Locus 9780

Sequence ID dm3.chr3R
Location 8,924,881 – 8,924,938
Length 57
Max. P 0.994901
window13417 window13418

overview

Window 7

Location 8,924,881 – 8,924,938
Length 57
Sequences 6
Columns 60
Reading direction forward
Mean pairwise identity 78.62
Shannon entropy 0.39896
G+C content 0.59795
Mean single sequence MFE -23.10
Consensus MFE -14.28
Energy contribution -14.62
Covariance contribution 0.34
Combinations/Pair 1.44
Mean z-score -1.95
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.27
SVM RNA-class probability 0.918563
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8924881 57 + 27905053
UGGGUGCCUGGCUCUUGGCACUGGGCUCCCAGUACUCAAGCCAAGCUCCGUAC-AUCC--
.(((((..(((..(((((((((((....)))))......))))))..)))..)-))))-- ( -24.20, z-score =  -2.33, R)
>droSim1.chr3R 15020677 57 - 27517382
UGGGUGCCUGGCUCUUGGCACUGGGCUCCCAGUACUCAAGCCAAGCUCCAUGC-AUCC--
.((((((.(((..(((((((((((....)))))......))))))..))).))-))))-- ( -28.80, z-score =  -3.57, R)
>droSec1.super_0 8048584 57 - 21120651
UGGGUGCCUGGCUCUUGGCACUGGGCUCCCAGUACUCAAGCCAAGCUCCAUGC-AUCC--
.((((((.(((..(((((((((((....)))))......))))))..))).))-))))-- ( -28.80, z-score =  -3.57, R)
>droYak2.chr3R 13227361 57 + 28832112
UGGGUGCCUGCCUCCUGGCACUGGGCUCCCAGUACUCAAGCCAAGCUCCAUGC-AUCC--
.((((((.((...(.(((((((((....)))))......)))).)...)).))-))))-- ( -20.50, z-score =  -0.89, R)
>droEre2.scaffold_4770 5028967 57 - 17746568
UGGGUACCCGGUUCUUGGCACUGGGCUCCCAGUACUCAAGCCCAGCUCCAUGC-AUCC--
.((....))(((.(.(((..(((((((...........)))))))..))).).-))).-- ( -18.40, z-score =  -0.54, R)
>droMoj3.scaffold_6540 25988043 60 - 34148556
UAGGCAACUGGCAACUGGCAACUGCUUCGGCUACCUCAAUGUAAGCCUUAUGUUGUGCCA
..((((...((((...(((....((....))(((......))).)))...)))).)))). ( -17.90, z-score =  -0.83, R)
>consensus
UGGGUGCCUGGCUCUUGGCACUGGGCUCCCAGUACUCAAGCCAAGCUCCAUGC_AUCC__
((((.((.(((((...((.(((((....))))).))..))))).)))))).......... (-14.28 = -14.62 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 8,924,881 – 8,924,938
Length 57
Sequences 6
Columns 60
Reading direction reverse
Mean pairwise identity 78.62
Shannon entropy 0.39896
G+C content 0.59795
Mean single sequence MFE -26.07
Consensus MFE -19.33
Energy contribution -20.33
Covariance contribution 1.00
Combinations/Pair 1.21
Mean z-score -2.53
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.75
SVM RNA-class probability 0.994901
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8924881 57 - 27905053
--GGAU-GUACGGAGCUUGGCUUGAGUACUGGGAGCCCAGUGCCAAGAGCCAGGCACCCA
--....-....((.(((((((((..(((((((....)))))))...))))))))).)).. ( -30.90, z-score =  -4.40, R)
>droSim1.chr3R 15020677 57 + 27517382
--GGAU-GCAUGGAGCUUGGCUUGAGUACUGGGAGCCCAGUGCCAAGAGCCAGGCACCCA
--....-....((.(((((((((..(((((((....)))))))...))))))))).)).. ( -30.60, z-score =  -3.86, R)
>droSec1.super_0 8048584 57 + 21120651
--GGAU-GCAUGGAGCUUGGCUUGAGUACUGGGAGCCCAGUGCCAAGAGCCAGGCACCCA
--....-....((.(((((((((..(((((((....)))))))...))))))))).)).. ( -30.60, z-score =  -3.86, R)
>droYak2.chr3R 13227361 57 - 28832112
--GGAU-GCAUGGAGCUUGGCUUGAGUACUGGGAGCCCAGUGCCAGGAGGCAGGCACCCA
--....-....((.(((((.((((.(((((((....)))))))))))...))))).)).. ( -25.10, z-score =  -1.51, R)
>droEre2.scaffold_4770 5028967 57 + 17746568
--GGAU-GCAUGGAGCUGGGCUUGAGUACUGGGAGCCCAGUGCCAAGAACCGGGUACCCA
--....-....((.(((.((((((.(((((((....)))))))))))..)).))).)).. ( -24.20, z-score =  -1.83, R)
>droMoj3.scaffold_6540 25988043 60 + 34148556
UGGCACAACAUAAGGCUUACAUUGAGGUAGCCGAAGCAGUUGCCAGUUGCCAGUUGCCUA
.((((((((....((((.((......))))))...((....))..)))).....)))).. ( -15.00, z-score =   0.27, R)
>consensus
__GGAU_GCAUGGAGCUUGGCUUGAGUACUGGGAGCCCAGUGCCAAGAGCCAGGCACCCA
...........((.((((((((((.(((((((....)))))))))))..)))))).)).. (-19.33 = -20.33 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:10:59 2011