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Phaeodactylum tricornutum vs Giardia lamblia LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Giardia lamblia (Giardia lamblia, GL2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 lamblia
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: 27,268,096 out of 27,568,093
Covered: 299,997 out of 27,568,093

Uncovered: 17,584,378 out of 17,873,974
Matches: 170,435 out of 17,873,974
Mismatches: 108,948 out of 17,873,974
Insertions: 10,213 out of 17,873,974
Identity over aligned base-pairs: 58.9%

Giardia lamblia

Uncovered: 10,944,797 out of 11,192,215
Covered: 247,418 out of 11,192,215

Uncovered: 9,078,410 out of 9,322,001
Matches: 142,767 out of 9,322,001
Mismatches: 91,372 out of 9,322,001
Insertions: 9,452 out of 9,322,001
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
47
3.6 kb
100 bp - 1 kb
625
247.0 kb
382
187.2 kb
1 kb - 10 kb
72
94.0 kb
109
157.9 kb