Locus 8944

Sequence ID	dm3.chr3R
Location	2,835,294 – 2,835,426
Length	132
Max. P	0.701336

overview

Window 6

Location	2,835,294 – 2,835,390
Length	96
Sequences	3
Columns	102
Reading direction	forward
Mean pairwise identity	92.67
Shannon entropy	0.09903
G+C content	0.53064
Mean single sequence MFE	-32.70
Consensus MFE	-31.55
Energy contribution	-31.67
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.16
Structure conservation index	0.96
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.45
SVM RNA-class probability	0.701336
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2835294 96 + 27905053
------GCAGUGGCAGUUGCAGUUGCAGUUGCAUUUCUGCUGCGUUUUGUGUCUCCGCUGCAGUUAAAACGGAACCCGUCGUCGUCGAUGGUGACUCUACUC
------(((((((.((.(((((.((((((.........))))))..))))).))))))))).........(((.(((((((....)))))).)..))).... ( -32.50, z-score =  -1.46, R)
>droSec1.super_6 2926063 96 + 4358794
------GCAGUGGCAGUUGCAGUUGCAGUUGCAUUUCUGCUGCGCUUUGUGUCUCCGCUACAGUUAAAACGGAACCCGUCGUCGUCGAUGGUGACUCCACUU
------((.(..((((.(((((......)))))...))))..))).....(((((((............))))..((((((....)))))).)))....... ( -29.40, z-score =  -0.40, R)
>droYak2.chr3R_random 715349 102 + 3277457
ACAGUUGCAGUGGCAGUUGCAGUUGCAGUGGCAUUUCUGCUGCGUUUUGUGUCUCCGCUGCAGUUAAAACGGAACCCGUCGUCGUCGAUGGUGACUCUACUC
....(((((((((.((.(((((.(((((..(.....)..)))))..))))).))))))))))).......(((.(((((((....)))))).)..))).... ( -36.20, z-score =  -1.62, R)
>consensus
______GCAGUGGCAGUUGCAGUUGCAGUUGCAUUUCUGCUGCGUUUUGUGUCUCCGCUGCAGUUAAAACGGAACCCGUCGUCGUCGAUGGUGACUCUACUC
......(((((((.((.(((((.(((((..(.....)..)))))..))))).))))))))).........(((.(((((((....)))))).)..))).... (-31.55 = -31.67 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	2,835,318 – 2,835,426
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	96.85
Shannon entropy	0.05578
G+C content	0.50000
Mean single sequence MFE	-30.56
Consensus MFE	-27.64
Energy contribution	-27.92
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-1.44
Structure conservation index	0.90
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.02
SVM RNA-class probability	0.506692
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2835318 108 + 27905053
GCAUUUCUGCUGCGUUUUGUGUCUCCGCUGCAGUUAAAACGGAACCCGUCGUCGUCGAUGGUGACUCUACUCCGGCGACGACGAAAACGACAACGACUUAAUUAAAAC
(((.......)))(((...((((((((.(........).))))...(((((((((((..((((....)))).))))))))))).....))))..)))........... ( -32.20, z-score =  -1.79, R)
>droSim1.chr3R 2875246 108 + 27517382
GCAUUUCUGCUGCGCUUUGUGUCUCCGCUGCAGUUAAAACGGAACCCGUCGUAGUCGAUGGUGACUCUACUCCGGCGACGACGAAAACGACAACGACUUAAUUAAAAC
(((.......)))...(((((((((((.(........).))))...((((((.((((..((((....)))).)))).)))))).....))).))))............ ( -25.20, z-score =   0.18, R)
>droSec1.super_6 2926087 108 + 4358794
GCAUUUCUGCUGCGCUUUGUGUCUCCGCUACAGUUAAAACGGAACCCGUCGUCGUCGAUGGUGACUCCACUUUGGCGACGACGAAAACGACAACGACUUAAUUAAAAC
(((.......)))...(((((((((((............))))...((((((((((((.((((....)))))))))))))))).....))).))))............ ( -33.00, z-score =  -2.56, R)
>droYak2.chr3R_random 715379 108 + 3277457
GCAUUUCUGCUGCGUUUUGUGUCUCCGCUGCAGUUAAAACGGAACCCGUCGUCGUCGAUGGUGACUCUACUCCGGCGACGACGAAAACGACAACGACUUAAUUAAAAC
(((.......)))(((...((((((((.(........).))))...(((((((((((..((((....)))).))))))))))).....))))..)))........... ( -32.20, z-score =  -1.79, R)
>droEre2.scaffold_4770 3088104 108 + 17746568
CCAUUUCUGCUGCGUUUUGUGUCUCCGCUGCAGUUAAAACGGAACCCGUCGUCGUCGAUGGCGACUCUACUCCGGCGACGACGAAAACGACAACGACUUAAUUAAAAC
((.(((..((((((....(((....)))))))))..))).))....(((((((((((..(.........)..)))))))))))......................... ( -30.20, z-score =  -1.26, R)
>consensus
GCAUUUCUGCUGCGUUUUGUGUCUCCGCUGCAGUUAAAACGGAACCCGUCGUCGUCGAUGGUGACUCUACUCCGGCGACGACGAAAACGACAACGACUUAAUUAAAAC
(((.......)))...(((((((((((.(........).))))...(((((((((((..((((....)))).))))))))))).....))).))))............ (-27.64 = -27.92 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:55:08 2011