In this section

Tetrahymena thermophila vs Emiliania huxleyi LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Tetrahymena thermophila 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

ParameterTetrahymena thermophilaEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,641 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,686,403 out of 103,014,375
Covered: 327,972 out of 103,014,375

Uncovered: 47,894,378 out of 48,193,658
Matches: 175,976 out of 48,193,658
Mismatches: 119,366 out of 48,193,658
Insertions: 3,938 out of 48,193,658
Identity over aligned base-pairs: 58.8%

Emiliania huxleyi

Uncovered: 167,249,196 out of 167,675,649
Covered: 426,453 out of 167,675,649

Uncovered: 39,359,692 out of 39,740,234
Matches: 233,481 out of 39,740,234
Mismatches: 142,413 out of 39,740,234
Insertions: 4,648 out of 39,740,234
Identity over aligned base-pairs: 61.4%

Block size distribution

Size range All 2,641 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
56.0 bp
10 bp - 100 bp
766
58.5 kb
418
33.9 kb
100 bp - 1 kb
1,820
455.5 kb
972
314.4 kb
1 kb - 10 kb
47
62.5 kb
137
228.3 kb