Locus 12987

Sequence ID dm3.chrX
Location 3,768,747 – 3,768,886
Length 139
Max. P 0.933681
window17850 window17851 window17852 window17853

overview

Window 0

Location 3,768,747 – 3,768,860
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.99
Shannon entropy 0.50733
G+C content 0.41399
Mean single sequence MFE -27.37
Consensus MFE -11.99
Energy contribution -15.31
Covariance contribution 3.31
Combinations/Pair 1.25
Mean z-score -1.70
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.684298
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3768747 113 + 22422827
AGGGCAUACCAGGCUUAUCUAAUUAUUUAUAGGUAAAGCCCUCAGUGUACUCA-------UUUUUCAAUUAGCUUGUUGAAAAUUACGGAGUAUCAGCGACUCCGAUUGGUCUACGGCUU
.((((......((((((((((........))))).)))))....(((.(((..-------.((((((((......))))))))...((((((.......))))))...))).))).)))) ( -28.90, z-score =  -1.55, R)
>droEre2.scaffold_4690 1152798 113 + 18748788
AAGGCAUGCCAGGCUUAUCUAAUUAUUUAUAGGUAAAGCCCUCACUGUACUCA-------UUUUUCAAUUAGCCAGUUGGAAAUGACGGAGUAUCAGCGACUCCCAUUGGUCUACCCCUU
((((...((((((((((((((........))))).))))).((.((((((((.-------.(((((((((....))))))))).....))))).))).)).......)))).....)))) ( -30.00, z-score =  -1.78, R)
>droYak2.chrX 17124524 119 - 21770863
AAGGCAUACCAGGCUUAUUUAAUUAUUUAUAGGCAAAGCCCCCACUGCCCUCACUCAUUUUUUUUCAAUUAGCUUGUUGGAAAUUUCGGAGUAUCAGUGACUCCGAU-AGUCUACGCCCU
..(((....((((((.((((((....)))..((((..........)))).................))).)))))).((((....(((((((.......))))))).-..)))).))).. ( -26.50, z-score =  -1.35, R)
>droSec1.super_4 3240516 113 - 6179234
AAGGCAUACCAGGCUUAUCUAAUUAUUUAUAGGCAAAGCCCUCACUGUACUCA-------UUUUUCAUUUGGCUUGUUGGAAAUUACGGAGUAUCAGCGACUACGAUUGGUCUACGCCUU
(((((..(((((((((.((((........))))..))))).((.((((((((.-------.((((((..........)))))).....))))).))).)).......))))....))))) ( -27.90, z-score =  -1.53, R)
>droSim1.chrX 2774721 113 + 17042790
AAGGCAUACCAGGCUUAUCUAAUUAUUUAUAGGUAAAGCCCUCACUGUACUCA-------UUUUUCAAUUAGCUUGUUGGAAAUUACGGAGUAUCAGCGACUACGAUUGGUCUACGCUUU
(((((..((((((((((((((........))))).))))).((.((((((((.-------.((((((((......)))))))).....))))).))).)).......))))....))))) ( -30.80, z-score =  -2.89, R)
>droPer1.super_25 250627 91 + 1448063
GAUCCGCAGUAGAGUGACCU------UCAAAAAUGGUGACCCCAUGCCGCUUG-------------AAUUUG---AAUGCAAUUUGAAGAGCAUUA-CAGCUCCGA---GUCCAUCU---
((..((.(((.(((((..((------(((((...(((........)))((...-------------......---...))..)))))))..)))).-).))).)).---.)).....--- ( -20.10, z-score =  -1.09, R)
>consensus
AAGGCAUACCAGGCUUAUCUAAUUAUUUAUAGGUAAAGCCCUCACUGUACUCA_______UUUUUCAAUUAGCUUGUUGGAAAUUACGGAGUAUCAGCGACUCCGAUUGGUCUACGCCUU
.((((......((((((((((........))))))).))).((.((((((((.........((((((((......)))))))).....))))).))).)).........))))....... (-11.99 = -15.31 +   3.31)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,768,747 – 3,768,860
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.99
Shannon entropy 0.50733
G+C content 0.41399
Mean single sequence MFE -27.95
Consensus MFE -14.88
Energy contribution -15.97
Covariance contribution 1.09
Combinations/Pair 1.35
Mean z-score -1.42
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.779832
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3768747 113 - 22422827
