Locus 1399

Sequence ID dm3.chr2L
Location 10,887,286 – 10,887,403
Length 117
Max. P 0.936290
window1905 window1906

overview

Window 5

Location 10,887,286 – 10,887,403
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.26
Shannon entropy 0.14464
G+C content 0.42849
Mean single sequence MFE -35.95
Consensus MFE -31.28
Energy contribution -32.56
Covariance contribution 1.28
Combinations/Pair 1.14
Mean z-score -2.16
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.936290
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10887286 117 + 23011544
UCUUAUUUUCGGUUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGUUCUUGUUAAGACCCAU-GUCUGGUUGGGAAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCU
.........(((....)))((((((.((((((((......(.((..((((((((.((((((...((((....-))))...))))))))))))))..))--)...)))))))).)))))). ( -38.90, z-score =  -2.85, R)
>droSim1.chr2L 10686469 117 + 22036055
UCUUAUUCUCGGUUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGCUCUUGUUAAGACCCAU-GUCUGGUUGGGAAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCU
.........(((....)))((((((.((((((((......(.((..((((((((..(((((...((((....-))))...))))).))))))))..))--)...)))))))).)))))). ( -38.80, z-score =  -2.54, R)
>droYak2.chr2L 7286803 117 + 22324452
UCUUAUUCUCGGUUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGUUCUUGUUAAGACCCAU-GUCUGGUUUGAAAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCU
.........(((....)))((((((.((((((((......(.((..((((((((.(((......((((....-)))).....))).))))))))..))--)...)))))))).)))))). ( -37.40, z-score =  -2.90, R)
>droEre2.scaffold_4929 12089361 117 - 26641161
UCUUAUUCUCGGUUCACUGGCCUGAAUGGUCAAGAUGAUUGACUUCAUGCAAAUGUUCUUGUUAAGACCCAU-GUCUGGUCGGAGAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCU
.........(((....)))(((.((.((((((((......(.((..((((((((.((((.....((((....-))))....)))).))))))))..))--)...)))))))).)).))). ( -33.70, z-score =  -1.31, R)
>droSec1.super_3 6296413 117 + 7220098
UCUUAUUCUCGGUUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGCUCUUGUUAAGACCCAU-GUCUGGUUGGGAAAUUUGCAUUUGG--CUUGUUUGACCAGUCUGGCU
.........(((....)))((((((.((((((((......(.((..((((((((..(((((...((((....-))))...))))).))))))))..))--)...)))))))).)))))). ( -38.80, z-score =  -2.54, R)
>droAna3.scaffold_12916 14742429 115 + 16180835
UCUUAUUUUCAGUUCAGUGACCAG-----CCGAGAUGAUUGACUUCAUGCAAAUUUUCUUGUUAAGCCCGAUUGUCUGGUCAGAAAAUUUGCAUUUGGUUCUUGUUUGACCAGACUGGCU
........((((((..(((((.((-----(((((((((......))))(((((((((((..(((..(......)..)))..))))))))))).)))))))...)))..))..)))))).. ( -28.10, z-score =  -0.82, R)
>consensus
UCUUAUUCUCGGUUCACUGGCCAGAAUGGUCGAGAUGAUUGACUUCAUGCAAAUGUUCUUGUUAAGACCCAU_GUCUGGUUGGAAAAUUUGCAUUUGG__CUUGUUUGACCAGUCUGGCU
.........(((....)))((((((.((((((((........((..((((((((.((((.....((((.....))))....)))).))))))))..))......)))))))).)))))). (-31.28 = -32.56 +   1.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,887,286 – 10,887,403
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.26
Shannon entropy 0.14464
G+C content 0.42849
Mean single sequence MFE -30.63
Consensus MFE -24.11
Energy contribution -24.53
Covariance contribution 0.42
Combinations/Pair 1.14
Mean z-score -2.36
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.888418
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10887286 117 - 23011544
AGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUUCCCAACCAGAC-AUGGGUCUUAACAAGAACAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAACCGAAAAUAAGA
.((((((.(((((.......--....(((((((((((......((((-....))))......))).))))))))((......)).....))))).))))))................... ( -30.60, z-score =  -2.73, R)
>droSim1.chr2L 10686469 117 - 22036055
AGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUUCCCAACCAGAC-AUGGGUCUUAACAAGAGCAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAACCGAGAAUAAGA
.((((((.(((((......(--(.((((((......((((.......-.))))(((.....)))))))))))((((......))))...))))).))))))................... ( -33.50, z-score =  -3.01, R)
>droYak2.chr2L 7286803 117 - 22324452
AGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUUUCAAACCAGAC-AUGGGUCUUAACAAGAACAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAACCGAGAAUAAGA
.((((((.(((((.......--....((((((((.(((.....((((-....))))......))).))))))))((......)).....))))).))))))................... ( -31.40, z-score =  -2.76, R)
>droEre2.scaffold_4929 12089361 117 + 26641161
AGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUCUCCGACCAGAC-AUGGGUCUUAACAAGAACAUUUGCAUGAAGUCAAUCAUCUUGACCAUUCAGGCCAGUGAACCGAGAAUAAGA
......(((((((.......--....(((((((((((..((((....-...))))......)))..))))))))((((((((.....)))))..))).)))))))............... ( -26.80, z-score =  -1.03, R)
>droSec1.super_3 6296413 117 - 7220098
AGCCAGACUGGUCAAACAAG--CCAAAUGCAAAUUUCCCAACCAGAC-AUGGGUCUUAACAAGAGCAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAACCGAGAAUAAGA
.((((((.(((((......(--(.((((((......((((.......-.))))(((.....)))))))))))((((......))))...))))).))))))................... ( -33.50, z-score =  -3.01, R)
>droAna3.scaffold_12916 14742429 115 - 16180835
AGCCAGUCUGGUCAAACAAGAACCAAAUGCAAAUUUUCUGACCAGACAAUCGGGCUUAACAAGAAAAUUUGCAUGAAGUCAAUCAUCUCGG-----CUGGUCACUGAACUGAAAAUAAGA
.((((((((((((......).)))).(((((((((((((..((........))........)))))))))))))...............))-----)))))................... ( -28.00, z-score =  -1.61, R)
>consensus
AGCCAGACUGGUCAAACAAG__CCAAAUGCAAAUUUCCCAACCAGAC_AUGGGUCUUAACAAGAACAUUUGCAUGAAGUCAAUCAUCUCGACCAUUCUGGCCAGUGAACCGAGAAUAAGA
.((((((.(((((.............(((((((((((......((((.....))))......))).))))))))((......)).....))))).))))))................... (-24.11 = -24.53 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:31:10 2011