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Tetrahymena thermophila vs Giardia intestinalis - GCA_000002435.2 LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Tetrahymena thermophila 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

ParameterTetrahymena thermophilaGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,942 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,546,006 out of 103,014,375
Covered: 468,369 out of 103,014,375

Uncovered: 47,766,356 out of 48,193,658
Matches: 249,716 out of 48,193,658
Mismatches: 165,557 out of 48,193,658
Insertions: 12,029 out of 48,193,658
Identity over aligned base-pairs: 58.4%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,821,426 out of 12,078,186
Covered: 256,760 out of 12,078,186

Uncovered: 9,218,972 out of 9,469,365
Matches: 145,182 out of 9,469,365
Mismatches: 96,168 out of 9,469,365
Insertions: 9,043 out of 9,469,365
Identity over aligned base-pairs: 58.0%

Block size distribution

Size range All 1,942 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
28.0 bp
10 bp - 100 bp
541
39.6 kb
371
28.4 kb
100 bp - 1 kb
1,339
405.8 kb
674
246.6 kb
1 kb - 10 kb
57
80.3 kb
126
250.6 kb