Locus 1579

Sequence ID dm3.chr2L
Location 12,257,641 – 12,257,733
Length 92
Max. P 0.876982
window2158 window2159

overview

Window 8

Location 12,257,641 – 12,257,733
Length 92
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 68.05
Shannon entropy 0.48274
G+C content 0.47809
Mean single sequence MFE -13.51
Consensus MFE -8.19
Energy contribution -7.87
Covariance contribution -0.31
Combinations/Pair 1.17
Mean z-score -1.22
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763903
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12257641 92 + 23011544
UUUUGUUGUUC-GAGGGAAGCCCAUAAUUAUGAUUAUGAGUACUCCCUCAGAAUUUUCCUGCCGCCCCCCCCCCCCCUCCCCCUUCCCACCAU
.......((((-((((((.((.((((((....)))))).))..)))))).))))....................................... ( -16.50, z-score =  -2.69, R)
>droSim1.chr2L 12059409 70 + 22036055
UUUUGUUGUUC-GAGGGAAGCCCAUAAUUAUGAUUAUGAGUACUCCCCCAGCAUUUUCCUGCCCCCCGCCC----------------------
......((((.-(.((((.((.((((((....)))))).))..))))).))))..................---------------------- ( -12.80, z-score =  -1.37, R)
>droSec1.super_16 447813 70 + 1878335
UUUUGUUGUUC-GAGGGAAGCCCAUAAUUAUGAUUAUGAGUACUCCCCCAGCAUUUUCCUGCCCCCCGCCC----------------------
......((((.-(.((((.((.((((((....)))))).))..))))).))))..................---------------------- ( -12.80, z-score =  -1.37, R)
>dp4.chr4_group3 5815173 79 - 11692001
UUUUGCUGUGAAGAAGGAAGCACAUAAUUAUGAUUAUG-GUGCCUCUAUAUCUCUCUCUUUCUGCCCAUCAUCAUUGUUG-------------
...((((...........))))..((((.(((((.(((-(.((....................)))))).))))).))))------------- ( -11.95, z-score =   0.55, R)
>consensus
UUUUGUUGUUC_GAGGGAAGCCCAUAAUUAUGAUUAUGAGUACUCCCCCAGCAUUUUCCUGCCCCCCGCCC______________________
..............((((.((.((((((....)))))).))..)))).............................................. ( -8.19 =  -7.87 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,257,641 – 12,257,733
Length 92
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 68.05
Shannon entropy 0.48274
G+C content 0.47809
Mean single sequence MFE -20.20
Consensus MFE -11.35
Energy contribution -11.35
Covariance contribution -0.00
Combinations/Pair 1.29
Mean z-score -1.61
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.876982
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12257641 92 - 23011544
AUGGUGGGAAGGGGGAGGGGGGGGGGGGGCGGCAGGAAAAUUCUGAGGGAGUACUCAUAAUCAUAAUUAUGGGCUUCCCUC-GAACAACAAAA
.((.((....((((((((...........(..(((((...)))))..).....((((((((....))))))))))))))))-...)).))... ( -23.50, z-score =  -1.09, R)
>droSim1.chr2L 12059409 70 - 22036055
----------------------GGGCGGGGGGCAGGAAAAUGCUGGGGGAGUACUCAUAAUCAUAAUUAUGGGCUUCCCUC-GAACAACAAAA
----------------------(..((...((((......))))(((((((..((((((((....))))))))))))))))-)..)....... ( -22.00, z-score =  -2.65, R)
>droSec1.super_16 447813 70 - 1878335
----------------------GGGCGGGGGGCAGGAAAAUGCUGGGGGAGUACUCAUAAUCAUAAUUAUGGGCUUCCCUC-GAACAACAAAA
----------------------(..((...((((......))))(((((((..((((((((....))))))))))))))))-)..)....... ( -22.00, z-score =  -2.65, R)
>dp4.chr4_group3 5815173 79 + 11692001
-------------CAACAAUGAUGAUGGGCAGAAAGAGAGAGAUAUAGAGGCAC-CAUAAUCAUAAUUAUGUGCUUCCUUCUUCACAGCAAAA
-------------......................(((..((.....(((((((-.(((((....))))))))))))))..)))......... ( -13.30, z-score =  -0.03, R)
>consensus
______________________GGGCGGGCGGCAGGAAAAUGCUGGGGGAGUACUCAUAAUCAUAAUUAUGGGCUUCCCUC_GAACAACAAAA
............................................((((((((...((((((....)))))).))))))))............. (-11.35 = -11.35 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:34:40 2011