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Trypanosoma brucei vs Paramecium tetraurelia LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) 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 bruceiParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,751 alignment blocks

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

Uncovered: 25,161,238 out of 25,789,186
Covered: 627,948 out of 25,789,186

Uncovered: 12,556,651 out of 13,171,744
Matches: 352,201 out of 13,171,744
Mismatches: 242,031 out of 13,171,744
Insertions: 20,861 out of 13,171,744
Identity over aligned base-pairs: 57.3%

Paramecium tetraurelia

Uncovered: 70,455,428 out of 72,094,543
Covered: 1,639,115 out of 72,094,543

Uncovered: 52,492,636 out of 54,044,574
Matches: 892,941 out of 54,044,574
Mismatches: 604,160 out of 54,044,574
Insertions: 54,837 out of 54,044,574
Identity over aligned base-pairs: 57.5%

Block size distribution

Size range All 3,751 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
14.0 bp
10 bp - 100 bp
367
26.3 kb
179
13.6 kb
100 bp - 1 kb
2,951
1.2 Mb
1,918
917.6 kb
1 kb - 10 kb
430
622.4 kb
481
898.3 kb
10 kb - 100 kb
2
21.5 kb