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Phaeodactylum tricornutum vs Tetrahymena thermophila LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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 tricornutumTetrahymena thermophila
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,496 alignment blocks

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

Uncovered: 26,978,222 out of 27,568,093
Covered: 589,871 out of 27,568,093

Uncovered: 17,318,151 out of 17,873,974
Matches: 333,071 out of 17,873,974
Mismatches: 207,710 out of 17,873,974
Insertions: 15,042 out of 17,873,974
Identity over aligned base-pairs: 59.9%

Tetrahymena thermophila

Uncovered: 102,225,498 out of 103,014,375
Covered: 788,877 out of 103,014,375

Uncovered: 47,472,153 out of 48,193,658
Matches: 432,515 out of 48,193,658
Mismatches: 271,007 out of 48,193,658
Insertions: 17,983 out of 48,193,658
Identity over aligned base-pairs: 59.9%

Block size distribution

Size range All 3,496 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
44.0 bp
10 bp - 100 bp
726
54.7 kb
334
26.5 kb
100 bp - 1 kb
2,690
782.2 kb
1,442
551.0 kb
1 kb - 10 kb
72
99.8 kb
240
359.2 kb