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Schizosaccharomyces cryophilus vs Trichoderma virens LastZ results

Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Schizosaccharomyces cryophilus 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 cryophilusTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,033 alignment blocks

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

Uncovered: 9,524,270 out of 11,554,764
Covered: 2,030,494 out of 11,554,764

Uncovered: 5,025,486 out of 7,004,290
Matches: 1,197,764 out of 7,004,290
Mismatches: 736,550 out of 7,004,290
Insertions: 44,490 out of 7,004,290
Identity over aligned base-pairs: 60.5%

Trichoderma virens

Uncovered: 36,906,086 out of 39,022,666
Covered: 2,116,580 out of 39,022,666

Uncovered: 15,514,520 out of 17,541,951
Matches: 1,203,129 out of 17,541,951
Mismatches: 749,816 out of 17,541,951
Insertions: 74,486 out of 17,541,951
Identity over aligned base-pairs: 59.3%

Block size distribution

Size range All 5,033 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
42.0 bp
10 bp - 100 bp
634
44.9 kb
89
6.7 kb
100 bp - 1 kb
3,801
1.5 Mb
1,465
789.2 kb
1 kb - 10 kb
590
907.4 kb
936
1.6 Mb