Locus 9110

Sequence ID	dm3.chr3R
Location	4,181,714 – 4,181,844
Length	130
Max. P	0.955509

overview

Window 6

Location	4,181,714 – 4,181,818
Length	104
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	91.55
Shannon entropy	0.13854
G+C content	0.45870
Mean single sequence MFE	-24.48
Consensus MFE	-22.70
Energy contribution	-22.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.93
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.62
SVM RNA-class probability	0.955509
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 4181714 104 + 27905053
GUGAGAUUGAUAAACAAAGAGCGCCGCGCUGAUCGAUUCGCUUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAACACCAGCCAAUACAAAACUAUA-CUAU
(((...(((.....))).((((((((.((.((.....)))).))))..(((((....))))).....)))).......)))...................-.... ( -23.90, z-score =  -2.16, R)
>droSim1.chr3R 10434348 104 - 27517382
GUGAGAUUGAUAAACAAAGAGCGCCGCGCUGAUCGAUUCGCCUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAACACCAAGCGAUACAAUCCUAUA-AUAU
(((.(((((.........((((((((.((.((.....)))).))))..(((((....))))).....))))..........(....)...))))).))).-.... ( -25.00, z-score =  -2.02, R)
>droSec1.super_0 3473101 99 - 21120651
GUGAGAUUGAUAAACAAAGAGCGCCGCGCUGAUCGAUUCGCCUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAACACCAAGCGAUACAAUACUAU------
(((...(((.....))).((((((((.((.((.....)))).))))..(((((....))))).....)))).......)))..................------ ( -23.90, z-score =  -1.81, R)
>droEre2.scaffold_4770 358048 103 - 17746568
GUGCGAUUGAUAAACAAAGAGCGCCGCGCUGAUCGAUUCGCCUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAAC--CAAGCAAUACUAUACUAUUUAUAU
.(((..(((.....))).((((((((.((.((.....)))).))))..(((((....))))).....))))........--...))).................. ( -25.10, z-score =  -1.98, R)
>consensus
GUGAGAUUGAUAAACAAAGAGCGCCGCGCUGAUCGAUUCGCCUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAACACCAAGCAAUACAAUACUAUA_AUAU
..................((((((((.((.((.....)))).))))..(((((....))))).....)))).................................. (-22.70 = -22.70 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	4,181,754 – 4,181,844
Length	90
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	85.26
Shannon entropy	0.22848
G+C content	0.37268
Mean single sequence MFE	-13.29
Consensus MFE	-9.38
Energy contribution	-9.45
Covariance contribution	0.06
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.71
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.48
SVM RNA-class probability	0.713068
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 4181754 90 + 27905053
CUUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAACACCAGCCAAUACAAAACUA------UACUAUA-UAUAC---UCAGAUACAAAUAAAGCAAA
.(((((.....((((((...(((......))).))))))....)))))..........------.......-.....---.................... ( -11.40, z-score =  -1.56, R)
>droSim1.chr3R 10434388 90 - 27517382
CCUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAACACCAAGCGAUACAAUCCUA------UAAUAUA-UAUAC---UCAGAUACAAAUAAAGCACA
.((((...(((((....)))))....((((.............))))...........------.......-.....---))))................ ( -13.02, z-score =  -1.78, R)
>droSec1.super_0 3473141 85 - 21120651
CCUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAACACCAAGCGAUACAA-----------UACUAUA-UAUAC---UCAGAUACAAAUAAAGCAAA
.((((...(((((....)))))....((((.............))))......-----------.......-.....---))))................ ( -13.02, z-score =  -2.02, R)
>droEre2.scaffold_4770 358088 98 - 17746568
CCUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAAC--CAAGCAAUACUAUACUAUUUAUAUACUAUACUAUAUGAAUCAGAUACAAAAAAAGCACA
....((..(((((....))))).....(((.........--..))).........(((((((((((......))))))))).))...........))... ( -15.70, z-score =  -2.72, R)
>consensus
CCUGGCAACCCGUUUUAACGGGACAACGCUCCAUAAAACACCAAGCAAUACAAUACUA______UACUAUA_UAUAC___UCAGAUACAAAUAAAGCAAA
....((..(((((....))))).....(((.............))).................................................))... ( -9.38 =  -9.45 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:58:12 2011