Locus 5309

Sequence ID dm3.chr2R
Location 19,381,735 – 19,381,789
Length 54
Max. P 0.657910
window7277 window7278

overview

Window 7

Location 19,381,735 – 19,381,789
Length 54
Sequences 5
Columns 58
Reading direction forward
Mean pairwise identity 67.43
Shannon entropy 0.58320
G+C content 0.50864
Mean single sequence MFE -13.44
Consensus MFE -5.94
Energy contribution -6.62
Covariance contribution 0.68
Combinations/Pair 1.29
Mean z-score -1.31
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.657910
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19381735 54 + 21146708
AGCAACUGCCGAAAAAUACAGCUCUCUGGAGACUCGUACAUUUGGCCC----CGCUAU
(((....((((((...((((((((....))).)).)))..))))))..----.))).. ( -13.80, z-score =  -1.84, R)
>droSim1.chr2R 17963306 54 + 19596830
AGCAACAGCCGAAAAAUACAGCUCUCCGGAGACUCGUACAUUUGGCCU----CGCUAA
(((....((((((...((((((((....))).)).)))..))))))..----.))).. ( -13.80, z-score =  -1.72, R)
>droSec1.super_9 2670664 54 + 3197100
AGCAACGGCCGAAAAAUACAGCUCUCUGGAGACUCGUACAUUUGGCCU----CGCUAG
(((...(((((((...((((((((....))).)).)))..))))))).----.))).. ( -17.50, z-score =  -2.68, R)
>droYak2.chr2R 19349716 58 + 21139217
AGCAACAGCCGAAAAAUACGGCUCUCUGGAGACUCGUACAUUUGGCUAGGUGCGCUGG
.(((..(((((((...((((..(((....)))..))))..)))))))...)))..... ( -19.40, z-score =  -2.01, R)
>droMoj3.scaffold_6496 12342582 51 + 26866924
-------UGAGAAAAUUACCAGCCACCAGUCACUUGUUUCGACGUCUAGCCAUGCCGU
-------..............((.....(((.........))).....))........ (  -2.70, z-score =   1.70, R)
>consensus
AGCAACAGCCGAAAAAUACAGCUCUCUGGAGACUCGUACAUUUGGCCA____CGCUAG
.......((((((...((((((((....))).)).)))..))))))............ ( -5.94 =  -6.62 +   0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 19,381,735 – 19,381,789
Length 54
Sequences 5
Columns 58
Reading direction reverse
Mean pairwise identity 67.43
Shannon entropy 0.58320
G+C content 0.50864
Mean single sequence MFE -15.80
Consensus MFE -6.46
Energy contribution -7.74
Covariance contribution 1.28
Combinations/Pair 1.40
Mean z-score -1.34
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.540442
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19381735 54 - 21146708
AUAGCG----GGGCCAAAUGUACGAGUCUCCAGAGAGCUGUAUUUUUCGGCAGUUGCU
..((((----(.((((((.((((.((.(((....))))))))).))).)))..))))) ( -15.40, z-score =  -0.98, R)
>droSim1.chr2R 17963306 54 - 19596830
UUAGCG----AGGCCAAAUGUACGAGUCUCCGGAGAGCUGUAUUUUUCGGCUGUUGCU
..((((----((((((((.((((.((.(((....))))))))).))).)))).))))) ( -16.70, z-score =  -1.31, R)
>droSec1.super_9 2670664 54 - 3197100
CUAGCG----AGGCCAAAUGUACGAGUCUCCAGAGAGCUGUAUUUUUCGGCCGUUGCU
..((((----((((((((.((((.((.(((....))))))))).))).)))).))))) ( -19.40, z-score =  -2.63, R)
>droYak2.chr2R 19349716 58 - 21139217
CCAGCGCACCUAGCCAAAUGUACGAGUCUCCAGAGAGCCGUAUUUUUCGGCUGUUGCU
.....(((..((((((((.(((((.(.(((....))))))))).))).))))).))). ( -17.80, z-score =  -2.28, R)
>droMoj3.scaffold_6496 12342582 51 - 26866924
ACGGCAUGGCUAGACGUCGAAACAAGUGACUGGUGGCUGGUAAUUUUCUCA-------
.((((...(((((.((.(.......))).))))).))))............------- (  -9.70, z-score =   0.51, R)
>consensus
AUAGCG____AGGCCAAAUGUACGAGUCUCCAGAGAGCUGUAUUUUUCGGCUGUUGCU
...........(((((((.(((((..(((....)))..))))).))).))))...... ( -6.46 =  -7.74 +   1.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:45:46 2011