Locus 1552

Sequence ID dm3.chr2L
Location 12,006,494 – 12,006,655
Length 161
Max. P 0.854099
window2124 window2125

overview

Window 4

Location 12,006,494 – 12,006,556
Length 62
Sequences 5
Columns 62
Reading direction reverse
Mean pairwise identity 98.06
Shannon entropy 0.03493
G+C content 0.56129
Mean single sequence MFE -15.47
Consensus MFE -15.35
Energy contribution -15.03
Covariance contribution -0.32
Combinations/Pair 1.20
Mean z-score -1.39
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.93
SVM RNA-class probability 0.854099
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12006494 62 - 23011544
UUCUCAUUCUCGUUCUCGUUGGCCUCGCCCGCUAACAUUAACCUUCGGCUGGUGGAGCACUC
...........(((((.((((((.......))))))....(((.......)))))))).... ( -13.50, z-score =  -0.71, R)
>droEre2.scaffold_4929 13233326 62 + 26641161
UUCUCAUUCUCGUUCUCGCUGGCCUCGCCCGCUAGCAUUAACCUUCGGCUGGUGGAGCACUC
...........(((((.((((((.......))))))....(((.......)))))))).... ( -15.90, z-score =  -0.75, R)
>droYak2.chr2L 8425433 62 - 22324452
UUCUCAUUCUCGUUCUCGCUGGCCUCGCCCGCUAACAUUAACCUUCGGCUGGUGGAGCACUC
...........((((.(((..(((......................)))..))))))).... ( -15.85, z-score =  -1.57, R)
>droSec1.super_16 202009 62 - 1878335
UUCUCAUUCUCGUUCUCACUGGCCUCGCCCGCUAACAUUAACCUUCGGCUGGUGGAGCACUC
...........((((.(((..(((......................)))..))))))).... ( -16.25, z-score =  -2.36, R)
>droSim1.chr2L 11810605 62 - 22036055
UUCUCAUUCUCGUUCUCGCUGGCCUCGCCCGCUAACAUUAACCUUCGGCUGGUGGAGCACUC
...........((((.(((..(((......................)))..))))))).... ( -15.85, z-score =  -1.57, R)
>consensus
UUCUCAUUCUCGUUCUCGCUGGCCUCGCCCGCUAACAUUAACCUUCGGCUGGUGGAGCACUC
...........((((.(((..(((......................)))..))))))).... (-15.35 = -15.03 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,006,556 – 12,006,655
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 84.02
Shannon entropy 0.27821
G+C content 0.56874
Mean single sequence MFE -28.65
Consensus MFE -22.94
Energy contribution -22.14
Covariance contribution -0.80
Combinations/Pair 1.20
Mean z-score -1.31
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.595549
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12006556 99 - 23011544
-CCCUUCCUUAAUACCGUUUAAGCCAAUAUGCUCGAAAGUGCAGGGUACUGCGGGAGCGAGACCCCUGCUGACACAUAGCCGUCGUCCCGCUCUGGCACA
-(((...(((((......)))))......(((.(....).))))))...(((.((((((.(((..(.((((.....)))).)..))).)))))).))).. ( -34.90, z-score =  -2.44, R)
>droSim1.chr2L 11810667 99 - 22036055
-CUCUUCCUUAAUACCGUUUAAACCAAUAUGCCCGAGAGUGCAGGGCACUGCGGGAGCGAGACCCCUGCUGACACAUAGCCGCCAUCCCGCUCUGGCACA
-............................((((..(((((((((....))))(((((((((....))((((.....)))))))..))))))))))))).. ( -27.30, z-score =  -0.43, R)
>droSec1.super_16 202071 100 - 1878335
CCCAUUCCCUCAUACCGUUAAAACCAAUAUGCCGGCAAGCGCAGGUCACUGCGGGAGCGAGACCCCUGCUGACACAUAGCCGCCAUCCCGCUCUGGCACA
.............................((((((..(((((((....))))(((((((((....))((((.....)))))))..))))))))))))).. ( -29.00, z-score =  -0.99, R)
>droYak2.chr2L 8425495 94 - 22324452
----UUCCUUAAUACCGUUAAAGCCAAUAUGCCUCCAAGUGCAGGGCAUUGCGUGAGCGAGACCCCUGCUGACACACAGCCGCCAUCCCGCUCUGGCA--
----............((((..((......))........((((((..((((....))))...))))))))))........((((........)))).-- ( -26.80, z-score =  -1.14, R)
>droEre2.scaffold_4929 13233388 91 + 26641161
----UCCCUUAAUAUCGUUAUA-CUAAUACGCCUCAAAUUGCAGGGCAUUGCGUGAGCGAGACCCCUGCUGA--CACAGCCGCCAUCCCGCUCUGGCA--
----..................-.......((........((((((..((((....))))...))))))...--....)).((((........)))).-- ( -25.26, z-score =  -1.58, R)
>consensus
_C__UUCCUUAAUACCGUUAAAACCAAUAUGCCCGAAAGUGCAGGGCACUGCGGGAGCGAGACCCCUGCUGACACAUAGCCGCCAUCCCGCUCUGGCACA
..............................(((......(((((....))))).(((((.((...(.((((.....)))).)...)).))))).)))... (-22.94 = -22.14 +  -0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:34:11 2011