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Puccinia graminis vs Trichoderma virens LastZ results

Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Puccinia graminis 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 graminisTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,363 alignment blocks

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

Uncovered: 86,865,916 out of 88,724,376
Covered: 1,858,460 out of 88,724,376

Uncovered: 17,104,593 out of 18,687,338
Matches: 971,669 out of 18,687,338
Mismatches: 545,211 out of 18,687,338
Insertions: 65,865 out of 18,687,338
Identity over aligned base-pairs: 61.4%

Trichoderma virens

Uncovered: 37,440,673 out of 39,022,666
Covered: 1,581,993 out of 39,022,666

Uncovered: 16,071,804 out of 17,541,951
Matches: 913,779 out of 17,541,951
Mismatches: 520,338 out of 17,541,951
Insertions: 36,030 out of 17,541,951
Identity over aligned base-pairs: 62.2%

Block size distribution

Size range All 7,363 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
52.0 bp
10 bp - 100 bp
1,626
117.5 kb
224
16.9 kb
100 bp - 1 kb
5,498
1.6 Mb
1,789
793.0 kb
1 kb - 10 kb
228
320.2 kb
720
1.3 Mb
10 kb - 100 kb
1
11.2 kb
2
23.9 kb