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Trichoderma virens vs Fusarium oxysporum Translated Blat results

Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) and Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Fungi release 94. Trichoderma virens was used as the reference species. After running Translated Blat, the raw Translated Blat 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
Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

ParameterTrichoderma virensFusarium oxysporum
Chunk size1,000,00025,000
Overlap10,00010,000
Group set size100,000,00010,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 55,329 alignment blocks

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

Uncovered: 30,111,443 out of 39,022,666
Covered: 8,911,223 out of 39,022,666

Uncovered: 8,989,831 out of 17,541,951
Matches: 6,067,667 out of 17,541,951
Mismatches: 2,478,804 out of 17,541,951
Insertions: 5,649 out of 17,541,951
Identity over aligned base-pairs: 70.9%

Fusarium oxysporum

Uncovered: 51,331,519 out of 61,470,697
Covered: 10,139,178 out of 61,470,697

Uncovered: 12,839,362 out of 21,631,774
Matches: 6,230,014 out of 21,631,774
Mismatches: 2,557,594 out of 21,631,774
Insertions: 4,804 out of 21,631,774
Identity over aligned base-pairs: 70.9%

Block size distribution

Size range All 55,329 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
356
1.5 kb
10 bp - 100 bp
46,194
2.7 Mb
261
20.7 kb
100 bp - 1 kb
62,296
16.2 Mb
6,093
2.4 Mb
1 kb - 10 kb
1,812
2.6 Mb
2,814
6.9 Mb
10 kb - 100 kb
224
7.2 Mb
100 kb - 1 Mb
30
4.9 Mb