Locus 12940

Sequence ID dm3.chrX
Location 3,462,106 – 3,462,203
Length 97
Max. P 0.988125
window17792 window17793

overview

Window 2

Location 3,462,106 – 3,462,198
Length 92
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 72.78
Shannon entropy 0.44110
G+C content 0.58716
Mean single sequence MFE -25.46
Consensus MFE -16.12
Energy contribution -16.56
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -2.13
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979649
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3462106 92 + 22422827
CUAAUGGCGGAGCACAGCGGGCGGCGUCACACGCCUACCAAAUCCAAAACCGCUCUCCAUA----AGACCACCUCCGUCAGUCUCACUGACAAAAA
....((((((((......((..((((.....))))..))............(.(((.....----))).)..))))))))(((.....)))..... ( -26.20, z-score =  -2.68, R)
>droSim1.chrX_random 1465447 70 + 5698898
CUAAUGGCGGAGCACAGCGGGCAGCGUCACACGCCUCCCAAAUCCAAAACCGCUCCCCA---------------------GUCUCACUGAC-----
....(((.(((((.....(((..(((.....)))..)))...(....)...))))))))---------------------(((.....)))----- ( -20.10, z-score =  -1.73, R)
>droSec1.super_4 2967551 70 - 6179234
CUAAUGGCGGAGCACAGCGGGCAGCGUCACACGCCUCCCAAAUCCAAAACCGCUCCCCA---------------------GUCUCACUGAC-----
....(((.(((((.....(((..(((.....)))..)))...(....)...))))))))---------------------(((.....)))----- ( -20.10, z-score =  -1.73, R)
>droYak2.chrX 16844803 87 - 21770863
CUAAUGGCGGAGCACAGCGGGCGGCGCCAAAUGCCUCCCAAAUCCCAAACUGCUCCACAUA----GGAGCUUCUCCGCCAAUCACACUGAG-----
....((((((((......(((.((((.....)))).)))............(((((.....----)))))..))))))))...........----- ( -35.00, z-score =  -4.21, R)
>droEre2.scaffold_4690 874465 90 + 18748788
CUAAUGGCGGAGCACAGCGGGCGGCCUACAAUGCCUCCCAAAUCCCAA-CUGCUCCACAUAUGUAAGAGCUACUCCUCCAAUGGCACUGGG-----
(((.(((.((((......(((.(((.......))).))).........-..((((.((....))..))))..)))).))).))).......----- ( -25.90, z-score =  -0.32, R)
>consensus
CUAAUGGCGGAGCACAGCGGGCGGCGUCACACGCCUCCCAAAUCCAAAACCGCUCCCCAUA_____GA_C__CUCC__CAGUCUCACUGAC_____
.....(((((.((...))(((.((((.....)))).)))..........))))).......................................... (-16.12 = -16.56 +   0.44)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 3,462,111 – 3,462,203
Length 92
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 72.14
Shannon entropy 0.44862
G+C content 0.58081
Mean single sequence MFE -25.00
Consensus MFE -15.92
Energy contribution -16.36
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -2.23
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.31
SVM RNA-class probability 0.988125
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3462111 92 + 22422827
GGCGGAGCACAGCGGGCGGCGUCACACGCCUACCAAAUCCAAAACCGCUCUCCAUA----AGACCACCUCCGUCAGUCUCACUGACAAAAAAAAAA
(((((((......((..((((.....))))..))............(.(((.....----))).)..))))))).(((.....))).......... ( -25.20, z-score =  -2.82, R)
>droSim1.chrX_random 1465452 69 + 5698898
GGCGGAGCACAGCGGGCAGCGUCACACGCCUCCCAAAUCCAAAACCGCUCCCCA---------------------GUCUCACUGACAAAA------
((.(((((.....(((..(((.....)))..)))...(....)...))))))).---------------------(((.....)))....------ ( -20.80, z-score =  -2.35, R)
>droSec1.super_4 2967556 69 - 6179234
GGCGGAGCACAGCGGGCAGCGUCACACGCCUCCCAAAUCCAAAACCGCUCCCCA---------------------GUCUCACUGACAAAA------
((.(((((.....(((..(((.....)))..)))...(....)...))))))).---------------------(((.....)))....------ ( -20.80, z-score =  -2.35, R)
>droYak2.chrX 16844808 86 - 21770863
GGCGGAGCACAGCGGGCGGCGCCAAAUGCCUCCCAAAUCCCAAACUGCUCCACAUA----GGAGCUUCUCCGCCAAUCACACUGAGAAAA------
(((((((......(((.((((.....)))).)))............(((((.....----)))))..)))))))................------ ( -34.00, z-score =  -3.82, R)
>droEre2.scaffold_4690 874470 89 + 18748788
GGCGGAGCACAGCGGGCGGCCUACAAUGCCUCCCAAAUCCCAA-CUGCUCCACAUAUGUAAGAGCUACUCCUCCAAUGGCACUGGGAAAA------
.((........))(((.(((.......))).)))...(((((.-..((((.((....))..))))....((......))...)))))...------ ( -24.20, z-score =   0.20, R)
>consensus
GGCGGAGCACAGCGGGCGGCGUCACACGCCUCCCAAAUCCAAAACCGCUCCCCAUA_____GA_C__CUCC__CAGUCUCACUGACAAAA______
(((((.((...))(((.((((.....)))).)))..........)))))............................................... (-15.92 = -16.36 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:11:42 2011