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Trichoderma virens vs Puccinia triticina - GCA_000151525.2 LastZ results

Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. Trichoderma virens 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

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

Statistics over 7,784 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Trichoderma virens

Uncovered: 37,369,140 out of 39,022,666
Covered: 1,653,526 out of 39,022,666

Uncovered: 15,974,309 out of 17,541,951
Matches: 979,680 out of 17,541,951
Mismatches: 546,811 out of 17,541,951
Insertions: 41,151 out of 17,541,951
Identity over aligned base-pairs: 62.5%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,377,372 out of 135,343,689
Covered: 1,966,317 out of 135,343,689

Uncovered: 15,815,843 out of 17,522,293
Matches: 1,050,943 out of 17,522,293
Mismatches: 579,623 out of 17,522,293
Insertions: 75,884 out of 17,522,293
Identity over aligned base-pairs: 61.6%

Block size distribution

Size range All 7,784 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
18
82.0 bp
10 bp - 100 bp
1,585
112.8 kb
185
14.0 kb
100 bp - 1 kb
5,940
1.8 Mb
1,924
861.1 kb
1 kb - 10 kb
241
322.0 kb
751
1.3 Mb
10 kb - 100 kb
1
11.8 kb