In this section

Paramecium tetraurelia vs Guillardia theta CCMP2712 LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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 tetraureliaGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,234 alignment blocks

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

Uncovered: 69,980,018 out of 72,094,543
Covered: 2,114,525 out of 72,094,543

Uncovered: 52,022,961 out of 54,044,574
Matches: 1,190,190 out of 54,044,574
Mismatches: 772,238 out of 54,044,574
Insertions: 59,185 out of 54,044,574
Identity over aligned base-pairs: 58.9%

Guillardia theta CCMP2712

Uncovered: 86,335,530 out of 87,266,873
Covered: 931,343 out of 87,266,873

Uncovered: 29,788,104 out of 30,644,092
Matches: 494,502 out of 30,644,092
Mismatches: 328,850 out of 30,644,092
Insertions: 32,636 out of 30,644,092
Identity over aligned base-pairs: 57.8%

Block size distribution

Size range All 6,234 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
73.0 bp
10 bp - 100 bp
1,053
75.1 kb
293
22.0 kb
100 bp - 1 kb
4,660
1.7 Mb
2,658
1.1 Mb
1 kb - 10 kb
506
797.5 kb
665
1.2 Mb
10 kb - 100 kb
12
139.8 kb