Locus 8557

Sequence ID	dm3.chr3RHet
Location	659,146 – 659,238
Length	92
Max. P	0.993553

overview

Window 7

Location	659,146 – 659,238
Length	92
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	75.98
Shannon entropy	0.39766
G+C content	0.50191
Mean single sequence MFE	-34.58
Consensus MFE	-20.51
Energy contribution	-21.58
Covariance contribution	1.06
Combinations/Pair	1.25
Mean z-score	-2.86
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.62
SVM RNA-class probability	0.993553
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 659146 92 + 2517507
------------------GGAGCGAC-GAGUUGGCACUGACGUUAGCAGAAGCAGCGACAGUGCUGGGGGGUAUAAAUAUCACCCAAUUUUGUACUUUAAAUUUAGUUCCG
------------------(((((...-...(..((((((.((((.((....)))))).))))))..)((((((((((...........)))))))))).......))))). ( -31.90, z-score =  -3.62, R)
>droSim1.chrU 2292476 104 - 15797150
GGAGCGACGAUGGCAGAGUCAGCAACGGAGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCU-------AUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGUUCCG
((((((((.........)))....(((((((((((((((.((((.((....)))))).)))))).-------............)))))))))............))))). ( -31.81, z-score =  -2.22, R)
>droSec1.super_42 220670 111 - 298440
GGAGCGACGAUGGCAGAGCCAGCAACUGAGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCUGGGGGGUAUAAAUACCACCCAAAUAUGUACUUUAAAUUUAGUUCCG
(((((..((....(((.((((((......)))))).))).((((.((....)))))).))((((((((.((((....)))).)))).....))))..........))))). ( -41.40, z-score =  -3.64, R)
>droYak2.chrU 17377185 110 + 28119190
GGAGCAACGAGGGCAGAGGCAGCGACGGAGCCAGCACCGACGCCAACAGAGGCAGCGACGGUGCUGGGAGGUAUAAAUAACACCCAAAU-UGUAAAAUAGCUUUAGUUCAA
.((((..((...((....))..))..(((((((((((((.(((...........))).))))))))((..((.......))..))....-.........))))).)))).. ( -33.20, z-score =  -1.96, R)
>consensus
GGAGCGACGAUGGCAGAGGCAGCAACGGAGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCUGGGGGGUAUAAAUACCACCCAAAUUUGUACUUUAAAUUUAGUUCCG
.......................(((.((((((((((((.((((.((....)))))).)))))))(((.((((....)))).)))..............))))).)))... (-20.51 = -21.58 +   1.06)

alignment

secondary structure

dotplot

Window 8

Location	659,146 – 659,238
Length	92
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	75.98
Shannon entropy	0.39766
G+C content	0.50191
Mean single sequence MFE	-27.70
Consensus MFE	-16.20
Energy contribution	-17.32
Covariance contribution	1.12
Combinations/Pair	1.24
Mean z-score	-1.47
Structure conservation index	0.58
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.02
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>dm3.chr3RHet 659146 92 - 2517507
CGGAACUAAAUUUAAAGUACAAAAUUGGGUGAUAUUUAUACCCCCCAGCACUGUCGCUGCUUCUGCUAACGUCAGUGCCAACUC-GUCGCUCC------------------
.((.(((........)))........(((((.......))))).)).((((((.((..((....))...)).))))))......-........------------------ ( -20.50, z-score =  -1.42, R)
>droSim1.chrU 2292476 104 + 15797150
CGGAACUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAU-------AGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACUCCGUUGCUGACUCUGCCAUCGUCGCUCC
.((((((........))).........(((((((.....-------.((((.(.((((((....)).)))).).))))((((...)))).......))))))).....))) ( -25.80, z-score =  -0.56, R)
>droSec1.super_42 220670 111 + 298440
CGGAACUAAAUUUAAAGUACAUAUUUGGGUGGUAUUUAUACCCCCCAGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACUCAGUUGCUGGCUCUGCCAUCGUCGCUCC
.(.((((..................((((.((((....)))).))))((((.(.((((((....)).)))).).))))......)))).)((((...)))).......... ( -32.10, z-score =  -1.67, R)
>droYak2.chrU 17377185 110 - 28119190
UUGAACUAAAGCUAUUUUACA-AUUUGGGUGUUAUUUAUACCUCCCAGCACCGUCGCUGCCUCUGUUGGCGUCGGUGCUGGCUCCGUCGCUGCCUCUGCCCUCGUUGCUCC
.........(((.........-....((((((.....)))))).(((((((((.((((.........)))).))))))))).......))).................... ( -32.40, z-score =  -2.23, R)
>consensus
CGGAACUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAUACCCCCCAGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACUCCGUCGCUGCCUCUGCCAUCGUCGCUCC
..........................(((((.......)))))....((((((.((((((....)).)))).))))))................................. (-16.20 = -17.32 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:47:52 2011