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Trypanosoma brucei vs Phytophthora kernoviae LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 bruceiPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,166 alignment blocks

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

Uncovered: 24,721,041 out of 25,789,186
Covered: 1,068,145 out of 25,789,186

Uncovered: 12,120,503 out of 13,171,744
Matches: 620,964 out of 13,171,744
Mismatches: 388,657 out of 13,171,744
Insertions: 41,620 out of 13,171,744
Identity over aligned base-pairs: 59.1%

Phytophthora kernoviae

Uncovered: 41,932,981 out of 43,208,681
Covered: 1,275,700 out of 43,208,681

Uncovered: 10,438,180 out of 11,344,308
Matches: 530,905 out of 11,344,308
Mismatches: 335,563 out of 11,344,308
Insertions: 39,660 out of 11,344,308
Identity over aligned base-pairs: 58.6%

Block size distribution

Size range All 3,166 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6
24.0 bp
10 bp - 100 bp
331
23.4 kb
106
7.8 kb
100 bp - 1 kb
2,458
983.7 kb
1,456
694.1 kb
1 kb - 10 kb
371
587.3 kb
476
844.2 kb
10 kb - 100 kb
4
48.4 kb