In this section

Hyaloperonospora arabidopsidis vs Trypanosoma brucei LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) 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 arabidopsidisTrypanosoma brucei
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,458 alignment blocks

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

Uncovered: 78,035,316 out of 78,897,814
Covered: 862,498 out of 78,897,814

Uncovered: 12,421,421 out of 13,171,834
Matches: 441,875 out of 13,171,834
Mismatches: 277,359 out of 13,171,834
Insertions: 31,179 out of 13,171,834
Identity over aligned base-pairs: 58.9%

Trypanosoma brucei

Uncovered: 24,982,155 out of 25,789,186
Covered: 807,031 out of 25,789,186

Uncovered: 12,380,383 out of 13,171,744
Matches: 468,335 out of 13,171,744
Mismatches: 294,806 out of 13,171,744
Insertions: 28,220 out of 13,171,744
Identity over aligned base-pairs: 59.2%

Block size distribution

Size range All 2,458 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
5.0 bp
10 bp - 100 bp
384
28.4 kb
212
16.2 kb
100 bp - 1 kb
1,809
714.3 kb
1,106
524.8 kb
1 kb - 10 kb
264
374.1 kb
380
575.8 kb