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Schizosaccharomyces octosporus vs Trichoderma virens LastZ results

Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Schizosaccharomyces octosporus 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

ParameterSchizosaccharomyces octosporusTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,029 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Schizosaccharomyces octosporus

Uncovered: 9,607,796 out of 11,634,473
Covered: 2,026,677 out of 11,634,473

Uncovered: 4,951,032 out of 6,921,651
Matches: 1,192,819 out of 6,921,651
Mismatches: 734,173 out of 6,921,651
Insertions: 43,627 out of 6,921,651
Identity over aligned base-pairs: 60.5%

Trichoderma virens

Uncovered: 36,877,772 out of 39,022,666
Covered: 2,144,894 out of 39,022,666

Uncovered: 15,500,241 out of 17,541,951
Matches: 1,211,681 out of 17,541,951
Mismatches: 754,598 out of 17,541,951
Insertions: 75,431 out of 17,541,951
Identity over aligned base-pairs: 59.3%

Block size distribution

Size range All 5,029 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
50.0 bp
10 bp - 100 bp
620
43.7 kb
84
6.2 kb
100 bp - 1 kb
3,795
1.5 Mb
1,481
793.3 kb
1 kb - 10 kb
605
951.3 kb
930
1.6 Mb
10 kb - 100 kb
2
28.1 kb