Locus 12141

Sequence ID	dm3.chr3R
Location	26,025,417 – 26,025,536
Length	119
Max. P	0.998295

overview

Window 4

Location	26,025,417 – 26,025,520
Length	103
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	81.55
Shannon entropy	0.30490
G+C content	0.30725
Mean single sequence MFE	-18.87
Consensus MFE	-10.77
Energy contribution	-13.84
Covariance contribution	3.06
Combinations/Pair	1.19
Mean z-score	-3.19
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.27
SVM RNA-class probability	0.987157
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26025417 103 + 27905053
GCCCAUAAUUAGUUUCGUACUCACAUUUAGGCAAUAACAAACAUAAAAUGGCUGUAAUUUAUAACAUUUACACUUCCUCAUUUUAUGUUUGUAGUUAUCUCAU
(((.......(((.....)))........)))(((.(((((((((((((((.(((((..........))))).....))))))))))))))).)))....... ( -20.76, z-score =  -4.03, R)
>droEre2.scaffold_4820 8497433 92 - 10470090
GCCCAGAAUUAGUGUGGUACUCACAUA-AAGCAAUUAUAAAUAUAAAAUUGCCGUCAUUUAUUACAUUUACACUUC----------GUCCAUAGUUAUCACAC
...........((((((((........-..((((((.((....)).))))))...................(((..----------......))))))))))) ( -11.70, z-score =  -0.85, R)
>droSec1.super_4 4877887 103 + 6179234
GCCCAUAAUUAGUUUCGUACUCACAUUUAGGCAAACACAAACAUAAAAUAGCUGUAAUUUAUAACAUUUACAAUUCGUUAUUUUAUGUUUGCAGCUAACACAU
(((.......(((.....)))........))).....((((((((((((((((((((..........)))))....)))))))))))))))............ ( -20.46, z-score =  -3.71, R)
>droSim1.chr3R 25693219 103 + 27517382
GCCCAUAAUAAGUUUCGUACUCACAUUUAGGCAAUCACAAACAUAAAAUGGCUGUAAUUUAUAACAUUUACACUUCGCUAUUUUAUGUUUGCAGCUAUCACAU
(((.......(((.....)))........))).....((((((((((((((((((((..........)))))....)))))))))))))))............ ( -22.56, z-score =  -4.17, R)
>consensus
GCCCAUAAUUAGUUUCGUACUCACAUUUAGGCAAUCACAAACAUAAAAUGGCUGUAAUUUAUAACAUUUACACUUCGUUAUUUUAUGUUUGCAGCUAUCACAU
(((.......(((.....)))........))).....((((((((((((((((((((..........)))))....)))))))))))))))............ (-10.77 = -13.84 +   3.06)

alignment

secondary structure

dotplot

Window 5

Location	26,025,433 – 26,025,536
Length	103
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	80.91
Shannon entropy	0.30966
G+C content	0.26714
Mean single sequence MFE	-17.47
Consensus MFE	-12.75
Energy contribution	-14.25
Covariance contribution	1.50
Combinations/Pair	1.15
Mean z-score	-3.48
Structure conservation index	0.73
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.31
SVM RNA-class probability	0.998295
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26025433 103 + 27905053
GUACUCACAUUUAGGCAAUAACAAACAUAAAAUGGCUGUAAUUUAUAACAUUUACACUUCCUCAUUUUAUGUUUGUAGUUAUCUCAUUUAUAUUUUCAAAACC
............((..(((.(((((((((((((((.(((((..........))))).....))))))))))))))).)))..))................... ( -19.00, z-score =  -3.94, R)
>droYak2.chr3R 26959209 83 + 28832112
--------AUUUAAGAAAUCACAAACAUAAAAUG---------CAUUAUAUUUACACUUCGCUAUUUUAUGUUUGAAGUUAUCACAUUUAUAU---CGAAGCC
--------......(((((..(((((((((((((---------(................)).))))))))))))..))).))..........---....... ( -12.59, z-score =  -2.18, R)
>droSec1.super_4 4877903 103 + 6179234
GUACUCACAUUUAGGCAAACACAAACAUAAAAUAGCUGUAAUUUAUAACAUUUACAAUUCGUUAUUUUAUGUUUGCAGCUAACACAUUUAUAUUUUCAAAACC
.............(((.....((((((((((((((((((((..........)))))....)))))))))))))))..)))....................... ( -18.10, z-score =  -3.59, R)
>droSim1.chr3R 25693235 103 + 27517382
GUACUCACAUUUAGGCAAUCACAAACAUAAAAUGGCUGUAAUUUAUAACAUUUACACUUCGCUAUUUUAUGUUUGCAGCUAUCACAUUUAUAUUUUCAAAACC
.............(((.....((((((((((((((((((((..........)))))....)))))))))))))))..)))....................... ( -20.20, z-score =  -4.24, R)
>consensus
GUACUCACAUUUAGGCAAUCACAAACAUAAAAUGGCUGUAAUUUAUAACAUUUACACUUCGCUAUUUUAUGUUUGCAGCUAUCACAUUUAUAUUUUCAAAACC
.....................((((((((((((((((((((..........)))))....)))))))))))))))............................ (-12.75 = -14.25 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:56:33 2011