Locus 259

Sequence ID	dm3.chr2L
Location	1,885,440 – 1,885,539
Length	99
Max. P	0.903355

overview

Window 3

Location	1,885,440 – 1,885,539
Length	99
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	86.01
Shannon entropy	0.21888
G+C content	0.57774
Mean single sequence MFE	-41.75
Consensus MFE	-28.11
Energy contribution	-29.68
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-2.59
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.17
SVM RNA-class probability	0.903355
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1885440 99 + 23011544
AGACCAGAAAGACCGUUUUCGAAGGCAAACGGGCGGGCGGCGGAUUUGGAUCCAGAACCACCCCCUUUUGGGGGUGCUUUUCGCUCUCAGCUGGGCUUG
...((((..(((((((((.(....).))))))(((((.(((((.((((....)))).))((((((....))))))))).))))))))...))))..... ( -44.00, z-score =  -2.44, R)
>droEre2.scaffold_4929 1930966 84 + 26641161
AGACCAGAAAGAGCGUUUUCGAAGGCGG---------------AUUUGGAUCCAGAGCCACCCCCUUUUGGGGGUGGUUUUCGCUCUCAGCUGUGCUUG
((..(((..((((((...........((---------------((....))))((((((((((((....))))))))))))))))))...)))..)).. ( -38.40, z-score =  -3.55, R)
>droSec1.super_14 1833001 99 + 2068291
AGACCAGAAAGACCGUUUUCGAAGGCGGACGGGGGGGCGGCGGUUUUGGAUCCAGAACCACCCCCUUUUGGGGGUGCUUUUCGCUCUCAGCUGGGCUUG
...((((.....(((((..(....)..)))))((((((((.(((((((....)))))))((((((....)))))).....))))))))..))))..... ( -49.20, z-score =  -3.16, R)
>droSim1.chr2L_random 96872 91 + 909653
AGACCAGAAAGACCGUUUUCAAAGGCGG--------GCGGCGGUAUUGGAUCCAGAACCACCCCCUUUUGGGGGUGCUUUUCGCUCUCAGCUGGGCUUG
...((((..(((((((((....))))))--------((((.(((.(((....))).)))((((((....)))))).....)))))))...))))..... ( -35.40, z-score =  -1.23, R)
>consensus
AGACCAGAAAGACCGUUUUCGAAGGCGG________GCGGCGGAUUUGGAUCCAGAACCACCCCCUUUUGGGGGUGCUUUUCGCUCUCAGCUGGGCUUG
...((((..(((.((.....((((((...............(((((((....)))))))((((((....)))))))))))))).)))...))))..... (-28.11 = -29.68 +   1.56)

alignment

secondary structure

dotplot

Window 4

Location	1,885,440 – 1,885,539
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	86.01
Shannon entropy	0.21888
G+C content	0.57774
Mean single sequence MFE	-34.00
Consensus MFE	-26.05
Energy contribution	-26.30
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.94
Structure conservation index	0.77
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.71
SVM RNA-class probability	0.795400
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1885440 99 - 23011544
CAAGCCCAGCUGAGAGCGAAAAGCACCCCCAAAAGGGGGUGGUUCUGGAUCCAAAUCCGCCGCCCGCCCGUUUGCCUUCGAAAACGGUCUUUCUGGUCU
..((.((((..(((((((......((((((....))))))(((..(((((....)))))..))))))((((((........)))))))))).)))).)) ( -37.30, z-score =  -1.93, R)
>droEre2.scaffold_4929 1930966 84 - 26641161
CAAGCACAGCUGAGAGCGAAAACCACCCCCAAAAGGGGGUGGCUCUGGAUCCAAAU---------------CCGCCUUCGAAAACGCUCUUUCUGGUCU
...((.(((..(((((((....((((((((....))))))))....((((....))---------------))...........))))))).))))).. ( -35.40, z-score =  -4.11, R)
>droSec1.super_14 1833001 99 - 2068291
CAAGCCCAGCUGAGAGCGAAAAGCACCCCCAAAAGGGGGUGGUUCUGGAUCCAAAACCGCCGCCCCCCCGUCCGCCUUCGAAAACGGUCUUUCUGGUCU
..((.((((..(((((((....((((((((....))))))((((.((....)).)))))))))....((((.((....))...)))))))).)))).)) ( -32.90, z-score =  -0.93, R)
>droSim1.chr2L_random 96872 91 - 909653
CAAGCCCAGCUGAGAGCGAAAAGCACCCCCAAAAGGGGGUGGUUCUGGAUCCAAUACCGCCGC--------CCGCCUUUGAAAACGGUCUUUCUGGUCU
..((.((((..(((((((....((((((((....))))))(((..((....))..))))))))--------(((..........))))))).)))).)) ( -30.40, z-score =  -0.78, R)
>consensus
CAAGCCCAGCUGAGAGCGAAAAGCACCCCCAAAAGGGGGUGGUUCUGGAUCCAAAACCGCCGC________CCGCCUUCGAAAACGGUCUUUCUGGUCU
..((.((((..((((.((.....(((((((....)))))))....((....))...............................)).)))).)))).)) (-26.05 = -26.30 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:09:34 2011