Locus 12879

Sequence ID dm3.chrX
Location 2,933,805 – 2,933,877
Length 72
Max. P 0.976742
window17709 window17710

overview

Window 9

Location 2,933,805 – 2,933,877
Length 72
Sequences 11
Columns 72
Reading direction forward
Mean pairwise identity 94.49
Shannon entropy 0.12835
G+C content 0.50273
Mean single sequence MFE -19.90
Consensus MFE -18.84
Energy contribution -19.22
Covariance contribution 0.37
Combinations/Pair 1.05
Mean z-score -1.07
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.637344
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2933805 72 + 22422827
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUUACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ ( -21.39, z-score =  -1.40, R)
>droSim1.chrX 2072570 72 + 17042790
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUUACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ ( -21.39, z-score =  -1.40, R)
>droSec1.super_10 2673686 72 + 3036183
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUUACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ ( -21.39, z-score =  -1.40, R)
>droYak2.chrX 16341049 72 - 21770863
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUUACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ ( -21.39, z-score =  -1.40, R)
>droEre2.scaffold_4690 361531 72 + 18748788
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUUACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ ( -21.39, z-score =  -1.40, R)
>droAna3.scaffold_12613 2246 72 - 519072
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUAACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ ( -21.39, z-score =  -1.49, R)
>dp4.chrXL_group1e 2412553 72 + 12523060
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUUACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ ( -21.39, z-score =  -1.40, R)
>droPer1.super_18 1282218 72 + 1952607
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUUACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ ( -21.39, z-score =  -1.40, R)
>droWil1.scaffold_181096 10072705 72 - 12416693
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAAGGCCUUAAAC
(((((((((.(((((................)))))...)))..(((((....))))))).))))....... ( -17.59, z-score =  -0.40, R)
>droVir3.scaffold_12726 274775 65 + 2840439
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCAUAGCC-------
((...((((.(((((................)))))...)))).(((((....)))))....)).------- ( -12.39, z-score =   0.63, R)
>droGri2.scaffold_15203 2488335 67 + 11997470
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGUGCAGCGAGGCCUG-----
(((((((((.(((((................)))))...)))..(((((....)))))))))))...----- ( -17.79, z-score =  -0.71, R)
>consensus
GCCUCGUCAAAACGUCAAUCGGUGUAAUCAAGCGUUAAGUGAUUCUGCGGAAGCGCAGCGAGGCCUUUACUU
(((((((((.(((((................)))))...)))..(((((....)))))))))))........ (-18.84 = -19.22 +   0.37) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,933,805 – 2,933,877
Length 72
Sequences 11
Columns 72
Reading direction reverse
Mean pairwise identity 94.49
Shannon entropy 0.12835
G+C content 0.50273
Mean single sequence MFE -20.36
Consensus MFE -20.07
Energy contribution -20.11
Covariance contribution 0.04
Combinations/Pair 1.09
Mean z-score -1.89
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.976742
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2933805 72 - 22422827
AAGUAAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -21.60, z-score =  -2.08, R)
>droSim1.chrX 2072570 72 - 17042790
AAGUAAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -21.60, z-score =  -2.08, R)
>droSec1.super_10 2673686 72 - 3036183
AAGUAAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -21.60, z-score =  -2.08, R)
>droYak2.chrX 16341049 72 + 21770863
AAGUAAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -21.60, z-score =  -2.08, R)
>droEre2.scaffold_4690 361531 72 - 18748788
AAGUAAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -21.60, z-score =  -2.08, R)
>droAna3.scaffold_12613 2246 72 + 519072
AAGUUAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -21.60, z-score =  -2.11, R)
>dp4.chrXL_group1e 2412553 72 - 12523060
AAGUAAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -21.60, z-score =  -2.08, R)
>droPer1.super_18 1282218 72 - 1952607
AAGUAAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -21.60, z-score =  -2.08, R)
>droWil1.scaffold_181096 10072705 72 + 12416693
GUUUAAGGCCUUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
.......((((.(((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) ( -17.80, z-score =  -0.97, R)
>droVir3.scaffold_12726 274775 65 - 2840439
-------GGCUAUGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
-------.(((.(((((((....)))))..(((...((((.(..(((.....)))..))))).))))).))) ( -13.20, z-score =  -0.16, R)
>droGri2.scaffold_15203 2488335 67 - 11997470
-----CAGGCCUCGCUGCACUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
-----...((((((((((......))))..(((...((((.(..(((.....)))..))))).))))))))) ( -20.20, z-score =  -2.99, R)
>consensus
AAGUAAAGGCCUCGCUGCGCUUCCGCAGAAUCACUUAACGCUUGAUUACACCGAUUGACGUUUUGACGAGGC
........(((((((((((....)))))..(((...((((.(..(((.....)))..))))).))))))))) (-20.07 = -20.11 +   0.04) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:10:34 2011