Locus 12775

Sequence ID	dm3.chrX
Location	2,101,144 – 2,101,225
Length	81
Max. P	0.957675

overview

Window 1

Location	2,101,144 – 2,101,225
Length	81
Sequences	5
Columns	87
Reading direction	forward
Mean pairwise identity	86.56
Shannon entropy	0.23041
G+C content	0.51987
Mean single sequence MFE	-30.34
Consensus MFE	-17.32
Energy contribution	-17.88
Covariance contribution	0.56
Combinations/Pair	1.22
Mean z-score	-2.80
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.96
SVM RNA-class probability	0.861549
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2101144 81 + 22422827
AGAGCGGCAGAGAGCGGCCACAUAAAUAGAUGUGGCCGGCCGGAUAUGUGGAUCGCGUACGUACAUACA------UAUAUGCCCAUG
...(.((((.....(((((((((......))))))))).....(((((((...((....))....))))------))).)))))... ( -28.50, z-score =  -2.01, R)
>droEre2.scaffold_4644 2064139 83 + 2521924
AGAGCGGCGGAGAGUGGCCACAUAAAUAGAUGUG----GCCGGAUACGUGGAUCGUGUACGUAGGUACAUAUGUAUAUAUGUACAUG
.((.(.(((.....(((((((((......)))))----))))....))).).))(((((((((.((((....)))).))))))))). ( -33.90, z-score =  -4.78, R)
>droYak2.chrX_random 199467 82 + 1802292
AGAGCGGCGGAGAGCGGCCACAUAAAUAGAUGUG--UGGCCGGAUAUGUGGAUCGUCUUUGUACGUAGACG---AUAUAUGCCCAUG
...(.(((......((((((((((......))))--)))))).....(((.(((((((........)))))---)).)))))))... ( -31.70, z-score =  -3.39, R)
>droSec1.super_10 1884538 81 + 3036183
AGAGCGGCAGAGAGCGGCCACAUAAAUAGAUGUGGCCGGCCGGAUAUGUGGAUCGCGGACGUACAUACA------UAUAUGCCCAUG
...(.((((.....(((((((((......))))))))).....(((((((...((....))....))))------))).)))))... ( -28.50, z-score =  -2.06, R)
>droSim1.chrX_random 1199170 81 + 5698898
AGAGCGGCGGAGAGCGGCCACAUAAAUAGAUGUGGCCGGCCGGAUAUGUGGAUCGCGUACGUACAUACA------UAUAUGCCCAUG
...(.(((((....(((((((((......))))))))).))..(((((((...((....))....))))------)))..))))... ( -29.10, z-score =  -1.74, R)
>consensus
AGAGCGGCGGAGAGCGGCCACAUAAAUAGAUGUGGCCGGCCGGAUAUGUGGAUCGCGUACGUACAUACA______UAUAUGCCCAUG
.(.(((((......(((((((((......))))))))))))...((((((...((....)))))))).............)).)... (-17.32 = -17.88 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	2,101,144 – 2,101,225
Length	81
Sequences	5
Columns	87
Reading direction	reverse
Mean pairwise identity	86.56
Shannon entropy	0.23041
G+C content	0.51987
Mean single sequence MFE	-27.04
Consensus MFE	-17.16
Energy contribution	-18.88
Covariance contribution	1.72
Combinations/Pair	1.14
Mean z-score	-2.96
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.64
SVM RNA-class probability	0.957675
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2101144 81 - 22422827
CAUGGGCAUAUA------UGUAUGUACGUACGCGAUCCACAUAUCCGGCCGGCCACAUCUAUUUAUGUGGCCGCUCUCUGCCGCUCU
...((((..(((------(((..((.((....))))..))))))..((((((((((((......)))))))))......))))))). ( -28.50, z-score =  -2.38, R)
>droEre2.scaffold_4644 2064139 83 - 2521924
CAUGUACAUAUAUACAUAUGUACCUACGUACACGAUCCACGUAUCCGGC----CACAUCUAUUUAUGUGGCCACUCUCCGCCGCUCU
...((((((((....)))))))).(((((.........)))))...(((----(((((......))))))))............... ( -23.10, z-score =  -3.84, R)
>droYak2.chrX_random 199467 82 - 1802292
CAUGGGCAUAUAU---CGUCUACGUACAAAGACGAUCCACAUAUCCGGCCA--CACAUCUAUUUAUGUGGCCGCUCUCCGCCGCUCU
....(((....((---(((((........))))))).........((((((--((.(......).))))))))......)))..... ( -26.60, z-score =  -3.95, R)
>droSec1.super_10 1884538 81 - 3036183
CAUGGGCAUAUA------UGUAUGUACGUCCGCGAUCCACAUAUCCGGCCGGCCACAUCUAUUUAUGUGGCCGCUCUCUGCCGCUCU
...((((..(((------(((..((.((....))))..))))))..((((((((((((......)))))))))......))))))). ( -28.50, z-score =  -2.39, R)
>droSim1.chrX_random 1199170 81 - 5698898
CAUGGGCAUAUA------UGUAUGUACGUACGCGAUCCACAUAUCCGGCCGGCCACAUCUAUUUAUGUGGCCGCUCUCCGCCGCUCU
...((((..(((------(((..((.((....))))..))))))..((((((((((((......)))))))))......))))))). ( -28.50, z-score =  -2.24, R)
>consensus
CAUGGGCAUAUA______UGUAUGUACGUACGCGAUCCACAUAUCCGGCCGGCCACAUCUAUUUAUGUGGCCGCUCUCCGCCGCUCU
...((((...........(((((....)))))..............((((((((((((......)))))))))......))))))). (-17.16 = -18.88 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:08:33 2011