Locus 2006

Sequence ID	dm3.chr2L
Location	15,489,361 – 15,489,492
Length	131
Max. P	0.997708

overview

Window 6

Location	15,489,361 – 15,489,468
Length	107
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	90.32
Shannon entropy	0.15226
G+C content	0.43255
Mean single sequence MFE	-31.23
Consensus MFE	-27.07
Energy contribution	-28.57
Covariance contribution	1.50
Combinations/Pair	1.07
Mean z-score	-3.65
Structure conservation index	0.87
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.16
SVM RNA-class probability	0.997708
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15489361 107 + 23011544
AAAAAAAAGAAAAGUAAACAGCACAUAUCUGUUUACAAUAACAAAGGGGGAAAAAUAUCGUGGUUGGGGCUUUCGGUUUAGAGUCCGAUUCCGCGUCCAAGUCUCCC
.............((((((((.......)))))))).........((((((.......(((((.(.(((((((......))))))).)..)))))......)))))) ( -33.32, z-score =  -4.07, R)
>droSim1.chr2L 15243172 99 + 22036055
-------ACAAAAGUAAACAGCACAUAUCUGUUUACAAUAACAAAGGGGGAAAA-UAUCGUGGUUGGGGCUUUCGGUUUAGAGUCUCAUACCGCGUCCAAGUCUCCC
-------......((((((((.......)))))))).........((((((...-...(((((((((((((((......))))))))).))))))......)))))) ( -36.60, z-score =  -5.81, R)
>droYak2.chr2L 2482821 100 - 22324452
-------ACAAAAGUAAACAGCACAUAUCUAUUUACAAUAACAAAGGGGGAAAAAUAUCGUGGUUGGGCAUUUCGGUUUAGAGUCGGAUUCCGCGUCCAAGUCUCCC
-------......(((((.((.......)).))))).........((((((.......(((((((.(((...((......))))).))..)))))......)))))) ( -20.92, z-score =  -0.83, R)
>droEre2.scaffold_4929 7235317 99 + 26641161
-------ACAAAAGUAAACAGCACAUAUCUGUUUACAAUAACAAAGGGGGAAAA-CGUCGUGGUUUGGGCUUUCGGUUUAGAGUCCGAUUCCGCGUCCAAGUCGCCC
-------......((((((((.......)))))))).........(((.((...-.(.(((((.(((((((((......)))))))))..))))).)....)).))) ( -34.10, z-score =  -3.91, R)
>consensus
_______ACAAAAGUAAACAGCACAUAUCUGUUUACAAUAACAAAGGGGGAAAA_UAUCGUGGUUGGGGCUUUCGGUUUAGAGUCCGAUUCCGCGUCCAAGUCUCCC
.............((((((((.......)))))))).........((((((.......(((((.(((((((((......)))))))))..)))))......)))))) (-27.07 = -28.57 +   1.50)

alignment

secondary structure

dotplot

Window 7

Location	15,489,390 – 15,489,492
Length	102
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	88.27
Shannon entropy	0.18140
G+C content	0.46124
Mean single sequence MFE	-27.61
Consensus MFE	-22.25
Energy contribution	-23.25
Covariance contribution	1.00
Combinations/Pair	1.10
Mean z-score	-1.67
Structure conservation index	0.81
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.28
SVM RNA-class probability	0.626231
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15489390 102 + 23011544
UGUUUACAAUAACAAAGGGGGAAAAAUAUCGUGGUUGGGGCUUUCGGUUUAGAGUCCGAUUCCGCGUCCAAGUCUCCCCAACUACUCGUA---UCCGUACAAUAG
((((......))))..((((((.......(((((.(.(((((((......))))))).)..)))))......)).))))........(((---....)))..... ( -27.42, z-score =  -1.23, R)
>droSim1.chr2L 15243194 104 + 22036055
UGUUUACAAUAACAAAGGGGGAAAA-UAUCGUGGUUGGGGCUUUCGGUUUAGAGUCUCAUACCGCGUCCAAGUCUCCCCAACUACUCGUACAAUCCGUACAAUAG
((((......))))..((((((...-...(((((((((((((((......))))))))).))))))......)).))))........((((.....))))..... ( -33.80, z-score =  -3.71, R)
>droYak2.chr2L 2482843 96 - 22324452
UAUUUACAAUAACAAAGGGGGAAAAAUAUCGUGGUUGGGCAUUUCGGUUUAGAGUCGGAUUCCGCGUCCAAGUCUCCCCAACUA---------UCCGUACAAUAG
................((((((.......(((((((.(((...((......))))).))..)))))......)).)))).....---------............ ( -19.62, z-score =   0.28, R)
>droEre2.scaffold_4929 7235339 95 + 26641161
UGUUUACAAUAACAAAGGGGGAAAA-CGUCGUGGUUUGGGCUUUCGGUUUAGAGUCCGAUUCCGCGUCCAAGUCGCCCCAACUA---------UCCGCACAAUAG
((((......))))..((((((...-.(.(((((.(((((((((......)))))))))..))))).)....)).)))).....---------............ ( -29.60, z-score =  -2.03, R)
>consensus
UGUUUACAAUAACAAAGGGGGAAAA_UAUCGUGGUUGGGGCUUUCGGUUUAGAGUCCGAUUCCGCGUCCAAGUCUCCCCAACUA_________UCCGUACAAUAG
................((((((.......(((((.(((((((((......)))))))))..)))))......)).)))).......................... (-22.25 = -23.25 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:42:57 2011