Locus 13385

Sequence ID	dm3.chrX
Location	6,246,550 – 6,246,604
Length	54
Max. P	0.996691

overview

Window 1

Location	6,246,550 – 6,246,604
Length	54
Sequences	6
Columns	62
Reading direction	forward
Mean pairwise identity	72.29
Shannon entropy	0.50034
G+C content	0.44316
Mean single sequence MFE	-12.52
Consensus MFE	-8.57
Energy contribution	-9.93
Covariance contribution	1.36
Combinations/Pair	1.15
Mean z-score	-2.30
Structure conservation index	0.68
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.97
SVM RNA-class probability	0.996691
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6246550 54 + 22422827
--UGCUUUUCGACCAGUGUAUCGAAUUCCCAUGCUUUCCUGGGAUCUCUAUCCACC------
--.............(((.((.((..(((((........)))))..)).)).))).------ ( -10.90, z-score =  -1.47, R)
>droSim1.chrX 4919752 54 + 17042790
--UGCUUUUCGUUCAGUGUAUCGAAUUCCCAUGCUUUCCUGGGAUCUCUAUACACC------
--.............((((((.((..(((((........)))))..)).)))))).------ ( -15.50, z-score =  -3.97, R)
>droSec1.super_4 5655668 54 - 6179234
--UGCUUUUCGUUCAGUGUAUCGAAUUCCCAUGCUUUCCUGGGAUCUCUAUACACC------
--.............((((((.((..(((((........)))))..)).)))))).------ ( -15.50, z-score =  -3.97, R)
>droYak2.chrX 2240357 58 + 21770863
--UGAUUUUCGUCGAGUGUAUUGAAUUCCCAUGCUUUCCUGGGAUCUCUAUACAUAUAUC--
--.............((((((.((..(((((........)))))..)).)))))).....-- ( -14.20, z-score =  -2.31, R)
>droEre2.scaffold_4690 15211072 54 + 18748788
--UGCUUUUCGUCCAGUGUAUUGAAUUCCCAUGCUUUCCUGGGAUCUCUAUACAUC------
--.............((((((.((..(((((........)))))..)).)))))).------ ( -13.60, z-score =  -3.03, R)
>droAna3.scaffold_13335 1205502 60 - 3335858
UGUACUACUCCCCCUAC-UAUUCCACCCACACAGUUUCC-GAGUUUUCCGGAUUGGAUUCCU
.................-...((((...........(((-(.......)))).))))..... (  -5.40, z-score =   0.96, R)
>consensus
__UGCUUUUCGUCCAGUGUAUCGAAUUCCCAUGCUUUCCUGGGAUCUCUAUACACC______
...............((((((.((..(((((........)))))..)).))))))....... ( -8.57 =  -9.93 +   1.36)

alignment

secondary structure

dotplot

Window 2

Location	6,246,550 – 6,246,604
Length	54
Sequences	6
Columns	62
Reading direction	reverse
Mean pairwise identity	72.29
Shannon entropy	0.50034
G+C content	0.44316
Mean single sequence MFE	-14.78
Consensus MFE	-7.76
Energy contribution	-9.28
Covariance contribution	1.53
Combinations/Pair	1.08
Mean z-score	-2.62
Structure conservation index	0.52
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.71
SVM RNA-class probability	0.994580
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6246550 54 - 22422827
------GGUGGAUAGAGAUCCCAGGAAAGCAUGGGAAUUCGAUACACUGGUCGAAAAGCA--
------((((....(((.(((((........))))).)))....))))............-- ( -14.40, z-score =  -1.84, R)
>droSim1.chrX 4919752 54 - 17042790
------GGUGUAUAGAGAUCCCAGGAAAGCAUGGGAAUUCGAUACACUGAACGAAAAGCA--
------(((((((.(((.(((((........))))).))).)))))))............-- ( -18.00, z-score =  -4.42, R)
>droSec1.super_4 5655668 54 + 6179234
------GGUGUAUAGAGAUCCCAGGAAAGCAUGGGAAUUCGAUACACUGAACGAAAAGCA--
------(((((((.(((.(((((........))))).))).)))))))............-- ( -18.00, z-score =  -4.42, R)
>droYak2.chrX 2240357 58 - 21770863
--GAUAUAUGUAUAGAGAUCCCAGGAAAGCAUGGGAAUUCAAUACACUCGACGAAAAUCA--
--......(((((.(((.(((((........))))).))).)))))..............-- ( -13.80, z-score =  -2.66, R)
>droEre2.scaffold_4690 15211072 54 - 18748788
------GAUGUAUAGAGAUCCCAGGAAAGCAUGGGAAUUCAAUACACUGGACGAAAAGCA--
------..(((((.(((.(((((........))))).))).)))))..............-- ( -13.80, z-score =  -2.92, R)
>droAna3.scaffold_13335 1205502 60 + 3335858
AGGAAUCCAAUCCGGAAAACUC-GGAAACUGUGUGGGUGGAAUA-GUAGGGGGAGUAGUACA
.....(((..(((((.....))-))).(((((.........)))-))....)))........ ( -10.70, z-score =   0.53, R)
>consensus
______GGUGUAUAGAGAUCCCAGGAAAGCAUGGGAAUUCAAUACACUGGACGAAAAGCA__
........(((((.(((.(((((........))))).))).)))))................ ( -7.76 =  -9.28 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:20:24 2011