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Fusarium oxysporum vs Puccinia triticina - GCA_000151525.2 LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. Fusarium oxysporum 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

ParameterFusarium oxysporumPuccinia triticina - GCA_000151525.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,418 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Fusarium oxysporum

Uncovered: 59,524,927 out of 61,470,697
Covered: 1,945,770 out of 61,470,697

Uncovered: 20,011,347 out of 21,631,774
Matches: 1,006,650 out of 21,631,774
Mismatches: 571,648 out of 21,631,774
Insertions: 42,129 out of 21,631,774
Identity over aligned base-pairs: 62.1%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,348,077 out of 135,343,689
Covered: 1,995,612 out of 135,343,689

Uncovered: 15,839,820 out of 17,522,293
Matches: 1,028,408 out of 17,522,293
Mismatches: 579,500 out of 17,522,293
Insertions: 74,565 out of 17,522,293
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 8,418 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
71.0 bp
10 bp - 100 bp
1,706
121.4 kb
224
17.0 kb
100 bp - 1 kb
6,388
2.0 Mb
2,166
970.1 kb
1 kb - 10 kb
311
432.6 kb
893
1.5 Mb
10 kb - 100 kb
1
11.7 kb