Locus 4504

Sequence ID dm3.chr2R
Location 13,548,114 – 13,548,211
Length 97
Max. P 0.824136
window6160 window6161

overview

Window 0

Location 13,548,114 – 13,548,211
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 84.36
Shannon entropy 0.25675
G+C content 0.55523
Mean single sequence MFE -30.10
Consensus MFE -27.21
Energy contribution -27.03
Covariance contribution -0.19
Combinations/Pair 1.20
Mean z-score -1.30
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.824136
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13548114 97 + 21146708
CCGCUUUUCCGUCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCUCUG
..((...((((.(((((....(((.....)))..)))..((((((((........))))))))..........)).))))....))........... ( -28.10, z-score =  -1.06, R)
>droSec1.super_1 11047444 97 + 14215200
CCGCUUUUCCGCCCGACUUUAGGCAUUUCGCCGCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCUCUG
..((.....(((((((((...(((.....))).......((((((((........))))))))..........)))))))))..))........... ( -32.60, z-score =  -1.93, R)
>droEre2.scaffold_4845 7777672 97 + 22589142
CCGCUUUUCCAGCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCCCUG
..((...((((((((((....(((.....)))..)))..((((((((........))))))))..........)))))))....))........... ( -33.00, z-score =  -2.25, R)
>droAna3.scaffold_13266 9250781 77 - 19884421
---------GGCCUGGCUUUCGGCAUUUUGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCCCAGUUAAUUGGUUGGGUGUUGC-----------
---------.(((..(((...(((.....))).......((((((((........))))))))..........)))..))).....----------- ( -26.70, z-score =   0.03, R)
>consensus
CCGCUUUUCCGCCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCUCUG
.........(((((((((...(((.....))).......((((((((........))))))))..........)))))))))............... (-27.21 = -27.03 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,548,114 – 13,548,211
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 84.36
Shannon entropy 0.25675
G+C content 0.55523
Mean single sequence MFE -30.10
Consensus MFE -27.21
Energy contribution -27.03
Covariance contribution -0.19
Combinations/Pair 1.20
Mean z-score -1.30
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.824136
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13548114 97 + 21146708
CCGCUUUUCCGUCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCUCUG
..((...((((.(((((....(((.....)))..)))..((((((((........))))))))..........)).))))....))........... ( -28.10, z-score =  -1.06, R)
>droSec1.super_1 11047444 97 + 14215200
CCGCUUUUCCGCCCGACUUUAGGCAUUUCGCCGCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCUCUG
..((.....(((((((((...(((.....))).......((((((((........))))))))..........)))))))))..))........... ( -32.60, z-score =  -1.93, R)
>droEre2.scaffold_4845 7777672 97 + 22589142
CCGCUUUUCCAGCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCCCUG
..((...((((((((((....(((.....)))..)))..((((((((........))))))))..........)))))))....))........... ( -33.00, z-score =  -2.25, R)
>droAna3.scaffold_13266 9250781 77 - 19884421
---------GGCCUGGCUUUCGGCAUUUUGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCCCAGUUAAUUGGUUGGGUGUUGC-----------
---------.(((..(((...(((.....))).......((((((((........))))))))..........)))..))).....----------- ( -26.70, z-score =   0.03, R)
>consensus
CCGCUUUUCCGCCCGACUUUCGGCAUUUCGCCCCGUCACGGGCCAUUUUGUGCACAAUGGCCCACAGUUAAUUGGUUGGGUGUUGCCCAUUUCUCUG
.........(((((((((...(((.....))).......((((((((........))))))))..........)))))))))............... (-27.21 = -27.03 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:18 2011