Locus 10278

Sequence ID dm3.chr3R
Location 12,648,469 – 12,648,601
Length 132
Max. P 0.987887
window14129 window14130 window14131

overview

Window 9

Location 12,648,469 – 12,648,562
Length 93
Sequences 7
Columns 100
Reading direction reverse
Mean pairwise identity 73.28
Shannon entropy 0.50010
G+C content 0.62118
Mean single sequence MFE -39.63
Consensus MFE -25.60
Energy contribution -28.34
Covariance contribution 2.74
Combinations/Pair 1.30
Mean z-score -1.93
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.30
SVM RNA-class probability 0.987887
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12648469 93 - 27905053
CGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCG-------ACUGCCGACUGCAUUGGGCCGGCUAAUGC
.....(((((.....)))))((((((((((..(((((.((.....)))))))((..(((....)-------))..)).......))))))))))...... ( -45.30, z-score =  -2.68, R)
>droSim1.chr3R 18690351 93 + 27517382
CGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCG-------ACUGCCGACUGCAGUGGGCCGGCUAAUGC
.....(((((.....)))))(((((.(((.(((((((.((.....)))))))))))).))(((.-------(((((.....))))).))).)))...... ( -46.80, z-score =  -2.77, R)
>droSec1.super_12 617890 93 + 2123299
CGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCG-------ACUGCCGACUGCAGUGGGCCGGCUGAUGC
.....(((((.....)))))(((((.(((.(((((((.((.....)))))))))))).))(((.-------(((((.....))))).))).)))...... ( -46.80, z-score =  -2.51, R)
>droYak2.chr3R 17088590 100 + 28832112
CGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCGACUGCUAACUGCCGACUGCAGUGGGCCGGCUAAUGC
.....(((((.....)))))(((((.(((.(((((((.((.....)))))))))))).))(((.(((((............))))).))).)))...... ( -46.90, z-score =  -2.31, R)
>droEre2.scaffold_4770 8760136 93 + 17746568
CGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCG-------ACUGUCGACUGCAGUGGGCCGGCUAAUGC
.....(((((.....)))))(((((.(((.(((((((.((.....)))))))))))).))(((.-------(((((.....))))).))).)))...... ( -45.10, z-score =  -2.61, R)
>droAna3.scaffold_13340 16449848 73 + 23697760
CGUGGUCUGCUUAGAGCGGAGCCGGUUGAACUGGCCAGAGGUUCACUGUGCUGGUGGUCUAC---------UCGGCUAAUUC------------------
((.(.(((((.....))))).)))...(((.(((((.(((..(((((.....)))))....)---------))))))).)))------------------ ( -25.20, z-score =  -0.76, R)
>droWil1.scaffold_181130 11715586 75 + 16660200
CUUGGUCCACUUUGGCUGAAGCCGGUUGAGCUGGU-----GGCCACUUGGUUGGUGGUCUACAAA--AAUUGCAGUUGCUUG------------------
.(((..(((.((..((((....))))..)).))).-----(((((((.....)))))))..))).--....((....))...------------------ ( -21.30, z-score =   0.15, R)
>consensus
CGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCG_______ACUGCCGACUGCAGUGGGCCGGCUAAUGC
.....(((((.....)))))(((((((((((((((((.((.....))))))))))((((.((............)).))))....)))))))))...... (-25.60 = -28.34 +   2.74)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,648,489 – 12,648,601
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.04
Shannon entropy 0.38941
G+C content 0.62320
Mean single sequence MFE -44.63
Consensus MFE -31.68
Energy contribution -33.08
Covariance contribution 1.41
Combinations/Pair 1.14
Mean z-score -1.44
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.813512
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12648489 112 + 27905053
-------GUCGGCAGUCGGCGGACCACCGGCCGAGUGAACCUCCGGCCAGUUGGACCGGCUCCACUUUAAGUAGACCACGA-UGGUCGGCCUGGAGGAGGAGAAGAUGUCGGCGAUAUCG
-------(((((((.((..(((.((((.(((((((.....)).))))).).))).))).((((.(((((.((.((((....-.)))).)).)))))..))))..)))))))))....... ( -47.10, z-score =  -1.32, R)
>droSim1.chr3R 18690371 112 - 27517382
-------GUCGGCAGUCGGCGGACCACCGGCCGAGUGAACCUCCGGCCAGUUGGACCGGCUCCACUUUAAGUAGACCACGA-UGGUCGGCCUGGAGGAGGAGGAGAUGUCGGCGAUAUGA
-------(((((((.((..(((.((((.(((((((.....)).))))).).))).))).((((.(((((.((.((((....-.)))).)).)))))..))))))..)))))))....... ( -47.50, z-score =  -1.20, R)
>droSec1.super_12 617910 112 - 2123299
-------GUCGGCAGUCGGCGGACCACCGGCCGAGUGAACCUCCGGCCAGUUGGACCGGCUCCACUUUAAGUAGACCACGA-UGGCCGGUCUGGAGGAGGAGGAGAUGUCGGCGAUAUGA
