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Tetrahymena thermophila vs Phytophthora kernoviae LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,176 alignment blocks

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

Uncovered: 101,833,447 out of 103,014,375
Covered: 1,180,928 out of 103,014,375

Uncovered: 47,084,578 out of 48,193,658
Matches: 651,327 out of 48,193,658
Mismatches: 427,819 out of 48,193,658
Insertions: 29,934 out of 48,193,658
Identity over aligned base-pairs: 58.7%

Phytophthora kernoviae

Uncovered: 42,192,710 out of 43,208,681
Covered: 1,015,971 out of 43,208,681

Uncovered: 10,647,090 out of 11,344,308
Matches: 410,780 out of 11,344,308
Mismatches: 269,193 out of 11,344,308
Insertions: 17,245 out of 11,344,308
Identity over aligned base-pairs: 58.9%

Block size distribution

Size range All 5,176 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
23
115.0 bp
10 bp - 100 bp
886
62.6 kb
267
19.8 kb
100 bp - 1 kb
4,135
1.3 Mb
1,961
784.5 kb
1 kb - 10 kb
132
195.6 kb
352
679.1 kb
10 kb - 100 kb
3
35.3 kb