Locus 6346

Sequence ID	3R_DroMel_CAF1
Location	16,608,732 – 16,608,869
Length	137
Max. P	0.962266

overview

Window 1

Location	16,608,732 – 16,608,832
Length	100
Sequences	3
Columns	103
Reading direction	reverse
Mean pairwise identity	90.20
Mean single sequence MFE	-34.63
Consensus MFE	-30.81
Energy contribution	-31.14
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.89
SVM decision value	0.76
SVM RNA-class probability	0.842540
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16608732 100 - 27905053
CCGGUUCUCGGUUCGCCAACGUCUGAGAAUCGAACUGAGAAUCGAGAACUCAGAAUCGGCAGCAGCAGCAG---CAGAAUCAGAAGCAGAGGCUGUGGCCGCU
.((((((((((((((....(......)...))))))))))))))............((((.(((((..(.(---(..........)).)..))))).)))).. ( -36.60)
>DroSec_CAF1 165176 103 - 1
CCGGUUCUCGGUUCGCCAACGUCUGAGAAUCGAACUGAGAAUCGAGAACUCAGAAUCGGCAGCAGCAGCAGAAACAGAAUCAGAAGCAGAGGCUGUGGCCGCU
.((((((((((((((....(......)...))))))))))))))............((((.(((((.((................))....))))).)))).. ( -34.29)
>DroYak_CAF1 165555 89 - 1
CCGGUUCUCGGUUCGCCAACGUCUGAGAAUCGAACUGAG-------AA-UCAGAAUCGGCAGCAGCAG------CAGAAUCAGAAGCAGAGGCUGUAGCCGCU
..(((((((((((((....(......)...)))))))))-------))-)).....((((.(((((.(------(..........))....))))).)))).. ( -33.00)
>consensus
CCGGUUCUCGGUUCGCCAACGUCUGAGAAUCGAACUGAGAAUCGAGAACUCAGAAUCGGCAGCAGCAGCAG___CAGAAUCAGAAGCAGAGGCUGUGGCCGCU
.((((((((((..((....)).))))))))))..(((((.........)))))...((((.(((((.........................))))).)))).. (-30.81 = -31.14 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	16,608,766 – 16,608,869
Length	103
Sequences	3
Columns	103
Reading direction	reverse
Mean pairwise identity	94.82
Mean single sequence MFE	-37.70
Consensus MFE	-36.20
Energy contribution	-36.53
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.40
Structure conservation index	0.96
SVM decision value	1.54
SVM RNA-class probability	0.962266
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16608766 103 - 27905053
CGCGUUGUAAUAAUGGCGGACGGCAACGUCUACGUCACCGGUUCUCGGUUCGCCAACGUCUGAGAAUCGAACUGAGAAUCGAGAACUCAGAAUCGGCAGCAGC
.(((((((.....(((((((((....))))..))))).((((((((((((((....(......)...))))))))))))))..............))))).)) ( -38.30)
>DroSec_CAF1 165213 103 - 1
CGCGUUGUAAUAAUGGCGGACGGCAACGUCUACGUCACCGGUUCUCGGUUCGCCAACGUCUGAGAAUCGAACUGAGAAUCGAGAACUCAGAAUCGGCAGCAGC
.(((((((.....(((((((((....))))..))))).((((((((((((((....(......)...))))))))))))))..............))))).)) ( -38.30)
>DroYak_CAF1 165586 95 - 1
CGCGUUGUAAUAAUGGCGGACGGCAACGUCUACGUCACCGGUUCUCGGUUCGCCAACGUCUGAGAAUCGAACUGAG-------AA-UCAGAAUCGGCAGCAGC
.(((((((.....(((((((((....))))..)))))..(((((((((((((....(......)...)))))))))-------))-)).......))))).)) ( -36.50)
>consensus
CGCGUUGUAAUAAUGGCGGACGGCAACGUCUACGUCACCGGUUCUCGGUUCGCCAACGUCUGAGAAUCGAACUGAGAAUCGAGAACUCAGAAUCGGCAGCAGC
.(((((((.....(((((((((....))))..))))).((((((((((..((....)).))))))))))..(((((.........))))).....))))).)) (-36.20 = -36.53 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:17 2006