Locus 2413

Sequence ID dm3.chr2L
Location 18,850,744 – 18,850,850
Length 106
Max. P 0.967183
window3316 window3317 window3318

overview

Window 6

Location 18,850,744 – 18,850,795
Length 51
Sequences 5
Columns 51
Reading direction forward
Mean pairwise identity 94.12
Shannon entropy 0.11038
G+C content 0.47843
Mean single sequence MFE -13.52
Consensus MFE -13.84
Energy contribution -13.52
Covariance contribution -0.32
Combinations/Pair 1.18
Mean z-score -0.97
Structure conservation index 1.02
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.87
SVM RNA-class probability 0.839980
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18850744 51 + 23011544
CGAAAGCUGAAAAAAGAGGGGCUGCAAGCGAAGAGUUUAAUGCCUCUCCAU
...............(((((((...((((.....))))...)))))))... ( -14.40, z-score =  -1.58, R)
>droSim1.chr2L 18540442 51 + 22036055
CAAGAGCUGGAAAAAGAGGGGCUGCAGGCGAAGAGUUUAAUGCUUCUCCAU
...............(((((((...((((.....))))...)))))))... ( -11.20, z-score =   0.22, R)
>droSec1.super_7 2477137 51 + 3727775
CAAAAGCUGGAAAAAGAGGGGCUGCAGGCGAAGAGUUUAAUGCCUCUCCAU
...............(((((((...((((.....))))...)))))))... ( -14.00, z-score =  -0.85, R)
>droYak2.chr2R 5365643 51 + 21139217
CAAAAUCUGCAAAAAGAGGGGCUGCAGGCGAAGAGUUUAAUGCCUCUCCAU
...............(((((((...((((.....))))...)))))))... ( -14.00, z-score =  -1.17, R)
>droEre2.scaffold_4845 17163660 51 - 22589142
CAAAAACUGGAAAAAGAGGGGCUGCAGGCGAAGAGUUUAAUGCCUCUCCAU
...............(((((((...((((.....))))...)))))))... ( -14.00, z-score =  -1.45, R)
>consensus
CAAAAGCUGGAAAAAGAGGGGCUGCAGGCGAAGAGUUUAAUGCCUCUCCAU
...............(((((((...((((.....))))...)))))))... (-13.84 = -13.52 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,850,795 – 18,850,850
Length 55
Sequences 6
Columns 55
Reading direction forward
Mean pairwise identity 89.33
Shannon entropy 0.20781
G+C content 0.51055
Mean single sequence MFE -17.73
Consensus MFE -13.40
Energy contribution -13.65
Covariance contribution 0.25
Combinations/Pair 1.13
Mean z-score -2.66
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967183
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18850795 55 + 23011544
CGAUGGGAAAAUUGGUUAAGAUAGGGCAUGUCCUCUACGAGAGAGAUGUGCCGAC
((((......))))..........(((((((((((.....))).))))))))... ( -16.60, z-score =  -2.98, R)
>droAna3.scaffold_12943 4645105 54 + 5039921
CGAUGCAGAAGU-GGAUAAGAUAGAGCAGGUCCUCUUCUGCAAAGAUGUGCUGAC
...((((((((.-((((..(......)..)))).))))))))............. ( -18.00, z-score =  -2.71, R)
>droEre2.scaffold_4845 17163711 55 - 22589142
CGAUGGGCAAAUUGCUUAAGAUAGGGCAUGUCCUCUGCGAGAGAGAUGUGCCGAC
...(((((.....)))))......(((((((((((.....))).))))))))... ( -19.30, z-score =  -2.83, R)
>droYak2.chr2R 5365694 55 + 21139217
CGAUGGGCAAAUUGCUUAAGAUAGGGCAUGUCCUCUACGAGAGAGAUGUGCCGAC
...(((((.....)))))......(((((((((((.....))).))))))))... ( -19.30, z-score =  -3.31, R)
>droSec1.super_7 2477188 55 + 3727775
CGAUGGGCAAAUUGGUUAAGAUAGGGCAUGUCCUCUGCGAGAGAGAUGUGCCGAC
((((......))))..........(((((((((((.....))).))))))))... ( -16.60, z-score =  -2.05, R)
>droSim1.chr2L 18540493 55 + 22036055
CGAUGGGCAAAUUGGUUAAGAUAGGGCAUGUCCUCUGCGAGAGAGAUGUGCCGAC
((((......))))..........(((((((((((.....))).))))))))... ( -16.60, z-score =  -2.05, R)
>consensus
CGAUGGGCAAAUUGGUUAAGAUAGGGCAUGUCCUCUGCGAGAGAGAUGUGCCGAC
((((......))))..........(((((((((((.....))).))))))))... (-13.40 = -13.65 +   0.25)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 18,850,795 – 18,850,850
Length 55
Sequences 6
Columns 55
Reading direction reverse
Mean pairwise identity 89.33
Shannon entropy 0.20781
G+C content 0.51055
Mean single sequence MFE -10.94
Consensus MFE -8.83
Energy contribution -8.58
Covariance contribution -0.25
Combinations/Pair 1.22
Mean z-score -1.56
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.616434
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18850795 55 - 23011544
GUCGGCACAUCUCUCUCGUAGAGGACAUGCCCUAUCUUAACCAAUUUUCCCAUCG
...((((..((.(((.....)))))..))))........................ ( -10.10, z-score =  -2.26, R)
>droAna3.scaffold_12943 4645105 54 - 5039921
GUCAGCACAUCUUUGCAGAAGAGGACCUGCUCUAUCUUAUCC-ACUUCUGCAUCG
.............((((((((.(((..............)))-.))))))))... ( -13.94, z-score =  -2.32, R)
>droEre2.scaffold_4845 17163711 55 + 22589142
GUCGGCACAUCUCUCUCGCAGAGGACAUGCCCUAUCUUAAGCAAUUUGCCCAUCG
...((((..((.(((.....)))))..)))).........((.....))...... ( -10.70, z-score =  -0.90, R)
>droYak2.chr2R 5365694 55 - 21139217
GUCGGCACAUCUCUCUCGUAGAGGACAUGCCCUAUCUUAAGCAAUUUGCCCAUCG
...((((..((.(((.....)))))..)))).........((.....))...... ( -10.70, z-score =  -1.13, R)
>droSec1.super_7 2477188 55 - 3727775
GUCGGCACAUCUCUCUCGCAGAGGACAUGCCCUAUCUUAACCAAUUUGCCCAUCG
...((((..((.(((.....)))))..))))........................ ( -10.10, z-score =  -1.39, R)
>droSim1.chr2L 18540493 55 - 22036055
GUCGGCACAUCUCUCUCGCAGAGGACAUGCCCUAUCUUAACCAAUUUGCCCAUCG
...((((..((.(((.....)))))..))))........................ ( -10.10, z-score =  -1.39, R)
>consensus
GUCGGCACAUCUCUCUCGCAGAGGACAUGCCCUAUCUUAACCAAUUUGCCCAUCG
...((((..((.(((.....)))))..))))........................ ( -8.83 =  -8.58 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:50:43 2011