Locus 12795

Sequence ID dm3.chrX
Location 2,213,915 – 2,214,082
Length 167
Max. P 0.987987
window17585 window17586 window17587

overview

Window 5

Location 2,213,915 – 2,214,009
Length 94
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 85.38
Shannon entropy 0.22383
G+C content 0.61918
Mean single sequence MFE -35.95
Consensus MFE -27.66
Energy contribution -28.35
Covariance contribution 0.69
Combinations/Pair 1.08
Mean z-score -1.79
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.710309
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2213915 94 + 22422827
UUCCCAUCCCCCUUACCCCGGGCCAGGAUUUUCCCAUUUCGACUGACAGGC-----GGUGGCGGCGGUGGACGUCAGCGUUUCUGUUGACGUCUCCCGU
..((((((((..(((...((((...((.....))...))))..)))..)).-----))))).)((((..((((((((((....))))))))))..)))) ( -33.80, z-score =  -0.60, R)
>droEre2.scaffold_4644 2171411 92 + 2521924
-------UUCCCACCCUCUGUGCCCGGAUUUUCCCAUUUCGACUGACAGGCAGAGUGGCGGUGGCGGUGGACGUCAUCGUUUCUGUUGACGUCUCCCGU
-------...(((((((((.((((.((......))...((....))..)))).)).)).)))))(((..(((((((.((....)).)))))))..))). ( -35.00, z-score =  -1.60, R)
>droSec1.super_10 1990715 88 + 3036183
------UUCCCACCCCCCUGUGCCCGGAUUUUCCCAUUUCGACUGACAGGC-----GGUGGCGGCGGCGGACGUCAGCGUUUCUGUUGACGUCUCCCGU
------..((((((..(((((...((((.........))))....))))).-----))))).)((((.(((((((((((....))))))))))).)))) ( -37.50, z-score =  -2.49, R)
>droSim1.chrX 1561412 88 + 17042790
------UUCCCACCCCCCUGUGCCCGGAUUUUCCCAUUUCGACUGACAGGC-----GGUGGCGGCGGCGGACGUCAGCGUUUCUGUUGACGUCUCCCGU
------..((((((..(((((...((((.........))))....))))).-----))))).)((((.(((((((((((....))))))))))).)))) ( -37.50, z-score =  -2.49, R)
>consensus
______UUCCCACCCCCCUGUGCCCGGAUUUUCCCAUUUCGACUGACAGGC_____GGUGGCGGCGGCGGACGUCAGCGUUUCUGUUGACGUCUCCCGU
.........(((((.......(((.((......))...((....))..))).....)))))..((((..((((((((((....))))))))))..)))) (-27.66 = -28.35 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 2,213,949 – 2,214,044
Length 95
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 92.39
Shannon entropy 0.12524
G+C content 0.58558
Mean single sequence MFE -40.88
Consensus MFE -37.84
Energy contribution -37.60
Covariance contribution -0.24
Combinations/Pair 1.10
Mean z-score -2.55
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.30
SVM RNA-class probability 0.987987
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2213949 95 + 22422827
CAUUUCGACUGACAGGC-----GGUGGCGGCGGUGGACGUCAGCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUUCAUUACCUUCGAGGGACAUUGUCG
..............(((-----(((((((((((..((((((((((....))))))))))..))))))).............(((....))).))))))). ( -42.20, z-score =  -3.39, R)
>droEre2.scaffold_4644 2171438 100 + 2521924
CAUUUCGACUGACAGGCAGAGUGGCGGUGGCGGUGGACGUCAUCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUCCAUUACCUUCGAGGGGCAUUGUCG
..........(((((((.((((((((.((((((..(((((((.((....)).)))))))..))))))))))))))......(((....))))).))))). ( -38.50, z-score =  -1.58, R)
>droYak2.chrX 15649714 100 - 21770863
CAUUUUGACUGACGGGCGGAGUGGCGGUGGCGGUGGACGUCAUCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUCCAUUACCUUCGAGGGGCAUUGUCG
..........((((((((((..((((.((((((..(((((((.((....)).)))))))..))))))))))...)))....(((....))))).))))). ( -40.50, z-score =  -1.72, R)
