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Phaeodactylum tricornutum vs Paramecium tetraurelia LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phaeodactylum tricornutum 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

ParameterPhaeodactylum tricornutumParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,409 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 26,891,296 out of 27,568,093
Covered: 676,797 out of 27,568,093

Uncovered: 17,237,395 out of 17,873,974
Matches: 368,197 out of 17,873,974
Mismatches: 245,175 out of 17,873,974
Insertions: 23,207 out of 17,873,974
Identity over aligned base-pairs: 57.8%

Paramecium tetraurelia

Uncovered: 70,405,011 out of 72,094,543
Covered: 1,689,532 out of 72,094,543

Uncovered: 52,445,743 out of 54,044,574
Matches: 942,227 out of 54,044,574
Mismatches: 610,743 out of 54,044,574
Insertions: 45,861 out of 54,044,574
Identity over aligned base-pairs: 58.9%

Block size distribution

Size range All 4,409 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6
26.0 bp
10 bp - 100 bp
541
38.5 kb
180
13.4 kb
100 bp - 1 kb
3,527
1.4 Mb
2,219
1.0 Mb
1 kb - 10 kb
335
462.5 kb
546
823.4 kb