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Pythium ultimum vs Giardia intestinalis - GCA_000002435.2 LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Pythium ultimum 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 ultimumGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,875 alignment blocks

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

Uncovered: 44,230,961 out of 44,913,582
Covered: 682,621 out of 44,913,582

Uncovered: 19,270,116 out of 19,826,256
Matches: 327,671 out of 19,826,256
Mismatches: 206,008 out of 19,826,256
Insertions: 22,461 out of 19,826,256
Identity over aligned base-pairs: 58.9%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,637,856 out of 12,078,186
Covered: 440,330 out of 12,078,186

Uncovered: 9,043,902 out of 9,469,365
Matches: 223,284 out of 9,469,365
Mismatches: 183,970 out of 9,469,365
Insertions: 18,209 out of 9,469,365
Identity over aligned base-pairs: 52.5%

Block size distribution

Size range All 1,875 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
6.0 bp
10 bp - 100 bp
300
21.8 kb
157
12.2 kb
100 bp - 1 kb
1,414
511.1 kb
840
348.4 kb
1 kb - 10 kb
157
230.5 kb
202
392.4 kb
10 kb - 100 kb
3
64.3 kb
3
74.7 kb