Locus 9333

Sequence ID dm3.chr3R
Location 5,984,455 – 5,984,535
Length 80
Max. P 0.997602
window12796 window12797

overview

Window 6

Location 5,984,455 – 5,984,535
Length 80
Sequences 6
Columns 82
Reading direction forward
Mean pairwise identity 70.50
Shannon entropy 0.55681
G+C content 0.40833
Mean single sequence MFE -21.95
Consensus MFE -6.71
Energy contribution -8.47
Covariance contribution 1.75
Combinations/Pair 1.32
Mean z-score -2.51
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.884136
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5984455 80 + 27905053
AGUGUGUCCUCGGAUAUUUACCGCAUUUGAAAAUGUUGGCCACAU--AUAAAGCCAAUCAUUUUCGGGUGGAUCAUCCAAAG
...........(((((((((((.....(((((((((((((.....--.....))))).))))))))))))))).)))).... ( -23.50, z-score =  -2.72, R)
>droVir3.scaffold_12855 5320536 64 - 10161210
--UAUUUACGCAACGAAUAGUCACAAUCCCAACUAUUGUCUAUAAUAAUAGAUGUGAUUGUGUCUA----------------
--...............(((.(((((((.((.(((((((.....))))))).)).))))))).)))---------------- ( -17.60, z-score =  -4.38, R)
>droSim1.chr3R 12126312 80 - 27517382
AGUGUGUCCUUGGAUAUUUACCGCACUCGGAAAUGUUGGCCACAU--AUAGAGCCAAUCAUUUUCGGGUGGAGCAUCCAAAG
.........((((((.(((....((((((((((((((((((....--...).))))).))))))))))))))).)))))).. ( -27.60, z-score =  -3.12, R)
>droSec1.super_0 5190180 80 - 21120651
AGUGUGUCCUUGGAUAUUUACCACACUUGGAAAUGAUGGCCACAU--AUAGGGCCAAUCAUUUUCGGGUGGAGCAUCCAAAG
.........((((((.(((....((((((((((((((((((....--....)))).))))))))))))))))).)))))).. ( -30.00, z-score =  -3.42, R)
>droYak2.chr3R 10033084 80 + 28832112
AGUGUGUCCUCGGAUAUUUACUGCAUUCUGAAAUGUUGGCCACAU--AUAAAGCCAAUCCCUUUCAAGUGGAGCAUCCGAAG
.........((((((.((((((......(((((.((((((.....--.....))))))...)))))))))))..)))))).. ( -19.40, z-score =  -1.49, R)
>droEre2.scaffold_4770 2138534 80 - 17746568
AGUGUGUCCUUGGAUAUUUACUGCAUUUUGAAAUGUUGUCCACAU--AUAAAGCCAAUCACUUUCAAGUGGAGCAUCCAAAG
.........((((((.....(.(((((....))))).)(((((..--..((((.......))))...)))))..)))))).. ( -13.60, z-score =   0.08, R)
>consensus
AGUGUGUCCUCGGAUAUUUACCGCAUUCGGAAAUGUUGGCCACAU__AUAAAGCCAAUCAUUUUCAGGUGGAGCAUCCAAAG
.........((((((.((((((.......((((.((((((............))))))...)))).))))))..)))))).. ( -6.71 =  -8.47 +   1.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,984,455 – 5,984,535
Length 80
Sequences 6
Columns 82
Reading direction reverse
Mean pairwise identity 70.50
Shannon entropy 0.55681
G+C content 0.40833
Mean single sequence MFE -23.12
Consensus MFE -10.24
Energy contribution -10.63
Covariance contribution 0.39
Combinations/Pair 1.54
Mean z-score -2.96
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.14
SVM RNA-class probability 0.997602
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5984455 80 - 27905053
CUUUGGAUGAUCCACCCGAAAAUGAUUGGCUUUAU--AUGUGGCCAACAUUUUCAAAUGCGGUAAAUAUCCGAGGACACACU
(((((((((..((.(..(((((((.((((((....--....)))))))))))))....).))....)))))))))....... ( -25.70, z-score =  -3.76, R)
>droVir3.scaffold_12855 5320536 64 + 10161210
----------------UAGACACAAUCACAUCUAUUAUUAUAGACAAUAGUUGGGAUUGUGACUAUUCGUUGCGUAAAUA--
----------------(((.(((((((.((.(((((.........))))).)).))))))).)))...............-- ( -13.50, z-score =  -1.92, R)
>droSim1.chr3R 12126312 80 + 27517382
CUUUGGAUGCUCCACCCGAAAAUGAUUGGCUCUAU--AUGUGGCCAACAUUUCCGAGUGCGGUAAAUAUCCAAGGACACACU
(((((((((((.(((.((.(((((.((((((....--....))))))))))).)).))).)))....))))))))....... ( -27.40, z-score =  -3.69, R)
>droSec1.super_0 5190180 80 + 21120651
CUUUGGAUGCUCCACCCGAAAAUGAUUGGCCCUAU--AUGUGGCCAUCAUUUCCAAGUGUGGUAAAUAUCCAAGGACACACU
(((((((((..((((.(..(((((((.(((((...--..).)))))))))))....).))))....)))))))))....... ( -28.80, z-score =  -3.85, R)
>droYak2.chr3R 10033084 80 - 28832112
CUUCGGAUGCUCCACUUGAAAGGGAUUGGCUUUAU--AUGUGGCCAACAUUUCAGAAUGCAGUAAAUAUCCGAGGACACACU
(((((((((((.((.((((((..(.((((((....--....))))))).))))))..)).)))....))))))))....... ( -23.70, z-score =  -2.55, R)
>droEre2.scaffold_4770 2138534 80 + 17746568
CUUUGGAUGCUCCACUUGAAAGUGAUUGGCUUUAU--AUGUGGACAACAUUUCAAAAUGCAGUAAAUAUCCAAGGACACACU
(((((((((.(((((...(((((.....)))))..--..)))))...((((....)))).......)))))))))....... ( -19.60, z-score =  -1.97, R)
>consensus
CUUUGGAUGCUCCACCCGAAAAUGAUUGGCUCUAU__AUGUGGCCAACAUUUCCAAAUGCGGUAAAUAUCCAAGGACACACU
(((((((((......(((.......((((((.((....)).))))))((((....)))))))....)))))))))....... (-10.24 = -10.63 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:02:23 2011