Locus 6545

Sequence ID dm3.chr3L
Location 7,573,193 – 7,573,330
Length 137
Max. P 0.998449
window9010 window9011 window9012 window9013

overview

Window 0

Location 7,573,193 – 7,573,292
Length 99
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 86.49
Shannon entropy 0.18551
G+C content 0.29156
Mean single sequence MFE -24.03
Consensus MFE -20.22
Energy contribution -19.23
Covariance contribution -0.99
Combinations/Pair 1.23
Mean z-score -3.89
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.36
SVM RNA-class probability 0.998449
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7573193 99 + 24543557
AAAAGGCCAGAACUGACAAGAACAAUAACUUGUUUACAAAACUAAUCCUAUUAACUUAGGAUUAGGAAAGCAUAAGAAUCUAUUAUUUUUCUUCUUGUU
..............((((((((...................(((((((((......)))))))))(((((.((((.......))))))))))))))))) ( -21.10, z-score =  -2.89, R)
>droSim1.chr3L 7087425 98 + 22553184
AAAAGACCAGAACUAACAAGAACAAUAAACUCUUUACAAA-CCAAUCCUAUAAUAUUAGGAUUGGGGUAUCAUAAGAAUCUAUUAGUUCUUUUCUUGUU
..((((..((((((((..(((.............(((...-(((((((((......))))))))).)))((....)).))).))))))))..))))... ( -26.60, z-score =  -4.83, R)
>droSec1.super_2 7502780 98 + 7591821
AAGAGACCAGAACUGACAAAAACAAUAAACUCUUUACAAA-CCAAUCCUAUAAUCUUAGGAUUGGGAUAUCAUAAGAACCUAUUAGUUCUUUUCUUGUU
..((((..((((((((........................-(((((((((......)))))))))....((....)).....))))))))..))))... ( -24.40, z-score =  -3.94, R)
>consensus
AAAAGACCAGAACUGACAAGAACAAUAAACUCUUUACAAA_CCAAUCCUAUAAUCUUAGGAUUGGGAUAUCAUAAGAAUCUAUUAGUUCUUUUCUUGUU
..((((..((((((((.........................(((((((((......)))))))))(....)...........))))))))..))))... (-20.22 = -19.23 +  -0.99)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,573,193 – 7,573,292
Length 99
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 86.49
Shannon entropy 0.18551
G+C content 0.29156
Mean single sequence MFE -26.90
Consensus MFE -21.49
Energy contribution -21.50
Covariance contribution 0.01
Combinations/Pair 1.12
Mean z-score -3.78
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.18
SVM RNA-class probability 0.997790
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7573193 99 - 24543557
AACAAGAAGAAAAAUAAUAGAUUCUUAUGCUUUCCUAAUCCUAAGUUAAUAGGAUUAGUUUUGUAAACAAGUUAUUGUUCUUGUCAGUUCUGGCCUUUU
......(((((.((((((................(((((((((......)))))))))..(((....))))))))).)))))((((....))))..... ( -19.30, z-score =  -1.66, R)
>droSim1.chr3L 7087425 98 - 22553184
AACAAGAAAAGAACUAAUAGAUUCUUAUGAUACCCCAAUCCUAAUAUUAUAGGAUUGG-UUUGUAAAGAGUUUAUUGUUCUUGUUAGUUCUGGUCUUUU
...((((..(((((((((((((((((...(((..(((((((((......)))))))))-..))).))))))).........))))))))))..)))).. ( -32.20, z-score =  -5.61, R)
>droSec1.super_2 7502780 98 - 7591821
AACAAGAAAAGAACUAAUAGGUUCUUAUGAUAUCCCAAUCCUAAGAUUAUAGGAUUGG-UUUGUAAAGAGUUUAUUGUUUUUGUCAGUUCUGGUCUCUU
....(((..((((((((((..(((((...(((..(((((((((......)))))))))-..))).)))))..)))).........))))))..)))... ( -29.20, z-score =  -4.07, R)
>consensus
AACAAGAAAAGAACUAAUAGAUUCUUAUGAUAUCCCAAUCCUAAGAUUAUAGGAUUGG_UUUGUAAAGAGUUUAUUGUUCUUGUCAGUUCUGGUCUUUU
