Locus 13326

Sequence ID dm3.chrX
Location 5,859,773 – 5,859,868
Length 95
Max. P 0.986039
window18343 window18344

overview

Window 3

Location 5,859,773 – 5,859,868
Length 95
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 81.07
Shannon entropy 0.32296
G+C content 0.53606
Mean single sequence MFE -31.86
Consensus MFE -21.00
Energy contribution -22.24
Covariance contribution 1.24
Combinations/Pair 1.21
Mean z-score -2.76
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.22
SVM RNA-class probability 0.986039
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5859773 95 + 22422827
GAGAGAGGACGAGAGUAAGAGCGAGAGAAAACUCUUUCUCCAGUAGCCAAAACUCCCCAAAAA-GCGCUCCGCUUACGCACCACUCUCGCUCUCCU----
.((.(((..(((((((..(((((.((((((....)))))).(((.......))).........-.))))).((....))...)))))))..)))))---- ( -29.60, z-score =  -2.52, R)
>droEre2.scaffold_4690 3197634 93 + 18748788
----GAGGGAGAAAGAGCGAGCGAGAGAAAACUCUUCCUCCAGUCGCUAAAACUCCCCAAAAA-GUGCUCCACUUACGCGCCGCUCUCUCCCUCUCCU--
----((((((((..(((((((((((((..........)))...)))))...............-((((.........)))))))))))))))))....-- ( -33.00, z-score =  -3.61, R)
>droYak2.chrX 14713045 94 + 21770863
------GAGAGAGAGAGAGAGCGAGAGUGAAUUCUUUCUCCAGUCGCCAAAACUCCCCAAAAAAGUGCUCUACUUGCGCGCCACUCUCUCGCGCUCUCCU
------(((((.(((((((.(((((((........)))))........................((((.......))))))..)))))))...))))).. ( -30.90, z-score =  -1.86, R)
>droSec1.super_4 5274120 95 - 6179234
GAGAGAGGAAGAGAGUGAGAGCGAGAGAAAACUCUUUCUCCAGUAGCCAAAACUCCCCAAAAA-GCGCCCCGCUUACGCGUCACUCUCGCUCUCCU----
..(((((...((((((((..(((.((((((....)))))).....................((-(((...))))).))).)))))))).)))))..---- ( -33.50, z-score =  -3.08, R)
>droSim1.chrX 4586163 95 + 17042790
GAGAGAGGAAGAGAGUGAGAGCGAGAGAAAACUCUUUCUCCAGUAGCCAAAACUCCCCAAAAA-GCGCACCGCUUACGCGCCACUCUCGCUCUCCU----
..(((((...(((((((.(.(((.((((((....)))))).....................((-(((...))))).))).)))))))).)))))..---- ( -32.30, z-score =  -2.71, R)
>consensus
GAGAGAGGAAGAGAGUGAGAGCGAGAGAAAACUCUUUCUCCAGUAGCCAAAACUCCCCAAAAA_GCGCUCCGCUUACGCGCCACUCUCGCUCUCCU____
....((((.((((((((.(((.(((((....))))).)))........................((((.........)))))))))))).))))...... (-21.00 = -22.24 +   1.24)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,859,773 – 5,859,868
Length 95
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 81.07
Shannon entropy 0.32296
G+C content 0.53606
Mean single sequence MFE -38.40
Consensus MFE -30.24
Energy contribution -29.84
Covariance contribution -0.40
Combinations/Pair 1.36
Mean z-score -1.28
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.687815
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5859773 95 - 22422827
----AGGAGAGCGAGAGUGGUGCGUAAGCGGAGCGC-UUUUUGGGGAGUUUUGGCUACUGGAGAAAGAGUUUUCUCUCGCUCUUACUCUCGUCCUCUCUC
----.((((..((((((((..((....))((((((.-((((..(..(((....))).)..)))).((((....))))))))))))))))))..))))... ( -38.80, z-score =  -1.55, R)
>droEre2.scaffold_4690 3197634 93 - 18748788
--AGGAGAGGGAGAGAGCGGCGCGUAAGUGGAGCAC-UUUUUGGGGAGUUUUAGCGACUGGAGGAAGAGUUUUCUCUCGCUCGCUCUUUCUCCCUC----
--....(((((((((((.(((((....)).((((..-(((((.((..((....))..)).))))).(((......)))))))))))))))))))))---- ( -39.70, z-score =  -1.52, R)
>droYak2.chrX 14713045 94 - 21770863
AGGAGAGCGCGAGAGAGUGGCGCGCAAGUAGAGCACUUUUUUGGGGAGUUUUGGCGACUGGAGAAAGAAUUCACUCUCGCUCUCUCUCUCUCUC------
..(((((.(.((((((((((.((....)).(((..(((((((.((..((....))..)).)))))))..)))....)))))))))).).)))))------ ( -37.80, z-score =  -1.16, R)
>droSec1.super_4 5274120 95 + 6179234
----AGGAGAGCGAGAGUGACGCGUAAGCGGGGCGC-UUUUUGGGGAGUUUUGGCUACUGGAGAAAGAGUUUUCUCUCGCUCUCACUCUCUUCCUCUCUC
----.((((((.(((((((((((....)))(((((.-((((..(..(((....))).)..)))).((((....)))))))))))))))))...)))))). ( -40.10, z-score =  -1.69, R)
>droSim1.chrX 4586163 95 - 17042790
----AGGAGAGCGAGAGUGGCGCGUAAGCGGUGCGC-UUUUUGGGGAGUUUUGGCUACUGGAGAAAGAGUUUUCUCUCGCUCUCACUCUCUUCCUCUCUC
----.((((((.(((((((((((....)))(.(((.-((((..(..(((....))).)..)))).((((....))))))).)))))))))...)))))). ( -35.60, z-score =  -0.45, R)
>consensus
____AGGAGAGCGAGAGUGGCGCGUAAGCGGAGCGC_UUUUUGGGGAGUUUUGGCUACUGGAGAAAGAGUUUUCUCUCGCUCUCACUCUCUUCCUCUCUC
....(((((((.(((((((((((....)))((((.(.(((((.((.(((....))).)).))))).).))))....)))))))).)))))))........ (-30.24 = -29.84 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:19:13 2011