In this section

Tetrahymena thermophila vs Pythium irregulare LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 thermophilaPythium irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,704 alignment blocks

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

Uncovered: 102,150,764 out of 103,014,375
Covered: 863,611 out of 103,014,375

Uncovered: 47,372,683 out of 48,193,658
Matches: 476,370 out of 48,193,658
Mismatches: 326,637 out of 48,193,658
Insertions: 17,968 out of 48,193,658
Identity over aligned base-pairs: 58.0%

Pythium irregulare

Uncovered: 42,260,012 out of 42,968,084
Covered: 708,072 out of 42,968,084

Uncovered: 19,892,253 out of 20,543,058
Matches: 377,945 out of 20,543,058
Mismatches: 257,846 out of 20,543,058
Insertions: 15,014 out of 20,543,058
Identity over aligned base-pairs: 58.1%

Block size distribution

Size range All 3,704 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
79.0 bp
10 bp - 100 bp
659
47.6 kb
261
19.4 kb
100 bp - 1 kb
2,945
886.2 kb
1,350
527.9 kb
1 kb - 10 kb
87
127.2 kb
243
481.0 kb
10 kb - 100 kb
3
32.8 kb