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Magnaporthe oryzae vs Puccinia triticina - GCA_000151525.2 LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. Magnaporthe oryzae 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 oryzaePuccinia triticina - GCA_000151525.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,333 alignment blocks

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

Uncovered: 38,978,948 out of 41,027,733
Covered: 2,048,785 out of 41,027,733

Uncovered: 15,211,719 out of 16,744,523
Matches: 956,842 out of 16,744,523
Mismatches: 534,533 out of 16,744,523
Insertions: 41,429 out of 16,744,523
Identity over aligned base-pairs: 62.4%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,376,607 out of 135,343,689
Covered: 1,967,082 out of 135,343,689

Uncovered: 15,835,110 out of 17,522,293
Matches: 1,039,182 out of 17,522,293
Mismatches: 576,152 out of 17,522,293
Insertions: 71,849 out of 17,522,293
Identity over aligned base-pairs: 61.6%

Block size distribution

Size range All 8,333 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16
87.0 bp
10 bp - 100 bp
1,843
132.6 kb
221
16.4 kb
100 bp - 1 kb
5,967
1.8 Mb
2,103
918.4 kb
1 kb - 10 kb
507
653.1 kb
915
1.7 Mb
10 kb - 100 kb
1
11.7 kb