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Tetrahymena thermophila vs Paramecium tetraurelia LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) 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 thermophilaParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 46,119 alignment blocks

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

Uncovered: 90,836,416 out of 103,014,375
Covered: 12,177,959 out of 103,014,375

Uncovered: 40,519,430 out of 48,193,658
Matches: 4,516,503 out of 48,193,658
Mismatches: 2,522,140 out of 48,193,658
Insertions: 635,585 out of 48,193,658
Identity over aligned base-pairs: 58.9%

Paramecium tetraurelia

Uncovered: 55,485,439 out of 72,094,543
Covered: 16,609,104 out of 72,094,543

Uncovered: 40,469,383 out of 54,044,574
Matches: 8,360,257 out of 54,044,574
Mismatches: 4,561,141 out of 54,044,574
Insertions: 653,793 out of 54,044,574
Identity over aligned base-pairs: 61.6%

Block size distribution

Size range All 46,119 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
286
1.8 kb
10 bp - 100 bp
5,906
381.5 kb
2,935
190.7 kb
100 bp - 1 kb
33,999
13.5 Mb
13,681
6.1 Mb
1 kb - 10 kb
5,925
9.4 Mb
8,217
16.3 Mb
10 kb - 100 kb
3
33.1 kb
62
785.8 kb