Locus 2520

Sequence ID dm3.chr2L
Location 19,698,958 – 19,699,051
Length 93
Max. P 0.811764
window3467 window3468

overview

Window 7

Location 19,698,958 – 19,699,051
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 88.30
Shannon entropy 0.18952
G+C content 0.47161
Mean single sequence MFE -18.64
Consensus MFE -16.60
Energy contribution -16.40
Covariance contribution -0.20
Combinations/Pair 1.13
Mean z-score -1.52
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.811764
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19698958 93 + 23011544
ACCACCACUCCAAACAUCAAAAAUACUCCUCUGGCGUUUCCGCCGUAUGUUUGUCAUCCACAUUAGCGUAAUAUGCCGGAAAAAGGGAGCCUC
.........................((((((((((((...(((...((((.........))))..)))....)))))))).....)))).... ( -19.50, z-score =  -1.37, R)
>droSec1.super_7 3313893 83 + 3727775
---------CCAAACAUCGAAAAUACUCCUCCGGCAUUUCCGCCGUAUGUUUGUCAUCCACAUUAGCGUAAUAUGCCGGAAAA-GCGAGCGAC
---------.......(((......((..((((((((...(((...((((.........))))..)))....))))))))..)-)....))). ( -20.50, z-score =  -2.02, R)
>droSim1.chr2L 19366942 84 + 22036055
--------UCCAAACAUCGAAAAUACUCCUCCGGCAUUUCCGCCGUAUGUUUGUCAUCCACAUUAGCGUAAUAUGCCGGAAAA-GCGAGCGAC
--------........(((......((..((((((((...(((...((((.........))))..)))....))))))))..)-)....))). ( -20.50, z-score =  -2.00, R)
>droYak2.chr2R 6171786 82 + 21139217
----------UGAACAUCAUAAAUACUCCUCCGGCAUUUCCGCCGUAUGUUUGUCAUCCACAUUAGCGUAAUAUGCCGGAAAA-GCGAGCCUC
----------...............((((((((((((...(((...((((.........))))..)))....))))))))...-).))).... ( -19.10, z-score =  -1.91, R)
>droEre2.scaffold_4845 17975501 82 - 22589142
----------CGAACAUCAAAAAUACUCAUCCGUCGUUUCCGCCGUAUGUUUGUCAUCCACAUUAGCGUAAUAUGCCGGAAAA-GCGAGCCUC
----------.....................(((..((((((.(((((...((..(.......)..))..))))).)))))).-)))...... ( -13.60, z-score =  -0.30, R)
>consensus
_________CCAAACAUCAAAAAUACUCCUCCGGCAUUUCCGCCGUAUGUUUGUCAUCCACAUUAGCGUAAUAUGCCGGAAAA_GCGAGCCUC
.............................((((((((...(((...((((.........))))..)))....))))))))............. (-16.60 = -16.40 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,698,958 – 19,699,051
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 88.30
Shannon entropy 0.18952
G+C content 0.47161
Mean single sequence MFE -26.04
Consensus MFE -19.08
Energy contribution -20.08
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.610098
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19698958 93 - 23011544
GAGGCUCCCUUUUUCCGGCAUAUUACGCUAAUGUGGAUGACAAACAUACGGCGGAAACGCCAGAGGAGUAUUUUUGAUGUUUGGAGUGGUGGU
...((..((...(((((((((....(((....))).....((((.((((((((....))))......)))).))))))).)))))).))..)) ( -26.40, z-score =  -1.05, R)
>droSec1.super_7 3313893 83 - 3727775
GUCGCUCGC-UUUUCCGGCAUAUUACGCUAAUGUGGAUGACAAACAUACGGCGGAAAUGCCGGAGGAGUAUUUUCGAUGUUUGG---------
((((...((-(((((((((((....((((.((((.........))))..))))...))))))))))))).....))))......--------- ( -29.70, z-score =  -3.20, R)
>droSim1.chr2L 19366942 84 - 22036055
GUCGCUCGC-UUUUCCGGCAUAUUACGCUAAUGUGGAUGACAAACAUACGGCGGAAAUGCCGGAGGAGUAUUUUCGAUGUUUGGA--------
((((...((-(((((((((((....((((.((((.........))))..))))...))))))))))))).....)))).......-------- ( -29.70, z-score =  -2.94, R)
>droYak2.chr2R 6171786 82 - 21139217
GAGGCUCGC-UUUUCCGGCAUAUUACGCUAAUGUGGAUGACAAACAUACGGCGGAAAUGCCGGAGGAGUAUUUAUGAUGUUCA----------
.......((-(((((((((((....((((.((((.........))))..))))...)))))))))))))..............---------- ( -27.80, z-score =  -3.06, R)
>droEre2.scaffold_4845 17975501 82 + 22589142
GAGGCUCGC-UUUUCCGGCAUAUUACGCUAAUGUGGAUGACAAACAUACGGCGGAAACGACGGAUGAGUAUUUUUGAUGUUCG----------
.......((-((.((((.(((((((...)))))))................((....)).)))).))))..............---------- ( -16.60, z-score =   0.36, R)
>consensus
GAGGCUCGC_UUUUCCGGCAUAUUACGCUAAUGUGGAUGACAAACAUACGGCGGAAAUGCCGGAGGAGUAUUUUUGAUGUUUGG_________
...((((.....(((((((((....((((.((((.........))))..))))...)))))))))))))........................ (-19.08 = -20.08 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:52:48 2011