In this section

Albugo laibachii vs Giardia intestinalis - GCA_000002435.2 LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Albugo laibachii 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

ParameterAlbugo laibachiiGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,156 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 32,316,126 out of 32,766,811
Covered: 450,685 out of 32,766,811

Uncovered: 15,476,690 out of 15,902,867
Matches: 245,923 out of 15,902,867
Mismatches: 163,802 out of 15,902,867
Insertions: 16,452 out of 15,902,867
Identity over aligned base-pairs: 57.7%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,750,923 out of 12,078,186
Covered: 327,263 out of 12,078,186

Uncovered: 9,146,014 out of 9,469,365
Matches: 185,026 out of 9,469,365
Mismatches: 122,174 out of 9,469,365
Insertions: 16,151 out of 9,469,365
Identity over aligned base-pairs: 57.2%

Block size distribution

Size range All 1,156 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
4.0 bp
10 bp - 100 bp
160
11.7 kb
94
7.0 kb
100 bp - 1 kb
877
342.3 kb
521
241.7 kb
1 kb - 10 kb
118
171.1 kb
147
276.3 kb