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Schizosaccharomyces pombe vs Puccinia triticina - GCA_000151525.2 LastZ results

Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. 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 pombePuccinia triticina - GCA_000151525.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,529 alignment blocks

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

Uncovered: 11,434,343 out of 12,631,379
Covered: 1,197,036 out of 12,631,379

Uncovered: 6,008,236 out of 7,176,702
Matches: 728,341 out of 7,176,702
Mismatches: 421,373 out of 7,176,702
Insertions: 18,752 out of 7,176,702
Identity over aligned base-pairs: 62.3%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,973,961 out of 135,343,689
Covered: 1,369,728 out of 135,343,689

Uncovered: 16,322,065 out of 17,522,293
Matches: 727,338 out of 17,522,293
Mismatches: 423,944 out of 17,522,293
Insertions: 48,946 out of 17,522,293
Identity over aligned base-pairs: 60.6%

Block size distribution

Size range All 5,529 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
60.0 bp
10 bp - 100 bp
1,075
77.9 kb
107
8.4 kb
100 bp - 1 kb
4,271
1.2 Mb
1,391
630.5 kb
1 kb - 10 kb
174
242.9 kb
509
916.0 kb