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Schizosaccharomyces octosporus vs Puccinia triticina - GCA_000151525.2 LastZ results

Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. 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 octosporusPuccinia triticina - GCA_000151525.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,561 alignment blocks

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

Uncovered: 10,429,738 out of 11,634,473
Covered: 1,204,735 out of 11,634,473

Uncovered: 5,756,882 out of 6,921,651
Matches: 718,063 out of 6,921,651
Mismatches: 428,183 out of 6,921,651
Insertions: 18,523 out of 6,921,651
Identity over aligned base-pairs: 61.6%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,976,798 out of 135,343,689
Covered: 1,366,891 out of 135,343,689

Uncovered: 16,336,908 out of 17,522,293
Matches: 721,049 out of 17,522,293
Mismatches: 416,741 out of 17,522,293
Insertions: 47,595 out of 17,522,293
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 5,561 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
18
98.0 bp
10 bp - 100 bp
1,129
83.1 kb
123
9.3 kb
100 bp - 1 kb
4,267
1.2 Mb
1,404
630.6 kb
1 kb - 10 kb
146
205.1 kb
503
891.7 kb
10 kb - 100 kb
1
21.6 kb
1
21.6 kb