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Puccinia triticina vs Trichoderma virens LastZ results

Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Puccinia triticina 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

ParameterPuccinia triticinaTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,373 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Puccinia triticina

Uncovered: 160,778,431 out of 162,948,716
Covered: 2,170,285 out of 162,948,716

Uncovered: 12,413,644 out of 13,973,123
Matches: 960,786 out of 13,973,123
Mismatches: 527,823 out of 13,973,123
Insertions: 70,870 out of 13,973,123
Identity over aligned base-pairs: 61.6%

Trichoderma virens

Uncovered: 37,348,438 out of 39,022,666
Covered: 1,674,228 out of 39,022,666

Uncovered: 15,986,287 out of 17,541,951
Matches: 965,567 out of 17,541,951
Mismatches: 549,201 out of 17,541,951
Insertions: 40,896 out of 17,541,951
Identity over aligned base-pairs: 62.1%

Block size distribution

Size range All 8,373 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
21
97.0 bp
10 bp - 100 bp
1,678
119.0 kb
224
16.6 kb
100 bp - 1 kb
6,401
1.9 Mb
2,220
980.9 kb
1 kb - 10 kb
273
379.2 kb
788
1.4 Mb
10 kb - 100 kb
4
53.0 kb