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Phaeodactylum tricornutum vs Giardia intestinalis - GCA_000002435.2 LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Phaeodactylum tricornutum 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

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

Statistics over 805 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 27,268,106 out of 27,568,093
Covered: 299,987 out of 27,568,093

Uncovered: 17,584,388 out of 17,873,974
Matches: 170,437 out of 17,873,974
Mismatches: 108,931 out of 17,873,974
Insertions: 10,218 out of 17,873,974
Identity over aligned base-pairs: 58.9%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,831,385 out of 12,078,186
Covered: 246,801 out of 12,078,186

Uncovered: 9,226,331 out of 9,469,365
Matches: 142,404 out of 9,469,365
Mismatches: 91,292 out of 9,469,365
Insertions: 9,338 out of 9,469,365
Identity over aligned base-pairs: 58.6%

Block size distribution

Size range All 805 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
13.0 bp
10 bp - 100 bp
106
7.7 kb
46
3.5 kb
100 bp - 1 kb
625
246.5 kb
381
186.4 kb
1 kb - 10 kb
72
94.0 kb
109
158.2 kb