Locus 5825

Sequence ID	dm3.chr3L
Location	1,579,408 – 1,579,507
Length	99
Max. P	0.880077

overview

Window 3

Location	1,579,408 – 1,579,507
Length	99
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	76.67
Shannon entropy	0.37697
G+C content	0.43038
Mean single sequence MFE	-24.90
Consensus MFE	-13.45
Energy contribution	-15.33
Covariance contribution	1.88
Combinations/Pair	1.11
Mean z-score	-2.24
Structure conservation index	0.54
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.04
SVM RNA-class probability	0.880077
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1579408 99 + 24543557
AUUACUUAUACGCUAGCACUGUGAAAAGAAA--ACCCACGCACAAAACCCAAAAUAAGCGGAGAUAAGCUGUUGGGCAACCAAAAUAUCGUUUGCAGGCAG
...............((.(((..((......--.....(((................)))..((((.....((((....))))..)))).))..))))).. ( -20.09, z-score =  -0.63, R)
>droSim1.chr3L 1162151 99 + 22553184
AUUACUUA--CGCUAGCACUGUGAAUGGAAACCAUCCACUCACAAAACCCAAAAUAAGCAGAGAUAAGCUCUUGGGCAACCAAAAUAUCGUUUGCAGGCAG
........--.(((.((..(((((.((((.....)))).)))))...........((((.(((.....)))((((....))))......)))))).))).. ( -26.30, z-score =  -3.22, R)
>droSec1.super_2 1605831 99 + 7591821
AUUACUUA--CGCUAGCACUGUGAAUGGAAACCAUCCACUCACAAAGCCCAAAAUAAGCGGAGAUAAGCUCUUGGGCAACCAAAAUAUCGUUUGCAGGCAG
........--.(((.(((.(((((.((((.....)))).)))))..((((((....(((........))).))))))...............))).))).. ( -29.80, z-score =  -3.43, R)
>droYak2.chr3L 1529772 84 + 24197627
-----------------AUUGCCUAUGCUGGCAGCACCCACAAAAUACAUAAUAUAAGAGGAGAUAAGCUCUUGGGCAACCAAAAUAUCGGUUGCAGGCAA
-----------------.((((((.(((.....)))..................((((((........)))))).((((((........)))))))))))) ( -23.40, z-score =  -1.68, R)
>consensus
AUUACUUA__CGCUAGCACUGUGAAUGGAAACCACCCACUCACAAAACCCAAAAUAAGCGGAGAUAAGCUCUUGGGCAACCAAAAUAUCGUUUGCAGGCAG
...............((.((((((((((............................(((........))).((((....))))....)))))))))))).. (-13.45 = -15.33 +   1.88)

alignment

secondary structure

dotplot

Window 4

Location	1,579,408 – 1,579,507
Length	99
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	76.67
Shannon entropy	0.37697
G+C content	0.43038
Mean single sequence MFE	-27.62
Consensus MFE	-17.05
Energy contribution	-19.05
Covariance contribution	2.00
Combinations/Pair	1.27
Mean z-score	-1.64
Structure conservation index	0.62
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.45
SVM RNA-class probability	0.702048
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1579408 99 - 24543557
CUGCCUGCAAACGAUAUUUUGGUUGCCCAACAGCUUAUCUCCGCUUAUUUUGGGUUUUGUGCGUGGGU--UUUCUUUUCACAGUGCUAGCGUAUAAGUAAU
.....(((................((((((.(((........)))....)))))).((((((((.(((--...((......)).))).))))))))))).. ( -19.60, z-score =   0.95, R)
>droSim1.chr3L 1162151 99 - 22553184
CUGCCUGCAAACGAUAUUUUGGUUGCCCAAGAGCUUAUCUCUGCUUAUUUUGGGUUUUGUGAGUGGAUGGUUUCCAUUCACAGUGCUAGCG--UAAGUAAU
..((..(((...............((((((((((........))))...)))))).(((((((((((.....))))))))))))))..)).--........ ( -32.10, z-score =  -2.81, R)
>droSec1.super_2 1605831 99 - 7591821
CUGCCUGCAAACGAUAUUUUGGUUGCCCAAGAGCUUAUCUCCGCUUAUUUUGGGCUUUGUGAGUGGAUGGUUUCCAUUCACAGUGCUAGCG--UAAGUAAU
..((..(((...............((((((((((........))))...)))))).(((((((((((.....))))))))))))))..)).--........ ( -33.80, z-score =  -2.99, R)
>droYak2.chr3L 1529772 84 - 24197627
UUGCCUGCAACCGAUAUUUUGGUUGCCCAAGAGCUUAUCUCCUCUUAUAUUAUGUAUUUUGUGGGUGCUGCCAGCAUAGGCAAU-----------------
((((((((((((((....))))))))..(((((........))))).............(((.((.....)).))).)))))).----------------- ( -25.00, z-score =  -1.71, R)
>consensus
CUGCCUGCAAACGAUAUUUUGGUUGCCCAAGAGCUUAUCUCCGCUUAUUUUGGGUUUUGUGAGUGGAUGGUUUCCAUUCACAGUGCUAGCG__UAAGUAAU
..((..(((...............((((((((((........))))...)))))).(((((((((((.....))))))))))))))..))........... (-17.05 = -19.05 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:55:56 2011