Locus 4896

Sequence ID dm3.chr2R
Location 16,256,499 – 16,256,576
Length 77
Max. P 0.971399
window6736 window6737

overview

Window 6

Location 16,256,499 – 16,256,576
Length 77
Sequences 4
Columns 81
Reading direction forward
Mean pairwise identity 50.00
Shannon entropy 0.80583
G+C content 0.46909
Mean single sequence MFE -18.21
Consensus MFE -7.28
Energy contribution -6.03
Covariance contribution -1.25
Combinations/Pair 1.67
Mean z-score -1.33
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.66
SVM RNA-class probability 0.959114
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16256499 77 + 21146708
UUUGGUCAAUCGAGCCUUUAAUCGACUCUGCAGUUUCCCCCUACCAAAGGUAAGGGACUCAGA----GAAAGGCCAGCUCC
.((((((..((((........))))(((((.(((...(((.((((...)))).))))))))))----)...)))))).... ( -26.60, z-score =  -2.73, R)
>droSec1.super_43 56432 65 + 327307
UUUGGUUGUUUUGUUUUUCGAAAUUCUCUGCAGUUUUUUCGCACCAGUAGUAAAAAACUCAGAGA----------------
.......((((((.....))))))((((((.((((((((.((.......))))))))))))))))---------------- ( -15.10, z-score =  -2.19, R)
>droAna3.scaffold_13089 423646 71 - 978470
--------UUUGGUCCAUCGAGACACCCUGACGUUUUCCCC--CCUGUGGUAAGAGACUCAGGUUUUAAAAAACUGGCACC
--------...((((((.........(((((.(((((...(--(....))...))))))))))...........))).))) ( -13.95, z-score =   0.64, R)
>droPer1.super_164 85937 65 + 94152
--------GUUGGUCCUUCGAGACUCUCCGUUGUUUCCCCC---CUGUGGUAAGAG-CACGGA----GUUAAACCAGCUUC
--------((((((.(((((.(.(((((((..(........---)..)))..))))-).))))----)....))))))... ( -17.20, z-score =  -1.02, R)
>consensus
________UUUGGUCCUUCGAGACACUCUGCAGUUUCCCCC__CCAGUGGUAAGAGACUCAGA____GAAAAACCAGCUCC
..........................((((.((((((.((........))...)))))))))).................. ( -7.28 =  -6.03 +  -1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 16,256,499 – 16,256,576
Length 77
Sequences 4
Columns 81
Reading direction reverse
Mean pairwise identity 50.00
Shannon entropy 0.80583
G+C content 0.46909
Mean single sequence MFE -19.05
Consensus MFE -9.49
Energy contribution -9.55
Covariance contribution 0.06
Combinations/Pair 1.71
Mean z-score -0.92
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.85
SVM RNA-class probability 0.971399
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16256499 77 - 21146708
GGAGCUGGCCUUUC----UCUGAGUCCCUUACCUUUGGUAGGGGGAAACUGCAGAGUCGAUUAAAGGCUCGAUUGACCAAA
((..(.((((((((----(((((((((((((((...))))))))...))).)))))......))))))).).....))... ( -27.40, z-score =  -1.52, R)
>droSec1.super_43 56432 65 - 327307
----------------UCUCUGAGUUUUUUACUACUGGUGCGAAAAAACUGCAGAGAAUUUCGAAAAACAAAACAACCAAA
----------------((((((((((((((..((....))..)))))))).))))))........................ ( -13.30, z-score =  -2.39, R)
>droAna3.scaffold_13089 423646 71 + 978470
GGUGCCAGUUUUUUAAAACCUGAGUCUCUUACCACAGG--GGGGAAAACGUCAGGGUGUCUCGAUGGACCAAA--------
(((.(((......((...(((((((.(((..((...))--..)))..)).))))).))......))))))...-------- ( -18.30, z-score =   0.38, R)
>droPer1.super_164 85937 65 - 94152
GAAGCUGGUUUAAC----UCCGUG-CUCUUACCACAG---GGGGGAAACAACGGAGAGUCUCGAAGGACCAAC--------
.....(((.....(----(((((.-(((((.....))---)))(....).))))))....((....)))))..-------- ( -17.20, z-score =  -0.13, R)
>consensus
GGAGCUGGUUUUUC____UCUGAGUCUCUUACCACAGG__GGGGAAAACUGCAGAGAGUCUCGAAGGACCAAA________
..................(((((.(((((((((...))))))))).....))))).......................... ( -9.49 =  -9.55 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:38:10 2011