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Paramecium tetraurelia vs Giardia intestinalis - GCA_000002435.2 LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. 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 tetraureliaGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,481 alignment blocks

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

Uncovered: 71,040,095 out of 72,094,543
Covered: 1,054,448 out of 72,094,543

Uncovered: 53,041,536 out of 54,044,574
Matches: 574,281 out of 54,044,574
Mismatches: 397,334 out of 54,044,574
Insertions: 31,423 out of 54,044,574
Identity over aligned base-pairs: 57.3%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,776,771 out of 12,078,186
Covered: 301,415 out of 12,078,186

Uncovered: 9,175,382 out of 9,469,365
Matches: 163,872 out of 9,469,365
Mismatches: 117,025 out of 9,469,365
Insertions: 13,086 out of 9,469,365
Identity over aligned base-pairs: 55.7%

Block size distribution

Size range All 2,481 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
23.0 bp
10 bp - 100 bp
257
18.3 kb
136
10.5 kb
100 bp - 1 kb
2,006
836.2 kb
1,239
579.9 kb
1 kb - 10 kb
214
290.2 kb
294
554.3 kb