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Tetrahymena thermophila vs Pythium iwayamai LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Tetrahymena thermophila 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

ParameterTetrahymena thermophilaPythium iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,386 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,239,090 out of 103,014,375
Covered: 775,285 out of 103,014,375

Uncovered: 47,506,133 out of 48,193,658
Matches: 396,821 out of 48,193,658
Mismatches: 277,204 out of 48,193,658
Insertions: 13,500 out of 48,193,658
Identity over aligned base-pairs: 57.7%

Pythium iwayamai

Uncovered: 42,601,692 out of 43,199,174
Covered: 597,482 out of 43,199,174

Uncovered: 19,025,814 out of 19,552,457
Matches: 304,400 out of 19,552,457
Mismatches: 210,818 out of 19,552,457
Insertions: 11,425 out of 19,552,457
Identity over aligned base-pairs: 57.8%

Block size distribution

Size range All 3,386 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6
36.0 bp
10 bp - 100 bp
723
55.0 kb
408
32.5 kb
100 bp - 1 kb
2,567
753.3 kb
1,255
464.9 kb
1 kb - 10 kb
90
134.3 kb
202
411.5 kb
10 kb - 100 kb
3
33.8 kb