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Albugo laibachii vs Paramecium tetraurelia LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Albugo laibachii 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

ParameterAlbugo laibachiiParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,846 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 31,589,592 out of 32,766,811
Covered: 1,177,219 out of 32,766,811

Uncovered: 14,827,648 out of 15,902,867
Matches: 628,682 out of 15,902,867
Mismatches: 399,374 out of 15,902,867
Insertions: 47,163 out of 15,902,867
Identity over aligned base-pairs: 58.5%

Paramecium tetraurelia

Uncovered: 69,266,149 out of 72,094,543
Covered: 2,828,394 out of 72,094,543

Uncovered: 51,372,751 out of 54,044,574
Matches: 1,586,985 out of 54,044,574
Mismatches: 992,348 out of 54,044,574
Insertions: 92,490 out of 54,044,574
Identity over aligned base-pairs: 59.4%

Block size distribution

Size range All 6,846 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
24.0 bp
10 bp - 100 bp
714
51.2 kb
278
21.0 kb
100 bp - 1 kb
5,391
2.1 Mb
3,277
1.5 Mb
1 kb - 10 kb
736
1.1 Mb
951
1.7 Mb
10 kb - 100 kb
8
89.0 kb