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Pythium arrhenomanes vs Giardia intestinalis - GCA_000002435.2 LastZ results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes 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 arrhenomanesGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,559 alignment blocks

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

Uncovered: 44,083,677 out of 44,672,625
Covered: 588,948 out of 44,672,625

Uncovered: 17,857,541 out of 18,367,184
Matches: 298,945 out of 18,367,184
Mismatches: 189,704 out of 18,367,184
Insertions: 20,994 out of 18,367,184
Identity over aligned base-pairs: 58.7%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,678,343 out of 12,078,186
Covered: 399,843 out of 12,078,186

Uncovered: 9,076,527 out of 9,469,365
Matches: 227,081 out of 9,469,365
Mismatches: 146,393 out of 9,469,365
Insertions: 19,364 out of 9,469,365
Identity over aligned base-pairs: 57.8%

Block size distribution

Size range All 1,559 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6
30.0 bp
10 bp - 100 bp
162
11.9 kb
70
5.2 kb
100 bp - 1 kb
1,243
479.2 kb
755
339.2 kb
1 kb - 10 kb
148
219.8 kb
187
356.4 kb
10 kb - 100 kb
1
10.1 kb