We need your help! Has Ensembl saved you time or effort? Please take 15 minutes to fill in a survey and help EMBL-EBI make the case for why open data resources are critical to life science research.
https://www.surveymonkey.com/r/QGFMBH8?channel=[webpage]

In this section

Schizosaccharomyces japonicus vs Puccinia triticina - GCA_000151525.2 LastZ results

Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. Schizosaccharomyces japonicus 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

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

Statistics over 6,016 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Schizosaccharomyces japonicus

Uncovered: 10,400,324 out of 11,733,154
Covered: 1,332,830 out of 11,733,154

Uncovered: 5,614,924 out of 6,846,208
Matches: 771,849 out of 6,846,208
Mismatches: 437,332 out of 6,846,208
Insertions: 22,103 out of 6,846,208
Identity over aligned base-pairs: 62.7%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,891,480 out of 135,343,689
Covered: 1,452,209 out of 135,343,689

Uncovered: 16,256,979 out of 17,522,293
Matches: 769,789 out of 17,522,293
Mismatches: 440,958 out of 17,522,293
Insertions: 54,567 out of 17,522,293
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 6,016 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
65.0 bp
10 bp - 100 bp
1,217
88.7 kb
138
10.7 kb
100 bp - 1 kb
4,612
1.4 Mb
1,504
701.7 kb
1 kb - 10 kb
177
262.7 kb
565
1.0 Mb