Locus 1510

Sequence ID dm3.chr2L
Location 11,690,380 – 11,690,430
Length 50
Max. P 0.813632
window2063 window2064

overview

Window 3

Location 11,690,380 – 11,690,430
Length 50
Sequences 5
Columns 50
Reading direction forward
Mean pairwise identity 93.80
Shannon entropy 0.10957
G+C content 0.38000
Mean single sequence MFE -11.66
Consensus MFE -10.33
Energy contribution -10.37
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.813632
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11690380 50 + 23011544
AAUUGACCGAAUUAAAAUCCUGUCGAGGGCUCUCGACUAAUUUAGGCAAA
..(((.((((((((.......((((((....)))))))))))).))))). ( -11.61, z-score =  -1.66, R)
>droEre2.scaffold_4929 12921368 50 - 26641161
AAUUGACCGAAUUAAAAUCCUGUCGAGGGCACUUGACUAAUUUAGGCAAA
..(((.((((((((.......((((((....)))))))))))).))))). ( -10.71, z-score =  -1.71, R)
>droYak2.chr2L 8114414 50 + 22324452
AAUUGACCGAAUUAAAAUCCUGUCGAGGGUGCUCGACUAAUUUCGGCAAA
..(((.(((((..........((((((....))))))....)))))))). ( -14.34, z-score =  -2.48, R)
>droSec1.super_3 7082684 50 + 7220098
AAUUGACCGAAUUAAAAUCAUGUCGAGGGUUCUCGACUAAUUUAGGAAAA
......((((((((.......((((((....)))))))))))).)).... ( -10.01, z-score =  -1.06, R)
>droSim1.chr2L 11499917 50 + 22036055
AAUUGACCGAAUUAAAAUCAUGUCGAGGGUUCUCGACUAAUUUAGGCAAA
..(((.((((((((.......((((((....)))))))))))).))))). ( -11.61, z-score =  -1.95, R)
>consensus
AAUUGACCGAAUUAAAAUCCUGUCGAGGGUUCUCGACUAAUUUAGGCAAA
..(((.((((((((.......((((((....)))))))))))).))))). (-10.33 = -10.37 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,690,380 – 11,690,430
Length 50
Sequences 5
Columns 50
Reading direction reverse
Mean pairwise identity 93.80
Shannon entropy 0.10957
G+C content 0.38000
Mean single sequence MFE -11.20
Consensus MFE -9.08
Energy contribution -9.48
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.715052
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11690380 50 - 23011544
UUUGCCUAAAUUAGUCGAGAGCCCUCGACAGGAUUUUAAUUCGGUCAAUU
.(((((.......((((((....)))))).((((....)))))).))).. ( -12.90, z-score =  -2.26, R)
>droEre2.scaffold_4929 12921368 50 + 26641161
UUUGCCUAAAUUAGUCAAGUGCCCUCGACAGGAUUUUAAUUCGGUCAAUU
.(((((.......(((.((....)).))).((((....)))))).))).. (  -6.50, z-score =  -0.03, R)
>droYak2.chr2L 8114414 50 - 22324452
UUUGCCGAAAUUAGUCGAGCACCCUCGACAGGAUUUUAAUUCGGUCAAUU
.(((((((((((.((((((....))))))..))).....))))).))).. ( -13.50, z-score =  -2.57, R)
>droSec1.super_3 7082684 50 - 7220098
UUUUCCUAAAUUAGUCGAGAACCCUCGACAUGAUUUUAAUUCGGUCAAUU
.......((((((((((((....)))))).)))))).............. ( -10.70, z-score =  -2.32, R)
>droSim1.chr2L 11499917 50 - 22036055
UUUGCCUAAAUUAGUCGAGAACCCUCGACAUGAUUUUAAUUCGGUCAAUU
.(((((.((((((((((((....)))))).))))))......)).))).. ( -12.40, z-score =  -3.06, R)
>consensus
UUUGCCUAAAUUAGUCGAGAACCCUCGACAGGAUUUUAAUUCGGUCAAUU
.(((((.......((((((....))))))..((.......)))).))).. ( -9.08 =  -9.48 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:33:21 2011