Locus 2908

Sequence ID dm3.chr2RHet
Location 1,940,365 – 1,940,419
Length 54
Max. P 0.943837
window4002 window4003

overview

Window 2

Location 1,940,365 – 1,940,419
Length 54
Sequences 4
Columns 57
Reading direction forward
Mean pairwise identity 68.17
Shannon entropy 0.51819
G+C content 0.36606
Mean single sequence MFE -5.25
Consensus MFE -4.47
Energy contribution -4.72
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -0.79
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.904042
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 1940365 54 + 3288761
AAAGCUUAUAUAACGAAACUCCGGCACUUAGCCGU--UAAACCUUUUUAUUACAAA-
.....................((((.....)))).--...................- (  -5.90, z-score =  -0.80, R)
>droSim1.chr2R_random 2685591 53 - 2996586
CAAGCUCAUAAAUCGAAACUCCAGCGAUUCGCCGU--U--AUCUUCUUAUUAUCACG
.(((...((((..((((.(......).))))...)--)--))...)))......... (  -2.80, z-score =   0.52, R)
>droYak2.chrU 1939929 54 + 28119190
CAAGCUCAUAUAACGAAACUCCGGCACUUAGCCGU--UAAACCUUUUUAUUACAAA-
.....................((((.....)))).--...................- (  -5.90, z-score =  -1.11, R)
>droWil1.scaffold_181155 227040 55 - 3442787
AACAAUAAAGAAGCAUAACUCCGGCACUUAGCCGAAAUACAAUUUAUCAUCUCUA--
.....................((((.....)))).....................-- (  -6.40, z-score =  -1.76, R)
>consensus
AAAGCUCAUAAAACGAAACUCCGGCACUUAGCCGU__UAAACCUUUUUAUUACAAA_
.....................((((.....))))....................... ( -4.47 =  -4.72 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 1,940,365 – 1,940,419
Length 54
Sequences 4
Columns 57
Reading direction reverse
Mean pairwise identity 68.17
Shannon entropy 0.51819
G+C content 0.36606
Mean single sequence MFE -11.23
Consensus MFE -8.07
Energy contribution -7.70
Covariance contribution -0.37
Combinations/Pair 1.40
Mean z-score -1.20
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.49
SVM RNA-class probability 0.943837
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 1940365 54 - 3288761
-UUUGUAAUAAAAAGGUUUA--ACGGCUAAGUGCCGGAGUUUCGUUAUAUAAGCUUU
-...........((((((((--.((((.....))))(.....)......)))))))) ( -10.20, z-score =  -0.84, R)
>droSim1.chr2R_random 2685591 53 + 2996586
CGUGAUAAUAAGAAGAU--A--ACGGCGAAUCGCUGGAGUUUCGAUUUAUGAGCUUG
.((.((((...((((..--.--.(((((...)))))...))))...))))..))... ( -10.40, z-score =  -0.75, R)
>droYak2.chrU 1939929 54 - 28119190
-UUUGUAAUAAAAAGGUUUA--ACGGCUAAGUGCCGGAGUUUCGUUAUAUGAGCUUG
-...................--.((((.....))))((((((........)))))). ( -10.10, z-score =  -0.69, R)
>droWil1.scaffold_181155 227040 55 + 3442787
--UAGAGAUGAUAAAUUGUAUUUCGGCUAAGUGCCGGAGUUAUGCUUCUUUAUUGUU
--....((..(((((..((((((((((.....))))))...))))...)))))..)) ( -14.20, z-score =  -2.54, R)
>consensus
_UUUGUAAUAAAAAGGUUUA__ACGGCUAAGUGCCGGAGUUUCGUUAUAUGAGCUUG
.......................((((.....))))((((((........)))))). ( -8.07 =  -7.70 +  -0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:00:12 2011