>droSec1.super_10 1990743 95 + 3036183
CAUUUCGACUGACAGGC-----GGUGGCGGCGGCGGACGUCAGCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUUCAUUACCUUCGAGGGACAUUGUCG
..............(((-----(((((((((((.(((((((((((....))))))))))).))))))).............(((....))).))))))). ( -41.60, z-score =  -3.03, R)
>droSim1.chrX 1561440 95 + 17042790
CAUUUCGACUGACAGGC-----GGUGGCGGCGGCGGACGUCAGCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUUCAUUACCUUCGAGGGACAUUGUCG
..............(((-----(((((((((((.(((((((((((....))))))))))).))))))).............(((....))).))))))). ( -41.60, z-score =  -3.03, R)
>consensus
CAUUUCGACUGACAGGC_____GGUGGCGGCGGUGGACGUCAGCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUUCAUUACCUUCGAGGGACAUUGUCG
.....((((.(((..((......)).(((((((..((((((((((....))))))))))..))))))))))..........(((....))).....)))) (-37.84 = -37.60 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 2,213,975 – 2,214,082
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 86.52
Shannon entropy 0.22296
G+C content 0.52349
Mean single sequence MFE -29.45
Consensus MFE -24.16
Energy contribution -24.92
Covariance contribution 0.76
Combinations/Pair 1.12
Mean z-score -1.35
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.521521
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2213975 107 + 22422827
GGUGGACGUCAGCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUUCAUUACCUUCGAGGGACAUUGUCGUCACAAGACUCACACAUUCACAUUCACAUACAACAUGC
((..((((((((((....))))))))))..))(((.(.(((.............))).))))..(((.(((....)))..)))........................ ( -28.42, z-score =  -1.38, R)
>droEre2.scaffold_4644 2171469 100 + 2521924
GGUGGACGUCAUCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUCCAUUACCUUCGAGGGGCAUUGUCGUCACACAACUCGCACAUUCUCGUGUGCAUAC-------
((..(((((((.((....)).)))))))..))((.(((.((...((....((.....))))...)).))).)).......((((((....))))))....------- ( -29.70, z-score =  -1.22, R)
>droYak2.chrX 15649745 100 - 21770863
GGUGGACGUCAUCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUCCAUUACCUUCGAGGGGCAUUGUCGUCAGAAAACUCGCACAUACUCGUGUGCAUGC-------
((((.....)))).((((((.(((((...(((.(((....((.......))...))).)))...))))).))))))....((((((....))))))....------- ( -30.20, z-score =  -0.75, R)
>droSec1.super_10 1990769 94 + 3036183
GGCGGACGUCAGCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUUCAUUACCUUCGAGGGACAUUGUCGUCAGAAAACUCACACAUUCACAUGC-------------
((.(((((((((((....))))))))))).))...(.((.((((((....((.....))(((......))).))))))..)).)..........------------- ( -29.00, z-score =  -1.76, R)
>droSim1.chrX 1561466 96 + 17042790
GGCGGACGUCAGCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUUCAUUACCUUCGAGGGACAUUGUCGUCAGAAAACUCACACAUUCACAUGCGU-----------
((.(((((((((((....))))))))))).))..(((((.((((((....((.....))(((......))).))))))............))))).----------- ( -29.92, z-score =  -1.64, R)
>consensus
GGUGGACGUCAGCGUUUCUGUUGACGUCUCCCGUCGCGUCGUUUUCAUUACCUUCGAGGGACAUUGUCGUCAGAAAACUCACACAUUCACAUGCGCAU_C_______
((..((((((((((....))))))))))..))...(.((.((((((....((.....))(((......))).))))))..)).)....................... (-24.16 = -24.92 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:08:54 2011