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Trypanosoma brucei vs Bigelowiella natans LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) 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 bruceiBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,678 alignment blocks

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

Uncovered: 25,157,940 out of 25,789,186
Covered: 631,246 out of 25,789,186

Uncovered: 12,550,458 out of 13,171,744
Matches: 371,799 out of 13,171,744
Mismatches: 229,547 out of 13,171,744
Insertions: 19,940 out of 13,171,744
Identity over aligned base-pairs: 59.8%

Bigelowiella natans

Uncovered: 94,080,399 out of 94,701,163
Covered: 620,764 out of 94,701,163

Uncovered: 28,229,723 out of 28,817,508
Matches: 351,992 out of 28,817,508
Mismatches: 215,303 out of 28,817,508
Insertions: 20,490 out of 28,817,508
Identity over aligned base-pairs: 59.9%

Block size distribution

Size range All 2,678 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
56.0 bp
10 bp - 100 bp
716
50.5 kb
183
12.7 kb
100 bp - 1 kb
1,801
543.0 kb
993
403.5 kb
1 kb - 10 kb
152
240.8 kb
215
418.2 kb