Locus 15174

Sequence ID	dm3.chrX
Location	17,752,367 – 17,752,463
Length	96
Max. P	0.970259

overview

Window 3

Location	17,752,367 – 17,752,463
Length	96
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	67.01
Shannon entropy	0.51399
G+C content	0.27763
Mean single sequence MFE	-15.52
Consensus MFE	-7.06
Energy contribution	-7.62
Covariance contribution	0.56
Combinations/Pair	1.27
Mean z-score	-1.41
Structure conservation index	0.46
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.08
SVM RNA-class probability	0.532370
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17752367 96 + 22422827
---GUUCGAAAUUCACGGACAUAGCAAUAAGAAAAGCUUUAUU-CUUUGUUUUCGU---AAAUUUCUUUUGUUUUUUUUAAUAAAGUUUUUUAUUUGGCAAUC
---(((((.......)))))...((.....(((((((((((((-.........((.---..........))........))))))))))))).....)).... ( -14.13, z-score =  -0.90, R)
>droSim1.chrX 13812364 91 + 17042790
---GUUCGAAAUUCACGGACAAAGCAAUAAGAAAAGCUUUAUU-CUUUGUUUUCGU---AAAUUUCUUUUGUUUUUUU----AAAGUUUUUU-UUUGGCAAUC
---(((((.......)))))...((...(((((((((((((..-............---..................)----))))))))))-))..)).... ( -15.55, z-score =  -1.26, R)
>droSec1.super_8 62707 80 + 3762037
---GUUCGAAAUUCACGGACAAAGCAAUAAGAAAAGCUUUAUU-CUUUGUUUUCGU---AAAUUUCUUUUGUUUUUUU----------------UUGGCAAUC
---....((((((.((((((((((.((((((......))))))-)))))))..)))---.))))))..(((((.....----------------..))))).. ( -16.50, z-score =  -2.30, R)
>droMoj3.scaffold_6328 3113471 97 - 4453435
UAGAUGUGUUUUUCUUAAACGAAAAAAAAAAAACACGUUUAUUUCCUUAUUUUUAUUCUAACUGCCGUUUAGUGCUGU------AAGCUGCGCCUAAGAAAUC
(((((((((((((.((.........)).)))))))))))))..............((((...(((.(((((......)------)))).)))....))))... ( -15.90, z-score =  -1.20, R)
>consensus
___GUUCGAAAUUCACGGACAAAGCAAUAAGAAAAGCUUUAUU_CUUUGUUUUCGU___AAAUUUCUUUUGUUUUUUU______AGUUUUUU_UUUGGCAAUC
.......((((((.((((((((((.((((((......)))))).)))))))..)))....))))))..................................... ( -7.06 =  -7.62 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	17,752,367 – 17,752,463
Length	96
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	67.01
Shannon entropy	0.51399
G+C content	0.27763
Mean single sequence MFE	-16.52
Consensus MFE	-6.71
Energy contribution	-7.40
Covariance contribution	0.69
Combinations/Pair	1.24
Mean z-score	-2.55
Structure conservation index	0.41
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.83
SVM RNA-class probability	0.970259
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17752367 96 - 22422827
GAUUGCCAAAUAAAAAACUUUAUUAAAAAAAACAAAAGAAAUUU---ACGAAAACAAAG-AAUAAAGCUUUUCUUAUUGCUAUGUCCGUGAAUUUCGAAC---
........((((((....)))))).............(((((((---(((...(((.((-(((((........))))).)).))).))))))))))....--- ( -14.50, z-score =  -2.42, R)
>droSim1.chrX 13812364 91 - 17042790
GAUUGCCAAA-AAAAAACUUU----AAAAAAACAAAAGAAAUUU---ACGAAAACAAAG-AAUAAAGCUUUUCUUAUUGCUUUGUCCGUGAAUUUCGAAC---
..........-..........----............(((((((---(((...((((((-(((((........))))).)))))).))))))))))....--- ( -17.50, z-score =  -3.27, R)
>droSec1.super_8 62707 80 - 3762037
GAUUGCCAA----------------AAAAAAACAAAAGAAAUUU---ACGAAAACAAAG-AAUAAAGCUUUUCUUAUUGCUUUGUCCGUGAAUUUCGAAC---
.........----------------............(((((((---(((...((((((-(((((........))))).)))))).))))))))))....--- ( -17.50, z-score =  -3.60, R)
>droMoj3.scaffold_6328 3113471 97 + 4453435
GAUUUCUUAGGCGCAGCUU------ACAGCACUAAACGGCAGUUAGAAUAAAAAUAAGGAAAUAAACGUGUUUUUUUUUUUUCGUUUAAGAAAAACACAUCUA
..(((((((.......((.------((.((........)).)).))........)))))))......(((((((((((.........)))))))))))..... ( -16.56, z-score =  -0.92, R)
>consensus
GAUUGCCAAA_AAAAAACU______AAAAAAACAAAAGAAAUUU___ACGAAAACAAAG_AAUAAAGCUUUUCUUAUUGCUUUGUCCGUGAAUUUCGAAC___
.....................................(((((((...(((...((((((.(((((........))))).)))))).))))))))))....... ( -6.71 =  -7.40 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:54:20 2011