Locus 466

Sequence ID dm3.chr2L
Location 3,245,870 – 3,246,006
Length 136
Max. P 0.734338
window629 window630

overview

Window 9

Location 3,245,870 – 3,246,006
Length 136
Sequences 3
Columns 147
Reading direction forward
Mean pairwise identity 62.56
Shannon entropy 0.50711
G+C content 0.48807
Mean single sequence MFE -42.13
Consensus MFE -22.81
Energy contribution -23.27
Covariance contribution 0.46
Combinations/Pair 1.30
Mean z-score -1.30
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.721395
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3245870 136 + 23011544
AAAACAGAACAGCGCAGCACAGAAGGCAAGCAGCCGUAAUGUUUGCAGUCAACUUGUCUGCAGUCUCUCUGCAGUUGCAG-----CUGCAGCUGUAGCUGCAUCUGAAUCCGAAUCCAAAUACGAGUACGAAUCCAAAUCU------
....((((.....((((.(((((..(((((((.......)))))))..))....)))))))........(((((((((((-----(....))))))))))))))))...................................------ ( -42.20, z-score =  -1.64, R)
>droYak2.chr2L 3235695 136 + 22324452
AAAAGAGAACAGCGCAGUACAGAAAGCAAGCAGCCGUAAUGUUUGCAGUCAACUUGUCUGCAGUUUCACUACAACUGCAG-----CUGCAACUGCAACUGUAGCUGCAUCUGAAUUCAAAUACGUAUCCGAAUCAGAAUCU------
.....(((.(((((((((.(((...(((((((.......))))))).......((((((((((((.......))))))))-----..)))))))..))))).))))..(((((.(((............)))))))).)))------ ( -38.80, z-score =  -1.54, R)
>droGri2.scaffold_2190 1013 143 - 1372
AAAAGGAAACAGCGCUGCCGGCGAGGAUAUGGACAGCAAUUU---CGAGCAACUUGU-UGCAGCCCUCGCAGAAGAGCAGAGAUGCUCCAGCAGCAGCGGCAGCUGUACCUGAGACGGAACCAGAACCUGAAACCGAGUCCAAUGCU
....(....)((((((((((((((((.....((.(....).)---)..((((....)-)))...))))))....(((((....))))).........))))))).......((..(((...(((...)))...)))..))....))) ( -45.40, z-score =  -0.72, R)
>consensus
AAAAGAGAACAGCGCAGCACAGAAGGCAAGCAGCCGUAAUGUUUGCAGUCAACUUGUCUGCAGUCUCACUACAACUGCAG_____CUGCAGCUGCAGCUGCAGCUGAAUCUGAAUCCAAAUACGAAUCCGAAUCCGAAUCU______
...(((...(((((((((.......(((((((.......)))))))............((((((...........(((((.....)))))))))))))))).))))..))).................................... (-22.81 = -23.27 +   0.46)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,245,870 – 3,246,006
Length 136
Sequences 3
Columns 147
Reading direction reverse
Mean pairwise identity 62.56
Shannon entropy 0.50711
G+C content 0.48807
Mean single sequence MFE -48.80
Consensus MFE -22.74
Energy contribution -23.87
Covariance contribution 1.14
Combinations/Pair 1.37
Mean z-score -1.62
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.734338
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3245870 136 - 23011544
------AGAUUUGGAUUCGUACUCGUAUUUGGAUUCGGAUUCAGAUGCAGCUACAGCUGCAG-----CUGCAACUGCAGAGAGACUGCAGACAAGUUGACUGCAAACAUUACGGCUGCUUGCCUUCUGUGCUGCGCUGUUCUGUUUU
------..(((((((((((.(..((....))..).)))))))))))((((..(((((.((((-----(.(((.((((((.....)))))).(((((.(.(((.........)))).))))).....))))))))))))).))))... ( -47.40, z-score =  -1.52, R)
>droYak2.chr2L 3235695 136 - 22324452
------AGAUUCUGAUUCGGAUACGUAUUUGAAUUCAGAUGCAGCUACAGUUGCAGUUGCAG-----CUGCAGUUGUAGUGAAACUGCAGACAAGUUGACUGCAAACAUUACGGCUGCUUGCUUUCUGUACUGCGCUGUUCUCUUUU
------....((((((((((((....))))))).))))).(((((..((((.((((..((((-----..((((((((((((....(((((.(.....).)))))..))))))))))))))))...)))))))).)))))........ ( -49.70, z-score =  -2.88, R)
>droGri2.scaffold_2190 1013 143 + 1372
AGCAUUGGACUCGGUUUCAGGUUCUGGUUCCGUCUCAGGUACAGCUGCCGCUGCUGCUGGAGCAUCUCUGCUCUUCUGCGAGGGCUGCA-ACAAGUUGCUCG---AAAUUGCUGUCCAUAUCCUCGCCGGCAGCGCUGUUUCCUUUU
......(((..((((....(((.(((...((......))..)))..)))(((((((..((((((....))))))...(((((((..(((-(....))))..(---(........))....))))))))))))))))))..))).... ( -49.30, z-score =  -0.46, R)
>consensus
______AGAUUCGGAUUCGGAUUCGUAUUUGGAUUCAGAUACAGCUGCAGCUGCAGCUGCAG_____CUGCAAUUGUAGAGAGACUGCAGACAAGUUGACUGCAAACAUUACGGCUGCUUGCCUUCUGUGCUGCGCUGUUCUCUUUU
.......((((.(((((((((......))))))))).))).)....(((((.(((((.((((.....))))....((((((((...((((....((..............))..))))...))))))))))))))))))........ (-22.74 = -23.87 +   1.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:13:24 2011