Locus 15804

Sequence ID	dm3.chrX
Location	21,174,229 – 21,174,463
Length	234
Max. P	0.646639

overview

Window 1

Location	21,174,229 – 21,174,344
Length	115
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.01
Shannon entropy	0.15095
G+C content	0.31793
Mean single sequence MFE	-23.99
Consensus MFE	-19.26
Energy contribution	-19.04
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.70
Structure conservation index	0.80
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.03
SVM RNA-class probability	0.511000
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 21174229 115 - 22422827
UAGCUGCAAUAAAUGCUUAUCUUUACAUUCAAUAUUCAUUGGAUACGGUUAAUAAAAAUUUGCUCAAAGAGCUCAAAGGUUUUGUUUUA-----UAAGUCUUUGGGCUUUAUGAGUCCUC
((((((((.....)))..........(((((((....)))))))..)))))..........(((((.(((((((((((..((.......-----.))..))))))))))).))))).... ( -29.70, z-score =  -3.40, R)
>droSec1.super_8 3481563 120 - 3762037
UAUCUGCAAUAAAUGCUUAUCUUUACAUCCAAUACUCAUUAGAUACGGUUGAUAAAAAUUUGCUCAAAGAGCUCAAAGGUUUUGUUGUAUAUAGUAUGUCUUUGGGCUUUAUGAAUCCUC
.....((((...((..(((((..(..(((.(((....))).)))...)..)))))..))))))(((.((((((((((((..((((.....))))....)))))))))))).)))...... ( -21.20, z-score =  -0.31, R)
>droSim1.chrX_random 5481208 108 - 5698898
UAGCUGCAAUAAAUGCUUAUCUUUACAUCCAAUACUCAUUAGAUACGGUUAAUAAAAAUUUGCUCAAAGAGCUCAAAGGUUU------------UAUGUCUUUGGGCUUUAUGAAUCCUC
((((((((.....))).(((((..................))))).)))))............(((.((((((((((((...------------....)))))))))))).)))...... ( -21.07, z-score =  -1.37, R)
>consensus
UAGCUGCAAUAAAUGCUUAUCUUUACAUCCAAUACUCAUUAGAUACGGUUAAUAAAAAUUUGCUCAAAGAGCUCAAAGGUUUUGUU_UA_____UAUGUCUUUGGGCUUUAUGAAUCCUC
.....((((.....((((((((..................))))).)))..........))))(((.((((((((((((...................)))))))))))).)))...... (-19.26 = -19.04 +  -0.22)

alignment

secondary structure

dotplot

Window 2

Location	21,174,344 – 21,174,463
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	79.23
Shannon entropy	0.26784
G+C content	0.33592
Mean single sequence MFE	-20.53
Consensus MFE	-13.69
Energy contribution	-13.70
Covariance contribution	0.01
Combinations/Pair	1.12
Mean z-score	-1.92
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.33
SVM RNA-class probability	0.646639
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 21174344 119 - 22422827
UAUAACCACCAAAAAAUUACCGAAUCCUUUGGAUACAUAGUAUCUCGUUUUUU-GCUGAAAACAUGCAUAACUAACAUCAAUUGGGAACUCUCUCUCUUGAAAUGAAGAGAGAGAAUGUG
......(((..........((((.......((((((...)))))).((((((.-...))))))..................))))....((((((((((......))))))))))..))) ( -25.80, z-score =  -2.60, R)
>droSec1.super_8 3481683 97 - 3762037
-------------------CUUAAUCCUUUGGAUACAUAGUAUCUCGGUUUUUGGCUGAAAACAUACAAAACUAACAUGAAUUGCGAACUCUCUUU----AAAUGAAGAGAGACAAUAUG
-------------------....((((...)))).(((((((..((((((((((..((....))..))))...))).)))..)))...((((((((----....))))))))....)))) ( -18.00, z-score =  -1.84, R)
>droSim1.chrX_random 5481316 96 - 5698898
-------------------CUUAAUCCUUUGGAUACAUAGUAUCUCGGUUUUUGGCUGAAAACAUACAAAACUAACAUGAAUUGCGAACUCUCUUU----AAAUG-AGAGAGAGAAUAUG
-------------------....((((...)))).(((((((..((((((((((..((....))..))))...))).)))..)))...((((((((----.....-))))))))..)))) ( -17.80, z-score =  -1.34, R)
>consensus
___________________CUUAAUCCUUUGGAUACAUAGUAUCUCGGUUUUUGGCUGAAAACAUACAAAACUAACAUGAAUUGCGAACUCUCUUU____AAAUGAAGAGAGAGAAUAUG
.......................((((...)))).((((((((.(((((.....)))))....)))).....................((((((((..........))))))))..)))) (-13.69 = -13.70 +   0.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:06:14 2011