Locus 6883

Sequence ID	3R_DroMel_CAF1
Location	18,194,101 – 18,194,250
Length	149
Max. P	0.931382

overview

Window 3

Location	18,194,101 – 18,194,210
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	95.78
Mean single sequence MFE	-28.93
Consensus MFE	-26.96
Energy contribution	-27.00
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.42
Structure conservation index	0.93
SVM decision value	1.21
SVM RNA-class probability	0.931382
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18194101 109 - 27905053
CAGCUUCGUCUCGCUCGCACUGCCAUUAUGCAAGUGCGUGAGCAUCUACUUUCCUUUUAUCUUCCGCUCUCUCUUUCGCUCAUCGUGAGUGACACGCGCAGAAACCGUG
..((..(((.(((((((((((((......)).)))))((((((..................................))))))...)))))).))).)).......... ( -27.78)
>DroSec_CAF1 2291 109 - 1
CAGCUCCGUCUCGCUCGCACUGCCAUUAUGCAAGUGCGUGAGCAUCUACUUUCCUUUUAUCUUCCUCUCUCUCUUUCGCUCAUCGUGAGUGACACGCGCAGAAAGCGUG
.......((.(((((((((((((......)).)))))((((((..................................))))))...)))))).))((((.....)))). ( -28.98)
>DroSim_CAF1 2155 109 - 1
CAGCUCCGUCUCGCUCGCACUGCCAUUAUGCAAGUGCGUGAGCAUCUACUUUCCUUUUAUCUUCCUCUCUCUCUUUCGCUCAUCGUGAGUGACACGCGCAGAAAGCGUG
.......((.(((((((((((((......)).)))))((((((..................................))))))...)))))).))((((.....)))). ( -28.98)
>DroEre_CAF1 2442 109 - 1
CAGCUCCGUCCCGCUCGCACUGCCAUUAUGCAAGUGCGUGAGCAUCUACUUUCCUUUUAUCUUCUUCCCUCUCUUUCGUUCAUCGUGAGUGACACGCGCAGAAAGCGUG
...........(((((((..(((......))).((((....)))).......................................))))))).(((((.......))))) ( -25.70)
>DroYak_CAF1 2346 109 - 1
CAGCUUCGUCUCGCUCGCACUGCCAUUAUGCAAGUGCGUGAGCAUGGGCUUUCCUUUUAUCUUUCUCUCUCUCUUUCGCUCAUCGUGAGUGACACGCGCAGAAAGCGUG
.((((.((((((((..(((((((......)).)))))))))).))))))).........................((((((.....))))))(((((.......))))) ( -33.20)
>consensus
CAGCUCCGUCUCGCUCGCACUGCCAUUAUGCAAGUGCGUGAGCAUCUACUUUCCUUUUAUCUUCCUCUCUCUCUUUCGCUCAUCGUGAGUGACACGCGCAGAAAGCGUG
..((..(((.(((((((((((((......)).)))))((((((..................................))))))...)))))).))).)).......... (-26.96 = -27.00 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	18,194,130 – 18,194,250
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-30.65
Consensus MFE	-30.30
Energy contribution	-29.70
Covariance contribution	-0.60
Combinations/Pair	1.13
Mean z-score	-1.21
Structure conservation index	0.99
SVM decision value	0.89
SVM RNA-class probability	0.876146
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18194130 120 + 27905053
AGCGAAAGAGAGAGCGGAAGAUAAAAGGAAAGUAGAUGCUCACGCACUUGCAUAAUGGCAGUGCGAGCGAGACGAAGCUGUUUUCUGUGGAGGAGAUUAGGUUGUCAAGGUCAGCACAGU
.((........(((((....................)))))..(((((.((......)))))))((.(..(((((..(((.(((((.....))))).))).)))))..).)).))..... ( -30.35)
>DroSec_CAF1 2320 120 + 1
AGCGAAAGAGAGAGAGGAAGAUAAAAGGAAAGUAGAUGCUCACGCACUUGCAUAAUGGCAGUGCGAGCGAGACGGAGCUGCUUUCUGUGGAGGAGAUUAGGUUGUCAAGGUCAGCACAGU
.((.......................(((((((((.(((((.((((((.((......))))))))...))).))...))))))))).(((....(((......)))....)))))..... ( -30.00)
>DroSim_CAF1 2184 120 + 1
AGCGAAAGAGAGAGAGGAAGAUAAAAGGAAAGUAGAUGCUCACGCACUUGCAUAAUGGCAGUGCGAGCGAGACGGAGCUGUUUUCUGUGGAGGAGAUUAGGUUGUCAAGGUCAGCACAGU
..(....).......................((.(((((((..(((((.((......)))))))))))..(((((..(((.(((((.....))))).))).)))))...))).))..... ( -28.10)
>DroEre_CAF1 2471 120 + 1
AACGAAAGAGAGGGAAGAAGAUAAAAGGAAAGUAGAUGCUCACGCACUUGCAUAAUGGCAGUGCGAGCGGGACGGAGCUGUUCUCCGUGGAGGAGAUUAGGUUGUCAAGGUCAGCACAGU
..(....).......................((.(((((((..(((((.((......)))))))))))..(((((..(((.(((((.....))))).))).)))))...))).))..... ( -33.40)
>DroYak_CAF1 2375 120 + 1
AGCGAAAGAGAGAGAGAAAGAUAAAAGGAAAGCCCAUGCUCACGCACUUGCAUAAUGGCAGUGCGAGCGAGACGAAGCUGUUUUCCGUGGAGGAGAUUAGGUUGUCAAGGUCAGCACAGU
..(....).......................((((.(((((..(((((.((......)))))))))))).(((((..(((.(((((.....))))).))).)))))..))...))..... ( -31.40)
>consensus
AGCGAAAGAGAGAGAGGAAGAUAAAAGGAAAGUAGAUGCUCACGCACUUGCAUAAUGGCAGUGCGAGCGAGACGGAGCUGUUUUCUGUGGAGGAGAUUAGGUUGUCAAGGUCAGCACAGU
..(....).......................((.(((((((..(((((.((......)))))))))))..(((((..(((.(((((.....))))).))).)))))...))).))..... (-30.30 = -29.70 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:24 2006