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Entamoeba histolytica vs Paramecium tetraurelia LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 histolyticaParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,100 alignment blocks

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

Uncovered: 19,174,140 out of 20,835,395
Covered: 1,661,255 out of 20,835,395

Uncovered: 8,914,872 out of 10,244,611
Matches: 804,085 out of 10,244,611
Mismatches: 455,967 out of 10,244,611
Insertions: 69,687 out of 10,244,611
Identity over aligned base-pairs: 60.5%

Paramecium tetraurelia

Uncovered: 68,661,048 out of 72,094,543
Covered: 3,433,495 out of 72,094,543

Uncovered: 51,050,351 out of 54,044,574
Matches: 1,775,058 out of 54,044,574
Mismatches: 1,010,247 out of 54,044,574
Insertions: 208,918 out of 54,044,574
Identity over aligned base-pairs: 59.3%

Block size distribution

Size range All 7,100 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6
34.0 bp
10 bp - 100 bp
876
56.2 kb
770
49.6 kb
100 bp - 1 kb
4,986
2.3 Mb
3,990
1.9 Mb
1 kb - 10 kb
1,232
1.9 Mb
1,379
2.3 Mb