Locus 5613

Sequence ID dm3.chr3LHet
Location 2,077,501 – 2,077,557
Length 56
Max. P 0.984906
window7709 window7710

overview

Window 9

Location 2,077,501 – 2,077,557
Length 56
Sequences 3
Columns 57
Reading direction forward
Mean pairwise identity 69.51
Shannon entropy 0.40276
G+C content 0.49857
Mean single sequence MFE -20.13
Consensus MFE -11.45
Energy contribution -10.57
Covariance contribution -0.88
Combinations/Pair 1.23
Mean z-score -2.27
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.56
SVM RNA-class probability 0.950578
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 2077501 56 + 2555491
GGUGGCUCCAGGCUCUCUCGAAUUUUUGUUAGAGA-GCGAGAGAGCGAAGAGCGCUA
((((.(((...(((((((((..((((....)))).-.)))))))))...))))))). ( -24.60, z-score =  -2.40, R)
>dp4.chrXL_group3b 66965 50 + 386183
-------GUUGGCUCUCUGAAACUUUUUUGAAAGCCACGAGAGAGCUCGGAAAGCCA
-------..(((((.(((((..((((((((.......)))))))).))))).))))) ( -17.90, z-score =  -2.21, R)
>droPer1.super_56 87537 50 + 431378
-------GUUGGCUCUCUGAAACUUUUUUGAAAGCCACGAGAGAGCUCGGAAAGCCA
-------..(((((.(((((..((((((((.......)))))))).))))).))))) ( -17.90, z-score =  -2.21, R)
>consensus
_______GUUGGCUCUCUGAAACUUUUUUGAAAGCCACGAGAGAGCUCGGAAAGCCA
...........(((((((....((((....)))).....)))))))..((....)). (-11.45 = -10.57 +  -0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,077,501 – 2,077,557
Length 56
Sequences 3
Columns 57
Reading direction reverse
Mean pairwise identity 69.51
Shannon entropy 0.40276
G+C content 0.49857
Mean single sequence MFE -18.40
Consensus MFE -10.20
Energy contribution -11.53
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.70
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.18
SVM RNA-class probability 0.984906
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 2077501 56 - 2555491
UAGCGCUCUUCGCUCUCUCGC-UCUCUAACAAAAAUUCGAGAGAGCCUGGAGCCACC
..(.(((((..(((((((((.-...............)))))))))..))))))... ( -22.79, z-score =  -4.06, R)
>dp4.chrXL_group3b 66965 50 - 386183
UGGCUUUCCGAGCUCUCUCGUGGCUUUCAAAAAAGUUUCAGAGAGCCAAC-------
((((((((.(((....)))(..(((((....)))))..).))))))))..------- ( -16.20, z-score =  -2.02, R)
>droPer1.super_56 87537 50 - 431378
UGGCUUUCCGAGCUCUCUCGUGGCUUUCAAAAAAGUUUCAGAGAGCCAAC-------
((((((((.(((....)))(..(((((....)))))..).))))))))..------- ( -16.20, z-score =  -2.02, R)
>consensus
UGGCUUUCCGAGCUCUCUCGUGGCUUUCAAAAAAGUUUCAGAGAGCCAAC_______
...........(((((((...((((((....))))))..)))))))........... (-10.20 = -11.53 +   1.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:51:46 2011