Locus 5326

Sequence ID dm3.chr2R
Location 19,502,897 – 19,502,996
Length 99
Max. P 0.681351
window7300 window7301

overview

Window 0

Location 19,502,897 – 19,502,996
Length 99
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 79.26
Shannon entropy 0.34291
G+C content 0.41816
Mean single sequence MFE -23.47
Consensus MFE -15.38
Energy contribution -15.10
Covariance contribution -0.28
Combinations/Pair 1.07
Mean z-score -1.64
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.681351
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19502897 99 + 21146708
GCCUAAUAUUUCCGCCAAUUAUCAGAACACCUCAGAUGCUGAGGUUGG---UAGUGAAA-------CCUAAAAAAAAAAAACACUUCAAUUGGUCUCAAGUGGCGCUCC
............((((((((((((....(((((((...))))))))))---))))((.(-------((.......................))).))...))))).... ( -23.00, z-score =  -2.00, R)
>droSim1.chr2R 18073151 95 + 19596830
GCCUAAUAUUUCCGCCAAUUAUCAGAACACCUCAGAUGCUGAGGUUGG---UAGUUUA--------CCUAAAAAAAAA---CACUUCAAUUGGUCUCAAGUGGCGCUCC
(((..........(((((((........(((((((...))))))).((---((...))--------))..........---......))))))).......)))..... ( -20.73, z-score =  -1.35, R)
>droSec1.super_9 2782770 94 + 3197100
GCCUAAUAUUUCCGCCAAUUAUCAGAACACCUCAGAUGCUGAGGUUGG---UAGUCUA--------CCUACAAAAAA----CACCUCAAUUGGUCUCAAGUGGCGCUCC
............((((((((((((....(((((((...))))))))))---))))...--------...........----.(((......)))......))))).... ( -21.90, z-score =  -1.65, R)
>droYak2.chr2R 19477767 109 + 21139217
GCCUAAUAUUUCCGCCAAUUAUCAGAACACCUCAGAAGCUGAGGUUAGAGUUAAUGAAAAAGUGGUUUUUAAGUAGAAAAACACUCAGGUUCGUCUCGAGUGGCGCUAU
............(((((....((.....(((((((...)))))))..(((...(((((..((((.(((((.....))))).))))....)))))))))).))))).... ( -27.30, z-score =  -1.74, R)
>droEre2.scaffold_4845 20862403 109 + 22589142
GCCUAAUAUUUCCGCCAAUUAUCAGAACACCUCAGAUGCUGAGGUUAAAGUUAAUGAAAAAGCGGAUUUCAAGUAGAAAAACACUCAAUUUGCUCUCGAGUGGCGUUAC
(((((.....(((((...((.(((.((((((((((...)))))))....)))..))).)).))))).......))).....(((((...........)))))))..... ( -24.40, z-score =  -1.44, R)
>consensus
GCCUAAUAUUUCCGCCAAUUAUCAGAACACCUCAGAUGCUGAGGUUGG___UAGUGAAA_______CCUAAAAAAAAAAAACACUUCAAUUGGUCUCAAGUGGCGCUCC
............((((............(((((((...))))))).....................................((((...........)))))))).... (-15.38 = -15.10 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,502,897 – 19,502,996
Length 99
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 79.26
Shannon entropy 0.34291
G+C content 0.41816
Mean single sequence MFE -25.72
Consensus MFE -18.02
Energy contribution -17.66
Covariance contribution -0.36
Combinations/Pair 1.18
Mean z-score -1.34
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.538890
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19502897 99 - 21146708
GGAGCGCCACUUGAGACCAAUUGAAGUGUUUUUUUUUUUUAGG-------UUUCACUA---CCAACCUCAGCAUCUGAGGUGUUCUGAUAAUUGGCGGAAAUAUUAGGC
....(((((..(((((((((..((((......))))..)).))-------)))))...---...(((((((...)))))))...........)))))............ ( -26.30, z-score =  -1.52, R)
>droSim1.chr2R 18073151 95 - 19596830
GGAGCGCCACUUGAGACCAAUUGAAGUG---UUUUUUUUUAGG--------UAAACUA---CCAACCUCAGCAUCUGAGGUGUUCUGAUAAUUGGCGGAAAUAUUAGGC
....(((((..(.(((.(..........---..........((--------((...))---)).(((((((...)))))))).))).)....)))))............ ( -21.40, z-score =  -0.18, R)
>droSec1.super_9 2782770 94 - 3197100
GGAGCGCCACUUGAGACCAAUUGAGGUG----UUUUUUGUAGG--------UAGACUA---CCAACCUCAGCAUCUGAGGUGUUCUGAUAAUUGGCGGAAAUAUUAGGC
.....(((((((.(((....(((((((.----......((((.--------....)))---)..)))))))..))).)))).(((((........)))))......))) ( -23.80, z-score =  -0.34, R)
>droYak2.chr2R 19477767 109 - 21139217
AUAGCGCCACUCGAGACGAACCUGAGUGUUUUUCUACUUAAAAACCACUUUUUCAUUAACUCUAACCUCAGCUUCUGAGGUGUUCUGAUAAUUGGCGGAAAUAUUAGGC
....(((((.(((..(((((...((((((((((......))))).))))).)))..........(((((((...)))))))))..)))....)))))............ ( -26.50, z-score =  -1.90, R)
>droEre2.scaffold_4845 20862403 109 - 22589142
GUAACGCCACUCGAGAGCAAAUUGAGUGUUUUUCUACUUGAAAUCCGCUUUUUCAUUAACUUUAACCUCAGCAUCUGAGGUGUUCUGAUAAUUGGCGGAAAUAUUAGGC
....(((((.((.(((((.....(((((..((((.....))))..)))))..............(((((((...))))))))))))))....)))))............ ( -30.60, z-score =  -2.78, R)
>consensus
GGAGCGCCACUUGAGACCAAUUGAAGUGUUUUUUUUUUUUAGG_______UUUCACUA___CCAACCUCAGCAUCUGAGGUGUUCUGAUAAUUGGCGGAAAUAUUAGGC
....((((((((.((.....)).)))).....................................(((((((...)))))))............))))............ (-18.02 = -17.66 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:46:05 2011