Locus 2323

Sequence ID dm3.chr2L
Location 17,933,878 – 17,933,929
Length 51
Max. P 0.921669
window3200 window3201

overview

Window 0

Location 17,933,878 – 17,933,929
Length 51
Sequences 6
Columns 51
Reading direction forward
Mean pairwise identity 87.32
Shannon entropy 0.24154
G+C content 0.50830
Mean single sequence MFE -12.12
Consensus MFE -8.93
Energy contribution -9.07
Covariance contribution 0.14
Combinations/Pair 1.42
Mean z-score -2.07
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.847763
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17933878 51 + 23011544
CCUGAUUAUCCUUUAUGAGGACUGUCAGCUUUCGCUCACGCACUCCUCGCU
................(((((.(((.(((....)))...))).)))))... ( -12.00, z-score =  -2.06, R)
>droAna3.scaffold_12916 13218822 50 - 16180835
CCUGAUUAUCUUCAAUCGGGACAAG-GACAUCCGCUCACGCACCCAUCGCU
(((((((......)))))))....(-(....))((....)).......... ( -10.10, z-score =  -1.10, R)
>droEre2.scaffold_4845 16258521 51 - 22589142
CCUGAUUAUCCUUUAUGAGGAUUGUCAGCUUCCGCUCACGCACUCAUCGCU
.(((((.((((((...)))))).))))).....((....)).......... ( -12.20, z-score =  -2.00, R)
>droYak2.chr2R 17972907 51 - 21139217
CCUGAUUAUCCUUUAUGAGGAUUGUCAGCUUCCGCUCACGUCCUCAUCGCU
..............((((((((.((.(((....))).)))))))))).... ( -14.00, z-score =  -2.99, R)
>droSec1.super_7 1570051 51 + 3727775
CCUGAUUAUCCUUUAUGAGGAUUGUCAGCUUCCGCUCACGCACUCCUCGCU
.(((((.((((((...)))))).))))).....((....)).......... ( -12.20, z-score =  -2.12, R)
>droSim1.chr2L 17595355 51 + 22036055
CCUGAUUAUCCUUUAUGAGGAUUGUCAGCUUCCGCUCACGCACUCCUCGCU
.(((((.((((((...)))))).))))).....((....)).......... ( -12.20, z-score =  -2.12, R)
>consensus
CCUGAUUAUCCUUUAUGAGGAUUGUCAGCUUCCGCUCACGCACUCAUCGCU
.(((((.(((((.....))))).))))).....((....)).......... ( -8.93 =  -9.07 +   0.14)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,933,878 – 17,933,929
Length 51
Sequences 6
Columns 51
Reading direction reverse
Mean pairwise identity 87.32
Shannon entropy 0.24154
G+C content 0.50830
Mean single sequence MFE -16.23
Consensus MFE -10.73
Energy contribution -10.90
Covariance contribution 0.17
Combinations/Pair 1.25
Mean z-score -2.59
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.29
SVM RNA-class probability 0.921669
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17933878 51 - 23011544
AGCGAGGAGUGCGUGAGCGAAAGCUGACAGUCCUCAUAAAGGAUAAUCAGG
...(((((.(..((.(((....))).))).)))))................ ( -17.00, z-score =  -2.93, R)
>droAna3.scaffold_12916 13218822 50 + 16180835
AGCGAUGGGUGCGUGAGCGGAUGUC-CUUGUCCCGAUUGAAGAUAAUCAGG
..(((((((.((....))((....)-)....))).))))............ ( -12.10, z-score =  -0.15, R)
>droEre2.scaffold_4845 16258521 51 + 22589142
AGCGAUGAGUGCGUGAGCGGAAGCUGACAAUCCUCAUAAAGGAUAAUCAGG
.(((.....)))((.(((....))).)).(((((.....)))))....... ( -15.10, z-score =  -2.17, R)
>droYak2.chr2R 17972907 51 + 21139217
AGCGAUGAGGACGUGAGCGGAAGCUGACAAUCCUCAUAAAGGAUAAUCAGG
....(((((((.((.(((....))).))..))))))).............. ( -18.60, z-score =  -4.17, R)
>droSec1.super_7 1570051 51 - 3727775
AGCGAGGAGUGCGUGAGCGGAAGCUGACAAUCCUCAUAAAGGAUAAUCAGG
...(((((....((.(((....))).))..)))))................ ( -17.30, z-score =  -3.05, R)
>droSim1.chr2L 17595355 51 - 22036055
AGCGAGGAGUGCGUGAGCGGAAGCUGACAAUCCUCAUAAAGGAUAAUCAGG
...(((((....((.(((....))).))..)))))................ ( -17.30, z-score =  -3.05, R)
>consensus
AGCGAGGAGUGCGUGAGCGGAAGCUGACAAUCCUCAUAAAGGAUAAUCAGG
...((.......((.(((....))).)).(((((.....)))))..))... (-10.73 = -10.90 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:49:05 2011