Locus 12471

Sequence ID dm3.chrX
Location 420,222 – 420,286
Length 64
Max. P 0.924630
window17149 window17150

overview

Window 9

Location 420,222 – 420,286
Length 64
Sequences 5
Columns 71
Reading direction forward
Mean pairwise identity 76.02
Shannon entropy 0.40347
G+C content 0.43789
Mean single sequence MFE -14.91
Consensus MFE -9.95
Energy contribution -10.47
Covariance contribution 0.52
Combinations/Pair 1.08
Mean z-score -1.40
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.750795
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 420222 64 + 22422827
-------UAAAAUGAUCCUGCCAAUAGUAAUAAGGAUCGAGCGCUGCCCUCAAGGAUCGAUAGGCACUCCA
-------......((((((.............))))))(((.(((.(((....))...)...))).))).. ( -14.12, z-score =  -0.65, R)
>droSim1.chrX 314905 59 + 17042790
-------UAAAAUGAUCCUGACAAUAGUAA-AAGGAUCGAGCGC----CUCAAGGAUCAUUGAGCACUCCA
-------......((((((.((....))..-.))))))(((.((----.((((......)))))).))).. ( -18.00, z-score =  -3.64, R)
>droSec1.super_10 276538 59 + 3036183
-------UAAAAUGAUCCUGACAAUAGUAA-AAGGAUCGAGCGC----CUCAAGGAUCAUUGAGCACUCCA
-------......((((((.((....))..-.))))))(((.((----.((((......)))))).))).. ( -18.00, z-score =  -3.64, R)
>droYak2.chrX 347547 71 + 21770863
UAGUAGUAAAAGAGAUCCUGACAAUAACCAUAAGAAUCGAGCGCUUUUCUGGAGGAUCGCCGAGCACUCCA
..(.(((....(.((((((........(((.((((.........)))).)))))))))..)....))).). (  -9.30, z-score =   1.39, R)
>droEre2.scaffold_4644 371759 71 + 2521924
UAGUAGUAAAAGUGAUCCUGACAAUGAUAUUAAGGAUCGAGCGCUUUCCUCAAGGCUCUAUGAGCACUCCA
.............((((((.............))))))(((.((((.((....))......)))).))).. ( -15.12, z-score =  -0.47, R)
>consensus
_______UAAAAUGAUCCUGACAAUAGUAAUAAGGAUCGAGCGCU___CUCAAGGAUCAAUGAGCACUCCA
.............((((((.............))))))(((.(((.................))).))).. ( -9.95 = -10.47 +   0.52)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 420,222 – 420,286
Length 64
Sequences 5
Columns 71
Reading direction reverse
Mean pairwise identity 76.02
Shannon entropy 0.40347
G+C content 0.43789
Mean single sequence MFE -17.68
Consensus MFE -13.65
Energy contribution -13.49
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -1.50
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.31
SVM RNA-class probability 0.924630
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 420222 64 - 22422827
UGGAGUGCCUAUCGAUCCUUGAGGGCAGCGCUCGAUCCUUAUUACUAUUGGCAGGAUCAUUUUA-------
..((((((((.((((...)))).))..))))))((((((.............))))))......------- ( -16.62, z-score =  -0.48, R)
>droSim1.chrX 314905 59 - 17042790
UGGAGUGCUCAAUGAUCCUUGAG----GCGCUCGAUCCUU-UUACUAUUGUCAGGAUCAUUUUA-------
..((((((((((......)))).----))))))((((((.-..((....)).))))))......------- ( -19.90, z-score =  -3.21, R)
>droSec1.super_10 276538 59 - 3036183
UGGAGUGCUCAAUGAUCCUUGAG----GCGCUCGAUCCUU-UUACUAUUGUCAGGAUCAUUUUA-------
..((((((((((......)))).----))))))((((((.-..((....)).))))))......------- ( -19.90, z-score =  -3.21, R)
>droYak2.chrX 347547 71 - 21770863
UGGAGUGCUCGGCGAUCCUCCAGAAAAGCGCUCGAUUCUUAUGGUUAUUGUCAGGAUCUCUUUUACUACUA
..(((((((...(.........)...)))))))((((((.(..(...)..).))))))............. ( -14.30, z-score =   0.47, R)
>droEre2.scaffold_4644 371759 71 - 2521924
UGGAGUGCUCAUAGAGCCUUGAGGAAAGCGCUCGAUCCUUAAUAUCAUUGUCAGGAUCACUUUUACUACUA
..(((((((.......((....))..)))))))((((((..(((....))).))))))............. ( -17.70, z-score =  -1.06, R)
>consensus
UGGAGUGCUCAACGAUCCUUGAG___AGCGCUCGAUCCUUAUUACUAUUGUCAGGAUCAUUUUA_______
..((((((...................))))))((((((.............))))))............. (-13.65 = -13.49 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:56 2011