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Magnaporthe poae vs Trichoderma virens LastZ results

Magnaporthe poae (Magnaporthe poae ATCC 64411, Mag_poae_ATCC_64411_V1) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Magnaporthe poae 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

ParameterMagnaporthe poaeTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 18,212 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Magnaporthe poae

Uncovered: 29,012,353 out of 39,503,331
Covered: 10,490,978 out of 39,503,331

Uncovered: 6,927,862 out of 14,559,232
Matches: 4,901,737 out of 14,559,232
Mismatches: 2,398,599 out of 14,559,232
Insertions: 331,034 out of 14,559,232
Identity over aligned base-pairs: 64.2%

Trichoderma virens

Uncovered: 28,491,779 out of 39,022,666
Covered: 10,530,887 out of 39,022,666

Uncovered: 8,562,071 out of 17,541,951
Matches: 5,405,141 out of 17,541,951
Mismatches: 3,353,972 out of 17,541,951
Insertions: 220,767 out of 17,541,951
Identity over aligned base-pairs: 60.2%

Block size distribution

Size range All 18,212 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
38
222.0 bp
10 bp - 100 bp
2,016
134.3 kb
386
27.5 kb
100 bp - 1 kb
12,647
5.1 Mb
3,035
1.4 Mb
1 kb - 10 kb
3,482
6.4 Mb
3,225
8.5 Mb
10 kb - 100 kb
29
572.1 kb
142
2.3 Mb