-------(((((((.(((((((....)).))))).....(((((..((..(..((((((((....................-.))))))))..).)).)))))...)))))))....... ( -48.10, z-score =  -1.37, R)
>droYak2.chr3R 17088610 112 - 28832112
GUCGGCAGUUAGCAGUCGGCGGACCACCGGCCGAGUGAACCUCCGGCCAGUUGGACCGGCUCCACUUUAAGUAGACCACGA-UGGUCGGACUAGAGGAGGGGGAGAUGUCGGC-------
(((((((.....((.(((((((....)).))))).))...((((((((....)).))).((((.((((.(((.((((....-.))))..))).)))).))))))).)))))))------- ( -47.20, z-score =  -1.47, R)
>droEre2.scaffold_4770 8760156 112 - 17746568
-------GUCGACAGUCGGCGGACCACCGGCCGAGUGAACCUCCGGCCAGUUGGACCGGCUCCACUUUAAGUAGACCACGC-UGGUCGGGCUGGAGGAGGGGCAGAUGUCGGCGAUUUGG
-------(((((((.(((((((....)).))))).((..(((((..((((((.(((((((((.((.....)).))....))-))))).)))))).)))))..))..)))))))....... ( -57.20, z-score =  -3.34, R)
>droAna3.scaffold_13340 16449859 87 - 23697760
------------------GUAGACCACCAGCACAGUGAACCUCUGGCCAGUUCAACCGGCUCCGCUCUAAGCAGACCACGAAUGGCCCAGAUGCAGAUGGAAUAA---------------
------------------.....(((.(.(((..(....).((((((((.(((....((.((.((.....)).))))..)))))).)))))))).).))).....--------------- ( -20.70, z-score =   0.06, R)
>consensus
_______GUCGGCAGUCGGCGGACCACCGGCCGAGUGAACCUCCGGCCAGUUGGACCGGCUCCACUUUAAGUAGACCACGA_UGGUCGGCCUGGAGGAGGAGGAGAUGUCGGCGAUAUG_
.......(((((((.....(((.((((.(((((((.....)).))))).).))).))).((((.(((((....(((((....)))))....)))))..))))....)))))))....... (-31.68 = -33.08 +   1.41)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,648,489 – 12,648,601
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.04
Shannon entropy 0.38941
G+C content 0.62320
Mean single sequence MFE -42.62
Consensus MFE -31.42
Energy contribution -32.92
Covariance contribution 1.50
Combinations/Pair 1.19
Mean z-score -1.70
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.936335
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12648489 112 - 27905053
CGAUAUCGCCGACAUCUUCUCCUCCUCCAGGCCGACCA-UCGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCGACUGCCGAC-------
.......(((((........(((((.((((...((((.-....(((((((.....))))).))))))...))))..))))).....)))))(((..(((....)))..)))..------- ( -44.62, z-score =  -1.47, R)
>droSim1.chr3R 18690371 112 + 27517382
UCAUAUCGCCGACAUCUCCUCCUCCUCCAGGCCGACCA-UCGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCGACUGCCGAC-------
.......(((((.....(((((....((((...((((.-....(((((((.....))))).))))))...))))..))))).....)))))(((..(((....)))..)))..------- ( -45.60, z-score =  -2.02, R)
>droSec1.super_12 617910 112 + 2123299
UCAUAUCGCCGACAUCUCCUCCUCCUCCAGACCGGCCA-UCGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCGACUGCCGAC-------
.......(((((.....(((((.((....(((((((..-......(((((.....)))))))))))).....))..))))).....)))))(((..(((....)))..)))..------- ( -47.10, z-score =  -2.45, R)
>droYak2.chr3R 17088610 112 + 28832112
-------GCCGACAUCUCCCCCUCCUCUAGUCCGACCA-UCGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCGACUGCUAACUGCCGAC
-------(((((.((((((...(((.(((((..((((.-....)))).)))...)).)))(((((.....))))).))))))....)))))(((..((..((.....))..))..))).. ( -42.70, z-score =  -1.61, R)
>droEre2.scaffold_4770 8760156 112 + 17746568
CCAAAUCGCCGACAUCUGCCCCUCCUCCAGCCCGACCA-GCGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCGACUGUCGAC-------
.......(((((....((..(((((.((((...((((.-((....(((((.....))))))).))))...))))..)))))..)).)))))(((..(((....)))..)))..------- ( -43.30, z-score =  -1.25, R)
>droAna3.scaffold_13340 16449859 87 + 23697760
---------------UUAUUCCAUCUGCAUCUGGGCCAUUCGUGGUCUGCUUAGAGCGGAGCCGGUUGAACUGGCCAGAGGUUCACUGUGCUGGUGGUCUAC------------------
---------------.....(((((.((((.((((((........(((((.....)))))(((((.....)))))....))))))..)))).))))).....------------------ ( -32.40, z-score =  -1.38, R)
>consensus
_CAUAUCGCCGACAUCUCCUCCUCCUCCAGCCCGACCA_UCGUGGUCUACUUAAAGUGGAGCCGGUCCAACUGGCCGGAGGUUCACUCGGCCGGUGGUCCGCCGACUGCCGAC_______
.......(((((........((((((((.....(((((....))))).((.....)))))(((((.....))))).))))).....)))))(((..(((....)))..)))......... (-31.42 = -32.92 +   1.50)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:20:51 2011