Locus 13390

Sequence ID dm3.chrX
Location 6,283,078 – 6,283,156
Length 78
Max. P 0.606802
window18437 window18438

overview

Window 7

Location 6,283,078 – 6,283,156
Length 78
Sequences 6
Columns 81
Reading direction forward
Mean pairwise identity 71.62
Shannon entropy 0.53829
G+C content 0.57638
Mean single sequence MFE -27.90
Consensus MFE -13.08
Energy contribution -15.20
Covariance contribution 2.12
Combinations/Pair 1.41
Mean z-score -1.32
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.606802
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6283078 78 + 22422827
CAGAUGGCAGGAUAUCAGCGGGUUCUCCAUGGAGGACUCCUCCC-AAAAGGCGCAACCGGCGGU--GGCUUUCGCCUGCCU
.....((((((.....(((((((((((....)))))))).....-......(((.....)))..--.)))....)))))). ( -30.10, z-score =  -0.73, R)
>droSim1.chrX_random 2042575 77 + 5698898
CAGAUGGCAGGAUAUCAGUGGGUUCUCCAUGGAGCACUCCUCC--GAAAGGCGCAACCAGCGGU--GGCUUUCGCCUGCCU
.....((((((.....((.((((.(((....))).)))))).(--(((((.(((........))--).)))))))))))). ( -31.30, z-score =  -1.62, R)
>droSec1.super_4 5689156 77 - 6179234
CAGAUGGCAGGAUAUCAGUGGGUUCUCCAUGGAGCACUCCUCC--GAAAGGCGCAACCAGCGGU--GGCUUUCGCCUGCCU
.....((((((.....((.((((.(((....))).)))))).(--(((((.(((........))--).)))))))))))). ( -31.30, z-score =  -1.62, R)
>droYak2.chrX 2275897 77 + 21770863
CAGAUGGCAGGAUAUCAGGGGGUUUUCCAUGGAGGACUCCUCC--GCAAGGAGCAACCAGCGGU--GGCUUUCGCCUGCCU
.....((((((.......(((((((((....)))))))))(((--....)))((.(((...)))--.)).....)))))). ( -33.30, z-score =  -1.96, R)
>droEre2.scaffold_4690 15243863 70 + 18748788
CAGAUGGCUGGGUAUCAGGGGGUUUUCCAUGGAGGACUCCAUGGAGAAAGGCGCGGCCAGCGGU--GGCUUU---------
....((((((.((.((..(((((((((....)))))))))...)).....)).))))))((...--.))...--------- ( -28.20, z-score =  -2.42, R)
>droAna3.scaffold_13335 1237640 71 - 3335858
----UAUAUGUAUAUAUACAGGAUAUCUCUUAGCGAUUCCU----GGUGGCUGCCGUUUGCCGUCUGCCUUUCGCCUUU--
----....((((....))))............((((.....----(..(((........)))..)......))))....-- ( -13.20, z-score =   0.43, R)
>consensus
CAGAUGGCAGGAUAUCAGCGGGUUCUCCAUGGAGGACUCCUCC__GAAAGGCGCAACCAGCGGU__GGCUUUCGCCUGCCU
.....((((((........((((((((....))))))))......(((((.(...((.....))..).))))).)))))). (-13.08 = -15.20 +   2.12)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 8

Location 6,283,078 – 6,283,156
Length 78
Sequences 6
Columns 81
Reading direction reverse
Mean pairwise identity 71.62
Shannon entropy 0.53829
G+C content 0.57638
Mean single sequence MFE -25.54
Consensus MFE -9.33
Energy contribution -11.17
Covariance contribution 1.83
Combinations/Pair 1.27
Mean z-score -1.77
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.547728
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6283078 78 - 22422827
AGGCAGGCGAAAGCC--ACCGCCGGUUGCGCCUUUU-GGGAGGAGUCCUCCAUGGAGAACCCGCUGAUAUCCUGCCAUCUG
.(((((((....)))--...((.((((.(.((....-.(((((...)))))..)).))))).))........))))..... ( -31.10, z-score =  -1.62, R)
>droSim1.chrX_random 2042575 77 - 5698898
AGGCAGGCGAAAGCC--ACCGCUGGUUGCGCCUUUC--GGAGGAGUGCUCCAUGGAGAACCCACUGAUAUCCUGCCAUCUG
.((((((((..((((--(....))))).))))..((--((.((.((.(((....))).)))).)))).....))))..... ( -29.10, z-score =  -1.53, R)
>droSec1.super_4 5689156 77 + 6179234
AGGCAGGCGAAAGCC--ACCGCUGGUUGCGCCUUUC--GGAGGAGUGCUCCAUGGAGAACCCACUGAUAUCCUGCCAUCUG
.((((((((..((((--(....))))).))))..((--((.((.((.(((....))).)))).)))).....))))..... ( -29.10, z-score =  -1.53, R)
>droYak2.chrX 2275897 77 - 21770863
AGGCAGGCGAAAGCC--ACCGCUGGUUGCUCCUUGC--GGAGGAGUCCUCCAUGGAAAACCCCCUGAUAUCCUGCCAUCUG
.(((((((....)))--.(((.(((..(((((((..--.)))))))...)))))).................))))..... ( -29.20, z-score =  -2.11, R)
>droEre2.scaffold_4690 15243863 70 - 18748788
---------AAAGCC--ACCGCUGGCCGCGCCUUUCUCCAUGGAGUCCUCCAUGGAAAACCCCCUGAUACCCAGCCAUCUG
---------......--...(((((...((......((((((((....))))))))........))....)))))...... ( -18.84, z-score =  -2.41, R)
>droAna3.scaffold_13335 1237640 71 + 3335858
--AAAGGCGAAAGGCAGACGGCAAACGGCAGCCACC----AGGAAUCGCUAAGAGAUAUCCUGUAUAUAUACAUAUA----
--...(.(....).)....(((........)))..(----(((((((.......))).)))))..............---- ( -15.90, z-score =  -1.40, R)
>consensus
AGGCAGGCGAAAGCC__ACCGCUGGUUGCGCCUUUC__GGAGGAGUCCUCCAUGGAGAACCCACUGAUAUCCUGCCAUCUG
.((((((.............((.....))............((.((.(((....))).))))........))))))..... ( -9.33 = -11.17 +   1.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:20:29 2011