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Trypanosoma brucei vs Pythium iwayamai LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Trypanosoma brucei was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterTrypanosoma bruceiPythium iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,974 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Trypanosoma brucei

Uncovered: 24,825,882 out of 25,789,186
Covered: 963,304 out of 25,789,186

Uncovered: 12,220,378 out of 13,171,744
Matches: 557,536 out of 13,171,744
Mismatches: 358,904 out of 13,171,744
Insertions: 34,926 out of 13,171,744
Identity over aligned base-pairs: 58.6%

Pythium iwayamai

Uncovered: 42,143,171 out of 43,199,174
Covered: 1,056,003 out of 43,199,174

Uncovered: 18,627,849 out of 19,552,457
Matches: 541,020 out of 19,552,457
Mismatches: 343,591 out of 19,552,457
Insertions: 39,997 out of 19,552,457
Identity over aligned base-pairs: 58.5%

Block size distribution

Size range All 2,974 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
28.0 bp
10 bp - 100 bp
374
28.1 kb
141
11.3 kb
100 bp - 1 kb
2,298
844.5 kb
1,371
616.1 kb
1 kb - 10 kb
294
473.3 kb
365
661.1 kb
10 kb - 100 kb
5
57.3 kb