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Trypanosoma brucei vs Albugo laibachii LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Albugo laibachii (Albugo laibachii, ENA1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 bruceiAlbugo laibachii
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,562 alignment blocks

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

Uncovered: 24,927,634 out of 25,789,186
Covered: 861,552 out of 25,789,186

Uncovered: 12,336,268 out of 13,171,744
Matches: 490,661 out of 13,171,744
Mismatches: 315,486 out of 13,171,744
Insertions: 29,329 out of 13,171,744
Identity over aligned base-pairs: 58.7%

Albugo laibachii

Uncovered: 31,834,932 out of 32,766,811
Covered: 931,879 out of 32,766,811

Uncovered: 15,037,794 out of 15,902,867
Matches: 501,655 out of 15,902,867
Mismatches: 325,300 out of 15,902,867
Insertions: 38,118 out of 15,902,867
Identity over aligned base-pairs: 58.0%

Block size distribution

Size range All 2,562 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
19.0 bp
10 bp - 100 bp
337
24.9 kb
148
11.6 kb
100 bp - 1 kb
1,948
765.9 kb
1,091
509.3 kb
1 kb - 10 kb
272
413.9 kb
378
660.9 kb
10 kb - 100 kb
2
22.9 kb