Locus 8725

Sequence ID dm3.chr3R
Location 1,072,290 – 1,072,390
Length 100
Max. P 0.943425
window11976 window11977

overview

Window 6

Location 1,072,290 – 1,072,389
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 92.53
Shannon entropy 0.13378
G+C content 0.47554
Mean single sequence MFE -24.35
Consensus MFE -22.28
Energy contribution -21.80
Covariance contribution -0.48
Combinations/Pair 1.23
Mean z-score -1.87
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.915376
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1072290 99 + 27905053
CUUAAUGUGUGUAUUUUGGCGCGCUUACUUUUCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACGA
.......(((((....(((((((..........((((....))))........(((.((((.......))))...)))........)))))))))))). ( -26.10, z-score =  -2.42, R)
>droSim1.chr3R 1098624 99 + 27517382
CUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACCA
.....((.((((....(((((((..........((((....))))........(((.((((.......))))...)))........))))))))))))) ( -25.60, z-score =  -2.51, R)
>droSec1.super_6 1196063 99 + 4358794
CUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACCA
.....((.((((....(((((((..........((((....))))........(((.((((.......))))...)))........))))))))))))) ( -25.60, z-score =  -2.51, R)
>droYak2.chr3R 1439893 94 + 28832112
CUUAAUGCGUGAGUUUUGGUGCGCUU----UCCGAAACACUUUCCAUCAAUCAGCCCAUUGAAUUCCCUGAUCUGGGCAA-CACAUCGUGCCAACACCA
........(((.(((((((.......----.)))))))...............(((((...............)))))..-)))...(((....))).. ( -19.36, z-score =  -0.21, R)
>droEre2.scaffold_4770 1349338 99 + 17746568
CUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUUGAAUUCCCCGAUCUGGGCAAACACAACGCGCCAACGCCA
.....((.((((....(((((((..........((((....))))........(((.((((.......))))...)))........))))))))))))) ( -25.10, z-score =  -1.67, R)
>consensus
CUUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACCA
........((((....(((((((..........((((....))))........(((.((((.......))))...)))........))))))))))).. (-22.28 = -21.80 +  -0.48)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 7

Location 1,072,291 – 1,072,390
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 92.53
Shannon entropy 0.13378
G+C content 0.46533
Mean single sequence MFE -25.01
Consensus MFE -22.46
Energy contribution -22.18
Covariance contribution -0.28
Combinations/Pair 1.20
Mean z-score -2.09
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.49
SVM RNA-class probability 0.943425
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1072291 99 + 27905053
UUAAUGUGUGUAUUUUGGCGCGCUUACUUUUCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACGAU
......(((((....(((((((..........((((....))))........(((.((((.......))))...)))........)))))))))))).. ( -26.10, z-score =  -2.38, R)
>droSim1.chr3R 1098625 99 + 27517382
UUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACCAU
...(((.((((....(((((((..........((((....))))........(((.((((.......))))...)))........)))))))))))))) ( -26.70, z-score =  -2.90, R)
>droSec1.super_6 1196064 99 + 4358794
UUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACCAU
...(((.((((....(((((((..........((((....))))........(((.((((.......))))...)))........)))))))))))))) ( -26.70, z-score =  -2.90, R)
>droYak2.chr3R 1439894 94 + 28832112
UUAAUGCGUGAGUUUUGGUGCGCUU----UCCGAAACACUUUCCAUCAAUCAGCCCAUUGAAUUCCCUGAUCUGGGCAA-CACAUCGUGCCAACACCAU
.......(((.(((((((.......----.)))))))...............(((((...............)))))..-)))...(((....)))... ( -19.36, z-score =  -0.24, R)
>droEre2.scaffold_4770 1349339 99 + 17746568
UUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUUGAAUUCCCCGAUCUGGGCAAACACAACGCGCCAACGCCAU
...(((.((((....(((((((..........((((....))))........(((.((((.......))))...)))........)))))))))))))) ( -26.20, z-score =  -2.05, R)
>consensus
UUAAUGUGUGUAUUUUGGCGCGCUUACUUUCCGGAACACUUUCCAUCAAUCAGCCAAUCGAAUUCCCUGAUCUGGGCAAACACAACGCGCCAACACCAU
...(((.((((....(((((((..........((((....))))........(((.((((.......))))...)))........)))))))))))))) (-22.46 = -22.18 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:50:57 2011