Locus 5590

Sequence ID dm3.chr3LHet
Location 1,556,428 – 1,556,512
Length 84
Max. P 0.813574
window7678 window7679

overview

Window 8

Location 1,556,428 – 1,556,512
Length 84
Sequences 3
Columns 85
Reading direction forward
Mean pairwise identity 67.20
Shannon entropy 0.44294
G+C content 0.53373
Mean single sequence MFE -28.50
Consensus MFE -14.03
Energy contribution -12.93
Covariance contribution -1.10
Combinations/Pair 1.35
Mean z-score -1.92
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.781178
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 1556428 84 + 2555491
GGCUCUCUAGAAUUUUUGUUAGAGA-GCGAGAGAGCGAAGAGCGCUACAGCGAACAGCUCUUUUCAACGCACAAAGUGAUAGCAG
.(((((((((........)))))))-))((((((((......(((....)))....))))))))...(((.....)))....... ( -27.90, z-score =  -1.97, R)
>dp4.chrXL_group3b 66968 80 + 386183
GGCUCUCUGAAACUUUUUUGAAAGCCACGAGAGAGCUCGGAAAGCCACCGCGCUCUCACGCUGU--GUACAUGAGGCAGCCG---
((((.((.(((....))).)).))))....((((((.(((.......))).))))))..(((((--.(.....).)))))..--- ( -28.80, z-score =  -1.90, R)
>droPer1.super_56 87540 80 + 431378
GGCUCUCUGAAACUUUUUUGAAAGCCACGAGAGAGCUCGGAAAGCCACCGCGCUCUCACGCUGU--GUACAUGAGGCAGCCG---
((((.((.(((....))).)).))))....((((((.(((.......))).))))))..(((((--.(.....).)))))..--- ( -28.80, z-score =  -1.90, R)
>consensus
GGCUCUCUGAAACUUUUUUGAAAGCCACGAGAGAGCUCGGAAAGCCACCGCGCUCUCACGCUGU__GUACAUGAGGCAGCCG___
.(((((((....((((....)))).....))))))).......(((...(((......)))(((....)))...)))........ (-14.03 = -12.93 +  -1.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 1,556,428 – 1,556,512
Length 84
Sequences 3
Columns 85
Reading direction reverse
Mean pairwise identity 67.20
Shannon entropy 0.44294
G+C content 0.53373
Mean single sequence MFE -28.17
Consensus MFE -16.25
Energy contribution -18.03
Covariance contribution 1.79
Combinations/Pair 1.19
Mean z-score -1.61
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.813574
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 1556428 84 - 2555491
CUGCUAUCACUUUGUGCGUUGAAAAGAGCUGUUCGCUGUAGCGCUCUUCGCUCUCUCGC-UCUCUAACAAAAAUUCUAGAGAGCC
..((...........))...((..(((((.(..(((....)))..)...))))).))((-((((((..........)))))))). ( -21.30, z-score =  -0.76, R)
>dp4.chrXL_group3b 66968 80 - 386183
---CGGCUGCCUCAUGUAC--ACAGCGUGAGAGCGCGGUGGCUUUCCGAGCUCUCUCGUGGCUUUCAAAAAAGUUUCAGAGAGCC
---.(((..((...((...--.))((((....))))))..)))......(((((((.(..(((((....)))))..)))))))). ( -31.60, z-score =  -2.04, R)
>droPer1.super_56 87540 80 - 431378
---CGGCUGCCUCAUGUAC--ACAGCGUGAGAGCGCGGUGGCUUUCCGAGCUCUCUCGUGGCUUUCAAAAAAGUUUCAGAGAGCC
---.(((..((...((...--.))((((....))))))..)))......(((((((.(..(((((....)))))..)))))))). ( -31.60, z-score =  -2.04, R)
>consensus
___CGGCUGCCUCAUGUAC__ACAGCGUGAGAGCGCGGUGGCUUUCCGAGCUCUCUCGUGGCUUUCAAAAAAGUUUCAGAGAGCC
....(((((((...((......))((((....)))))))))))......(((((((.(..(((((....)))))..)))))))). (-16.25 = -18.03 +   1.79)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

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