.(((((((......((((((((((((((((....(((((((((......)))))))))..)))).)))))))))))))))))))............... (-21.49 = -21.50 +   0.01)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,573,230 – 7,573,330
Length 100
Sequences 3
Columns 100
Reading direction forward
Mean pairwise identity 72.56
Shannon entropy 0.34895
G+C content 0.27615
Mean single sequence MFE -19.64
Consensus MFE -16.13
Energy contribution -15.69
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -3.07
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.25
SVM RNA-class probability 0.998078
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 7573230 100 + 24543557
AAAACUAAUCCUAUUAACUUAGGAUUAGGAAAGCAUAAGAAUCUAUUAUUUUUCUUCUUGUUUAGCCAGUCUUUCAAAGAAUUUUAAUCUAGACCUUUGU
....(((((((((......)))))))))..(((((.(((((..........)))))..))))).....((((.....(((.......)))))))...... ( -18.30, z-score =  -1.23, R)
>droSim1.chr3L 7087462 77 + 22553184
-AAACCAAUCCUAUAAUAUUAGGAUUGGGGUAUCAUAAGAAUCUAUUAGUUCUUUUCUUGUUUAGCCAUUCUUUUAAA----------------------
-...(((((((((......)))))))))(((...(((((((.............)))))))...)))...........---------------------- ( -21.12, z-score =  -4.19, R)
>droSec1.super_2 7502817 77 + 7591821
-AAACCAAUCCUAUAAUCUUAGGAUUGGGAUAUCAUAAGAACCUAUUAGUUCUUUUCUUGUUUAGCCAUACUUUUAAA----------------------
-...(((((((((......)))))))))((((....((((((......))))))....))))................---------------------- ( -19.50, z-score =  -3.80, R)
>consensus
_AAACCAAUCCUAUAAUCUUAGGAUUGGGAUAUCAUAAGAAUCUAUUAGUUCUUUUCUUGUUUAGCCAUUCUUUUAAA______________________
....(((((((((......)))))))))......(((((((.............)))))))....................................... (-16.13 = -15.69 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,573,230 – 7,573,330
Length 100
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 72.56
Shannon entropy 0.34895
G+C content 0.27615
Mean single sequence MFE -16.32
Consensus MFE -12.66
Energy contribution -12.22
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -1.55
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.879669
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 7573230 100 - 24543557
ACAAAGGUCUAGAUUAAAAUUCUUUGAAAGACUGGCUAAACAAGAAGAAAAAUAAUAGAUUCUUAUGCUUUCCUAAUCCUAAGUUAAUAGGAUUAGUUUU
.((((((.............))))))...((..(((.....(((((.............)))))..))).))(((((((((......))))))))).... ( -16.74, z-score =  -0.30, R)
>droSim1.chr3L 7087462 77 - 22553184
----------------------UUUAAAAGAAUGGCUAAACAAGAAAAGAACUAAUAGAUUCUUAUGAUACCCCAAUCCUAAUAUUAUAGGAUUGGUUU-
----------------------.(((.((((((..(((.................))))))))).)))....(((((((((......)))))))))...- ( -13.93, z-score =  -1.79, R)
>droSec1.super_2 7502817 77 - 7591821
----------------------UUUAAAAGUAUGGCUAAACAAGAAAAGAACUAAUAGGUUCUUAUGAUAUCCCAAUCCUAAGAUUAUAGGAUUGGUUU-
----------------------........................(((((((....)))))))........(((((((((......)))))))))...- ( -18.30, z-score =  -2.56, R)
>consensus
______________________UUUAAAAGAAUGGCUAAACAAGAAAAGAACUAAUAGAUUCUUAUGAUAUCCCAAUCCUAAGAUUAUAGGAUUGGUUU_
.........................................(((((.............)))))........(((((((((......))))))))).... (-12.66 = -12.22 +  -0.44)

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 23:09:51 2011