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Phytophthora infestans vs Giardia intestinalis - GCA_000002435.2 LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Phytophthora infestans 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 infestansGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,068 alignment blocks

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

Uncovered: 227,646,754 out of 228,543,505
Covered: 896,751 out of 228,543,505

Uncovered: 21,817,469 out of 22,421,425
Matches: 356,906 out of 22,421,425
Mismatches: 224,535 out of 22,421,425
Insertions: 22,515 out of 22,421,425
Identity over aligned base-pairs: 59.1%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,645,999 out of 12,078,186
Covered: 432,187 out of 12,078,186

Uncovered: 9,046,527 out of 9,469,365
Matches: 229,307 out of 9,469,365
Mismatches: 173,487 out of 9,469,365
Insertions: 20,044 out of 9,469,365
Identity over aligned base-pairs: 54.2%

Block size distribution

Size range All 4,068 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
17.0 bp
10 bp - 100 bp
1,883
150.3 kb
1,784
143.5 kb
100 bp - 1 kb
2,026
589.5 kb
1,519
444.2 kb
1 kb - 10 kb
155
261.6 kb
199
405.0 kb
10 kb - 100 kb
1
15.1 kb
1
23.9 kb