Locus 12434

Sequence ID dm3.chrXHet
Location 159,485 – 159,596
Length 111
Max. P 0.999634
window17088 window17089

overview

Window 8

Location 159,485 – 159,581
Length 96
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 51.77
Shannon entropy 0.64923
G+C content 0.56749
Mean single sequence MFE -34.60
Consensus MFE -19.97
Energy contribution -19.53
Covariance contribution -0.43
Combinations/Pair 1.50
Mean z-score -1.44
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.35
SVM RNA-class probability 0.989060
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 159485 96 - 204112
----------AUCACCAUCGCGCCAAGGCGGCCUUGGCCGUGCUGGCAAGGAUGUUCACCAAGCAACAUCUUGGGCUAGCCCUGGUGCAGGAACCCUGGUAUAACC--
----------...(((...((((((.((((((....)))))((((((.((((((((........))))))))..))))))).))))))(((...))))))......-- ( -40.90, z-score =  -2.02, R)
>droYak2.chr3R 144096 90 - 28832112
----------AGCAAGGGUCCGCCGACAUAGCUUUGGUCCAAGAGCCAUGGAU-UGCCUCGGGCAAUGCCGUCGCCGGACUAAAGUCCUCCAAUUA--CAACC-----
----------.((...((((((.((((...(((((......)))))...((((-((((...)))))).)))))).))))))...))..........--.....----- ( -30.30, z-score =  -1.49, R)
>dp4.Unknown_singleton_3065 1778 107 - 2449
AUUACCAUGGAGAAAGAGCCCGCCGACAUAGCUUUAGUCCAGGAGCCGUGGAU-UGCGUCAGGCAACUCCGUGGCCGGGCUAGAGUCCUCAAAUUAAGCAGUAAGCAG
.......((..((...(((((((((((.........)))..)).(((((((((-(((.....)))).))))))))))))))....))..))......((.....)).. ( -32.60, z-score =  -0.79, R)
>consensus
__________AGCAAGAGCCCGCCGACAUAGCUUUGGUCCAGGAGCCAUGGAU_UGCAUCAGGCAACACCGUGGCCGGGCUAAAGUCCUCAAAUUA_GCAAUAA_C__
..............................((((((((((....(((((((...(((.....)))...))))))).))))))))))...................... (-19.97 = -19.53 +  -0.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 159,500 – 159,596
Length 96
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 47.95
Shannon entropy 0.70308
G+C content 0.58446
Mean single sequence MFE -41.73
Consensus MFE -19.97
Energy contribution -19.53
Covariance contribution -0.43
Combinations/Pair 1.50
Mean z-score -2.70
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.11
SVM RNA-class probability 0.999634
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 159500 96 - 204112
---------------AUAGCUCAGGUGAAAAUCACCAUCGCGCCAAGGCGGCCUUGGCCGUGCUGGCAAGGAUGUUCACCAAGCAACAUCUUGGGCUAGCCCUGGUGCAGG
---------------........((((.....))))...((((((.((((((....)))))((((((.((((((((........))))))))..))))))).))))))... ( -43.60, z-score =  -2.88, R)
>droYak2.chr3R 144109 85 - 28832112
----------------------AAGCGAAGAGCAAGGGUCCGCCGACAUAGCUUUGGUCCAAGAGCCAUGGAU-UGCCUCGGGCAAUGCCGUCGCCGGACUAAAGUCC---
----------------------..((.....))...((((((.((((...(((((......)))))...((((-((((...)))))).)))))).)))))).......--- ( -32.00, z-score =  -1.70, R)
>dp4.Unknown_singleton_3065 1795 110 - 2449
UAGCGUCGGUGGAGCUUCUCAUUACCAUGGAGAAAGAGCCCGCCGACAUAGCUUUAGUCCAGGAGCCGUGGAU-UGCGUCAGGCAACUCCGUGGCCGGGCUAGAGUCCUCA
....((((((((.(((((((.........))))...)))))))))))...((((((((((..(.(((((((((-(((.....)))).)))))))))))))))))))..... ( -49.60, z-score =  -3.50, R)
>consensus
________________U__C__AAGCGAAGAGCAAGAGCCCGCCGACAUAGCUUUGGUCCAGGAGCCAUGGAU_UGCAUCAGGCAACACCGUGGCCGGGCUAAAGUCC___
..................................................((((((((((....(((((((...(((.....)))...))))))).))))))))))..... (-19.97 = -19.53 +  -0.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:06 2011