AAGCCGUAGACCAAUCGGAGUCGCUGAUACUCCGUAAUUUUCAACAAGCUAAUUGAAAAA-------UGAGUACACUGAGGGCUUUACCUAUAAAUAAUUAGAUAAGCCUGGUAUGCCCU
.....(((.((((..((((((.......)))))).....((((....(((.(((....))-------).)))....))))(((((...(((........)))..))))))))).)))... ( -24.70, z-score =  -1.04, R)
>droEre2.scaffold_4690 1152798 113 - 18748788
AAGGGGUAGACCAAUGGGAGUCGCUGAUACUCCGUCAUUUCCAACUGGCUAAUUGAAAAA-------UGAGUACAGUGAGGGCUUUACCUAUAAAUAAUUAGAUAAGCCUGGCAUGCCUU
..((((((..((........((((((.(((((.((((........))))..(((....))-------))))))))))))((((((...(((........)))..))))))))..)))))) ( -33.60, z-score =  -1.84, R)
>droYak2.chrX 17124524 119 + 21770863
AGGGCGUAGACU-AUCGGAGUCACUGAUACUCCGAAAUUUCCAACAAGCUAAUUGAAAAAAAAUGAGUGAGGGCAGUGGGGGCUUUGCCUAUAAAUAAUUAAAUAAGCCUGGUAUGCCUU
((((((((....-.(((((((.......))))))).........((.(((..((....))..........((((((........))))))...............))).)).)))))))) ( -28.90, z-score =  -0.44, R)
>droSec1.super_4 3240516 113 + 6179234
AAGGCGUAGACCAAUCGUAGUCGCUGAUACUCCGUAAUUUCCAACAAGCCAAAUGAAAAA-------UGAGUACAGUGAGGGCUUUGCCUAUAAAUAAUUAGAUAAGCCUGGUAUGCCUU
(((((((..(((........((((((.(((((.....((((.............))))..-------.)))))))))))((((((...(((........)))..)))))))))))))))) ( -31.32, z-score =  -2.80, R)
>droSim1.chrX 2774721 113 - 17042790
AAAGCGUAGACCAAUCGUAGUCGCUGAUACUCCGUAAUUUCCAACAAGCUAAUUGAAAAA-------UGAGUACAGUGAGGGCUUUACCUAUAAAUAAUUAGAUAAGCCUGGUAUGCCUU
.(((.(((.(((........((((((.(((((.((........))......(((....))-------))))))))))))((((((...(((........)))..))))))))).)))))) ( -28.10, z-score =  -2.41, R)
>droPer1.super_25 250627 91 - 1448063
---AGAUGGAC---UCGGAGCUG-UAAUGCUCUUCAAAUUGCAUU---CAAAUU-------------CAAGCGGCAUGGGGUCACCAUUUUUGA------AGGUCACUCUACUGCGGAUC
---.....((.---.((((..((-.(((((..........)))))---))..))-------------)..((((..((((((.(((........------.))).)))))))))))..)) ( -21.10, z-score =  -0.01, R)
>consensus
AAGGCGUAGACCAAUCGGAGUCGCUGAUACUCCGUAAUUUCCAACAAGCUAAUUGAAAAA_______UGAGUACAGUGAGGGCUUUACCUAUAAAUAAUUAGAUAAGCCUGGUAUGCCUU
.....(((.(((........((((((.(((((....................................)))))))))))((((((...(((........)))..))))))))).)))... (-14.88 = -15.97 +   1.09)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,768,787 – 3,768,886
Length 99
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 83.50
Shannon entropy 0.27314
G+C content 0.42691
Mean single sequence MFE -27.32
Consensus MFE -17.88
Energy contribution -19.08
Covariance contribution 1.20
Combinations/Pair 1.06
Mean z-score -2.53
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.38
SVM RNA-class probability 0.933681
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3768787 99 + 22422827
CUCAGUGUACUCA-------UUUUUCAAUUAGCUUGUUGAAAAUUACGGAGUAUCAGCGACUCCGAUUGGUCUACGGCUUUUAUGGAGCCCAAUCGAGUGGAUUGA
.(((((.(((((.-------.((((((((......))))))))....(((((.......)))))((((((....)(((((.....))))))))))))))).))))) ( -32.80, z-score =  -3.37, R)
>droEre2.scaffold_4690 1152838 92 + 18748788
CUCACUGUACUCA-------UUUUUCAAUUAGCCAGUUGGAAAUGACGGAGUAUCAGCGACUCCCAUUGGUCUACCCCUUUUAUGAAGCUCAAUCGAGU-------
.(((((((((((.-------.(((((((((....))))))))).....))))).))).((((......))))...........))).((((....))))------- ( -19.30, z-score =  -0.59, R)
>droYak2.chrX 17124564 98 - 21770863
