Locus 6225

Sequence ID dm3.chr3L
Location 4,727,188 – 4,727,241
Length 53
Max. P 0.989166
window8554 window8555

overview

Window 4

Location 4,727,188 – 4,727,241
Length 53
Sequences 8
Columns 53
Reading direction forward
Mean pairwise identity 95.82
Shannon entropy 0.09182
G+C content 0.39242
Mean single sequence MFE -10.53
Consensus MFE -9.71
Energy contribution -10.09
Covariance contribution 0.38
Combinations/Pair 1.00
Mean z-score -1.25
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.548725
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4727188 53 + 24543557
UUUUGCCACAUGUCAGAGAUUGAUACUUGCGGCGAAAGUGAUUUAUAUACUGG
(((((((.((((((((...))))))..)).)))))))................ ( -11.50, z-score =  -1.60, R)
>droSim1.chr3L 4259804 53 + 22553184
UUUUGCCACAUGUCAGAGAUUGAUACUUGCGGCGAAAGUGAUUUAUAUACUGG
(((((((.((((((((...))))))..)).)))))))................ ( -11.50, z-score =  -1.60, R)
>droSec1.super_2 4711032 53 + 7591821
UUUUGCCACAUGUCAGAGAUUGAUACUUGCGGCGAAAGUGAUUUAUAUACUGG
(((((((.((((((((...))))))..)).)))))))................ ( -11.50, z-score =  -1.60, R)
>droYak2.chr3L 5309559 53 + 24197627
UUUUGCCACAUGUCAGAGAUUGAUACUUGCGGCGAAAGUGAUUUAUAUACUGG
(((((((.((((((((...))))))..)).)))))))................ ( -11.50, z-score =  -1.60, R)
>droEre2.scaffold_4784 7443252 53 + 25762168
UUUUGCCACAUGUCAGAGAUUGAUACUUGCGGCGAAAGUGAUUUAUAUACUGG
(((((((.((((((((...))))))..)).)))))))................ ( -11.50, z-score =  -1.60, R)
>droAna3.scaffold_13337 2816668 52 + 23293914
UUUUGCCACAUGUCAGAGAUUGAUACUUGCGGCGAAAGUGAUUUAUGUACUA-
(((((((.((((((((...))))))..)).)))))))...............- ( -11.50, z-score =  -1.48, R)
>dp4.chrXR_group8 2852271 53 + 9212921
UUUUGCCACAUGCCAGAGAUUGAUACUUGCGGCGAAAGUGAUUUAUAGACUGG
(((((((.((.................)).)))))))................ (  -8.03, z-score =  -0.10, R)
>droWil1.scaffold_180698 830047 53 - 11422946
UUUUGCCACAUGUCAGAGAUUGAUACUUAUAGCGAAAGUGAUUUAUUUACUGG
.(((((....((((((...))))))......)))))(((((.....))))).. (  -7.20, z-score =  -0.44, R)
>consensus
UUUUGCCACAUGUCAGAGAUUGAUACUUGCGGCGAAAGUGAUUUAUAUACUGG
(((((((.((((((((...))))))..)).)))))))................ ( -9.71 = -10.09 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,727,188 – 4,727,241
Length 53
Sequences 8
Columns 53
Reading direction reverse
Mean pairwise identity 95.82
Shannon entropy 0.09182
G+C content 0.39242
Mean single sequence MFE -9.36
Consensus MFE -9.80
Energy contribution -9.36
Covariance contribution -0.43
Combinations/Pair 1.50
Mean z-score -1.85
Structure conservation index 1.05
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.35
SVM RNA-class probability 0.989166
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4727188 53 - 24543557
CCAGUAUAUAAAUCACUUUCGCCGCAAGUAUCAAUCUCUGACAUGUGGCAAAA
....................((((((.((...........)).)))))).... (  -9.80, z-score =  -2.04, R)
>droSim1.chr3L 4259804 53 - 22553184
CCAGUAUAUAAAUCACUUUCGCCGCAAGUAUCAAUCUCUGACAUGUGGCAAAA
....................((((((.((...........)).)))))).... (  -9.80, z-score =  -2.04, R)
>droSec1.super_2 4711032 53 - 7591821
CCAGUAUAUAAAUCACUUUCGCCGCAAGUAUCAAUCUCUGACAUGUGGCAAAA
....................((((((.((...........)).)))))).... (  -9.80, z-score =  -2.04, R)
>droYak2.chr3L 5309559 53 - 24197627
CCAGUAUAUAAAUCACUUUCGCCGCAAGUAUCAAUCUCUGACAUGUGGCAAAA
....................((((((.((...........)).)))))).... (  -9.80, z-score =  -2.04, R)
>droEre2.scaffold_4784 7443252 53 - 25762168
CCAGUAUAUAAAUCACUUUCGCCGCAAGUAUCAAUCUCUGACAUGUGGCAAAA
....................((((((.((...........)).)))))).... (  -9.80, z-score =  -2.04, R)
>droAna3.scaffold_13337 2816668 52 - 23293914
-UAGUACAUAAAUCACUUUCGCCGCAAGUAUCAAUCUCUGACAUGUGGCAAAA
-...................((((((.((...........)).)))))).... (  -9.80, z-score =  -1.99, R)
>dp4.chrXR_group8 2852271 53 - 9212921
CCAGUCUAUAAAUCACUUUCGCCGCAAGUAUCAAUCUCUGGCAUGUGGCAAAA
....................((((((.((...........)).)))))).... ( -10.10, z-score =  -1.72, R)
>droWil1.scaffold_180698 830047 53 + 11422946
CCAGUAAAUAAAUCACUUUCGCUAUAAGUAUCAAUCUCUGACAUGUGGCAAAA
....................((((((.((...........)).)))))).... (  -6.00, z-score =  -0.90, R)
>consensus
CCAGUAUAUAAAUCACUUUCGCCGCAAGUAUCAAUCUCUGACAUGUGGCAAAA
....................((((((.((...........)).)))))).... ( -9.80 =  -9.36 +  -0.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:03:31 2011