Locus 6910

Sequence ID dm3.chr3L
Location 10,701,736 – 10,701,828
Length 92
Max. P 0.870473
window9513 window9514

overview

Window 3

Location 10,701,736 – 10,701,828
Length 92
Sequences 8
Columns 96
Reading direction forward
Mean pairwise identity 77.46
Shannon entropy 0.41511
G+C content 0.49185
Mean single sequence MFE -21.75
Consensus MFE -10.79
Energy contribution -12.17
Covariance contribution 1.38
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.818722
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10701736 92 + 24543557
---GGCGCCCGUGCUAAUUGUCACAG-UGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGC
---((((((.((((........((((-.((...............)))))).......((.(((......)))...))..))))...))))))... ( -20.86, z-score =  -2.81, R)
>droSim1.chr3L 10094622 92 + 22553184
---GGCGCCCGUGCUAAUUGUCACAG-UGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGC
---((((((.((((........((((-.((...............)))))).......((.(((......)))...))..))))...))))))... ( -20.86, z-score =  -2.81, R)
>droSec1.super_0 2922444 92 + 21120651
---GGCGCCCGUGCUAAUUGUCACAG-UGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGC
---((((((.((((........((((-.((...............)))))).......((.(((......)))...))..))))...))))))... ( -20.86, z-score =  -2.81, R)
>droYak2.chr3L 10712052 92 + 24197627
---GGCGCCCGUGCUAAUUGUCACAG-UGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGC
---((((((.((((........((((-.((...............)))))).......((.(((......)))...))..))))...))))))... ( -20.86, z-score =  -2.81, R)
>droEre2.scaffold_4784 10700630 92 + 25762168
---GGCGCCCGUGCUAAUUGUCACAG-UGUCUUCUCUUUUGCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGC
---((((((.((((........((((-.((...(......)....)))))).......((.(((......)))...))..))))...))))))... ( -20.90, z-score =  -1.99, R)
>droAna3.scaffold_13337 15613525 77 + 23293914
---GGCGCCCGUGCUAAUUGUCACAG-UGUCUUCCCC---------------CCCUCGAUGGCUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGG
---((((((.((((((((((......-.(((.((...---------------.....)).)))..))))))(.....)..))))...))))))... ( -20.60, z-score =  -1.23, R)
>dp4.chrXR_group6 6982737 78 - 13314419
GGGAAAAGCCGUGCUAAUUGCUGCUGCUGGCCUCUUGUUU------------------GUGGCUGCAAUUAGUUUUACAUGCACUUUGGCGCCUAC
(((....((((.(((((((((.((..(..((.....))..------------------)..)).))))))))).............)))).))).. ( -25.94, z-score =  -1.34, R)
>droPer1.super_82 267072 78 + 267963
GGGAAAAGCCGUGCUAAUUACUGCUGCUGGCCUCUUGUUU------------------GUGGCUGCAAUUAGUUUUACAUGCACUUUGGCGCCUAC
(((....(((((((.....((((.(((.((((.(......------------------).)))))))..)))).......))))...))).))).. ( -23.10, z-score =  -0.83, R)
>consensus
___GGCGCCCGUGCUAAUUGUCACAG_UGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGC
...((((((.((((((((((.............................................))))))(.....)..))))...))))))... (-10.79 = -12.17 +   1.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 10,701,736 – 10,701,828
Length 92
Sequences 8
Columns 96
Reading direction reverse
Mean pairwise identity 77.46
Shannon entropy 0.41511
G+C content 0.49185
Mean single sequence MFE -23.04
Consensus MFE -14.03
Energy contribution -13.86
Covariance contribution -0.17
Combinations/Pair 1.24
Mean z-score -1.76
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.870473
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10701736 92 - 24543557
GCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACA-CUGUGACAAUUAGCACGGGCGCC---
...((((((...((((..(.....)((((((......(((......)))(((...............))-).....)))))))))).))))))--- ( -25.66, z-score =  -2.95, R)
>droSim1.chr3L 10094622 92 - 22553184
GCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACA-CUGUGACAAUUAGCACGGGCGCC---
...((((((...((((..(.....)((((((......(((......)))(((...............))-).....)))))))))).))))))--- ( -25.66, z-score =  -2.95, R)
>droSec1.super_0 2922444 92 - 21120651
GCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACA-CUGUGACAAUUAGCACGGGCGCC---
...((((((...((((..(.....)((((((......(((......)))(((...............))-).....)))))))))).))))))--- ( -25.66, z-score =  -2.95, R)
>droYak2.chr3L 10712052 92 - 24197627
GCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACA-CUGUGACAAUUAGCACGGGCGCC---
...((((((...((((..(.....)((((((......(((......)))(((...............))-).....)))))))))).))))))--- ( -25.66, z-score =  -2.95, R)
>droEre2.scaffold_4784 10700630 92 - 25762168
GCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGCAAAAGAGAAGACA-CUGUGACAAUUAGCACGGGCGCC---
...((((((...((((..(.....)((((((......(((......)))(((...(......)....))-).....)))))))))).))))))--- ( -25.80, z-score =  -2.33, R)
>droAna3.scaffold_13337 15613525 77 - 23293914
CCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGCCAUCGAGGG---------------GGGGAAGACA-CUGUGACAAUUAGCACGGGCGCC---
...((((((...((((........((..((((.....))))..)---------------)((.......-))..........)))).))))))--- ( -22.90, z-score =  -1.20, R)
>dp4.chrXR_group6 6982737 78 + 13314419
GUAGGCGCCAAAGUGCAUGUAAAACUAAUUGCAGCCAC------------------AAACAAGAGGCCAGCAGCAGCAAUUAGCACGGCUUUUCCC
((.(((((......)).(((((......))))))))))------------------.....(((((((....((........))..)))))))... ( -16.50, z-score =   0.74, R)
>droPer1.super_82 267072 78 - 267963
GUAGGCGCCAAAGUGCAUGUAAAACUAAUUGCAGCCAC------------------AAACAAGAGGCCAGCAGCAGUAAUUAGCACGGCUUUUCCC
((.(((((......)).(((((......))))))))))------------------.....(((((((....((........))..)))))))... ( -16.50, z-score =   0.49, R)
>consensus
GCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACA_CUGUGACAAUUAGCACGGGCGCC___
...((((((...((((..(.....)((((((.............................................)))))))))).))))))... (-14.03 = -13.86 +  -0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:16:52 2011