CCCACUGCCCUCACUCAUUUUUUUUCAAUUAGCUUGUUGGAAAUUUCGGAGUAUCAGUGACUCCGAU-AGUCUACGCCCUUUAUGGAGCUCAAUCGAGU-------
..(((((.....((((.....((((((((......)))))))).....))))..)))))((((.(((-.(.....((((.....)).)).).)))))))------- ( -22.10, z-score =  -1.18, R)
>droSec1.super_4 3240556 98 - 6179234
CUCACUGUACUCA-------UUUUUCAUUUGGCUUGUUGGAAAUUACGGAGUAUCAGCGACUACGAUUGGUCUACGCCUUUUAUGGAGACCAAUCGAGUGGAUUG-
....((((((((.-------.((((((..........)))))).....))))).)))(.(((.((((((((((...((......))))))))))))))).)....- ( -30.50, z-score =  -3.31, R)
>droSim1.chrX 2774761 98 + 17042790
CUCACUGUACUCA-------UUUUUCAAUUAGCUUGUUGGAAAUUACGGAGUAUCAGCGACUACGAUUGGUCUACGCUUUUUAUGGAGACCAAUCGAGUGGAUUG-
....((((((((.-------.((((((((......)))))))).....))))).)))(.(((.((((((((((.((.......)).))))))))))))).)....- ( -31.90, z-score =  -4.20, R)
>consensus
CUCACUGUACUCA_______UUUUUCAAUUAGCUUGUUGGAAAUUACGGAGUAUCAGCGACUCCGAUUGGUCUACGCCUUUUAUGGAGCCCAAUCGAGUGGAUUG_
..(.((((((((.........((((((((......)))))))).....))))).))).)(((.(((((((.((.((.......)).)).))))))))))....... (-17.88 = -19.08 +   1.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,768,787 – 3,768,886
Length 99
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 83.50
Shannon entropy 0.27314
G+C content 0.42691
Mean single sequence MFE -23.58
Consensus MFE -14.89
Energy contribution -15.73
Covariance contribution 0.84
Combinations/Pair 1.19
Mean z-score -2.09
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.685434
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3768787 99 - 22422827
UCAAUCCACUCGAUUGGGCUCCAUAAAAGCCGUAGACCAAUCGGAGUCGCUGAUACUCCGUAAUUUUCAACAAGCUAAUUGAAAAA-------UGAGUACACUGAG
(((....(((((((((((((.......))))(....))))))(((((.......)))))....(((((((........))))))).-------.))))....))). ( -21.50, z-score =  -1.44, R)
>droEre2.scaffold_4690 1152838 92 - 18748788
-------ACUCGAUUGAGCUUCAUAAAAGGGGUAGACCAAUGGGAGUCGCUGAUACUCCGUCAUUUCCAACUGGCUAAUUGAAAAA-------UGAGUACAGUGAG
-------.(((.((((.(((((......)))))....)))))))..((((((.(((((.((((........))))..(((....))-------)))))))))))). ( -22.00, z-score =  -0.60, R)
>droYak2.chrX 17124564 98 + 21770863
-------ACUCGAUUGAGCUCCAUAAAGGGCGUAGACU-AUCGGAGUCACUGAUACUCCGAAAUUUCCAACAAGCUAAUUGAAAAAAAAUGAGUGAGGGCAGUGGG
-------...(.((((.((((......)))).......-.(((((((.......))))))).....((.....(((.(((.......))).)))...)))))).). ( -19.20, z-score =   0.55, R)
>droSec1.super_4 3240556 98 + 6179234
-CAAUCCACUCGAUUGGUCUCCAUAAAAGGCGUAGACCAAUCGUAGUCGCUGAUACUCCGUAAUUUCCAACAAGCCAAAUGAAAAA-------UGAGUACAGUGAG
-.......((((((((((((((......))...)))))))))).))((((((.(((((.....((((.............))))..-------.))))))))))). ( -28.02, z-score =  -4.40, R)
>droSim1.chrX 2774761 98 - 17042790
-CAAUCCACUCGAUUGGUCUCCAUAAAAAGCGUAGACCAAUCGUAGUCGCUGAUACUCCGUAAUUUCCAACAAGCUAAUUGAAAAA-------UGAGUACAGUGAG
-.......((((((((((((.(.........).)))))))))).))((((((.(((((.((........))......(((....))-------)))))))))))). ( -27.20, z-score =  -4.55, R)
>consensus
_CAAUCCACUCGAUUGGGCUCCAUAAAAGGCGUAGACCAAUCGGAGUCGCUGAUACUCCGUAAUUUCCAACAAGCUAAUUGAAAAA_______UGAGUACAGUGAG
........(((((((((.((.(.........).)).))))))).))((((((.(((((............(((.....))).............))))))))))). (-14.89 = -15.73 +   0.84)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:12:32 2011