Locus 2860

Sequence ID	dm3.chr2RHet
Location	891,067 – 891,225
Length	158
Max. P	0.800262

overview

Window 4

Location	891,067 – 891,155
Length	88
Sequences	4
Columns	88
Reading direction	forward
Mean pairwise identity	85.34
Shannon entropy	0.21569
G+C content	0.54230
Mean single sequence MFE	-24.93
Consensus MFE	-22.49
Energy contribution	-22.49
Covariance contribution	0.00
Combinations/Pair	1.05
Mean z-score	-1.37
Structure conservation index	0.90
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.73
SVM RNA-class probability	0.800262
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 891067 88 + 3288761
AUUAAGUUGAACUUGUGGCGCCCAGACUGAAGCCAGGUCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCGUGGAGGA
.....((((.((((((..((((.....(((.((((....)))).))).))))...))))))..)))).......((((.....)))). ( -26.20, z-score =  -0.59, R)
>droSim1.chrU 4942486 75 - 15797150
-------------UGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGA
-------------.(((..(((.((((((.....)))))))))..)))((((..............))))....((((.....)))). ( -26.34, z-score =  -1.18, R)
>droYak2.chrU 2414593 76 + 28119190
------------UUGUGGCGCCCAGACUAAAACCCAGUCUGGCAACACGGCGUAAACAAGUACUAACGCCAAGACCUUUCCUGGAUGA
------------..(((..(((.(((((.......))))))))..)))(((((............)))))....((......)).... ( -22.70, z-score =  -2.07, R)
>droEre2.scaffold_4784 371781 75 - 25762168
-------------UGUGGCGCCCAGACUAAAGCCCAGUCUGGCAACACGGCGUAAACAAGUACUAACGCCAAGACCUUUCCUGGAGGA
-------------.(((..(((.(((((.......))))))))..)))(((((............)))))....((((.....)))). ( -24.50, z-score =  -1.64, R)
>consensus
_____________UGUGGCGCCCAGACUAAAGCCCAGUCUGGCAACACGGCGAAAACAAGUACUAACGCCAAGACCUUUCCUGGAGGA
..............(((..(((.(((((.......))))))))..)))((((..............))))....((((.....)))). (-22.49 = -22.49 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	891,155 – 891,225
Length	70
Sequences	6
Columns	72
Reading direction	forward
Mean pairwise identity	74.41
Shannon entropy	0.49578
G+C content	0.51067
Mean single sequence MFE	-17.45
Consensus MFE	-7.43
Energy contribution	-8.48
Covariance contribution	1.06
Combinations/Pair	1.17
Mean z-score	-1.74
Structure conservation index	0.43
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.28
SVM RNA-class probability	0.624102
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 891155 70 + 3288761
CGAUAUCUUCUGAUAUCGUCAGACUGGACACACUGAAACUUCAGCUCCGC-GCGCAACAAGCUUA-CGGCAU
.((((((....))))))(((.....(((....((((....)))).)))..-((.......))...-.))).. ( -16.00, z-score =  -1.25, R)
>droAna3.scaffold_13250 842571 67 - 3535662
CGAUAUCGUAUGAGAGUAUCGAUAUCGCUUUUUCUGCGCCUCA----CGACAU-CGACAGCCUCAUCCGCAG
(((((((((((....))).))))))))......(((((.....----.(....-)((.....))...))))) ( -16.00, z-score =  -0.85, R)
>droSim1.chrU 4942561 69 - 15797150
CGAUAUCUUCUGAUAUCGUCAGACUGGACACUACAA--CUUCAACUCCGCCGCGCAACAAGCUUA-CGGUAU
.((((((....))))))(((......))).......--..........((((.((.....))...-)))).. ( -14.60, z-score =  -1.88, R)
>droYak2.chrU 2414669 70 + 28119190
CGAUAUCUUCUGAUAUCGUCAGACUGGCCACUCUGG-ACUUCAACCCCGCCGCGCAACAAGCUUA-CGGCAU
(((((((....)))))))(((((........)))))-...........((((.((.....))...-)))).. ( -18.60, z-score =  -1.99, R)
>droEre2.scaffold_4784 371856 70 - 25762168
CGAUAUCUUUUGAUAUCUUCAGACUGGCCACUCUGG-ACUCCAGCCUUGCCGCGCAACAAGCUUA-CGGCAU
.((((((....))))))...((.((((((.....))-...)))).))(((((.((.....))...-))))). ( -19.70, z-score =  -2.35, R)
>droSec1.super_94 45144 71 - 93855
CGAUAUCUUCUGAUAUCGUCAGACUGGACACACUGGUACUUCAGCUCUGCCGCGCAACAAGCUUA-CGGCAC
(((((((....)))))))..((((((((.((....))..))))).)))((((.((.....))...-)))).. ( -19.80, z-score =  -2.14, R)
>consensus
CGAUAUCUUCUGAUAUCGUCAGACUGGACACUCUGG_ACUUCAGCUCCGCCGCGCAACAAGCUUA_CGGCAU
.((((((....))))))...............................((((.((.....))....)))).. ( -7.43 =  -8.48 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:59:24 2011