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Paramecium tetraurelia vs Bigelowiella natans LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 tetraureliaBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,385 alignment blocks

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

Uncovered: 70,137,841 out of 72,094,543
Covered: 1,956,702 out of 72,094,543

Uncovered: 52,187,649 out of 54,044,574
Matches: 1,090,050 out of 54,044,574
Mismatches: 708,401 out of 54,044,574
Insertions: 58,474 out of 54,044,574
Identity over aligned base-pairs: 58.7%

Bigelowiella natans

Uncovered: 93,942,626 out of 94,701,163
Covered: 758,537 out of 94,701,163

Uncovered: 28,130,776 out of 28,817,508
Matches: 406,781 out of 28,817,508
Mismatches: 255,552 out of 28,817,508
Insertions: 24,399 out of 28,817,508
Identity over aligned base-pairs: 59.2%

Block size distribution

Size range All 6,385 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
26
136.0 bp
10 bp - 100 bp
1,426
102.6 kb
427
32.6 kb
100 bp - 1 kb
4,504
1.4 Mb
2,605
1.1 Mb
1 kb - 10 kb
429
693.4 kb
553
1.1 Mb