Locus 3038

Sequence ID dm3.chr2R
Location 1,718,869 – 1,718,963
Length 94
Max. P 0.789913
window4167 window4168

overview

Window 7

Location 1,718,869 – 1,718,963
Length 94
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 71.04
Shannon entropy 0.48022
G+C content 0.48705
Mean single sequence MFE -26.12
Consensus MFE -12.97
Energy contribution -13.17
Covariance contribution 0.20
Combinations/Pair 1.35
Mean z-score -1.70
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.70
SVM RNA-class probability 0.789913
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1718869 94 + 21146708
--------UUUCACUGUGUUCUUUCUCGGUCGGG-----GCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUCAAGCGUCAACUUUACCGGUCUCUACCCGCGCCGA-
--------.................(((((((((-----(((((...((((((.........))))))....)))))....(((.....))).....)))).)))))- ( -21.00, z-score =  -0.83, R)
>droAna3.scaffold_13266 819746 90 - 19884421
--------CUUCAGUGGGCCCUUCUUUGAUUUGG------UUUGCUUUGCUUUAUUACACUUAAAUUGU--UCAAGAGCUGGCAUCGGCGUCCUGGGCCCAC--UGAA
--------..(((((((((((......(((.(.(------..((((..(((((...(((.......)))--...))))).)))).).).)))..))))))))--))). ( -34.40, z-score =  -4.04, R)
>droEre2.scaffold_4929 6017819 105 - 26641161
UUUCACUGGGUUCUCGGGUUCUUUCCCGGCCGGGCCGGGGCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUGAAGCGUCAACUUUACCGGUCUCUACCCGC--CGA-
.......((((....(((......)))(((((((((((((....))))))).....((..(((((....))))).))..........))))))...))))..--...- ( -33.30, z-score =  -0.99, R)
>droYak2.chr2L 1506628 92 - 22324452
--------UCUUACUGGGUUCUAUCUCGGUCGUG-----GCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUCAAGCGUCAACUUAACCGGUCUCUACCCGC--CGA-
--------.......((((.....(.((((.((.-----(((((...((((((.........))))))....)))))....))...))))).....))))..--...- ( -18.50, z-score =  -0.49, R)
>droSec1.super_26 375646 92 + 826190
--------UUUCACUGGGUUCCUUCUCGGUCGGC-----GCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUCAAGCGUCAACUUUACCGGUCCCUACCCCA--CGA-
--------......((((..((.....(((.(((-----(((((...((((((.........))))))....)))))))).))).....))..)))).....--...- ( -23.40, z-score =  -2.13, R)
>consensus
________UUUCACUGGGUUCUUUCUCGGUCGGG_____GCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUCAAGCGUCAACUUUACCGGUCUCUACCCGC__CGA_
...............((((......(((((.........(((((...((((((.........))))))....))))).........))))).....))))........ (-12.97 = -13.17 +   0.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 8

Location 1,718,869 – 1,718,963
Length 94
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 71.04
Shannon entropy 0.48022
G+C content 0.48705
Mean single sequence MFE -26.12
Consensus MFE -12.97
Energy contribution -13.17
Covariance contribution 0.20
Combinations/Pair 1.35
Mean z-score -1.70
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.70
SVM RNA-class probability 0.789913
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1718869 94 + 21146708
--------UUUCACUGUGUUCUUUCUCGGUCGGG-----GCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUCAAGCGUCAACUUUACCGGUCUCUACCCGCGCCGA-
--------.................(((((((((-----(((((...((((((.........))))))....)))))....(((.....))).....)))).)))))- ( -21.00, z-score =  -0.83, R)
>droAna3.scaffold_13266 819746 90 - 19884421
--------CUUCAGUGGGCCCUUCUUUGAUUUGG------UUUGCUUUGCUUUAUUACACUUAAAUUGU--UCAAGAGCUGGCAUCGGCGUCCUGGGCCCAC--UGAA
--------..(((((((((((......(((.(.(------..((((..(((((...(((.......)))--...))))).)))).).).)))..))))))))--))). ( -34.40, z-score =  -4.04, R)
>droEre2.scaffold_4929 6017819 105 - 26641161
UUUCACUGGGUUCUCGGGUUCUUUCCCGGCCGGGCCGGGGCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUGAAGCGUCAACUUUACCGGUCUCUACCCGC--CGA-
.......((((....(((......)))(((((((((((((....))))))).....((..(((((....))))).))..........))))))...))))..--...- ( -33.30, z-score =  -0.99, R)
>droYak2.chr2L 1506628 92 - 22324452
--------UCUUACUGGGUUCUAUCUCGGUCGUG-----GCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUCAAGCGUCAACUUAACCGGUCUCUACCCGC--CGA-
--------.......((((.....(.((((.((.-----(((((...((((((.........))))))....)))))....))...))))).....))))..--...- ( -18.50, z-score =  -0.49, R)
>droSec1.super_26 375646 92 + 826190
--------UUUCACUGGGUUCCUUCUCGGUCGGC-----GCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUCAAGCGUCAACUUUACCGGUCCCUACCCCA--CGA-
--------......((((..((.....(((.(((-----(((((...((((((.........))))))....)))))))).))).....))..)))).....--...- ( -23.40, z-score =  -2.13, R)
>consensus
________UUUCACUGGGUUCUUUCUCGGUCGGG_____GCUUGCUUUGGUUUAAAGCACUCAAAUCAUUUUCAAGCGUCAACUUUACCGGUCUCUACCCGC__CGA_
...............((((......(((((.........(((((...((((((.........))))))....))))).........))))).....))))........ (-12.97 = -13.17 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:02:28 2011