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Phytophthora lateralis vs Giardia intestinalis - GCA_000002435.2 LastZ results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Phytophthora lateralis 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

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

Statistics over 1,346 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora lateralis

Uncovered: 43,501,780 out of 43,981,379
Covered: 479,599 out of 43,981,379

Uncovered: 13,830,628 out of 14,242,768
Matches: 241,547 out of 14,242,768
Mismatches: 154,614 out of 14,242,768
Insertions: 15,979 out of 14,242,768
Identity over aligned base-pairs: 58.6%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,715,983 out of 12,078,186
Covered: 362,203 out of 12,078,186

Uncovered: 9,112,965 out of 9,469,365
Matches: 206,779 out of 9,469,365
Mismatches: 131,696 out of 9,469,365
Insertions: 17,925 out of 9,469,365
Identity over aligned base-pairs: 58.0%

Block size distribution

Size range All 1,346 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
37.0 bp
10 bp - 100 bp
157
11.1 kb
73
5.3 kb
100 bp - 1 kb
1,065
394.0 kb
630
276.2 kb
1 kb - 10 kb
117
174.9 kb
141
298.4 kb