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Fusarium verticillioides vs Puccinia triticina - GCA_000151525.2 LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. Fusarium verticillioides 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 verticillioidesPuccinia triticina - GCA_000151525.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,771 alignment blocks

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

Uncovered: 40,174,349 out of 41,885,085
Covered: 1,710,736 out of 41,885,085

Uncovered: 16,270,759 out of 17,841,847
Matches: 977,743 out of 17,841,847
Mismatches: 552,560 out of 17,841,847
Insertions: 40,785 out of 17,841,847
Identity over aligned base-pairs: 62.2%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,402,424 out of 135,343,689
Covered: 1,941,265 out of 135,343,689

Uncovered: 15,848,891 out of 17,522,293
Matches: 1,026,460 out of 17,522,293
Mismatches: 572,390 out of 17,522,293
Insertions: 74,552 out of 17,522,293
Identity over aligned base-pairs: 61.3%

Block size distribution

Size range All 7,771 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
84.0 bp
10 bp - 100 bp
1,596
114.4 kb
229
17.6 kb
100 bp - 1 kb
5,923
1.8 Mb
1,937
871.7 kb
1 kb - 10 kb
239
329.4 kb
773
1.3 Mb
10 kb - 100 kb
1
11.9 kb