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Paramecium tetraurelia vs Pythium irregulare LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Paramecium tetraurelia 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

ParameterParamecium tetraureliaPythium irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,968 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Paramecium tetraurelia

Uncovered: 70,229,864 out of 72,094,543
Covered: 1,864,679 out of 72,094,543

Uncovered: 52,257,581 out of 54,044,574
Matches: 1,018,468 out of 54,044,574
Mismatches: 725,492 out of 54,044,574
Insertions: 43,033 out of 54,044,574
Identity over aligned base-pairs: 57.0%

Pythium irregulare

Uncovered: 42,142,101 out of 42,968,084
Covered: 825,983 out of 42,968,084

Uncovered: 19,794,656 out of 20,543,058
Matches: 421,037 out of 20,543,058
Mismatches: 305,241 out of 20,543,058
Insertions: 22,124 out of 20,543,058
Identity over aligned base-pairs: 56.3%

Block size distribution

Size range All 4,968 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
45.0 bp
10 bp - 100 bp
582
41.9 kb
180
13.4 kb
100 bp - 1 kb
3,944
1.4 Mb
2,218
998.1 kb
1 kb - 10 kb
430
630.1 kb
569
1.1 Mb
10 kb - 100 kb
5
57.6 kb