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Pythium vexans vs Giardia intestinalis - GCA_000002435.2 LastZ results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Pythium vexans 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

ParameterPythium vexansGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,677 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium vexans

Uncovered: 33,212,326 out of 33,844,883
Covered: 632,557 out of 33,844,883

Uncovered: 18,036,003 out of 18,608,353
Matches: 337,950 out of 18,608,353
Mismatches: 210,376 out of 18,608,353
Insertions: 24,024 out of 18,608,353
Identity over aligned base-pairs: 59.0%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,674,469 out of 12,078,186
Covered: 403,717 out of 12,078,186

Uncovered: 9,072,638 out of 9,469,365
Matches: 232,603 out of 9,469,365
Mismatches: 144,629 out of 9,469,365
Insertions: 19,495 out of 9,469,365
Identity over aligned base-pairs: 58.6%

Block size distribution

Size range All 1,677 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6
39.0 bp
10 bp - 100 bp
215
15.3 kb
70
5.2 kb
100 bp - 1 kb
1,297
483.7 kb
734
325.0 kb
1 kb - 10 kb
159
250.8 kb
209
409.6 kb
10 kb - 100 kb
1
10.0 kb