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Magnaporthe poae vs Schizosaccharomyces japonicus LastZ results

Magnaporthe poae (Magnaporthe poae ATCC 64411, Mag_poae_ATCC_64411_V1) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Magnaporthe poae 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

ParameterMagnaporthe poaeSchizosaccharomyces japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,637 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Magnaporthe poae

Uncovered: 37,696,036 out of 39,503,331
Covered: 1,807,295 out of 39,503,331

Uncovered: 12,953,182 out of 14,559,232
Matches: 963,052 out of 14,559,232
Mismatches: 582,559 out of 14,559,232
Insertions: 60,439 out of 14,559,232
Identity over aligned base-pairs: 60.0%

Schizosaccharomyces japonicus

Uncovered: 9,869,296 out of 11,733,154
Covered: 1,863,858 out of 11,733,154

Uncovered: 5,059,988 out of 6,846,208
Matches: 1,073,660 out of 6,846,208
Mismatches: 675,123 out of 6,846,208
Insertions: 37,437 out of 6,846,208
Identity over aligned base-pairs: 60.1%

Block size distribution

Size range All 4,637 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
79.0 bp
10 bp - 100 bp
650
44.7 kb
122
8.9 kb
100 bp - 1 kb
3,506
1.3 Mb
1,333
696.1 kb
1 kb - 10 kb
469
752.3 kb
783
1.4 Mb