Locus 1087

Sequence ID dm3.chr2L
Location 8,154,691 – 8,154,822
Length 131
Max. P 0.989199
window1486 window1487 window1488

overview

Window 6

Location 8,154,691 – 8,154,804
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.62
Shannon entropy 0.14399
G+C content 0.36249
Mean single sequence MFE -31.82
Consensus MFE -27.88
Energy contribution -27.72
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.68
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.20
SVM RNA-class probability 0.985375
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8154691 113 + 23011544
GAAAAUGGCAAUUUGAGUAUUUUGUACUCAAAUUCUGCGGAAUGCGGAAUA----AGAAAU---UAGCAUAAUUUCAAUUUCCUGUGCUUAAAGUUUUGGGAAACCCAGAAGCAAGGGUA
((((...((...((((((((...))))))))(((((((.....))))))).----......---..))....)))).....(((.((((......((((((...)))))))))).))).. ( -29.80, z-score =  -2.24, R)
>droEre2.scaffold_4929 17060731 110 + 26641161
UAAAAUGGCAAAUUGAGUAUUUUGUACUCAAAUUCUGCGGAAUGCGGAAUA----AUAAAU---UUGCAUAAUUUCAAUUUCCUGUGCU---GGGUUUGGGAAACCCAAAAGCAAGGGUA
.......(((((((((((((...))))))..(((((((.....))))))).----...)))---)))).............(((.((((---...((.((....)).)).)))).))).. ( -32.10, z-score =  -3.06, R)
>droYak2.chr2L 10786317 120 + 22324452
GAAAAUGGCGAAUUGAGUAUUUUGUACUCAAAUUCUGCGGAAUGCGGAAUACGGAAUAAAUCAUUUGCAUAAUUUCAACUUCCUGUGCUUAAGAUUUUGGGAAACCCAGAAGCAAGGGUA
((((...(((((((((((((...))))))))(((((((.....))))))).............)))))....)))).....(((.((((......((((((...)))))))))).))).. ( -32.00, z-score =  -2.31, R)
>droSec1.super_3 3651937 112 + 7220098
-GAAAUGGCAAUUUGAGUAUUUUGUACUCAAAUUCUGCGGAAUGCGGAAUA----AGAAAU---UAGCAUAAUUUCAAUUUCCUGUGCUUAAGGUUUUGGGAAACCCAGAAGCAAGGGUA
-(((((.((...((((((((...))))))))(((((((.....))))))).----......---..))...))))).....(((.(((((..(((((....)))))...))))).))).. ( -33.70, z-score =  -3.30, R)
>droSim1.chr2L 7936842 113 + 22036055
GAAAAUGGCAAUUUGAGUAUUUUGUACUCAAAUUCUGCGGAAUGCGGAAUU----AGAAAU---UAGCAUAAUUUCAAUUUCCUGUGCUUAAGGUUUUGGGAAACCCAGAAGCAAGGGUA
((((...((....(((((((...)))))))((((((((.....))))))))----......---..))....)))).....(((.(((((..(((((....)))))...))))).))).. ( -31.50, z-score =  -2.50, R)
>consensus
GAAAAUGGCAAUUUGAGUAUUUUGUACUCAAAUUCUGCGGAAUGCGGAAUA____AGAAAU___UAGCAUAAUUUCAAUUUCCUGUGCUUAAGGUUUUGGGAAACCCAGAAGCAAGGGUA
.......((...((((((((...))))))))(((((((.....)))))))................)).............(((.((((......((((((...)))))))))).))).. (-27.88 = -27.72 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,154,691 – 8,154,804
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.62
Shannon entropy 0.14399
G+C content 0.36249
Mean single sequence MFE -26.34
Consensus MFE -20.92
Energy contribution -21.04
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -3.23
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.36
SVM RNA-class probability 0.989199
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8154691 113 - 23011544
UACCCUUGCUUCUGGGUUUCCCAAAACUUUAAGCACAGGAAAUUGAAAUUAUGCUA---AUUUCU----UAUUCCGCAUUCCGCAGAAUUUGAGUACAAAAUACUCAAAUUGCCAUUUUC
......(((((..((((((....)))))).)))))..((((...(((((((...))---))))).----..))))((.....))..((((((((((.....))))))))))......... ( -25.20, z-score =  -2.94, R)
>droEre2.scaffold_4929 17060731 110 - 26641161
UACCCUUGCUUUUGGGUUUCCCAAACCC---AGCACAGGAAAUUGAAAUUAUGCAA---AUUUAU----UAUUCCGCAUUCCGCAGAAUUUGAGUACAAAAUACUCAAUUUGCCAUUUUA
...(((((((...(((((.....)))))---)))).)))....((((((...((((---(.....----.((((.((.....)).))))(((((((.....)))))))))))).)))))) ( -25.70, z-score =  -3.21, R)
>droYak2.chr2L 10786317 120 - 22324452
