Locus 14431

Sequence ID dm3.chrX
Location 13,288,919 – 13,289,059
Length 140
Max. P 0.984883
window19867 window19868

overview

Window 7

Location 13,288,919 – 13,289,059
Length 140
Sequences 3
Columns 143
Reading direction forward
Mean pairwise identity 84.83
Shannon entropy 0.20840
G+C content 0.54321
Mean single sequence MFE -44.93
Consensus MFE -37.92
Energy contribution -37.73
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -1.70
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.810588
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 13288919 140 + 22422827
AAUCCCAAAAAAAAAACCCUUCAAGGUCCUUUUUUGGAAGGGAACAACAAGGUCGAAUAUCCGGAUGACCCAGUGACCAGGCGACAAACUGGUCACCGGGUGACCGAGUGCGAUGCCGCAACUAUCCUACCGCGUCCACU---
..((((.((((((..(((......)))..))))))....)))).......((.((......(((.(.((((.((((((((........)))))))).)))).))))((((((....))).))).........)).))...--- ( -47.50, z-score =  -2.80, R)
>droSim1.chrX 10182388 122 + 17042790
AAUGCCAAAAA-----CCCAUCAAGGCCCUUUU--GGAAGGGAAGAACAAGGUCGAAUAUCCGGAUGACCCAGUGACCAGGCGAGGAACUGGUCACCGGGUGACCGA--------------CUAUCCUACCGCGUCCACUGCU
....((((((.-----.((.....))...))))--)).(((((.(.....(((.(.(((..(((.(.((((.((((((((........)))))))).)))).)))).--------------.))).).))).).))).))... ( -40.80, z-score =  -1.34, R)
>droSec1.super_21 1042301 136 + 1102487
AAUGCCAAAAA-----CCCAUCAAGGCCCUUUU--GGAAGGGAAGAACAAGGUCGAAUAUCCGGCUGACCCAGUGACCAGGCGAGGAACUGGUCACCGGGUGACCGAGUCCGAUGCGGCAACUAUCCUACCGCGUCCACUGCU
...(((.....-----.((.....))(((((..--..)))))........)))........(((.(.((((.((((((((........)))))))).)))).))))(((..(((((((...........))))))).)))... ( -46.50, z-score =  -0.97, R)
>consensus
AAUGCCAAAAA_____CCCAUCAAGGCCCUUUU__GGAAGGGAAGAACAAGGUCGAAUAUCCGGAUGACCCAGUGACCAGGCGAGGAACUGGUCACCGGGUGACCGAGU_CGAUGC_GCAACUAUCCUACCGCGUCCACUGCU
.................((.....))((((((....))))))........((.((......(((.(.((((.((((((((........)))))))).)))).)))).(((......))).............)).))...... (-37.92 = -37.73 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,288,919 – 13,289,059
Length 140
Sequences 3
Columns 143
Reading direction reverse
Mean pairwise identity 84.83
Shannon entropy 0.20840
G+C content 0.54321
Mean single sequence MFE -55.67
Consensus MFE -41.72
Energy contribution -42.39
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.97
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.18
SVM RNA-class probability 0.984883
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 13288919 140 - 22422827
---AGUGGACGCGGUAGGAUAGUUGCGGCAUCGCACUCGGUCACCCGGUGACCAGUUUGUCGCCUGGUCACUGGGUCAUCCGGAUAUUCGACCUUGUUGUUCCCUUCCAAAAAAGGACCUUGAAGGGUUUUUUUUUUGGGAUU
---....((((.(((.(((((..((((....)))).((((..(((((((((((((........)))))))))))))...)))).))))).))).))))..((((....((((((((((((....)))))))))))).)))).. ( -58.60, z-score =  -3.66, R)
>droSim1.chrX 10182388 122 - 17042790
AGCAGUGGACGCGGUAGGAUAG--------------UCGGUCACCCGGUGACCAGUUCCUCGCCUGGUCACUGGGUCAUCCGGAUAUUCGACCUUGUUCUUCCCUUCC--AAAAGGGCCUUGAUGGG-----UUUUUGGCAUU
.((...(((((.(((.(((((.--------------.(((..(((((((((((((........)))))))))))))...)))..))))).))).))))).........--..((((((((....)))-----))))).))... ( -52.20, z-score =  -3.05, R)
>droSec1.super_21 1042301 136 - 1102487
AGCAGUGGACGCGGUAGGAUAGUUGCCGCAUCGGACUCGGUCACCCGGUGACCAGUUCCUCGCCUGGUCACUGGGUCAGCCGGAUAUUCGACCUUGUUCUUCCCUUCC--AAAAGGGCCUUGAUGGG-----UUUUUGGCAUU
.((..((((.(((((((.....))))))).(((((.(((((.(((((((((((((........)))))))))))))..)))))...)))))..............)))--).((((((((....)))-----))))).))... ( -56.20, z-score =  -2.19, R)
>consensus
AGCAGUGGACGCGGUAGGAUAGUUGC_GCAUCG_ACUCGGUCACCCGGUGACCAGUUCCUCGCCUGGUCACUGGGUCAUCCGGAUAUUCGACCUUGUUCUUCCCUUCC__AAAAGGGCCUUGAUGGG_____UUUUUGGCAUU
......(((((.(((.(((((...............((((..(((((((((((((........)))))))))))))...)))).))))).))).)))))..(((((......)))))((.....))................. (-41.72 = -42.39 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:40:02 2011