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Entamoeba histolytica vs Giardia intestinalis - GCA_000002435.2 LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Entamoeba histolytica 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

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

Statistics over 746 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Entamoeba histolytica

Uncovered: 20,509,633 out of 20,835,395
Covered: 325,762 out of 20,835,395

Uncovered: 9,926,348 out of 10,244,611
Matches: 182,041 out of 10,244,611
Mismatches: 129,300 out of 10,244,611
Insertions: 6,922 out of 10,244,611
Identity over aligned base-pairs: 57.2%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,878,179 out of 12,078,186
Covered: 200,007 out of 12,078,186

Uncovered: 9,271,335 out of 9,469,365
Matches: 110,878 out of 9,469,365
Mismatches: 79,103 out of 9,469,365
Insertions: 8,049 out of 9,469,365
Identity over aligned base-pairs: 56.0%

Block size distribution

Size range All 746 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
10 bp - 100 bp
42
3.3 kb
22
1.7 kb
100 bp - 1 kb
636
264.7 kb
389
183.2 kb
1 kb - 10 kb
68
96.0 kb
116
179.2 kb