Locus 6506

Sequence ID	dm3.chr3L
Location	7,170,173 – 7,170,267
Length	94
Max. P	0.785128

overview

Window 7

Location	7,170,173 – 7,170,267
Length	94
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	86.43
Shannon entropy	0.21414
G+C content	0.45574
Mean single sequence MFE	-28.38
Consensus MFE	-22.25
Energy contribution	-23.38
Covariance contribution	1.12
Combinations/Pair	1.07
Mean z-score	-1.54
Structure conservation index	0.78
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.01
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>dm3.chr3L 7170173 94 + 24543557
ACUGGGUGCCACUUGCAUCUUGGCCCCUGCCACACUU------UCAAGUUGCAGAAGCGAAAAGUUUCGUGGCAAAAGUUUAUGAAAAAUUAUGAAUUUC
...(((.((((.........)))))))(((((((((.------...)))....(((((.....))))))))))).((((((((((....)))))))))). ( -28.70, z-score =  -2.47, R)
>droSec1.super_2 7096323 94 + 7591821
ACUGGGUGCCACCUGCAGCUUGGCCCCGGCCACAUUU------UCAAGUGGCAGAAGCGAAAAGUUUCGUGGCAAAAGUUUAUGAAAAAUUAUGAAUUUC
......((((((.(((....((((....))))((((.------...)))))))(((((.....))))))))))).((((((((((....)))))))))). ( -29.00, z-score =  -1.58, R)
>droYak2.chr3L 7767838 100 + 24197627
ACUGGGUGCCACUUGCAGCUUGGCCCUCUCCACUCUUUCUCUCUCAAGUGGCAAAAGCGAAAAGUUUCGUGGCUUAAGCUUAUGAAAUAUUAUGAAUUUC
.((...(((((((((.((..(((......)))..))........)))))))))..))......((((((((((....)).))))))))............ ( -22.30, z-score =  -0.11, R)
>droEre2.scaffold_4784 21584999 94 - 25762168
ACUGGGUGCCACUUGCAGCUUGGCCCCUUCCACUGCG------CCAAGUGGCAGAGGCGAAAAGUUUCGUGGCAAAAGCUUAUGAGAAAUUAUGAAUUUC
.((...((((((.(((.(((((((.(........).)------)))))).)))(((((.....)))))))))))..)).((((((....))))))..... ( -33.50, z-score =  -1.99, R)
>consensus
ACUGGGUGCCACUUGCAGCUUGGCCCCUGCCACACUU______UCAAGUGGCAGAAGCGAAAAGUUUCGUGGCAAAAGCUUAUGAAAAAUUAUGAAUUUC
.......(((((.(((.((((((....................)))))).)))(((((.....))))))))))..((((((((((....)))))))))). (-22.25 = -23.38 +   1.12)

alignment

secondary structure

dotplot

Window 8

Location	7,170,173 – 7,170,267
Length	94
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	86.43
Shannon entropy	0.21414
G+C content	0.45574
Mean single sequence MFE	-27.68
Consensus MFE	-23.94
Energy contribution	-24.88
Covariance contribution	0.94
Combinations/Pair	1.20
Mean z-score	-1.54
Structure conservation index	0.86
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.68
SVM RNA-class probability	0.785128
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7170173 94 - 24543557
GAAAUUCAUAAUUUUUCAUAAACUUUUGCCACGAAACUUUUCGCUUCUGCAACUUGA------AAGUGUGGCAGGGGCCAAGAUGCAAGUGGCACCCAGU
((((.........))))....(((..((((((.....((((.((((((((.(((...------.)))...)))))))).)))).....))))))...))) ( -26.60, z-score =  -1.75, R)
>droSec1.super_2 7096323 94 - 7591821
GAAAUUCAUAAUUUUUCAUAAACUUUUGCCACGAAACUUUUCGCUUCUGCCACUUGA------AAAUGUGGCCGGGGCCAAGCUGCAGGUGGCACCCAGU
((((.........))))....(((..(((((((((....)))(((((.(((((....------....))))).)))))..........))))))...))) ( -26.80, z-score =  -1.43, R)
>droYak2.chr3L 7767838 100 - 24197627
GAAAUUCAUAAUAUUUCAUAAGCUUAAGCCACGAAACUUUUCGCUUUUGCCACUUGAGAGAGAAAGAGUGGAGAGGGCCAAGCUGCAAGUGGCACCCAGU
(((((.......)))))..........(((((....((((((((((((....(((....))).)))))))))))).((......))..)))))....... ( -28.20, z-score =  -1.87, R)
>droEre2.scaffold_4784 21584999 94 + 25762168
GAAAUUCAUAAUUUCUCAUAAGCUUUUGCCACGAAACUUUUCGCCUCUGCCACUUGG------CGCAGUGGAAGGGGCCAAGCUGCAAGUGGCACCCAGU
(((((.....)))))......(((..(((((((((....)))((((((.(((((...------...))))).))))))..........))))))...))) ( -29.10, z-score =  -1.12, R)
>consensus
GAAAUUCAUAAUUUUUCAUAAACUUUUGCCACGAAACUUUUCGCUUCUGCCACUUGA______AAGAGUGGAAGGGGCCAAGCUGCAAGUGGCACCCAGU
.....................(((..(((((((((....)))(((((((((((((..........)))))))))))))..........))))))...))) (-23.94 = -24.88 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:09:04 2011