Locus 1610

Sequence ID dm3.chr2L
Location 12,469,404 – 12,469,530
Length 126
Max. P 0.934781
window2205 window2206

overview

Window 5

Location 12,469,404 – 12,469,505
Length 101
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 91.61
Shannon entropy 0.14171
G+C content 0.45936
Mean single sequence MFE -30.24
Consensus MFE -19.96
Energy contribution -20.28
Covariance contribution 0.32
Combinations/Pair 1.15
Mean z-score -2.50
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.628039
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12469404 101 - 23011544
ACCUGUUCGACAACUCACUUUGCAAAUGAUCUUAGCU---GGAGCCAGCUGAUCUCAGAUCUGCGAUCGCAGAUCUCAGCCGAGUUAAGAAAAUCACAAAUGCG
.....(((...(((((..........(((..((((((---(....)))))))..)))(((((((....)))))))......)))))..)))............. ( -30.40, z-score =  -2.32, R)
>droEre2.scaffold_4929 13691132 100 + 26641161
ACCUGUUCGACCACUUAC-UUGCAAAUGAUCUUAGCU---GGACCCAGCUGAUCUCAAAUCUCAAAUCUGAAAUCUCAGCCGAGUUGAGAAAAUCACAAAUGCG
..................-..(((..(((..((((((---(....)))))))..)))..((((((..((((....)))).....))))))..........))). ( -24.10, z-score =  -2.72, R)
>droYak2.chr2L 8906518 100 - 22324452
ACCUGUUCGACAACUCAC-UUGCAAAUGAUCUUAGCU---GGACACAGCUGAUCUCAAAUCUGCGAUCUGCGAUCUCAGUCGAGUUGAGAAAAUCACAAAUGCG
.....(((..((((((..-.......(((..((((((---(....)))))))..)))...(((.((((...)))).)))..)))))).)))............. ( -26.50, z-score =  -1.53, R)
>droSec1.super_16 660254 103 - 1878335
ACCUGUUCGACAACUCAC-UUGCAAAUGAUCUUAGCUGGUGGACCCAGCUGAUCUCAGAUCUGCGAUCGCAGAUCUCAGUCGAGUUGAGAAAAUCACAAAUGCG
.....(((..((((((((-(......(((..((((((((.....))))))))..)))(((((((....)))))))..))).)))))).)))............. ( -35.10, z-score =  -2.97, R)
>droSim1.chr2L 12278406 103 - 22036055
ACCUGUUCGACAACUCAC-UUGCAAAUGAUCUUAGCUGGUGGACCCAGCUGAUCUCAGAUCUGCGAUCGCAGAUCUCAGUCGAGUUGAGAAAAUCACAAAUGCG
.....(((..((((((((-(......(((..((((((((.....))))))))..)))(((((((....)))))))..))).)))))).)))............. ( -35.10, z-score =  -2.97, R)
>consensus
ACCUGUUCGACAACUCAC_UUGCAAAUGAUCUUAGCU___GGACCCAGCUGAUCUCAGAUCUGCGAUCGCAGAUCUCAGUCGAGUUGAGAAAAUCACAAAUGCG
.....................(((..(((((((((((...(....).(((((.....(((((((....))))))))))))..))))))))...)))....))). (-19.96 = -20.28 +   0.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,469,440 – 12,469,530
Length 90
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 85.52
Shannon entropy 0.24262
G+C content 0.42364
Mean single sequence MFE -23.72
Consensus MFE -15.46
Energy contribution -15.46
Covariance contribution -0.00
Combinations/Pair 1.08
Mean z-score -2.68
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.39
SVM RNA-class probability 0.934781
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12469440 90 + 23011544
GAUCGCAGAUCUGAGAUCAGCUGGCUCC---AGCUAAGAUCAUUUGCAAAGUGAGUUGUCGAACAGGUCCCCGAAAUAAAUGAAAAAAAAAAA
..(((..((((((.(((((((((....)---))))..)))).(((((((......))).))))))))))..)))................... ( -23.80, z-score =  -2.76, R)
>droEre2.scaffold_4929 13691168 79 - 26641161
GAUUUGAGAUUUGAGAUCAGCUGGGUCC---AGCUAAGAUCAUUUGCAA-GUAAGUGGUCGAACAGGUCCCCGAAAUAAAUAA----------
..((((.((((((.....(((((....)---))))..(((((((((...-.)))))))))...))))))..))))........---------- ( -23.10, z-score =  -2.81, R)
>droYak2.chr2L 8906554 77 + 22324452
GAUCGCAGAUUUGAGAUCAGCUGUGUCC---AGCUAAGAUCAUUUGCAA-GUGAGUUGUCGAACAGGUCCCCGAAAUAAAU------------
..(((..((((((.(((((((((....)---))))..)))).(((((((-.....))).))))))))))..))).......------------ ( -19.10, z-score =  -1.71, R)
>droSec1.super_16 660290 92 + 1878335
GAUCGCAGAUCUGAGAUCAGCUGGGUCCACCAGCUAAGAUCAUUUGCAA-GUGAGUUGUCGAACAGGUCCCCGAAAUAAAUGAAAAAUAAAUA
..(((..((((((.((((((((((.....))))))..)))).(((((((-.....))).))))))))))..)))................... ( -26.30, z-score =  -3.07, R)
>droSim1.chr2L 12278442 92 + 22036055
GAUCGCAGAUCUGAGAUCAGCUGGGUCCACCAGCUAAGAUCAUUUGCAA-GUGAGUUGUCGAACAGGUCCCCGAAAUAAAUGAAAAAUAAAUA
..(((..((((((.((((((((((.....))))))..)))).(((((((-.....))).))))))))))..)))................... ( -26.30, z-score =  -3.07, R)
>consensus
GAUCGCAGAUCUGAGAUCAGCUGGGUCC___AGCUAAGAUCAUUUGCAA_GUGAGUUGUCGAACAGGUCCCCGAAAUAAAUGAAAAA_AAA_A
..(((..((((((.((((((((.........))))..)))).(((((((......))).))))))))))..)))................... (-15.46 = -15.46 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:35:18 2011