Locus 1873

Sequence ID dm3.chr2L
Location 14,507,132 – 14,507,237
Length 105
Max. P 0.811691
window2581 window2582

overview

Window 1

Location 14,507,132 – 14,507,234
Length 102
Sequences 12
Columns 120
Reading direction forward
Mean pairwise identity 85.83
Shannon entropy 0.28264
G+C content 0.33366
Mean single sequence MFE -23.67
Consensus MFE -16.21
Energy contribution -15.81
Covariance contribution -0.40
Combinations/Pair 1.12
Mean z-score -1.91
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.726477
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14507132 102 + 23011544
CAAAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGCUCU------
...((((((.((......)).))))))...((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))..............------ ( -23.10, z-score =  -2.24, R)
>droSim1.chr2L 14254691 102 + 22036055
CAAAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGCUCU------
...((((((.((......)).))))))...((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))..............------ ( -23.10, z-score =  -2.24, R)
>droSec1.super_3 770367 102 + 7220098
CAAAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGCUCU------
...((((((.((......)).))))))...((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))..............------ ( -23.10, z-score =  -2.24, R)
>droYak2.chr2L 14615982 102 + 22324452
CAAAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGCUCU------
...((((((.((......)).))))))...((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))..............------ ( -25.80, z-score =  -3.05, R)
>droEre2.scaffold_4929 6261404 101 + 26641161
CAAAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGC-UGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGCUCU------
...((((((.((......)).))))))...((((((........((((((....)))))-).((------------(((.((....)).)))))))))))..............------ ( -22.50, z-score =  -2.08, R)
>droAna3.scaffold_12916 14869352 102 - 16180835
CAGAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGCCAGAUCC------
..(((((....(((((......)))))....(((((.......(((((((....))))))).((------------(((.((....)).)))))))))))))))..........------ ( -24.90, z-score =  -2.20, R)
>dp4.chr4_group1 1923611 120 - 5278887
CAGAAAUGUCGAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCCGGCUCAUACAUGCGAGUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAAAAAAUGCUCA
((....)).......(((((...((..((.((((((........((((((....))))))..((........))..(((((........))))))))))).))..)).....)))))... ( -24.60, z-score =  -0.36, R)
>droPer1.super_5 1868122 120 + 6813705
CAGAAAUGUCGAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCCGGCUCAUACAUGCGAGUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAAAAAAUGCUCA
((....)).......(((((...((..((.((((((........((((((....))))))..((........))..(((((........))))))))))).))..)).....)))))... ( -24.60, z-score =  -0.36, R)
>droWil1.scaffold_180764 2825537 102 + 3949147
CAGAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUUAAGUCUUUAC------
....(((((......)))))...((((((.((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))..))))))......------ ( -25.00, z-score =  -3.07, R)
>droVir3.scaffold_12723 2672223 92 + 5802038
CAGAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCUGGC------------AUAUAUGAGAAUUUAUGCGUCUCAUUUU----------------
...((((((.((......)).))))))...((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))....---------------- ( -24.40, z-score =  -3.09, R)
>droMoj3.scaffold_6500 15901159 98 + 32352404
CCGAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCUGGC------------UCAUAUGAGAAUUUAUGCGUCUCAUUUUGUCGCA----------
.(((((((.....((((((.....((((..((((.(.......(((((((....)))))))).)------------)))..)))).....))))))..))))))).....---------- ( -24.11, z-score =  -1.80, R)
>droGri2.scaffold_15126 7553577 98 - 8399593
CAGAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUCGGC------------ACAUAUGAGAAUUUAUGCGUCUCAUUUUGUCGCA----------
...((((((.((......)).)))))).......((........((((((....)))))).(((------------(...((((((.........))))))..)))))).---------- ( -18.80, z-score =  -0.17, R)
>consensus
CAGAAAUGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC____________AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGCUCU______
...((((((.((......)).))))))...((((((........((((((....)))))).................((((........)))).)))))).................... (-16.21 = -15.81 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,507,138 – 14,507,237
