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Schizosaccharomyces pombe vs Trichoderma virens LastZ results

Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Schizosaccharomyces pombe 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 pombeTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,999 alignment blocks

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

Uncovered: 10,579,047 out of 12,631,379
Covered: 2,052,332 out of 12,631,379

Uncovered: 5,180,145 out of 7,176,702
Matches: 1,203,903 out of 7,176,702
Mismatches: 749,530 out of 7,176,702
Insertions: 43,124 out of 7,176,702
Identity over aligned base-pairs: 60.3%

Trichoderma virens

Uncovered: 36,882,929 out of 39,022,666
Covered: 2,139,737 out of 39,022,666

Uncovered: 15,506,188 out of 17,541,951
Matches: 1,204,482 out of 17,541,951
Mismatches: 755,958 out of 17,541,951
Insertions: 75,323 out of 17,541,951
Identity over aligned base-pairs: 59.2%

Block size distribution

Size range All 4,999 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
66.0 bp
10 bp - 100 bp
649
45.5 kb
84
6.3 kb
100 bp - 1 kb
3,721
1.4 Mb
1,438
778.7 kb
1 kb - 10 kb
617
987.3 kb
940
1.6 Mb
10 kb - 100 kb
2
22.2 kb