In this section

Paramecium tetraurelia vs Pythium aphanidermatum LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Paramecium tetraurelia 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

ParameterParamecium tetraureliaPythium aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,804 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Paramecium tetraurelia

Uncovered: 69,741,562 out of 72,094,543
Covered: 2,352,981 out of 72,094,543

Uncovered: 51,807,047 out of 54,044,574
Matches: 1,282,859 out of 54,044,574
Mismatches: 891,082 out of 54,044,574
Insertions: 63,586 out of 54,044,574
Identity over aligned base-pairs: 57.3%

Pythium aphanidermatum

Uncovered: 34,838,767 out of 35,876,849
Covered: 1,038,082 out of 35,876,849

Uncovered: 17,104,127 out of 18,015,574
Matches: 517,563 out of 18,015,574
Mismatches: 360,843 out of 18,015,574
Insertions: 33,041 out of 18,015,574
Identity over aligned base-pairs: 56.8%

Block size distribution

Size range All 5,804 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16
63.0 bp
10 bp - 100 bp
652
47.0 kb
227
18.4 kb
100 bp - 1 kb
4,555
1.7 Mb
2,670
1.2 Mb
1 kb - 10 kb
581
906.0 kb
751
1.4 Mb
10 kb - 100 kb
8
91.7 kb