Locus 9924

Sequence ID dm3.chr3R
Location 9,826,506 – 9,826,564
Length 58
Max. P 0.938893
window13635 window13636

overview

Window 5

Location 9,826,506 – 9,826,564
Length 58
Sequences 5
Columns 71
Reading direction forward
Mean pairwise identity 78.96
Shannon entropy 0.34373
G+C content 0.38703
Mean single sequence MFE -13.78
Consensus MFE -6.98
Energy contribution -8.22
Covariance contribution 1.24
Combinations/Pair 1.07
Mean z-score -2.28
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.55
SVM RNA-class probability 0.740880
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9826506 58 + 27905053
GCACAUAGCGUUUAUGGGAAGAUGUUACUUUUAGUUUCGCAACAUUUUCCAUCGCUUU-------------
......((((......((((((((((.(..........).))))))))))..))))..------------- ( -13.80, z-score =  -2.95, R)
>droAna3.scaffold_13340 3052026 71 - 23697760
CCAGAUACAUUUUAUGGGAAGAUGUUACUUUUAGUUUCGCCACAUUUUUCCUCCAAGUGUGUCUCCAAUUU
..((((((((((...((((((((((................))))))))))...))))))))))....... ( -19.39, z-score =  -4.26, R)
>droYak2.chr3R 12227458 58 - 28832112
ACACAUAGCGUUUAUGUGAAGAUGUUACUCUUAGUUUCGCAACAUUUUCCUCCGCUUU-------------
......((((.....(.(((((((((.(..........).))))))))))..))))..------------- (  -9.50, z-score =  -1.47, R)
>droSec1.super_0 8933833 58 - 21120651
GCAUAUAGCGGUUAUGGGAAGAUGUUACUUUUAGUUUCGCAACAUUUUCCGCCGCUUU-------------
......((((((....((((((((((.(..........).))))))))))))))))..------------- ( -18.00, z-score =  -3.30, R)
>droSim1.chr3R 15915114 58 - 27517382
GCACAUAGCGUUUAUGGGAAGAUGUUACUUUUAGUUUCGCAAAAUUUUCCGCCGCUUU-------------
((.(((((...)))))(((((((((.((.....))...)))...))))))...))...------------- (  -8.20, z-score =   0.56, R)
>consensus
GCACAUAGCGUUUAUGGGAAGAUGUUACUUUUAGUUUCGCAACAUUUUCCGCCGCUUU_____________
......((((......((((((((((.(..........).))))))))))..))))............... ( -6.98 =  -8.22 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 9,826,506 – 9,826,564
Length 58
Sequences 5
Columns 71
Reading direction reverse
Mean pairwise identity 78.96
Shannon entropy 0.34373
G+C content 0.38703
Mean single sequence MFE -13.26
Consensus MFE -9.14
Energy contribution -9.70
Covariance contribution 0.56
Combinations/Pair 1.13
Mean z-score -2.08
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.938893
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9826506 58 - 27905053
-------------AAAGCGAUGGAAAAUGUUGCGAAACUAAAAGUAACAUCUUCCCAUAAACGCUAUGUGC
-------------..((((((((((.(((((((..........))))))).)).))))...))))...... ( -14.50, z-score =  -3.45, R)
>droAna3.scaffold_13340 3052026 71 + 23697760
AAAUUGGAGACACACUUGGAGGAAAAAUGUGGCGAAACUAAAAGUAACAUCUUCCCAUAAAAUGUAUCUGG
...(..((.(((.....((((((....(((.((..........)).))))))))).......))).))..) ( -10.90, z-score =  -0.22, R)
>droYak2.chr3R 12227458 58 + 28832112
-------------AAAGCGGAGGAAAAUGUUGCGAAACUAAGAGUAACAUCUUCACAUAAACGCUAUGUGU
-------------..((((...(((.(((((((..........))))))).))).......))))...... ( -13.20, z-score =  -2.14, R)
>droSec1.super_0 8933833 58 + 21120651
-------------AAAGCGGCGGAAAAUGUUGCGAAACUAAAAGUAACAUCUUCCCAUAACCGCUAUAUGC
-------------..(((((.((((.(((((((..........))))))).)))).....)))))...... ( -18.10, z-score =  -4.15, R)
>droSim1.chr3R 15915114 58 + 27517382
-------------AAAGCGGCGGAAAAUUUUGCGAAACUAAAAGUAACAUCUUCCCAUAAACGCUAUGUGC
-------------..((((..((((.((.((((..........)))).)).))))......))))...... (  -9.60, z-score =  -0.44, R)
>consensus
_____________AAAGCGGCGGAAAAUGUUGCGAAACUAAAAGUAACAUCUUCCCAUAAACGCUAUGUGC
...............((((..((((.(((((((..........))))))).))))......))))...... ( -9.14 =  -9.70 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:14:00 2011