Locus 13166

Sequence ID dm3.chrX
Location 4,780,643 – 4,780,796
Length 153
Max. P 0.995915
window18094 window18095

overview

Window 4

Location 4,780,643 – 4,780,697
Length 54
Sequences 6
Columns 61
Reading direction reverse
Mean pairwise identity 76.09
Shannon entropy 0.42908
G+C content 0.46490
Mean single sequence MFE -13.58
Consensus MFE -10.56
Energy contribution -10.70
Covariance contribution 0.14
Combinations/Pair 1.30
Mean z-score -2.41
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.86
SVM RNA-class probability 0.995915
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4780643 54 - 22422827
------UUUGCCAUCCUAUCAGCUUCG-UCAAUAUGUGCAGCCAAAGGUUGCACAUUUCCU
------.....................-.....((((((((((...))))))))))..... ( -13.50, z-score =  -2.79, R)
>droSim1.chrX 3692830 54 - 17042790
------UUUGCCAUCCCAUCAGCUUCG-UCAAUAUGUGCAGCCAAAGGUUGCACAUUUCCU
------.....................-.....((((((((((...))))))))))..... ( -13.50, z-score =  -2.83, R)
>droSec1.super_4 4216229 54 + 6179234
------UUUGCCAUCCCAUCAGCUUCG-UCAAUAUGUGCAGCCAAAGGUUGCACAUUUCCU
------.....................-.....((((((((((...))))))))))..... ( -13.50, z-score =  -2.83, R)
>droYak2.chrX 18104987 54 + 21770863
------UUUGCCAUCCCAUCUGCUUCG-UCAAUAUGUGCAACCUAGGGUUGCACAUUUCCU
------.....................-.....((((((((((...))))))))))..... ( -13.50, z-score =  -2.48, R)
>droEre2.scaffold_4690 2151628 55 - 18748788
------UUUGCCAUCCCAUCUGCUUCGACCAAUAUGUGCAGCCUAAGGUUGCACAUUUCCU
------...........................((((((((((...))))))))))..... ( -13.50, z-score =  -2.47, R)
>droAna3.scaffold_13417 123649 60 - 6960332
UUCGGAUCUUACGUGUCAGCUGAGCCACGUUCUGGCUACA-UCUUGGUUUGCACUUUUCCA
...(((......((((.((((.(((((.....)))))...-....)))).))))...))). ( -14.00, z-score =  -1.05, R)
>consensus
______UUUGCCAUCCCAUCAGCUUCG_UCAAUAUGUGCAGCCAAAGGUUGCACAUUUCCU
.................................((((((((((...))))))))))..... (-10.56 = -10.70 +   0.14)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 4,780,697 – 4,780,796
Length 99
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 57.97
Shannon entropy 0.71486
G+C content 0.41754
Mean single sequence MFE -22.02
Consensus MFE -7.08
Energy contribution -7.08
Covariance contribution 0.00
Combinations/Pair 1.67
Mean z-score -1.81
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.08
SVM RNA-class probability 0.888206
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4780697 99 - 22422827
CUUCUGUACACCUUAACAUAAAUC--------CACUUUAAAUUUUU-----AUUUAAAGAUCCCAAC------AUCUCCAAGUUGCCGAUGCUACCACGCAUCCGUAUGUACGGAAUA
.(((((((((..............--------..((((((((....-----))))))))........------..........(((.(((((......))))).)))))))))))).. ( -23.80, z-score =  -5.85, R)
>droSim1.chrX 3692884 112 - 17042790
CUUCUCUAUACCUUAGCAUAGAUUCAACUUGGCAUUUGGAGUUUUUU--GAAUUCAAAGAUUGGAGU----AGAUAUCCUAGUCGCCGUUGCUACCACGCAUCCGUGUGUGCGGAAUA
..........((.(((((...........((((.....((((((...--))))))...(((((((..----.....))).)))))))).))))).((((((....)))))).)).... ( -24.30, z-score =   0.10, R)
>droSec1.super_4 4216283 112 + 6179234
CUUCUCUAUACCUUAGCAUAGCUUCAGUUUGGCAUUUUGAGUUUUUU--GAAUUUAAAGAUUGGAGU----GGAUGUCCAAGUCGCCGUUGCUACCACGCAUCCGCAUGUGCGGAAUA
.............(((((.(((....))).(((.((((((((((...--))))))))))...((..(----((....)))..)))))..))))).......(((((....)))))... ( -26.00, z-score =  -0.06, R)
>droYak2.chrX 18105041 103 + 21770863
--------CCAUUUGGCAUUUAGAC-------UUUUUUGAAUUUUUUAAAGAUUUAAAGAUCCUAUCUACUCAAAGUCGCCGACGACGACGAUGCCACACAGCCCCAUGUGCGGCAUA
--------...(((((....(((..-------.(((((((((((.....)))))))))))..))).....)))))((((....))))....(((((.((((......)))).))))). ( -25.50, z-score =  -3.26, R)
>droEre2.scaffold_4690 2151683 87 - 18748788
----------------CUUUCAAG--------CACCUUAGACUUUUC-AGAAUUUCUAGAACCUAU------AUACUGCACGUCGCCGACGAUACCUCGCAUCCCUACGAGCGAAAUA
----------------.......(--------((...((.....(((-((.....)).)))....)------)...))).((((...)))).....((((.((.....)))))).... ( -10.50, z-score =   0.01, R)
>consensus
CUUCU_UACACCUUAGCAUAGAUUC_______CAUUUUGAAUUUUUU__GAAUUUAAAGAUCCGAGC_____AAUCUCCAAGUCGCCGAUGCUACCACGCAUCCGUAUGUGCGGAAUA
..................................((((((((((.....))))))))))..........................................(((((....)))))... ( -7.08 =  -7.08 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:15:51 2011