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Ashbya gossypii vs Puccinia triticina - GCA_000151525.2 LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. Ashbya gossypii 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

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

Statistics over 4,977 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Ashbya gossypii

Uncovered: 8,077,473 out of 9,119,312
Covered: 1,041,839 out of 9,119,312

Uncovered: 5,982,142 out of 7,019,450
Matches: 646,549 out of 7,019,450
Mismatches: 368,198 out of 7,019,450
Insertions: 22,561 out of 7,019,450
Identity over aligned base-pairs: 62.3%

Puccinia triticina - GCA_000151525.2

Uncovered: 134,068,852 out of 135,343,689
Covered: 1,274,837 out of 135,343,689

Uncovered: 16,380,886 out of 17,522,293
Matches: 697,167 out of 17,522,293
Mismatches: 395,324 out of 17,522,293
Insertions: 48,916 out of 17,522,293
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 4,977 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
51.0 bp
10 bp - 100 bp
1,007
74.0 kb
121
9.1 kb
100 bp - 1 kb
3,826
1.1 Mb
1,267
560.4 kb
1 kb - 10 kb
134
185.4 kb
485
822.4 kb