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Hyaloperonospora arabidopsidis vs Giardia lamblia LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Giardia lamblia (Giardia lamblia, GL2) 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 arabidopsidisGiardia lamblia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,074 alignment blocks

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

Uncovered: 78,540,176 out of 78,897,814
Covered: 357,638 out of 78,897,814

Uncovered: 12,858,990 out of 13,171,834
Matches: 186,093 out of 13,171,834
Mismatches: 116,567 out of 13,171,834
Insertions: 10,184 out of 13,171,834
Identity over aligned base-pairs: 59.5%

Giardia lamblia

Uncovered: 10,912,352 out of 11,192,215
Covered: 279,863 out of 11,192,215

Uncovered: 9,045,626 out of 9,322,001
Matches: 162,591 out of 9,322,001
Mismatches: 101,745 out of 9,322,001
Insertions: 12,039 out of 9,322,001
Identity over aligned base-pairs: 58.8%

Block size distribution

Size range All 1,074 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
4.0 bp
10 bp - 100 bp
196
14.6 kb
143
10.8 kb
100 bp - 1 kb
796
297.4 kb
501
235.0 kb
1 kb - 10 kb
80
108.0 kb
122
174.2 kb