Locus 8788

Sequence ID	dm3.chr3R
Location	1,642,490 – 1,642,582
Length	92
Max. P	0.994455

overview

Window 8

Location	1,642,490 – 1,642,582
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	65.70
Shannon entropy	0.57962
G+C content	0.60308
Mean single sequence MFE	-19.56
Consensus MFE	-11.08
Energy contribution	-11.32
Covariance contribution	0.24
Combinations/Pair	1.27
Mean z-score	-2.01
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.70
SVM RNA-class probability	0.994455
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1642490 92 + 27905053
CCACGUCCACAUCCACACCCACACCCGCACCCACACCAAUAUCCCUGCCCGCGACCCGUUCCCGGGCACAGGAUAGGGUUUCUUUCGCCCAG
.......................................(((((.((((((.((.....)).))))))..)))))((((.......)))).. ( -21.90, z-score =  -2.40, R)
>droSim1.chr3R 1675505 74 + 27517382
------------------CCACGUCCACACCCACACCAAUAUCCCUGCCCGCGACCCGUUCCCGGGCACAGGAUAGGGUUUCCUUCGCCCAG
------------------.....................(((((.((((((.((.....)).))))))..)))))((((.......)))).. ( -21.90, z-score =  -2.77, R)
>droSec1.super_6 1750634 74 + 4358794
------------------CCACGUCCACACCGACACCAAUAUCCCUGCCCGCGACCCGUUCCCGGGCACAGGAUAGGGUUUCCUUCGCCCAG
------------------....(((......))).....(((((.((((((.((.....)).))))))..)))))((((.......)))).. ( -24.00, z-score =  -3.02, R)
>droEre2.scaffold_4770 1909637 80 + 17746568
------------CCACGCCCACACCCAUGCCCACACCAAUGUCCCUUUCCUCGACCCGUUCCCGGGAACAGGAUAGGGUUUCCUUCGCACAG
------------...............(((..(((....)))((((.((((...((((....))))...)))).))))........)))... ( -18.40, z-score =  -1.08, R)
>droWil1.scaffold_181108 3883067 84 - 4707319
------UAUUAUCCACAUACAGGACAAA--CGACGAGUAUGCCCUCCUCCCGCACCAAUUACUUCUUAACGGACAAAGUUAGCUUUGCCCAG
------..............(((.((.(--(.....)).)).))).........................((.(((((....))))).)).. ( -11.60, z-score =  -0.80, R)
>consensus
____________CCAC__CCACGCCCACACCCACACCAAUAUCCCUGCCCGCGACCCGUUCCCGGGCACAGGAUAGGGUUUCCUUCGCCCAG
..........................................(((((.((....((((....))))....)).))))).............. (-11.08 = -11.32 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	1,642,490 – 1,642,582
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	65.70
Shannon entropy	0.57962
G+C content	0.60308
Mean single sequence MFE	-29.80
Consensus MFE	-19.54
Energy contribution	-18.30
Covariance contribution	-1.24
Combinations/Pair	1.56
Mean z-score	-1.58
Structure conservation index	0.66
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.41
SVM RNA-class probability	0.990324
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 1642490 92 - 27905053
CUGGGCGAAAGAAACCCUAUCCUGUGCCCGGGAACGGGUCGCGGGCAGGGAUAUUGGUGUGGGUGCGGGUGUGGGUGUGGAUGUGGACGUGG
(((.((........((((..((((((((((....)))).)))))).))))(((((.((......)).)))))..)).)))............ ( -31.50, z-score =  -0.56, R)
>droSim1.chr3R 1675505 74 - 27517382
CUGGGCGAAGGAAACCCUAUCCUGUGCCCGGGAACGGGUCGCGGGCAGGGAUAUUGGUGUGGGUGUGGACGUGG------------------
(((.((.((.....((((..((((((((((....)))).)))))).))))...)).)).)))............------------------ ( -28.30, z-score =  -1.09, R)
>droSec1.super_6 1750634 74 - 4358794
CUGGGCGAAGGAAACCCUAUCCUGUGCCCGGGAACGGGUCGCGGGCAGGGAUAUUGGUGUCGGUGUGGACGUGG------------------
....(((.......((((..((((((((((....)))).)))))).))))((((((....))))))...)))..------------------ ( -29.30, z-score =  -1.13, R)
>droEre2.scaffold_4770 1909637 80 - 17746568
CUGUGCGAAGGAAACCCUAUCCUGUUCCCGGGAACGGGUCGAGGAAAGGGACAUUGGUGUGGGCAUGGGUGUGGGCGUGG------------
(..(((........((((.((((...((((....))))...)))).))))(((((.(((....))).)))))..)))..)------------ ( -34.00, z-score =  -2.97, R)
>droWil1.scaffold_181108 3883067 84 + 4707319
CUGGGCAAAGCUAACUUUGUCCGUUAAGAAGUAAUUGGUGCGGGAGGAGGGCAUACUCGUCG--UUUGUCCUGUAUGUGGAUAAUA------
..((((((((....))))))))...............((((((((.((((((......))).--))).))))))))..........------ ( -25.90, z-score =  -2.16, R)
>consensus
CUGGGCGAAGGAAACCCUAUCCUGUGCCCGGGAACGGGUCGCGGGCAGGGAUAUUGGUGUGGGUGUGGACGUGG__GUGG____________
...((((.......((((.(((((.(((((....))))))).))).)))).......))))............................... (-19.54 = -18.30 +  -1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:52:14 2011