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Trypanosoma brucei vs Pythium irregulare LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,089 alignment blocks

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

Uncovered: 24,746,076 out of 25,789,186
Covered: 1,043,110 out of 25,789,186

Uncovered: 12,144,092 out of 13,171,744
Matches: 604,661 out of 13,171,744
Mismatches: 384,356 out of 13,171,744
Insertions: 38,635 out of 13,171,744
Identity over aligned base-pairs: 58.8%

Pythium irregulare

Uncovered: 41,788,370 out of 42,968,084
Covered: 1,179,714 out of 42,968,084

Uncovered: 19,460,749 out of 20,543,058
Matches: 630,084 out of 20,543,058
Mismatches: 404,180 out of 20,543,058
Insertions: 48,045 out of 20,543,058
Identity over aligned base-pairs: 58.2%

Block size distribution

Size range All 3,089 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
22.0 bp
10 bp - 100 bp
375
26.2 kb
116
8.5 kb
100 bp - 1 kb
2,365
916.7 kb
1,396
659.0 kb
1 kb - 10 kb
346
553.2 kb
427
782.2 kb
10 kb - 100 kb
4
46.6 kb