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Saccharomyces cerevisiae vs Puccinia triticina - GCA_000151525.2 LastZ results

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. Saccharomyces cerevisiae 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

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

Statistics over 5,171 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Saccharomyces cerevisiae

Uncovered: 11,050,597 out of 12,157,105
Covered: 1,106,508 out of 12,157,105

Uncovered: 7,496,726 out of 8,596,583
Matches: 682,311 out of 8,596,583
Mismatches: 396,874 out of 8,596,583
Insertions: 20,672 out of 8,596,583
Identity over aligned base-pairs: 62.0%

Puccinia triticina - GCA_000151525.2

Uncovered: 134,147,252 out of 135,343,689
Covered: 1,196,437 out of 135,343,689

Uncovered: 16,455,863 out of 17,522,293
Matches: 644,234 out of 17,522,293
Mismatches: 379,376 out of 17,522,293
Insertions: 42,820 out of 17,522,293
Identity over aligned base-pairs: 60.4%

Block size distribution

Size range All 5,171 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
55.0 bp
10 bp - 100 bp
1,042
74.4 kb
104
7.7 kb
100 bp - 1 kb
3,968
1.2 Mb
1,255
563.9 kb
1 kb - 10 kb
153
207.7 kb
498
867.1 kb