Locus 3241

Sequence ID dm3.chr2R
Location 3,663,343 – 3,663,479
Length 136
Max. P 0.978839
window4460 window4461

overview

Window 0

Location 3,663,343 – 3,663,460
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 82.36
Shannon entropy 0.31209
G+C content 0.45357
Mean single sequence MFE -32.69
Consensus MFE -18.57
Energy contribution -22.10
Covariance contribution 3.53
Combinations/Pair 1.12
Mean z-score -2.02
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.585511
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3663343 117 - 21146708
GUAAGGCAAAUCUGCAGUUCGCCUUACAGUUUCGAAACGCAUAUGUAGAACUGGAUUGGACUCCUCAUCACGCGGGGAUUUCCACUCAGAUUCGAAUCUCGACAGAGAUUUGCAAAU
(((((((.(((.....))).)))))))...........((.......(((((((..((((.(((((.......)))))..)))).)))).)))(((((((....))))))))).... ( -35.10, z-score =  -2.44, R)
>droSim1.chr2R 2397339 117 - 19596830
GUAAGGCAAAUUUGCAGUUCGCCUUACAGUUUCGAAACGCAUAUGCAGAAGUGGACUGGAGUUCCCAUCACGCGGGGAUUUCCACUCAGAUUCGAAUCUCGCCAGAGAUUUGCAAAU
(((((((.(((.....))).)))))))................(((.(((...((.(((((.((((........)))).))))).))...)))(((((((....))))))))))... ( -38.50, z-score =  -3.05, R)
>droSec1.super_1 1318073 117 - 14215200
GUAAGGCAAAUUUGCAGUUCGCCUUACAGUUUCGAAACGCAUAUGCAGAACUGGACUGGAGUUCCCAUCACGCGGGGAUUUCCACUCAGAUUCGAAUCUCGCCAGAGAUUUGCAAAU
(((((((.(((.....))).)))))))................(((.(((((((..(((((.((((........)))).))))).)))).)))(((((((....))))))))))... ( -38.70, z-score =  -3.26, R)
>droYak2.chr2L 16334284 99 - 22324452
GUAAGGCAAAUUUGCAGCUCGCCUUACAUUUUUGAAACGCAUGUGGAGAACUCAA--------CUCAUCACGCGGGGAUUUCCAGUCAGAUUCGA----------AGAUUUGCAAAU
(((((((.............)))))))(((((((((.(((.((..(((.......--------)))..)).))).((....)).......)))))----------))))........ ( -24.32, z-score =  -0.96, R)
>droEre2.scaffold_4929 7695095 109 + 26641161
GUAAGGCUUAUUUGCAGUUCGAUUUACAUUUUCGAGACGCUCAUGGAGAACUCAG--------CUCACCGUGCGGGGAUUUCCAGUCAGAUUCGAAUCUCGCUAAAGAUUUGCAAAU
.........((((((((.((..........((((((.(.....((((((.(((.(--------(.......)).))).))))))....).))))))..........)).)))))))) ( -26.85, z-score =  -0.39, R)
>consensus
GUAAGGCAAAUUUGCAGUUCGCCUUACAGUUUCGAAACGCAUAUGCAGAACUGGA_UGGA_U_CUCAUCACGCGGGGAUUUCCACUCAGAUUCGAAUCUCGCCAGAGAUUUGCAAAU
(((((((.(((.....))).)))))))...........((.......(((((((...(((.(((((.......))))).)))...)))).)))(((((((....))))))))).... (-18.57 = -22.10 +   3.53)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,663,380 – 3,663,479
Length 99
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 68.63
Shannon entropy 0.52433
G+C content 0.43939
Mean single sequence MFE -23.06
Consensus MFE -13.47
Energy contribution -14.03
Covariance contribution 0.56
Combinations/Pair 1.16
Mean z-score -1.85
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.978839
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3663380 99 + 21146708
AAUCCCCGCGUGAUGAGGAGUCCAAUCCAGUUCUACAUAUGCGUUUCGAAACUGUAAGGCGAACUGCAGAUUUGCCUUACAACAAAUGUUCGCAACGAA----------
.......(((((.((((((.(.......).)))).)))))))(((.((((..((((((((((((....).))))))))))).......)))).)))...---------- ( -24.90, z-score =  -1.43, R)
>droSim1.chr2R 2397376 84 + 19596830
AAUCCCCGCGUGAUGGGAACUCCAGUCCACUUCUGCAUAUGCGUUUCGAAACUGUAAGGCGAACUGCAAAUUUGCCUUACAACA-------------------------
......((((((.((((((...........)))).)))))))).........(((((((((((.......)))))))))))...------------------------- ( -20.40, z-score =  -1.25, R)
>droSec1.super_1 1318110 84 + 14215200
AAUCCCCGCGUGAUGGGAACUCCAGUCCAGUUCUGCAUAUGCGUUUCGAAACUGUAAGGCGAACUGCAAAUUUGCCUUACAACA-------------------------
......((((((.((((((((.......)))))).)))))))).........(((((((((((.......)))))))))))...------------------------- ( -25.30, z-score =  -2.56, R)
>droYak2.chr2L 16334311 100 + 22324452
AAUCCCCGCGUGAUG--------AGUUGAGUUCUCCACAUGCGUUUCAAAAAUGUAAGGCGAGCUGCAAAUUUGCCUUACAA-ACAUGUUCCAAAUGAAUAUGUAAAUA
......((((((..(--------((.......)))..)))))).........(((((((((((.......))))))))))).-((((((((.....))))))))..... ( -29.90, z-score =  -4.48, R)
>droEre2.scaffold_4929 7695132 100 - 26641161
AAUCCCCGCACGGUG--------AGCUGAGUUCUCCAUGAGCGUCUCGAAAAUGUAAAUCGAACUGCAAAUAAGCCUUACUA-ACAUGUUAAAAAUAAGUAUGUACGUA
.........((((((--------((((..((((.....))))((.((((.........))))))........)).)))))..-((((((((....))).))))).))). ( -14.80, z-score =   0.46, R)
>consensus
AAUCCCCGCGUGAUG_G_A_UCCAGUCCAGUUCUCCAUAUGCGUUUCGAAACUGUAAGGCGAACUGCAAAUUUGCCUUACAACA_AUGUU___AA__A___________
......((((((.((....................)))))))).........(((((((((((.......)))))))))))............................ (-13.47 = -14.03 +   0.56)

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 22:06:30 2011