Locus 8698

Sequence ID	dm3.chr3R
Location	802,747 – 802,798
Length	51
Max. P	0.948883

overview

Window 7

Location	802,747 – 802,798
Length	51
Sequences	6
Columns	61
Reading direction	forward
Mean pairwise identity	58.30
Shannon entropy	0.83912
G+C content	0.40813
Mean single sequence MFE	-13.60
Consensus MFE	-3.97
Energy contribution	-4.80
Covariance contribution	0.84
Combinations/Pair	1.62
Mean z-score	-1.84
Structure conservation index	0.29
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.54
SVM RNA-class probability	0.948883
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 802747 51 + 27905053
AAUUGAAUUGUUUUCAGUGGAAGUG---------GGACUAAAAACUUCUUGGAAACCAGG-
.........(((((((..((((((.---------.........)))))))))))))....- ( -10.50, z-score =  -0.65, R)
>droAna3.scaffold_13340 23019132 55 + 23697760
-----AAUUGUUUUUUCCAUAGCAAAGCUCACAUAGCCAAGGAUCUCCGUCGUCCUUCGU-
-----..(((((........)))))..........((.((((((.......)))))).))- (  -7.40, z-score =  -1.23, R)
>droEre2.scaffold_4770 1097538 61 + 17746568
AAUUGAAUUGUUUUCAGUGGAGGCAUGCGGCUCAAGACGGAAAACUUCUUGGAAACAAUGG
......(((((((((((.((((...(.((........)).)...))))))))))))))).. ( -15.90, z-score =  -2.07, R)
>droSim1.chr3R_random 182595 60 + 1307089
AAUUGAAUUGUUUUCAGUGGAAGGAUGCGGCUCCGGACUGAAAACUUCUUGGAAACAAGG-
.........(((((((((....(((......)))..)))))))))..((((....)))).- ( -19.20, z-score =  -3.05, R)
>droSec1.super_6 946911 60 + 4358794
AAUUGAAUUGUUUUCAGUGGAAGCAUGCGACUGCGGACUGAAAACUUCUUGGAAACAAGG-
.........(((((((((....(((......)))..)))))))))..((((....)))).- ( -19.00, z-score =  -3.65, R)
>droGri2.scaffold_15074 3063202 55 - 7742996
AAUGAAUCCAUUUUGAAUGGAAG---GCAGGCAAAGUUGUGAAACUACUUAGUCAAGA---
..((..(((((.....)))))..---.))(((.((((.(.....).)))).)))....--- (  -9.60, z-score =  -0.39, R)
>consensus
AAUUGAAUUGUUUUCAGUGGAAGCAUGCGGCUAAAGACUGAAAACUUCUUGGAAACAAGG_
.........(((((((((..................)))))))))..((((....)))).. ( -3.97 =  -4.80 +   0.84)

alignment

secondary structure

dotplot

Window 8

Location	802,747 – 802,798
Length	51
Sequences	6
Columns	61
Reading direction	reverse
Mean pairwise identity	58.30
Shannon entropy	0.83912
G+C content	0.40813
Mean single sequence MFE	-9.58
Consensus MFE	-2.49
Energy contribution	-3.35
Covariance contribution	0.86
Combinations/Pair	1.56
Mean z-score	-1.37
Structure conservation index	0.26
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.15
SVM RNA-class probability	0.566328
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 802747 51 - 27905053
-CCUGGUUUCCAAGAAGUUUUUAGUCC---------CACUUCCACUGAAAACAAUUCAAUU
-..(((...)))....(((((((((..---------.......)))))))))......... (  -7.20, z-score =  -0.77, R)
>droAna3.scaffold_13340 23019132 55 - 23697760
-ACGAAGGACGACGGAGAUCCUUGGCUAUGUGAGCUUUGCUAUGGAAAAAACAAUU-----
-.(....)..........(((.((((...(....)...)))).)))..........----- (  -7.80, z-score =   0.08, R)
>droEre2.scaffold_4770 1097538 61 - 17746568
CCAUUGUUUCCAAGAAGUUUUCCGUCUUGAGCCGCAUGCCUCCACUGAAAACAAUUCAAUU
................((((((.((...(((........))).)).))))))......... (  -7.20, z-score =  -0.27, R)
>droSim1.chr3R_random 182595 60 - 1307089
-CCUUGUUUCCAAGAAGUUUUCAGUCCGGAGCCGCAUCCUUCCACUGAAAACAAUUCAAUU
-.((((....))))..(((((((((..(((......)))....)))))))))......... ( -15.20, z-score =  -3.65, R)
>droSec1.super_6 946911 60 - 4358794
-CCUUGUUUCCAAGAAGUUUUCAGUCCGCAGUCGCAUGCUUCCACUGAAAACAAUUCAAUU
-.((((....))))..(((((((((..(((......)))....)))))))))......... ( -15.00, z-score =  -3.95, R)
>droGri2.scaffold_15074 3063202 55 + 7742996
---UCUUGACUAAGUAGUUUCACAACUUUGCCUGC---CUUCCAUUCAAAAUGGAUUCAUU
---...(((....((((...((......)).))))---..(((((.....))))).))).. (  -5.10, z-score =   0.36, R)
>consensus
_CCUUGUUUCCAAGAAGUUUUCAGUCCGGAGCCGCAUGCUUCCACUGAAAACAAUUCAAUU
................(((((((((..................)))))))))......... ( -2.49 =  -3.35 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:50:25 2011