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Pythium ultimum vs Paramecium tetraurelia LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum 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

ParameterPythium ultimumParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,055 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 43,878,090 out of 44,913,582
Covered: 1,035,492 out of 44,913,582

Uncovered: 18,942,085 out of 19,826,256
Matches: 503,463 out of 19,826,256
Mismatches: 352,823 out of 19,826,256
Insertions: 27,885 out of 19,826,256
Identity over aligned base-pairs: 56.9%

Paramecium tetraurelia

Uncovered: 69,954,031 out of 72,094,543
Covered: 2,140,512 out of 72,094,543

Uncovered: 52,007,286 out of 54,044,574
Matches: 1,177,644 out of 54,044,574
Mismatches: 805,963 out of 54,044,574
Insertions: 53,681 out of 54,044,574
Identity over aligned base-pairs: 57.8%

Block size distribution

Size range All 6,055 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
18
88.0 bp
10 bp - 100 bp
860
63.2 kb
353
28.2 kb
100 bp - 1 kb
4,679
1.7 Mb
2,729
1.2 Mb
1 kb - 10 kb
498
767.9 kb
694
1.2 Mb
10 kb - 100 kb
7
80.8 kb