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Guillardia theta CCMP2712 vs Giardia intestinalis - GCA_000002435.2 LastZ results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Guillardia theta CCMP2712 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

ParameterGuillardia theta CCMP2712Giardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,612 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Guillardia theta CCMP2712

Uncovered: 86,708,093 out of 87,266,873
Covered: 558,780 out of 87,266,873

Uncovered: 30,116,328 out of 30,644,092
Matches: 313,667 out of 30,644,092
Mismatches: 194,234 out of 30,644,092
Insertions: 19,863 out of 30,644,092
Identity over aligned base-pairs: 59.4%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,730,028 out of 12,078,186
Covered: 348,158 out of 12,078,186

Uncovered: 9,126,754 out of 9,469,365
Matches: 201,602 out of 9,469,365
Mismatches: 124,325 out of 9,469,365
Insertions: 16,684 out of 9,469,365
Identity over aligned base-pairs: 58.8%

Block size distribution

Size range All 1,612 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
318
22.5 kb
89
6.5 kb
100 bp - 1 kb
1,138
402.9 kb
621
269.5 kb
1 kb - 10 kb
151
235.1 kb
159
374.4 kb
10 kb - 100 kb
1
10.1 kb