In this section

Entamoeba histolytica vs Phaeodactylum tricornutum LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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 histolyticaPhaeodactylum tricornutum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,537 alignment blocks

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

Uncovered: 20,273,570 out of 20,835,395
Covered: 561,825 out of 20,835,395

Uncovered: 9,714,007 out of 10,244,611
Matches: 313,680 out of 10,244,611
Mismatches: 205,980 out of 10,244,611
Insertions: 10,944 out of 10,244,611
Identity over aligned base-pairs: 59.1%

Phaeodactylum tricornutum

Uncovered: 27,138,372 out of 27,568,093
Covered: 429,721 out of 27,568,093

Uncovered: 17,470,932 out of 17,873,974
Matches: 232,336 out of 17,873,974
Mismatches: 155,286 out of 17,873,974
Insertions: 15,420 out of 17,873,974
Identity over aligned base-pairs: 57.6%

Block size distribution

Size range All 1,537 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
16.0 bp
10 bp - 100 bp
179
12.7 kb
61
4.4 kb
100 bp - 1 kb
1,205
469.0 kb
747
348.5 kb
1 kb - 10 kb
148
210.4 kb
222
339.4 kb