUGGGGUUUGCUCUUCGAAUUCCGACG--GAGAAUUGGAGAGUCGGAGAGCAA-----
.(((((....)))))....(((((((((((.((((((..--.....))))))..)))))))))))----- ( -22.80, z-score =  -3.51, R)
>droSec1.super_19 1042908 63 - 1257711
ACAUUGUUGUUAUUGAGUUUCGCUCUUCAAAUUCCGACG--GAGAAUUGGAGAGUCGGAGAGCAA-----
............(((..(((((((((((((.((((...)--)))..)))))))).)))))..)))----- ( -17.80, z-score =  -1.51, R)
>droSim1.chr3L 18392893 63 - 22553184
ACAUUAUUGUUAUUGAGUUUCGCUCUUCGAAUUCCGACG--GAGAAUUGGAGAGUCGGAGAGCAA-----
.....................(((((((((.((((((..--.....))))))..)))))))))..----- ( -19.70, z-score =  -2.22, R)
>consensus
ACAAUAUUGUUAUUGGGUUUCGCUCUUCGAAUUCCGACG__GAGAAUUGGAGAGUCGGAGAGCAA_____
.(((((....)))))......(((((((((.((((((.........))))))..)))))))))....... (-16.80 = -17.40 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:37:04 2011