Locus 10454

Sequence ID	dm3.chr3R
Location	13,889,757 – 13,889,870
Length	113
Max. P	0.889861

overview

Window 8

Location	13,889,757 – 13,889,855
Length	98
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	77.19
Shannon entropy	0.40086
G+C content	0.40489
Mean single sequence MFE	-14.10
Consensus MFE	-9.47
Energy contribution	-9.55
Covariance contribution	0.08
Combinations/Pair	1.20
Mean z-score	-1.65
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.03
SVM RNA-class probability	0.878048
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13889757 98 - 27905053
AGCCCCCAAGAA-CCCAGU-GCCCAGUGCCCAG---AACCAAGUUGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAACAG
............-....(.-.(...)..)....---....(((((((((((.......((((((........)))))).....))))).))))))........ ( -15.00, z-score =  -1.92, R)
>droYak2.chr3R 2483545 79 - 28832112
---------------------ACGAGAGCCUAG---AACCGAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAACCAAUUUUACAACUUUAUAACAC
---------------------............---....((((.((((((.......((((((........)))))).....))))).).))))........ ( -11.10, z-score =  -1.82, R)
>droEre2.scaffold_4770 10000854 79 + 17746568
---------------------CCAAGAGCCCAG---AACCAAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAACAG
---------------------............---....((((.((((((.......((((((........)))))).....))))).).))))........ ( -10.70, z-score =  -1.92, R)
>droSec1.super_12 1847211 100 + 2123299
AGCCUCCAAGAACCCCAGUGGCCCAGUGCCCAG---ACCCAAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAACAG
.((.((((.........(.(((.....))))..---.....(((((...((((........))))...)))))..)))).))..................... ( -16.20, z-score =  -1.20, R)
>droSim1.chr3R 19915841 90 + 27517382
--------AGAA-CCUAGU-GCCCAGUGCCCAG---AACCAAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAACAG
--------....-.((.(.-((.....))).))---....((((.((((((.......((((((........)))))).....))))).).))))........ ( -11.20, z-score =  -0.42, R)
>droAna3.scaffold_13340 11865664 92 + 23697760
-----------AGUCGAAUGCGAAAGCUUUCAGUAAAACCAAGCCCGAGUCCAAAAUGCCAUCAUAAACGAUUGAUGGAGGCAAUUUUACAACUUUAUAACAG
-----------....(((.((....)).))).((((((....(((.(....)......((((((........)))))).)))..))))))............. ( -20.40, z-score =  -2.62, R)
>consensus
___________A_CC_AGU_GCCCAGUGCCCAG___AACCAAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAACAG
........................................((((..(((((.......((((((........)))))).....)))))...))))........ ( -9.47 =  -9.55 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	13,889,760 – 13,889,870
Length	110
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	73.25
Shannon entropy	0.46789
G+C content	0.42443
Mean single sequence MFE	-14.58
Consensus MFE	-9.47
Energy contribution	-9.55
Covariance contribution	0.08
Combinations/Pair	1.20
Mean z-score	-1.41
Structure conservation index	0.65
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.09
SVM RNA-class probability	0.889861
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13889760 110 - 27905053
CCCCUAUAGCCCCAAAGCCCCCAAGAA-CCCAGU-GCCCAGUGCCCAG---AACCAAGUUGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAA
...........................-....(.-.(...)..)....---....(((((((((((.......((((((........)))))).....))))).))))))..... ( -15.00, z-score =  -1.66, R)
>droYak2.chr3R 2483548 87 - 28832112
------------------UCCCCAAAGCCACG-------AGAGCCUAG---AACCGAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAACCAAUUUUACAACUUUAUAA
------------------..............-------.........---....((((.((((((.......((((((........)))))).....))))).).))))..... ( -11.10, z-score =  -1.18, R)
>droEre2.scaffold_4770 10000857 87 + 17746568
------------------CCCCCAAAGCCCCA-------AGAGCCCAG---AACCAAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAA
------------------..............-------.........---....((((.((((((.......((((((........)))))).....))))).).))))..... ( -10.70, z-score =  -1.58, R)
>droSec1.super_12 1847214 112 + 2123299
ACCCCAUAGCCCCCAAGCCUCCAAGAACCCCAGUGGCCCAGUGCCCAG---ACCCAAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAA
................((.((((.........(.(((.....))))..---.....(((((...((((........))))...)))))..)))).)).................. ( -16.20, z-score =  -1.09, R)
>droSim1.chr3R 19915844 102 + 27517382
--------CCCCCAUGGCCCCCAAGAA-CCUAGU-GCCCAGUGCCCAG---AACCAAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAA
--------....((((((.(.......-....).-)))..))).....---....((((.((((((.......((((((........)))))).....))))).).))))..... ( -12.20, z-score =   0.36, R)
>droAna3.scaffold_13340 11865667 97 + 23697760
------------------CUAAAAAAAGUCGAAUGCGAAAGCUUUCAGUAAAACCAAGCCCGAGUCCAAAAUGCCAUCAUAAACGAUUGAUGGAGGCAAUUUUACAACUUUAUAA
------------------......(((((.(((.((....)).))).((((((....(((.(....)......((((((........)))))).)))..)))))).))))).... ( -22.30, z-score =  -3.29, R)
>consensus
__________________CCCCAAAAACCCCAGU_GCCCAGUGCCCAG___AACCAAGUCGAAAAUGAAAACGCCAUCAUAAACGAUUGAUGGAAGCAAUUUUACAACUUUAUAA
.......................................................((((..(((((.......((((((........)))))).....)))))...))))..... ( -9.47 =  -9.55 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:24:17 2011