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Entamoeba histolytica vs Tetrahymena thermophila LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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 histolyticaTetrahymena thermophila
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,300 alignment blocks

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

Uncovered: 19,100,492 out of 20,835,395
Covered: 1,734,903 out of 20,835,395

Uncovered: 9,046,729 out of 10,244,611
Matches: 724,486 out of 10,244,611
Mismatches: 405,975 out of 10,244,611
Insertions: 67,421 out of 10,244,611
Identity over aligned base-pairs: 60.5%

Tetrahymena thermophila

Uncovered: 100,752,770 out of 103,014,375
Covered: 2,261,605 out of 103,014,375

Uncovered: 46,809,936 out of 48,193,658
Matches: 803,648 out of 48,193,658
Mismatches: 458,448 out of 48,193,658
Insertions: 121,626 out of 48,193,658
Identity over aligned base-pairs: 58.1%

Block size distribution

Size range All 5,300 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
18
104.0 bp
10 bp - 100 bp
540
36.8 kb
308
21.4 kb
100 bp - 1 kb
3,857
1.6 Mb
1,861
834.3 kb
1 kb - 10 kb
885
1.5 Mb
1,112
2.3 Mb