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OPENSEQ.org
rfa1 and rfa2 c term actual
Genes: A B A+B
Length: 40 42 80
Sequences: 553 438 45
Seq/Len: 13.82 10.43 0.56
MirrorTree (Pazo et al. 2001) 0.55
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.03 0.01
2 0.03 0.04 0.01
5 0.03 0.04 0.01
10 0.03 0.04 0.01
20 0.03 0.04 0.01
100 0.03 0.04 0.11
∞ 0.04 0.04 0.55
Paired alignment generation
None of the genomes have hits within 20 Δgene.
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results
  • ERROR: Not enough sequences to run GREMLIN analysis on (0.56 < 0.6).
ID Seq/Len Name Options I_Prob Status
10214 0.56 rfa1 and rfa2 c term actual Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
10213 0.56 rfa1 and rfa2 c term actual Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
10211 0.56 rfa1 and rfa2 c term actual Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
10208 0.01 rfa1 and rfa2 c term actual Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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