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Trypanosoma brucei vs Guillardia theta CCMP2712 LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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 bruceiGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,879 alignment blocks

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

Uncovered: 24,997,911 out of 25,789,186
Covered: 791,275 out of 25,789,186

Uncovered: 12,394,552 out of 13,171,744
Matches: 464,717 out of 13,171,744
Mismatches: 285,412 out of 13,171,744
Insertions: 27,063 out of 13,171,744
Identity over aligned base-pairs: 59.8%

Guillardia theta CCMP2712

Uncovered: 86,321,726 out of 87,266,873
Covered: 945,147 out of 87,266,873

Uncovered: 29,768,083 out of 30,644,092
Matches: 516,087 out of 30,644,092
Mismatches: 321,234 out of 30,644,092
Insertions: 38,688 out of 30,644,092
Identity over aligned base-pairs: 58.9%

Block size distribution

Size range All 2,879 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
19.0 bp
10 bp - 100 bp
566
39.7 kb
138
9.9 kb
100 bp - 1 kb
2,059
729.2 kb
1,116
497.5 kb
1 kb - 10 kb
250
432.9 kb
328
638.1 kb
10 kb - 100 kb
5
56.5 kb