Locus 9448

Sequence ID dm3.chr3R
Location 6,754,104 – 6,754,204
Length 100
Max. P 0.737454
window12956 window12957

overview

Window 6

Location 6,754,104 – 6,754,204
Length 100
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 85.09
Shannon entropy 0.19855
G+C content 0.43596
Mean single sequence MFE -11.47
Consensus MFE -10.39
Energy contribution -11.17
Covariance contribution 0.78
Combinations/Pair 1.07
Mean z-score -1.26
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.55
SVM RNA-class probability 0.737454
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6754104 100 + 27905053
-----------UCUUUUUUUUCUUGGCCAACAUCUUAGACUCCAUCUCAAUCCAGUUGGCCAGCUCGCUUUCUUUCGCACUUUCCACUUAUUGUUUCGCCACCUCCUCUUU
-----------...........(((((((((.....(((.....))).......)))))))))...((........))................................. ( -13.80, z-score =  -2.20, R)
>droSim1.chr3R 12912528 99 - 27517382
------------UCUUUUUUUCUUGGCCAACAUCUUAGACUCCAUCUCAAUCCAGUUGGCCAGCUCGCUUUCUUUCGCACUUUCCACUUAUUGUUUCGCCACCUCCUCUUU
------------..........(((((((((.....(((.....))).......)))))))))...((........))................................. ( -13.80, z-score =  -2.23, R)
>droEre2.scaffold_4770 2892850 111 - 17746568
UCAAUUUUUGUUUUUUUUCUGUCCCACCAACGUCUUAGACUCCAUCUCAAUCCAGUUGGCCAGCUCGCUUUCUAUCGCACUUUCCACUUAUUGUUUCGCCACCUUCUCUUU
.((((...((................(((((.....(((.....))).......))))).......((........))......))...)))).................. (  -6.80, z-score =   0.67, R)
>consensus
___________UUUUUUUUUUCUUGGCCAACAUCUUAGACUCCAUCUCAAUCCAGUUGGCCAGCUCGCUUUCUUUCGCACUUUCCACUUAUUGUUUCGCCACCUCCUCUUU
......................(((((((((.....(((.....))).......)))))))))...((........))................................. (-10.39 = -11.17 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 6,754,104 – 6,754,204
Length 100
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 85.09
Shannon entropy 0.19855
G+C content 0.43596
Mean single sequence MFE -19.27
Consensus MFE -17.01
Energy contribution -16.90
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.40
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.727948
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6754104 100 - 27905053
AAAGAGGAGGUGGCGAAACAAUAAGUGGAAAGUGCGAAAGAAAGCGAGCUGGCCAACUGGAUUGAGAUGGAGUCUAAGAUGUUGGCCAAGAAAAAAAAGA-----------
.......((.(.((...((.....))........(....)...)).).))(((((((((((((.......))))))....))))))).............----------- ( -20.00, z-score =  -1.79, R)
>droSim1.chr3R 12912528 99 + 27517382
AAAGAGGAGGUGGCGAAACAAUAAGUGGAAAGUGCGAAAGAAAGCGAGCUGGCCAACUGGAUUGAGAUGGAGUCUAAGAUGUUGGCCAAGAAAAAAAGA------------
.......((.(.((...((.....))........(....)...)).).))(((((((((((((.......))))))....)))))))............------------ ( -20.00, z-score =  -1.77, R)
>droEre2.scaffold_4770 2892850 111 + 17746568
AAAGAGAAGGUGGCGAAACAAUAAGUGGAAAGUGCGAUAGAAAGCGAGCUGGCCAACUGGAUUGAGAUGGAGUCUAAGACGUUGGUGGGACAGAAAAAAAACAAAAAUUGA
..................((((...((.....(((........))).(((.((((((((((((.......))))))....)))))).)).)..........))...)))). ( -17.80, z-score =  -0.65, R)
>consensus
AAAGAGGAGGUGGCGAAACAAUAAGUGGAAAGUGCGAAAGAAAGCGAGCUGGCCAACUGGAUUGAGAUGGAGUCUAAGAUGUUGGCCAAGAAAAAAAAAA___________
..........((((.((.((((.(((((..(((.((........)).)))..)).)))..))))((((...))))......)).))))....................... (-17.01 = -16.90 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:04:36 2011