Locus 779

Sequence ID	dm3.chr2L
Location	5,519,909 – 5,519,987
Length	78
Max. P	0.845050

overview

Window 9

Location	5,519,909 – 5,519,987
Length	78
Sequences	5
Columns	78
Reading direction	forward
Mean pairwise identity	72.68
Shannon entropy	0.49664
G+C content	0.40642
Mean single sequence MFE	-16.63
Consensus MFE	-9.48
Energy contribution	-10.84
Covariance contribution	1.36
Combinations/Pair	1.18
Mean z-score	-1.43
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.89
SVM RNA-class probability	0.845050
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5519909 78 + 23011544
CACAUUUUCACCAAUUAGCGGGUUAUCGGGCUAUUCCCGCUAAAAUGGCUAUAGCCAGCUAGAAUGGCGUUUUUAUUA
..((((((......((((((((.............))))))))..((((....))))...))))))............ ( -20.52, z-score =  -1.43, R)
>droEre2.scaffold_4929 5606040 78 + 26641161
CACGUUUUCAUCCAUUAGCGGAUUAUCGAGCCAUUCCCGCUAAAAUAGCUAUAGCCAGCUAUAAUGGUGGGUUCAUUA
...((((..((((......))))....))))....(((((((..((((((......))))))..)))))))....... ( -20.40, z-score =  -2.11, R)
>droYak2.chr2L 8649445 62 - 22324452
CACAUGUUUAUUACGUAGCGUGAUAUCGAGCCAUUUCCACUAAAAUAGUUAUAGCCAAAGGU----------------
..((((((........))))))......(((.((((......)))).)))............---------------- (  -5.10, z-score =   1.12, R)
>droSec1.super_5 3598413 74 + 5866729
CACAUUUUCACCAAUUAGCGGGUUAUCGAGCUAUUCCCGAUAAAAUGGCAAUAGCCAGCUAGAAUACUGUUAUU----
..............(((((.((((((...((((((........)))))).)))))).)))))............---- ( -16.10, z-score =  -1.83, R)
>droSim1.chr2L 5322593 78 + 22036055
CAUAUUUUCACCAAUUAGCGGGUUAUCGAGCUAUUCCCGCUAAAAUGGCUAUAGCCAGCUAGAAUGGUCACAUCAUUC
.........((((.((((((((.............))))))))..((((....)))).......)))).......... ( -21.02, z-score =  -2.89, R)
>consensus
CACAUUUUCACCAAUUAGCGGGUUAUCGAGCUAUUCCCGCUAAAAUGGCUAUAGCCAGCUAGAAUGGUGUUAUCAUU_
...............((((.((((((..(((((((........))))))))))))).))))................. ( -9.48 = -10.84 +   1.36)

alignment

secondary structure

dotplot

Window 0

Location	5,519,909 – 5,519,987
Length	78
Sequences	5
Columns	78
Reading direction	reverse
Mean pairwise identity	72.68
Shannon entropy	0.49664
G+C content	0.40642
Mean single sequence MFE	-17.59
Consensus MFE	-10.10
Energy contribution	-10.58
Covariance contribution	0.48
Combinations/Pair	1.25
Mean z-score	-1.43
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.89
SVM RNA-class probability	0.845050
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5519909 78 - 23011544
UAAUAAAAACGCCAUUCUAGCUGGCUAUAGCCAUUUUAGCGGGAAUAGCCCGAUAACCCGCUAAUUGGUGAAAAUGUG
.........(((((.......((((....))))..((((((((.............)))))))).)))))........ ( -23.02, z-score =  -2.63, R)
>droEre2.scaffold_4929 5606040 78 - 26641161
UAAUGAACCCACCAUUAUAGCUGGCUAUAGCUAUUUUAGCGGGAAUGGCUCGAUAAUCCGCUAAUGGAUGAAAACGUG
.........((((((..((((.(..((((((((((((....)))))))))..)))..).)))))))).))........ ( -17.80, z-score =  -0.98, R)
>droYak2.chr2L 8649445 62 + 22324452
----------------ACCUUUGGCUAUAACUAUUUUAGUGGAAAUGGCUCGAUAUCACGCUACGUAAUAAACAUGUG
----------------....((((((((..((((....))))..))))).)))(((.(((...))).)))........ (  -7.70, z-score =   0.37, R)
>droSec1.super_5 3598413 74 - 5866729
----AAUAACAGUAUUCUAGCUGGCUAUUGCCAUUUUAUCGGGAAUAGCUCGAUAACCCGCUAAUUGGUGAAAAUGUG
----.....((.((...((((((((....))))..((((((((.....))))))))...))))..)).))........ ( -18.80, z-score =  -1.97, R)
>droSim1.chr2L 5322593 78 - 22036055
GAAUGAUGUGACCAUUCUAGCUGGCUAUAGCCAUUUUAGCGGGAAUAGCUCGAUAACCCGCUAAUUGGUGAAAAUAUG
........(.((((.......((((....))))..((((((((.............)))))))).)))).)....... ( -20.62, z-score =  -1.93, R)
>consensus
_AAUAAAAACACCAUUCUAGCUGGCUAUAGCCAUUUUAGCGGGAAUAGCUCGAUAACCCGCUAAUUGGUGAAAAUGUG
.....................((((....))))..((((((((.............)))))))).............. (-10.10 = -10.58 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:19:17 2011