Locus 4017

Sequence ID dm3.chr2R
Location 9,716,614 – 9,716,677
Length 63
Max. P 0.875023
window5493 window5494

overview

Window 3

Location 9,716,614 – 9,716,677
Length 63
Sequences 5
Columns 63
Reading direction forward
Mean pairwise identity 80.49
Shannon entropy 0.33444
G+C content 0.45913
Mean single sequence MFE -16.46
Consensus MFE -12.10
Energy contribution -12.50
Covariance contribution 0.40
Combinations/Pair 1.19
Mean z-score -1.22
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.523235
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9716614 63 + 21146708
GCUGCAGUUGCAGCUGUAGCUGCGUUCGAGCAAUCAUUGCAAUCCAAUUAAAUGGACAUUCGA
...((((((((....))))))))..(((((((.....)))..((((......))))...)))) ( -20.00, z-score =  -1.66, R)
>droAna3.scaffold_13266 17018458 50 + 19884421
-------------UGGCGAUGGCGUUUGAGCAAUCAUUGCAAUCCAAUUAAAUGGACAGUCGA
-------------...((((.(((..(((....))).)))..((((......))))..)))). ( -11.70, z-score =  -0.67, R)
>droEre2.scaffold_4845 6485858 55 - 22589142
--------UGCAGCUGUAGCUGCAUUCGAGCAAUCAUUGCAAUCCAAUUAAAUGGACAGUCGA
--------((((((....)))))).(((((((.....)))..((((......))))...)))) ( -17.20, z-score =  -2.32, R)
>droSec1.super_1 7243745 62 + 14215200
GCUGCAAUUGCAGCUGUAGCUGCGUUCG-GCAAUCAUUGCAAUCCAAUUAAAUGGACAGUCGA
((((.(((.(((((....))))))))))-))..((((((...((((......)))))))).)) ( -17.80, z-score =  -0.90, R)
>droSim1.chr2R 8155633 57 + 19596830
------GCUGCAGCUGUAGCUGCGUUCGGGCAAUCAUUGCAAUCCAAUUAAAUGGACAGUCGA
------...(((((....)))))..(((((((.....)))..((((......))))...)))) ( -15.60, z-score =  -0.55, R)
>consensus
________UGCAGCUGUAGCUGCGUUCGAGCAAUCAUUGCAAUCCAAUUAAAUGGACAGUCGA
.........(((((....)))))..(((((((.....)))..((((......))))...)))) (-12.10 = -12.50 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,716,614 – 9,716,677
Length 63
Sequences 5
Columns 63
Reading direction reverse
Mean pairwise identity 80.49
Shannon entropy 0.33444
G+C content 0.45913
Mean single sequence MFE -15.98
Consensus MFE -11.88
Energy contribution -12.56
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.875023
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9716614 63 - 21146708
UCGAAUGUCCAUUUAAUUGGAUUGCAAUGAUUGCUCGAACGCAGCUACAGCUGCAACUGCAGC
((((..(((((......))))).(((.....)))))))..(((((....)))))......... ( -18.50, z-score =  -1.71, R)
>droAna3.scaffold_13266 17018458 50 - 19884421
UCGACUGUCCAUUUAAUUGGAUUGCAAUGAUUGCUCAAACGCCAUCGCCA-------------
..(...(((((......)))))..)...(((.((......)).)))....------------- (  -9.20, z-score =  -0.65, R)
>droEre2.scaffold_4845 6485858 55 + 22589142
UCGACUGUCCAUUUAAUUGGAUUGCAAUGAUUGCUCGAAUGCAGCUACAGCUGCA--------
((((..(((((......))))).(((.....))))))).((((((....))))))-------- ( -18.10, z-score =  -2.74, R)
>droSec1.super_1 7243745 62 - 14215200
UCGACUGUCCAUUUAAUUGGAUUGCAAUGAUUGC-CGAACGCAGCUACAGCUGCAAUUGCAGC
......(((((......)))))(((((((.....-)....(((((....))))).)))))).. ( -17.40, z-score =  -1.49, R)
>droSim1.chr2R 8155633 57 - 19596830
UCGACUGUCCAUUUAAUUGGAUUGCAAUGAUUGCCCGAACGCAGCUACAGCUGCAGC------
(((...(((((......))))).(((.....))).)))..(((((....)))))...------ ( -16.70, z-score =  -2.08, R)
>consensus
UCGACUGUCCAUUUAAUUGGAUUGCAAUGAUUGCUCGAACGCAGCUACAGCUGCA________
(((...(((((......))))).(((.....))).)))..(((((....)))))......... (-11.88 = -12.56 +   0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:21:01 2011