Locus 124

Sequence ID dm3.chr2L
Location 842,067 – 842,159
Length 92
Max. P 0.860637
window178 window179

overview

Window 8

Location 842,067 – 842,159
Length 92
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 73.86
Shannon entropy 0.43496
G+C content 0.58498
Mean single sequence MFE -34.60
Consensus MFE -19.72
Energy contribution -19.76
Covariance contribution 0.04
Combinations/Pair 1.10
Mean z-score -1.48
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.658006
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 842067 92 + 23011544
--------------UGCCCCAAGCCCCAAGACAUGACUCGUUGCUUGGCAACCGAAAGCGGUGUGGUGAUGAUCU--CGGGGAGAUGCAGAAGAAUGACUCUGGGGCC
--------------.(((((...((((.((((((.(((((..(((((....)...))))..)).))).))).)))--.))))(((..((......))..)))))))). ( -36.30, z-score =  -2.40, R)
>droEre2.scaffold_4929 898847 82 + 26641161
---------------------UGCCCCAAGACAUGACUCGUUGCUUGGCCACCGAAAGGG-----GAGGAGAGAUCUCGCAGAGCUGGAGAGGAAUGGCUCCGGGGCC
---------------------.(((((.((.(((..(((...((((.((..((....)).-----...(((....))))).))))....)))..))).))..))))). ( -34.00, z-score =  -1.68, R)
>droYak2.chr2L 825677 87 + 22324452
---------------------UGCCCCAAGACAUGACUCGUUGCUUGGCAACCGUAGAAGAGUGAGAGGAGAGAUCUCGACGAGAUGGAGAAGAAUGACUCUGGGGCC
---------------------.(((((.........((((((((((.((....))....))))((((.......))))))))))..((((........))))))))). ( -27.60, z-score =  -1.94, R)
>droSec1.super_14 812680 108 + 2068291
UGCCCCAAGCUCCAAGCCCCAAGCCCCAAGACAUGACUCGUUGCUUGGCAACCGAGAGCGGUGUGGAGAUGAUCUCUCGGGGAGAUGCAGAAGAAUGACUCUGGGGCC
.((((((..(((((....((((((..(.((......)).)..))))))..((((....)))).))))).(((((((.....))))).))............)))))). ( -36.20, z-score =  -0.13, R)
>droSim1.chr2L 840931 101 + 22036055
-------UGCCCCAAGCUCCAAGCCCCAAGACAUGACUCGUUGCUUGGCAACCGAGAGCGGUGUGGAGAUGAUCUCUCGGGGAGAUGCAGCAGAAUGACUCUGGGGCC
-------.(((((..(((.((..((((....(((.((.((((.(((((...))))))))))))))((((.....))))))))...)).)))(((.....)))))))). ( -38.90, z-score =  -1.24, R)
>consensus
_______________GC_CCAAGCCCCAAGACAUGACUCGUUGCUUGGCAACCGAAAGCGGUGUGGAGAUGAUCUCUCGGGGAGAUGCAGAAGAAUGACUCUGGGGCC
......................(((((.........((((((((...))))).............((((.....))))...))).......(((.....)))))))). (-19.72 = -19.76 +   0.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 842,067 – 842,159
Length 92
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 73.86
Shannon entropy 0.43496
G+C content 0.58498
Mean single sequence MFE -34.45
Consensus MFE -22.58
Energy contribution -23.70
Covariance contribution 1.12
Combinations/Pair 1.12
Mean z-score -1.47
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.860637
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 842067 92 - 23011544
GGCCCCAGAGUCAUUCUUCUGCAUCUCCCCG--AGAUCAUCACCACACCGCUUUCGGUUGCCAAGCAACGAGUCAUGUCUUGGGGCUUGGGGCA--------------
.(((((((((......))))......(((((--(((.(((.(((....((....))(((((...)))))).)).)))))))))))...))))).-------------- ( -32.70, z-score =  -1.64, R)
>droEre2.scaffold_4929 898847 82 - 26641161
GGCCCCGGAGCCAUUCCUCUCCAGCUCUGCGAGAUCUCUCCUC-----CCCUUUCGGUGGCCAAGCAACGAGUCAUGUCUUGGGGCA---------------------
.(((((((((........)))).((((((((((....)))..(-----(((....)).))....)))..))))........))))).--------------------- ( -27.70, z-score =  -0.40, R)
>droYak2.chr2L 825677 87 - 22324452
GGCCCCAGAGUCAUUCUUCUCCAUCUCGUCGAGAUCUCUCCUCUCACUCUUCUACGGUUGCCAAGCAACGAGUCAUGUCUUGGGGCA---------------------
.((((((.((.(((....(((.........((((.......))))...........(((((...))))))))..))).)))))))).--------------------- ( -26.10, z-score =  -2.13, R)
>droSec1.super_14 812680 108 - 2068291
GGCCCCAGAGUCAUUCUUCUGCAUCUCCCCGAGAGAUCAUCUCCACACCGCUCUCGGUUGCCAAGCAACGAGUCAUGUCUUGGGGCUUGGGGCUUGGAGCUUGGGGCA
.(((((((((....(((..((........))..)))....)))......(((((.((((.((((((..((((......))))..)))))))))).))))).)))))). ( -45.00, z-score =  -1.62, R)
>droSim1.chr2L 840931 101 - 22036055
GGCCCCAGAGUCAUUCUGCUGCAUCUCCCCGAGAGAUCAUCUCCACACCGCUCUCGGUUGCCAAGCAACGAGUCAUGUCUUGGGGCUUGGAGCUUGGGGCA-------
.((((((((((......)))((......(((((((...............)))))))...((((((..((((......))))..)))))).))))))))).------- ( -40.76, z-score =  -1.56, R)
>consensus
GGCCCCAGAGUCAUUCUUCUGCAUCUCCCCGAGAGAUCAUCUCCACACCGCUUUCGGUUGCCAAGCAACGAGUCAUGUCUUGGGGCUUGG_GC_______________
.((((((.((.(((..(((..........((((((...............))))))(((((...))))))))..))).))))))))...................... (-22.58 = -23.70 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:07:08 2011