Locus 9420

Sequence ID dm3.chr3R
Location 6,561,827 – 6,561,908
Length 81
Max. P 0.952933
window12916 window12917

overview

Window 6

Location 6,561,827 – 6,561,908
Length 81
Sequences 4
Columns 89
Reading direction forward
Mean pairwise identity 77.67
Shannon entropy 0.37395
G+C content 0.35281
Mean single sequence MFE -20.23
Consensus MFE -11.94
Energy contribution -11.75
Covariance contribution -0.19
Combinations/Pair 1.21
Mean z-score -2.36
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.952933
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6561827 81 + 27905053
CAUAAAGCUUGUAAUGGGUAUCGGAUAGUUGAGUUGUUCAACUACAUCGUCUUCU--------UUUUGGUACUUAUCCCUCUUUAUUAG
.((((((...(..((((((((((((.((..(((.(((......))).).))..))--------.))))))))))))..).))))))... ( -17.50, z-score =  -2.08, R)
>droYak2.chr3R 10601890 87 + 28832112
UACUAAUUUCCUAG-GGGUAUUUUAUAGUCGAGCCGCUCGAUUAUAGCGUCUUCUAGAAUCU-UUUUGGUACUUGUACCUCUUUAUUAG
..(((((...((((-(((.((.(((((((((((...))))))))))).))))))))).....-....((((....)))).....))))) ( -24.20, z-score =  -3.09, R)
>droSec1.super_0 5740574 89 - 21120651
CAUAAGGAUAGUAAUGGGUAUCGGAUAGUUGACUUGCUCAACUACACCGUCUUCUGUAAUUUUUUUUGGUACUUAUCCCUCUUUAUUAG
.(((((((..(..((((((((((((..(((((.....)))))((((........))))......))))))))))))..))))))))... ( -18.80, z-score =  -1.36, R)
>droSim1.chr3R 12717917 89 - 27517382
CAUAAUGAUUGUAAUGGGUAUCGGAUAGUUGACUUGCUCAACUACAAUGUCUUUUGUAAUCUUUUUUGGUACUUAUCCCUCUUUAUUAG
..((((((..(..((((((((((((..(((((.....)))))(((((......)))))......))))))))))))..)...)))))). ( -20.40, z-score =  -2.92, R)
>consensus
CAUAAAGAUUGUAAUGGGUAUCGGAUAGUUGACUUGCUCAACUACAACGUCUUCUGUAAUCU_UUUUGGUACUUAUCCCUCUUUAUUAG
.............(((((((((((((((((((.....)))))))....................))))))))))))............. (-11.94 = -11.75 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 6,561,827 – 6,561,908
Length 81
Sequences 4
Columns 89
Reading direction reverse
Mean pairwise identity 77.67
Shannon entropy 0.37395
G+C content 0.35281
Mean single sequence MFE -15.07
Consensus MFE -8.76
Energy contribution -8.45
Covariance contribution -0.31
Combinations/Pair 1.20
Mean z-score -1.67
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.582799
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6561827 81 - 27905053
CUAAUAAAGAGGGAUAAGUACCAAAA--------AGAAGACGAUGUAGUUGAACAACUCAACUAUCCGAUACCCAUUACAAGCUUUAUG
...((((((.((........))....--------......((..((((((((.....)))))))).))..............)))))). ( -13.80, z-score =  -2.04, R)
>droYak2.chr3R 10601890 87 - 28832112
CUAAUAAAGAGGUACAAGUACCAAAA-AGAUUCUAGAAGACGCUAUAAUCGAGCGGCUCGACUAUAAAAUACCC-CUAGGAAAUUAGUA
(((((.....((((....))))....-...((((((.......((((.(((((...))))).))))........-)))))).))))).. ( -16.86, z-score =  -1.52, R)
>droSec1.super_0 5740574 89 + 21120651
CUAAUAAAGAGGGAUAAGUACCAAAAAAAAUUACAGAAGACGGUGUAGUUGAGCAAGUCAACUAUCCGAUACCCAUUACUAUCCUUAUG
.........(((((((.(((.............(....).(((.((((((((.....)))))))))))........))))))))))... ( -18.30, z-score =  -2.32, R)
>droSim1.chr3R 12717917 89 + 27517382
CUAAUAAAGAGGGAUAAGUACCAAAAAAGAUUACAAAAGACAUUGUAGUUGAGCAAGUCAACUAUCCGAUACCCAUUACAAUCAUUAUG
..........(((....(((...........)))..........((((((((.....))))))))......)))............... ( -11.30, z-score =  -0.80, R)
>consensus
CUAAUAAAGAGGGAUAAGUACCAAAA_AGAUUACAGAAGACGAUGUAGUUGAGCAACUCAACUAUCCGAUACCCAUUACAAUCUUUAUG
..........((........))......................((((((((.....))))))))........................ ( -8.76 =  -8.45 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:04:03 2011