Locus 13995

Sequence ID dm3.chrX
Location 10,465,491 – 10,465,625
Length 134
Max. P 0.890020
window19251 window19252

overview

Window 1

Location 10,465,491 – 10,465,625
Length 134
Sequences 5
Columns 142
Reading direction forward
Mean pairwise identity 83.95
Shannon entropy 0.28861
G+C content 0.52922
Mean single sequence MFE -47.28
Consensus MFE -31.43
Energy contribution -33.03
Covariance contribution 1.60
Combinations/Pair 1.06
Mean z-score -2.25
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.886090
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10465491 134 + 22422827
GUGUGCCACUUGAAGGAACUUGUCAUUGCAGUUUAGAUGACAAUGUUGACGGUGUGGCACAAAUUGCAGAACGCAAGGAGCAGGUGGACCAA--A------GCAGCCAAGGUGCCACGAGCUCGAAAGGAGUUGCGAGGACC
.((((((((.....(.(((((((((((........)))))))).)))..)...))))))))..((((((..(....)((((..(((((((..--.------........))).))))..))))........))))))..... ( -45.40, z-score =  -1.72, R)
>droYak2.chrX 19033263 142 + 21770863
GUGUGCCACUUGAAGCAACUUGUCAUUGCAGUUUAGAUGACAAUGUUGACGGUGUGGCACAAAUUGCAGGGCGCAAGUAGCAGGUGGACCAAUGGAGUCGAGCAGCCAAGGAGCCACAAAGUCGAAAGGAGUGGCGAGAAGC
.((((((((......((((((((((((........)))))))).)))).....))))))))....((..(((((.....)).(.(.((((....).))).).).))).....(((((....((....)).))))).....)) ( -50.00, z-score =  -2.52, R)
>droEre2.scaffold_4690 14083582 128 - 18748788
GUGUGCCACUUGAAGCAACUUGUCAUUGCAGUUUAGAUGACAAUGUUGA--------------UUGCAGAACGCAAGGAGCAGGUGGACCCAAGGAGCCAAGAAGCCAAGGAGCCACCAAGUCGAAAGAAGAUCCGAGGAGC
....((..((((..((..(((((..((((((((.(.((....)).).))--------------))))))...)))))..)).(((((..((...(.((......)))..))..)))))...((....)).....))))..)) ( -38.00, z-score =  -2.05, R)
>droSec1.super_15 1169320 140 + 1954846
GCGUGCCACUUGAAGCAACUUGUCAUUGCAGUUCAGAUGACAAUGUUGACGUUGUGGCACAAAUUGCAGAACGCAAGGAGCAGGUGGACCUG--GCUCGUGGCAGCCAAGGAGCCACGAGCUCGAAAGGAGAUCCGAGGACC
..(((((((......((((((((((((........)))))))).)))).....)))))))...((((.....))))(((.((((....))))--(((((((((..(....).)))))))))((....))...)))....... ( -57.40, z-score =  -3.35, R)
>droSim1.chrX 8117663 134 + 17042790
GCGUGCCACUUGAAGCAACUUGUCAUUGCAGUUCAGAUGACAAUGUUGACGUUGUGGCACAAAUUGCCGAACGCAAGGAGCAGGUGGACCAA--G------GCAGCCAAGGAGCCACGAGCUCGAAAGGAGAUCCGAGGACC
..(((((((......((((((((((((........)))))))).)))).....)))))))......((...(....)((((..((((.((..--(------(...))..))..))))..))))....((....))..))... ( -45.60, z-score =  -1.64, R)
>consensus
GUGUGCCACUUGAAGCAACUUGUCAUUGCAGUUUAGAUGACAAUGUUGACGGUGUGGCACAAAUUGCAGAACGCAAGGAGCAGGUGGACCAA__G______GCAGCCAAGGAGCCACGAGCUCGAAAGGAGAUCCGAGGACC
..(((((((......((((((((((((........)))))))).)))).....)))))))...((((.....))))(((.(..((((.((...................))..))))....((....)).).)))....... (-31.43 = -33.03 +   1.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,465,491 – 10,465,625
