Locus 2189

Sequence ID dm3.chr2L
Location 16,882,620 – 16,882,718
Length 98
Max. P 0.996234
window3026 window3027

overview

Window 6

Location 16,882,620 – 16,882,718
Length 98
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 87.04
Shannon entropy 0.21237
G+C content 0.49410
Mean single sequence MFE -28.30
Consensus MFE -20.38
Energy contribution -22.42
Covariance contribution 2.04
Combinations/Pair 1.04
Mean z-score -1.97
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.647333
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16882620 98 + 23011544
GCGGCAAGAAUUCCACGGCAAGUUGCAAUAAUGCAAUAAUGACCUCCUCUCUCUCAAAUGGCCGGCAAUUAUAGGCCAGCCAUUUGUAAGUCGUUGCC
..(((((((.......((((.((((((....))))))..)).))......((..((((((((.(((........))).))))))))..)))).))))) ( -31.80, z-score =  -2.92, R)
>droEre2.scaffold_4845 15237698 85 - 22589142
GCGGCCAGAAAUCCACGGCAAGCUGCAAUUAUGA-----------CCUCUCUC--AAAUGGCCAGCGAUUAUAGGCCAGCCGUUUGUAAGUCGUUGCC
(((((................)))))......((-----------(..((..(--(((((((..((........))..))))))))..))..)))... ( -23.09, z-score =  -0.32, R)
>droYak2.chr2R 16916703 85 - 21139217
GCGGCAAGAAUUUCACGGCAAGUUGCAAUAACGA-----------CCUCUCUC--AAAUGGCCAGCAAUUAUAGGCCAGCCAUUUGUAAGUCGUUGCC
..(((............((.....))...(((((-----------(......(--(((((((..((........))..))))))))...))))))))) ( -24.60, z-score =  -1.94, R)
>droSec1.super_7 519569 96 + 3727775
GCGGCAAGAAUUCCACGGCAAGUUGCAAUAAUGCAAUAAUGACCUCCUCUCUC--AAAUGGCCGGCAAUUAUAGGCCAGCCAUUUGCAAGUCGUUGCC
..(((((((.......((((.((((((....))))))..)).))....((..(--(((((((.(((........))).))))))))..)))).))))) ( -31.00, z-score =  -2.34, R)
>droSim1.chr2L 16566333 96 + 22036055
GCGGCAAGAAUUCCACGGCAAGUUGCAAUAAUGCAAUAAUGACCUCCUCUCUC--AAAUGGCCGGCAAUUAUAGGCCAGCCAUUUGCAAGUCGUUGCC
..(((((((.......((((.((((((....))))))..)).))....((..(--(((((((.(((........))).))))))))..)))).))))) ( -31.00, z-score =  -2.34, R)
>consensus
GCGGCAAGAAUUCCACGGCAAGUUGCAAUAAUGCAAUAAUGACCUCCUCUCUC__AAAUGGCCGGCAAUUAUAGGCCAGCCAUUUGUAAGUCGUUGCC
..((((........(((((..(((((......)))))..................(((((((.(((........))).)))))))....))))))))) (-20.38 = -22.42 +   2.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,882,620 – 16,882,718
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 87.04
Shannon entropy 0.21237
G+C content 0.49410
Mean single sequence MFE -35.92
Consensus MFE -26.46
Energy contribution -27.66
Covariance contribution 1.20
Combinations/Pair 1.07
Mean z-score -3.56
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.90
SVM RNA-class probability 0.996234
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16882620 98 - 23011544
GGCAACGACUUACAAAUGGCUGGCCUAUAAUUGCCGGCCAUUUGAGAGAGAGGAGGUCAUUAUUGCAUUAUUGCAACUUGCCGUGGAAUUCUUGCCGC
(((((.(((((.((((((((((((........)))))))))))).)))......((.((...(((((....)))))..)))).......))))))).. ( -38.70, z-score =  -4.18, R)
>droEre2.scaffold_4845 15237698 85 + 22589142
GGCAACGACUUACAAACGGCUGGCCUAUAAUCGCUGGCCAUUU--GAGAGAGG-----------UCAUAAUUGCAGCUUGCCGUGGAUUUCUGGCCGC
(((.........((((.(((..((........))..))).)))--)..(((((-----------((...((.((.....)).)).))))))).))).. ( -28.20, z-score =  -1.33, R)
>droYak2.chr2R 16916703 85 + 21139217
GGCAACGACUUACAAAUGGCUGGCCUAUAAUUGCUGGCCAUUU--GAGAGAGG-----------UCGUUAUUGCAACUUGCCGUGAAAUUCUUGCCGC
(((((((((((.((((((((..((........))..)))))))--)....)))-----------)))((((.((.....)).)))).....))))).. ( -34.10, z-score =  -4.41, R)
>droSec1.super_7 519569 96 - 3727775
GGCAACGACUUGCAAAUGGCUGGCCUAUAAUUGCCGGCCAUUU--GAGAGAGGAGGUCAUUAUUGCAUUAUUGCAACUUGCCGUGGAAUUCUUGCCGC
((((((..(((.((((((((((((........)))))))))))--)...)))..).......(((((....))))).)))))((((........)))) ( -39.30, z-score =  -3.93, R)
>droSim1.chr2L 16566333 96 - 22036055
GGCAACGACUUGCAAAUGGCUGGCCUAUAAUUGCCGGCCAUUU--GAGAGAGGAGGUCAUUAUUGCAUUAUUGCAACUUGCCGUGGAAUUCUUGCCGC
((((((..(((.((((((((((((........)))))))))))--)...)))..).......(((((....))))).)))))((((........)))) ( -39.30, z-score =  -3.93, R)
>consensus
GGCAACGACUUACAAAUGGCUGGCCUAUAAUUGCCGGCCAUUU__GAGAGAGGAGGUCAUUAUUGCAUUAUUGCAACUUGCCGUGGAAUUCUUGCCGC
(((((...(((..(((((((((((........)))))))))))..)))..............(((((....))))).)))))((((........)))) (-26.46 = -27.66 +   1.20)

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 21:46:40 2011