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OPENSEQ.org
CarO-Oxa23redo4
Genes: A B A+B
Length: 246 273 512
Sequences: 197 11667 118
Seq/Len: 0.8 42.74 0.23
MirrorTree (Pazo et al. 2001) 0.31
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.03 0.00
2 0.01 0.03 0.01
5 0.01 0.04 0.01
10 0.01 0.05 0.01
20 0.01 0.06 0.01
100 0.01 0.15 0.06
∞ 0.02 0.23 0.23
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
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 (0.23 < 0.6).
ID Seq/Len Name Options I_Prob Status
2771 0.04 CarO-Oxa23 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
2770 0.37 CarO-Oxa23 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
1299 0.18 CarO-Oxa23 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0696 0.23 CarO-Oxa23redo4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) Killed - Shared
0692 0.14 CarO-Oxa23redo4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0690 0.01 CarO-Oxa23redo3 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0688 0 CarO-Oxa23 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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