Locus 368

Sequence ID dm3.chr2L
Location 2,533,114 – 2,533,204
Length 90
Max. P 0.634309
window504 window505

overview

Window 4

Location 2,533,114 – 2,533,204
Length 90
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 64.17
Shannon entropy 0.62918
G+C content 0.58745
Mean single sequence MFE -39.10
Consensus MFE -15.56
Energy contribution -18.32
Covariance contribution 2.76
Combinations/Pair 1.36
Mean z-score -1.29
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.634309
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2533114 90 + 23011544
AUGCGUGUGC-AUUGUAGCUUAACUUGAGCUCUCCGGCAA-CUUAUGCCGAC--ACGGACUCAGCUGCUCCUGCA------GGUGCCAGUCUCCGGCACC------------------
.......(((-(..((((((......(((.(((.(((((.-....)))))..--..))))))))))))...))))------((((((.......))))))------------------ ( -31.40, z-score =  -1.15, R)
>droYak2.chr2L 2525464 114 + 22324452
AUGCGUGUGC-AUUCUGGCUUAACUUGAGCUCUCCGGCAA-CUUAUGCCGAC--ACGGACUCAGAUGCUCCUGCAUCCUGGACUGGGGGCUUAAGGCACUGCCCCAGUGCCCGGCUCC
..((.((.((-(((..(((....((((((((((.(((((.-....)))))..--.(((.((..(((((....)))))..)).))))))))))))).....)))..))))).))))... ( -44.40, z-score =  -1.82, R)
>droSec1.super_5 706979 114 + 5866729
AUGCGUGUGC-AUUGUGGCUUAACUUGAGCUCUCCGGCAA-CUUAUGCCGAC--ACGGACUCAGCUGCUCCUGCAUCCUGGACCGGGGGCUUAAGGCGCUGCCCCAGUCUCCGGCACC
......((((-((((.(((....((((((((((((((((.-....)))))..--..((.(.(((.(((....)))..)))).))))))))))))).....))).)))).....)))). ( -42.40, z-score =  -0.65, R)
>droSim1.chr2L 2495388 114 + 22036055
AUGCGUGUGC-AUUGUGGCUUAACUUAAGCUCUCCGGCAA-CUUAUGCCGAC--ACGGACUCAGCUGCUCCUGCAUCCUGGACCGGGGGCUUAAGGCGCUGCCCCAGUCUCCGGCAGC
..((....((-......))....((((((((((((((((.-....)))))..--..((.(.(((.(((....)))..)))).)))))))))))))))((((((.........)))))) ( -42.80, z-score =  -0.56, R)
>droVir3.scaffold_12963 10222759 103 - 20206255
------CUGCUAUGCCAGGUCAAACAAAGCCACGCAACAAACAAAAGCCGCCCCACAGGCUUAAGACGGCAGGCAUC--AGGCCACAUGCAUUGUCUGAUGCUUCGCAGUC-------
------((((..((((.(((........))).............(((((........))))).....))))((((((--((((..........))))))))))..))))..------- ( -34.50, z-score =  -2.26, R)
>consensus
AUGCGUGUGC_AUUGUGGCUUAACUUGAGCUCUCCGGCAA_CUUAUGCCGAC__ACGGACUCAGCUGCUCCUGCAUCCUGGACCGGGGGCUUAAGGCGCUGCCCCAGUCUCCGGC__C
................(((....((((((((((((((((......)))))......(((..(((......)))..)))......))))))))))).....)))............... (-15.56 = -18.32 +   2.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,533,114 – 2,533,204
Length 90
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 64.17
Shannon entropy 0.62918
G+C content 0.58745
Mean single sequence MFE -41.58
Consensus MFE -15.94
Energy contribution -17.26
Covariance contribution 1.32
Combinations/Pair 1.54
Mean z-score -1.30
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.536656
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2533114 90 - 23011544
------------------GGUGCCGGAGACUGGCACC------UGCAGGAGCAGCUGAGUCCGU--GUCGGCAUAAG-UUGCCGGAGAGCUCAAGUUAAGCUACAAU-GCACACGCAU
------------------(((((((....).))))))------((((..((((((((((..(..--.((((((....-.)))))).)..))).))))..)))....)-)))....... ( -38.60, z-score =  -2.72, R)
>droYak2.chr2L 2525464 114 - 22324452
GGAGCCGGGCACUGGGGCAGUGCCUUAAGCCCCCAGUCCAGGAUGCAGGAGCAUCUGAGUCCGU--GUCGGCAUAAG-UUGCCGGAGAGCUCAAGUUAAGCCAGAAU-GCACACGCAU
.((((((((((((((((....((.....)))))))))...((((((....))))))..))))).--.((((((....-.))))))...)))).............((-((....)))) ( -43.80, z-score =  -1.26, R)
>droSec1.super_5 706979 114 - 5866729
GGUGCCGGAGACUGGGGCAGCGCCUUAAGCCCCCGGUCCAGGAUGCAGGAGCAGCUGAGUCCGU--GUCGGCAUAAG-UUGCCGGAGAGCUCAAGUUAAGCCACAAU-GCACACGCAU
.((((..(.((((((((..((.......))))))))))).(..((((.(.(((((((((..(..--.((((((....-.)))))).)..))).))))..)))....)-)))..))))) ( -43.80, z-score =  -0.76, R)
>droSim1.chr2L 2495388 114 - 22036055
GCUGCCGGAGACUGGGGCAGCGCCUUAAGCCCCCGGUCCAGGAUGCAGGAGCAGCUGAGUCCGU--GUCGGCAUAAG-UUGCCGGAGAGCUUAAGUUAAGCCACAAU-GCACACGCAU
(((((((....)...))))))(((((((((((((((.((((..(((....))).))).).))).--...((((....-.)))))).).)))))))....((......-))....)).. ( -42.70, z-score =  -0.49, R)
>droVir3.scaffold_12963 10222759 103 + 20206255
-------GACUGCGAAGCAUCAGACAAUGCAUGUGGCCU--GAUGCCUGCCGUCUUAAGCCUGUGGGGCGGCUUUUGUUUGUUGCGUGGCUUUGUUUGACCUGGCAUAGCAG------
-------..((((...((.((((((((.(((((..((..--((((...(((((((((......)))))))))...)))).))..))).)).))))))))....))...))))------ ( -39.00, z-score =  -1.28, R)
>consensus
G__GCCGGACACUGGGGCAGCGCCUUAAGCCCCCGGUCCAGGAUGCAGGAGCAGCUGAGUCCGU__GUCGGCAUAAG_UUGCCGGAGAGCUCAAGUUAAGCCACAAU_GCACACGCAU
..........(((((((..((.......)))))))))..........((...((((((((.(.....((((((......)))))).).)))).))))...))................ (-15.94 = -17.26 +   1.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:11:39 2011