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Trypanosoma brucei vs Giardia intestinalis - GCA_000002435.2 LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Trypanosoma brucei 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

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

Statistics over 1,052 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Trypanosoma brucei

Uncovered: 25,368,686 out of 25,789,186
Covered: 420,500 out of 25,789,186

Uncovered: 12,760,673 out of 13,171,744
Matches: 240,490 out of 13,171,744
Mismatches: 157,268 out of 13,171,744
Insertions: 13,313 out of 13,171,744
Identity over aligned base-pairs: 58.5%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,759,752 out of 12,078,186
Covered: 318,434 out of 12,078,186

Uncovered: 9,157,277 out of 9,469,365
Matches: 178,420 out of 9,469,365
Mismatches: 117,340 out of 9,469,365
Insertions: 16,328 out of 9,469,365
Identity over aligned base-pairs: 57.2%

Block size distribution

Size range All 1,052 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
9.0 bp
10 bp - 100 bp
119
8.6 kb
75
5.9 kb
100 bp - 1 kb
826
334.3 kb
541
244.7 kb
1 kb - 10 kb
105
153.5 kb
125
245.9 kb