UACCCUUGCUUCUGGGUUUCCCAAAAUCUUAAGCACAGGAAGUUGAAAUUAUGCAAAUGAUUUAUUCCGUAUUCCGCAUUCCGCAGAAUUUGAGUACAAAAUACUCAAUUCGCCAUUUUC
(((...(((((..((((((....)))))).)))))..((((....(((((((....))))))).)))))))....((.....)).(((((.(((((.....))))))))))......... ( -24.80, z-score =  -1.94, R)
>droSec1.super_3 3651937 112 - 7220098
UACCCUUGCUUCUGGGUUUCCCAAAACCUUAAGCACAGGAAAUUGAAAUUAUGCUA---AUUUCU----UAUUCCGCAUUCCGCAGAAUUUGAGUACAAAAUACUCAAAUUGCCAUUUC-
......(((((..((((((....)))))).)))))..((((...(((((((...))---))))).----..))))((.....))..((((((((((.....))))))))))........- ( -28.00, z-score =  -4.08, R)
>droSim1.chr2L 7936842 113 - 22036055
UACCCUUGCUUCUGGGUUUCCCAAAACCUUAAGCACAGGAAAUUGAAAUUAUGCUA---AUUUCU----AAUUCCGCAUUCCGCAGAAUUUGAGUACAAAAUACUCAAAUUGCCAUUUUC
......(((((..((((((....)))))).)))))..((((...(((((((...))---))))).----..))))((.....))..((((((((((.....))))))))))......... ( -28.00, z-score =  -3.97, R)
>consensus
UACCCUUGCUUCUGGGUUUCCCAAAACCUUAAGCACAGGAAAUUGAAAUUAUGCUA___AUUUCU____UAUUCCGCAUUCCGCAGAAUUUGAGUACAAAAUACUCAAAUUGCCAUUUUC
...((((((((..((((((....)))))).))))).))).....(((((...((................((((.((.....)).))))(((((((.....)))))))...)).))))). (-20.92 = -21.04 +   0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,154,731 – 8,154,822
Length 91
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.17
Shannon entropy 0.35814
G+C content 0.34692
Mean single sequence MFE -17.98
Consensus MFE -12.48
Energy contribution -13.24
Covariance contribution 0.76
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.94
SVM RNA-class probability 0.856339
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8154731 91 - 23011544
----------------------AAAAACACUAUAAAAAAGUACCCUUGCUUCUGGGUUUCCCAAAACUUUAAGCACAGGAAAUUGAAAUUAUGCUAAUUUCUUAUUCCGCAUU-------
----------------------.................((.....(((((..((((((....)))))).)))))..((((...(((((((...)))))))...))))))...------- ( -15.20, z-score =  -1.54, R)
>droEre2.scaffold_4929 17060771 110 - 26641161
GCCCUAGACAGAAUGGACACAUUAAGACCAACAACAAAAGUACCCUUGCUUUUGGGUUUCCCAAACCC---AGCACAGGAAAUUGAAAUUAUGCAAAUUUAUUAUUCCGCAUU-------
((.........((((....))))............(((((((....)))))))(((((.....)))))---.))...((((....(((((.....)))))....)))).....------- ( -16.70, z-score =  -0.01, R)
>droYak2.chr2L 10786357 102 - 22324452
------------------ACAUUAAAACCCUCUGCAAGAUUACCCUUGCUUCUGGGUUUCCCAAAAUCUUAAGCACAGGAAGUUGAAAUUAUGCAAAUGAUUUAUUCCGUAUUCCGCAUU
------------------......((((((...(((((......)))))....)))))).............((...((((....(((((((....))))))).))))(.....)))... ( -22.00, z-score =  -2.17, R)
>droSec1.super_3 3651976 93 - 7220098
-------------------AAUUAAAACACCAU-AAAAAGUACCCUUGCUUCUGGGUUUCCCAAAACCUUAAGCACAGGAAAUUGAAAUUAUGCUAAUUUCUUAUUCCGCAUU-------
-------------------..............-.....((.....(((((..((((((....)))))).)))))..((((...(((((((...)))))))...))))))...------- ( -18.00, z-score =  -2.40, R)
>droSim1.chr2L 7936882 94 - 22036055
-------------------AAUUAAAACACUAUAAAAAAGUACCCUUGCUUCUGGGUUUCCCAAAACCUUAAGCACAGGAAAUUGAAAUUAUGCUAAUUUCUAAUUCCGCAUU-------
-------------------....................((.....(((((..((((((....)))))).)))))..((((...(((((((...)))))))...))))))...------- ( -18.00, z-score =  -2.56, R)
>consensus
___________________AAUUAAAACACUAUAAAAAAGUACCCUUGCUUCUGGGUUUCCCAAAACCUUAAGCACAGGAAAUUGAAAUUAUGCUAAUUUCUUAUUCCGCAUU_______
..............................................(((((..((((((....)))))).)))))..((((...((((((.....))))))...))))............ (-12.48 = -13.24 +   0.76)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:25:22 2011