Locus 8655

Sequence ID dm3.chr3R
Location 404,288 – 404,340
Length 52
Max. P 0.699736
window11883 window11884

overview

Window 3

Location 404,288 – 404,340
Length 52
Sequences 4
Columns 65
Reading direction forward
Mean pairwise identity 56.41
Shannon entropy 0.64672
G+C content 0.44231
Mean single sequence MFE -10.77
Consensus MFE -6.40
Energy contribution -5.77
Covariance contribution -0.63
Combinations/Pair 1.50
Mean z-score -0.25
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.550912
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 404288 52 + 27905053
UUGCGGCUUGCUGUUCCCAGCACCCAUGUCUGAGAAUAUUAUUUCCUUAUUU-------------
....((..((.(((((.(((((....)).))).))))).))...))......------------- (  -7.60, z-score =  -0.41, R)
>droPer1.super_3 4318049 52 - 7375914
CCGAGGCUGGCUACUUGUAGCACCCAUUUUGUAAUGUUUUUUUGCGAAACUU-------------
....((...((((....))))..)).((((((((.......))))))))...------------- ( -11.10, z-score =  -1.06, R)
>dp4.chr2 10487869 52 - 30794189
CCGAGGCUGGCUACUAGUAGCACCCAUUUUCUAAUGUUUUUUUGCGAAACUU-------------
....((...((((....))))..))..........(((((.....)))))..------------- (  -7.70, z-score =   0.29, R)
>droAna3.scaffold_13340 13314561 64 + 23697760
UUGCGGCUUGCUGUUGUUGGCACCCAUGGUGAAGCAU-UUGCUGGAUGAUUGUCCAGGACUUUGU
..((((....))))((((..((((...)))).)))).-...((((((....))))))........ ( -16.70, z-score =   0.19, R)
>consensus
CCGAGGCUGGCUACUAGUAGCACCCAUGUUGUAAUAUUUUUUUGCGAAACUU_____________
....((...((((....))))..))........................................ ( -6.40 =  -5.77 +  -0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 404,288 – 404,340
Length 52
Sequences 4
Columns 65
Reading direction reverse
Mean pairwise identity 56.41
Shannon entropy 0.64672
G+C content 0.44231
Mean single sequence MFE -9.35
Consensus MFE -6.62
Energy contribution -6.62
Covariance contribution 0.00
Combinations/Pair 1.22
Mean z-score -0.07
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.699736
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 404288 52 - 27905053
-------------AAAUAAGGAAAUAAUAUUCUCAGACAUGGGUGCUGGGAACAGCAAGCCGCAA
-------------......((..........((((....))))(((((....)))))..)).... ( -12.30, z-score =  -1.86, R)
>droPer1.super_3 4318049 52 + 7375914
-------------AAGUUUCGCAAAAAAACAUUACAAAAUGGGUGCUACAAGUAGCCAGCCUCGG
-------------..((((.......))))..........((((((((....))))..))))... (  -7.30, z-score =   0.20, R)
>dp4.chr2 10487869 52 + 30794189
-------------AAGUUUCGCAAAAAAACAUUAGAAAAUGGGUGCUACUAGUAGCCAGCCUCGG
-------------..((((.......))))....((...(((.(((.....))).)))...)).. (  -8.20, z-score =   0.15, R)
>droAna3.scaffold_13340 13314561 64 - 23697760
ACAAAGUCCUGGACAAUCAUCCAGCAA-AUGCUUCACCAUGGGUGCCAACAACAGCAAGCCGCAA
........(((((......)))))...-............((.(((........)))..)).... (  -9.60, z-score =   1.23, R)
>consensus
_____________AAAUUACGCAAAAAAACACUACAAAAUGGGUGCUACAAACAGCAAGCCGCAA
.......................................(((((((((....))))..))).)). ( -6.62 =  -6.62 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:49:39 2011