In this section

Hyaloperonospora arabidopsidis vs Tetrahymena thermophila LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisTetrahymena thermophila
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,817 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 78,225,867 out of 78,897,814
Covered: 671,947 out of 78,897,814

Uncovered: 12,615,118 out of 13,171,834
Matches: 331,786 out of 13,171,834
Mismatches: 212,741 out of 13,171,834
Insertions: 12,189 out of 13,171,834
Identity over aligned base-pairs: 59.6%

Tetrahymena thermophila

Uncovered: 102,131,341 out of 103,014,375
Covered: 883,034 out of 103,014,375

Uncovered: 47,453,991 out of 48,193,658
Matches: 431,482 out of 48,193,658
Mismatches: 291,111 out of 48,193,658
Insertions: 17,074 out of 48,193,658
Identity over aligned base-pairs: 58.3%

Block size distribution

Size range All 3,817 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
56.0 bp
10 bp - 100 bp
901
66.7 kb
441
33.9 kb
100 bp - 1 kb
2,809
817.3 kb
1,460
575.4 kb
1 kb - 10 kb
97
158.9 kb
271
433.6 kb
10 kb - 100 kb
1
24.3 kb
1
24.3 kb