Locus 3132

Sequence ID dm3.chr2R
Location 2,795,476 – 2,795,538
Length 62
Max. P 0.993463
window4305 window4306

overview

Window 5

Location 2,795,476 – 2,795,538
Length 62
Sequences 3
Columns 62
Reading direction forward
Mean pairwise identity 84.27
Shannon entropy 0.20736
G+C content 0.68062
Mean single sequence MFE -29.63
Consensus MFE -26.34
Energy contribution -26.57
Covariance contribution 0.23
Combinations/Pair 1.11
Mean z-score -2.77
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.62
SVM RNA-class probability 0.993463
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2795476 62 + 21146708
UCCCGGCCACCUUGGGUGCAGUGUCCAGACGGUCAGGCGGCCAGGCGACCAGGUGGCCAAAU
....((((((((.((.(((...((....))((((....))))..))).)))))))))).... ( -28.80, z-score =  -1.55, R)
>droSec1.super_1 477811 54 + 14215200
UCCCGGCCACCUUGGGUGCAGUGUCCAGACGGUCAAGCGGCCAGGUGGCCAGGU--------
.((.((((((((.((.(((..((.((....)).)).))).)))))))))).)).-------- ( -30.30, z-score =  -3.33, R)
>droSim1.chr2R 1609031 53 + 19596830
UCCCGGCCACCUUGGGUGCAGUGUCCAGACGGUCAGGCAGCCAGGUGGCUAGG---------
.((..(((((((.((.(((..((.((....)).)).))).)))))))))..))--------- ( -29.80, z-score =  -3.44, R)
>consensus
UCCCGGCCACCUUGGGUGCAGUGUCCAGACGGUCAGGCGGCCAGGUGGCCAGGU________
.((.((((((((.((.(((..((.((....)).)).))).)))))))))).))......... (-26.34 = -26.57 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 2,795,476 – 2,795,538
Length 62
Sequences 3
Columns 62
Reading direction reverse
Mean pairwise identity 84.27
Shannon entropy 0.20736
G+C content 0.68062
Mean single sequence MFE -27.50
Consensus MFE -26.17
Energy contribution -26.07
Covariance contribution -0.11
Combinations/Pair 1.11
Mean z-score -2.42
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.53
SVM RNA-class probability 0.992270
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2795476 62 - 21146708
AUUUGGCCACCUGGUCGCCUGGCCGCCUGACCGUCUGGACACUGCACCCAAGGUGGCCGGGA
....((((....)))).(((((((((((.......(((.........)))))))))))))). ( -27.51, z-score =  -1.23, R)
>droSec1.super_1 477811 54 - 14215200
--------ACCUGGCCACCUGGCCGCUUGACCGUCUGGACACUGCACCCAAGGUGGCCGGGA
--------.(((((((((((((..((.((.((....)).))..))..)).))))))))))). ( -29.60, z-score =  -3.54, R)
>droSim1.chr2R 1609031 53 - 19596830
---------CCUAGCCACCUGGCUGCCUGACCGUCUGGACACUGCACCCAAGGUGGCCGGGA
---------((..(((((((((.(((.((.((....)).))..))).)).)))))))..)). ( -25.40, z-score =  -2.49, R)
>consensus
________ACCUGGCCACCUGGCCGCCUGACCGUCUGGACACUGCACCCAAGGUGGCCGGGA
.........(((((((((((((..((.((.((....)).))..))..)).))))))))))). (-26.17 = -26.07 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:04:20 2011