Length 99
Sequences 12
Columns 117
Reading direction forward
Mean pairwise identity 84.01
Shannon entropy 0.32151
G+C content 0.34565
Mean single sequence MFE -23.27
Consensus MFE -15.36
Energy contribution -15.10
Covariance contribution -0.26
Combinations/Pair 1.10
Mean z-score -1.93
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.811691
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14507138 99 + 23011544
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGC---UCUUCG---
((.(.(((((......)))))...((((((.......(((((((....))))))).((------------(((.((....)).))))))))))).....).))..---......--- ( -22.70, z-score =  -2.14, R)
>droSim1.chr2L 14254697 99 + 22036055
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGC---UCUUCG---
((.(.(((((......)))))...((((((.......(((((((....))))))).((------------(((.((....)).))))))))))).....).))..---......--- ( -22.70, z-score =  -2.14, R)
>droSec1.super_3 770373 99 + 7220098
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGC---UCUUCG---
((.(.(((((......)))))...((((((.......(((((((....))))))).((------------(((.((....)).))))))))))).....).))..---......--- ( -22.70, z-score =  -2.14, R)
>droYak2.chr2L 14615988 99 + 22324452
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGC---UCUUCG---
((.(.(((((......)))))...((((((.......(((((((....))))))).((------------(((.((....)).))))))))))).....).))..---......--- ( -25.40, z-score =  -2.94, R)
>droEre2.scaffold_4929 6261410 98 + 26641161
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGC-UGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGC---UCUUCG---
((.(.(((((......)))))...((((((........((((((....)))))-).((------------(((.((....)).))))))))))).....).))..---......--- ( -22.10, z-score =  -1.93, R)
>droAna3.scaffold_12916 14869358 99 - 16180835
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGCCAGA---UCCUCG---
.(((.(((((......)))))...((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))....)))....---......--- ( -24.70, z-score =  -2.38, R)
>dp4.chr4_group1 1923617 117 - 5278887
UGUCGAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCCGGCUCAUACAUGCGAGUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAAAAAAUGCUCACGG
...((....(((((...((..((.((((((........((((((....))))))..((........))..(((((........))))))))))).))..)).....)))))...)). ( -25.00, z-score =  -0.61, R)
>droPer1.super_5 1868128 117 + 6813705
UGUCGAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCCGGCUCAUACAUGCGAGUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAAAAAAUGCUCACGG
...((....(((((...((..((.((((((........((((((....))))))..((........))..(((((........))))))))))).))..)).....)))))...)). ( -25.00, z-score =  -0.61, R)
>droWil1.scaffold_180764 2825543 99 + 3949147
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC------------AUAUAUGAAAAUUUAUGCGUCUCAUUUUAAGUCUUUACGGU------
.................((((((.((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))..)))))).........------ ( -23.30, z-score =  -2.61, R)
>droVir3.scaffold_12723 2672229 86 + 5802038
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCUGGC------------AUAUAUGAGAAUUUAUGCGUCUCAUUUU-------------------
.....(((((......)))))...((((((.......(((((((....))))))).((------------(((.((....)).)))))))))))....------------------- ( -23.70, z-score =  -3.26, R)
>droMoj3.scaffold_6500 15901165 95 + 32352404
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCCUGGC------------UCAUAUGAGAAUUUAUGCGUCUCAUUUUGUCGCAUCU----------
.......((((....(((......((((((.......(((((((....)))))))..(------------((....))).........))))))...))).))))..---------- ( -22.10, z-score =  -1.56, R)
>droGri2.scaffold_15126 7553583 98 - 8399593
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUCGGC------------ACAUAUGAGAAUUUAUGCGUCUCAUUUUGUCGCAUCUCUU-------
.....(((((......)))))....((((.........((((((....))))))((((------------(...((((((.........))))))..)))))..))))..------- ( -19.90, z-score =  -0.86, R)
>consensus
UGUCAAAAUGCAUUAACAUUUAAUUGAGGCUAAUUUAAGGCGAAAUAUUUCGCUUGGC____________AUAUAUGAAAAUUUAUGCGUCUCAUUUCGGUCAGC___UCUUCG___
.....(((((......)))))...((((((........((((((....)))))).................((((........)))).))))))....................... (-15.36 = -15.10 +  -0.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:40:31 2011