Length 134
Sequences 5
Columns 142
Reading direction reverse
Mean pairwise identity 83.95
Shannon entropy 0.28861
G+C content 0.52922
Mean single sequence MFE -42.51
Consensus MFE -26.88
Energy contribution -29.36
Covariance contribution 2.48
Combinations/Pair 1.06
Mean z-score -2.37
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.890020
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10465491 134 - 22422827
GGUCCUCGCAACUCCUUUCGAGCUCGUGGCACCUUGGCUGC------U--UUGGUCCACCUGCUCCUUGCGUUCUGCAAUUUGUGCCACACCGUCAACAUUGUCAUCUAAACUGCAAUGACAAGUUCCUUCAAGUGGCACAC
.((...(((((........((((..((((.(((..((...)------)--..)))))))..)))).)))))....))....((((((((......(((.(((((((..........)))))))))).......)))))))). ( -38.82, z-score =  -1.96, R)
>droYak2.chrX 19033263 142 - 21770863
GCUUCUCGCCACUCCUUUCGACUUUGUGGCUCCUUGGCUGCUCGACUCCAUUGGUCCACCUGCUACUUGCGCCCUGCAAUUUGUGCCACACCGUCAACAUUGUCAUCUAAACUGCAAUGACAAGUUGCUUCAAGUGGCACAC
((.....(((((.............))))).....(((.....((((.....)))).....((.....)))))..))....((((((((.....((((.(((((((..........)))))))))))......)))))))). ( -40.02, z-score =  -2.63, R)
>droEre2.scaffold_4690 14083582 128 + 18748788
GCUCCUCGGAUCUUCUUUCGACUUGGUGGCUCCUUGGCUUCUUGGCUCCUUGGGUCCACCUGCUCCUUGCGUUCUGCAA--------------UCAACAUUGUCAUCUAAACUGCAAUGACAAGUUGCUUCAAGUGGCACAC
.....(((((......)))))...(((((..((..((((....))))....))..)))))(((..((((......((((--------------(.....(((((((..........))))))))))))..))))..)))... ( -35.10, z-score =  -1.48, R)
>droSec1.super_15 1169320 140 - 1954846
GGUCCUCGGAUCUCCUUUCGAGCUCGUGGCUCCUUGGCUGCCACGAGC--CAGGUCCACCUGCUCCUUGCGUUCUGCAAUUUGUGCCACAACGUCAACAUUGUCAUCUGAACUGCAAUGACAAGUUGCUUCAAGUGGCACGC
((.(((((((......)))))(((((((((.(....)..)))))))))--..)).))....((...((((.....))))...(((((((.....((((.(((((((.((.....)))))))))))))......))))))))) ( -53.10, z-score =  -3.52, R)
>droSim1.chrX 8117663 134 - 17042790
GGUCCUCGGAUCUCCUUUCGAGCUCGUGGCUCCUUGGCUGC------C--UUGGUCCACCUGCUCCUUGCGUUCGGCAAUUUGUGCCACAACGUCAACAUUGUCAUCUGAACUGCAAUGACAAGUUGCUUCAAGUGGCACGC
((((....)))).......((((..((((..((..((...)------)--..)).))))..)))).((((.....))))...(((((((.....((((.(((((((.((.....)))))))))))))......))))))).. ( -45.50, z-score =  -2.28, R)
>consensus
GGUCCUCGGAUCUCCUUUCGAGCUCGUGGCUCCUUGGCUGC______C__UUGGUCCACCUGCUCCUUGCGUUCUGCAAUUUGUGCCACAACGUCAACAUUGUCAUCUAAACUGCAAUGACAAGUUGCUUCAAGUGGCACAC
((.(((((((......)))))....(..((......))..)...........)).)).........((((.....))))..((((((((.....((((.(((((((..........)))))))))))......)))))))). (-26.88 = -29.36 +   2.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:31:42 2011