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OPENSEQ.org
AraC-RNAP D whole genome
Genes: A B A+B
Length: 118 511 629
Sequences: 5 788 1
Seq/Len: 0.04 1.54 0
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 0.50 0.01 0.00
2 0.50 0.01 0.00
5 0.50 0.01 0.00
10 0.50 0.01 0.00
20 0.50 0.01 0.00
100 0.50 0.01 0.00
∞ 0.50 0.02 0.00
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 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.50 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
6558 0.33 AraC-RNAP D whole genome 1 iteration Δgene:(1, ∞) A:(1E-20, 1) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6557 1.37 AraC-RNAP D whole genome Δgene:(1, ∞) A:(1E-20, 4) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
6554 0 AraC-RNAP D whole genome Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6537 1.38 AraC-RNAP D whole genome Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6536 0.17 AraC-RNAP D Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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