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Tetrahymena thermophila vs Phytophthora lateralis LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Tetrahymena thermophila 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

ParameterTetrahymena thermophilaPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,934 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,118,677 out of 103,014,375
Covered: 895,698 out of 103,014,375

Uncovered: 47,385,129 out of 48,193,658
Matches: 471,485 out of 48,193,658
Mismatches: 317,587 out of 48,193,658
Insertions: 19,457 out of 48,193,658
Identity over aligned base-pairs: 58.3%

Phytophthora lateralis

Uncovered: 43,320,237 out of 43,981,379
Covered: 661,142 out of 43,981,379

Uncovered: 13,684,817 out of 14,242,768
Matches: 323,262 out of 14,242,768
Mismatches: 221,134 out of 14,242,768
Insertions: 13,555 out of 14,242,768
Identity over aligned base-pairs: 57.9%

Block size distribution

Size range All 3,934 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16
86.0 bp
10 bp - 100 bp
832
61.5 kb
423
33.0 kb
100 bp - 1 kb
3,007
907.6 kb
1,436
540.2 kb
1 kb - 10 kb
79
113.6 kb
236
476.6 kb
10 kb - 100 kb
3
33.0 kb