Locus 8815

Sequence ID	dm3.chr3R
Location	1,835,885 – 1,835,989
Length	104
Max. P	0.965919

overview

Window 3

Location	1,835,885 – 1,835,989
Length	104
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	76.33
Shannon entropy	0.32302
G+C content	0.35340
Mean single sequence MFE	-25.57
Consensus MFE	-16.19
Energy contribution	-16.63
Covariance contribution	0.45
Combinations/Pair	1.05
Mean z-score	-1.74
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.19
SVM RNA-class probability	0.586346
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1835885 104 + 27905053
-AAAUAUAUAAGUGUGAUCACCAAGUGACCGCAUUAGCAAGCAGUAAAGGCACUGCUUUAUCUAGCAGUG---------UUAUACAGGUGCAUAUGAGA-UGGCAAUACUUUAAA
-........((((((..((((((.((((((((....)).....(((..(((((((((......)))))))---------)).))).))).))).)).).-)))..)))))).... ( -27.90, z-score =  -1.59, R)
>droSec1.super_6 1945189 108 + 4358794
AAAAUGCAUAAGUGUAAUCACCAAGUGACCGCAUUAG-------AGAAGACACUGCUUUAUUAAGCAGUGAAUUGACUGCUGUAACGGUGGACAUGAGACUUAUAAUAUUUUAAA
((((((.((((((.(..(((((..((.((.(((...(-------(.....((((((((....))))))))..))...))).)).))))))).....).))))))..))))))... ( -25.10, z-score =  -2.04, R)
>droSim1.chr3R 1869993 108 + 27517382
AAGAUGCAUAAGUGUAAUCACCAAGUGACCGCAUUAG-------UGAAAACACUACUUUAUUAAGCAGUGAAUUGACUGCUGUAACGGUGCACAUGAGAUUAAUAAUAUUUUAAA
....(((((.(((((..((((..((((....)))).)-------)))..))))).........((((((......))))))......)))))..((((((.......)))))).. ( -23.70, z-score =  -1.60, R)
>consensus
AAAAUGCAUAAGUGUAAUCACCAAGUGACCGCAUUAG_______UGAAGACACUGCUUUAUUAAGCAGUGAAUUGACUGCUGUAACGGUGCACAUGAGA_UAAUAAUAUUUUAAA
...........((((...((((.((((....))))...............((((((((....))))))))................)))).)))).................... (-16.19 = -16.63 +   0.45)

alignment

secondary structure

dotplot

Window 4

Location	1,835,885 – 1,835,989
Length	104
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	76.33
Shannon entropy	0.32302
G+C content	0.35340
Mean single sequence MFE	-25.71
Consensus MFE	-15.54
Energy contribution	-14.77
Covariance contribution	-0.77
Combinations/Pair	1.20
Mean z-score	-2.68
Structure conservation index	0.60
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.76
SVM RNA-class probability	0.965919
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1835885 104 - 27905053
UUUAAAGUAUUGCCA-UCUCAUAUGCACCUGUAUAA---------CACUGCUAGAUAAAGCAGUGCCUUUACUGCUUGCUAAUGCGGUCACUUGGUGAUCACACUUAUAUAUUU-
......((((..(((-.....(((((....))))).---------.((((((((...((((((((....)))))))).)))..)))))....)))..)).))............- ( -26.70, z-score =  -2.20, R)
>droSec1.super_6 1945189 108 - 4358794
UUUAAAAUAUUAUAAGUCUCAUGUCCACCGUUACAGCAGUCAAUUCACUGCUUAAUAAAGCAGUGUCUUCU-------CUAAUGCGGUCACUUGGUGAUUACACUUAUGCAUUUU
..........(((((((.....(((.((((..((.(((.......((((((((....))))))))......-------....))).))....)))))))...)))))))...... ( -23.73, z-score =  -2.60, R)
>droSim1.chr3R 1869993 108 - 27517382
UUUAAAAUAUUAUUAAUCUCAUGUGCACCGUUACAGCAGUCAAUUCACUGCUUAAUAAAGUAGUGUUUUCA-------CUAAUGCGGUCACUUGGUGAUUACACUUAUGCAUCUU
.............((((((((.(((.(((((......(((.((..((((((((....))))))))..)).)-------))...)))))))).))).))))).............. ( -26.70, z-score =  -3.24, R)
>consensus
UUUAAAAUAUUAUAA_UCUCAUGUGCACCGUUACAGCAGUCAAUUCACUGCUUAAUAAAGCAGUGUCUUCA_______CUAAUGCGGUCACUUGGUGAUUACACUUAUGCAUUUU
....................((((.....................((((((((....)))))))).................((.((((((...)))))).)).....))))... (-15.54 = -14.77 +  -0.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:52:43 2011