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Tetrahymena thermophila vs Guillardia theta CCMP2712 LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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 thermophilaGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,081 alignment blocks

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

Uncovered: 102,136,199 out of 103,014,375
Covered: 878,176 out of 103,014,375

Uncovered: 47,365,829 out of 48,193,658
Matches: 489,799 out of 48,193,658
Mismatches: 313,826 out of 48,193,658
Insertions: 24,204 out of 48,193,658
Identity over aligned base-pairs: 59.2%

Guillardia theta CCMP2712

Uncovered: 86,511,905 out of 87,266,873
Covered: 754,968 out of 87,266,873

Uncovered: 29,940,125 out of 30,644,092
Matches: 416,549 out of 30,644,092
Mismatches: 266,210 out of 30,644,092
Insertions: 21,208 out of 30,644,092
Identity over aligned base-pairs: 59.2%

Block size distribution

Size range All 4,081 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
42.0 bp
10 bp - 100 bp
944
67.0 kb
221
16.9 kb
100 bp - 1 kb
2,994
900.1 kb
1,408
546.5 kb
1 kb - 10 kb
132
197.6 kb
234
531.7 kb
10 kb - 100 kb
6
69.7 kb