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Trypanosoma brucei vs Phaeodactylum tricornutum LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 bruceiPhaeodactylum tricornutum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,118 alignment blocks

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

Uncovered: 25,026,323 out of 25,789,186
Covered: 762,863 out of 25,789,186

Uncovered: 12,481,276 out of 13,171,744
Matches: 408,867 out of 13,171,744
Mismatches: 257,734 out of 13,171,744
Insertions: 23,867 out of 13,171,744
Identity over aligned base-pairs: 59.2%

Phaeodactylum tricornutum

Uncovered: 26,866,630 out of 27,568,093
Covered: 701,463 out of 27,568,093

Uncovered: 17,207,894 out of 17,873,974
Matches: 389,939 out of 17,873,974
Mismatches: 246,858 out of 17,873,974
Insertions: 29,283 out of 17,873,974
Identity over aligned base-pairs: 58.5%

Block size distribution

Size range All 2,118 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
59.0 bp
10 bp - 100 bp
270
18.7 kb
116
8.4 kb
100 bp - 1 kb
1,604
642.4 kb
892
418.7 kb
1 kb - 10 kb
236
325.0 kb
332
559.1 kb