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Trypanosoma brucei vs Tetrahymena thermophila LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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 bruceiTetrahymena thermophila
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,106 alignment blocks

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

Uncovered: 25,252,932 out of 25,789,186
Covered: 536,254 out of 25,789,186

Uncovered: 12,651,232 out of 13,171,744
Matches: 306,917 out of 13,171,744
Mismatches: 199,685 out of 13,171,744
Insertions: 13,910 out of 13,171,744
Identity over aligned base-pairs: 59.0%

Tetrahymena thermophila

Uncovered: 102,308,916 out of 103,014,375
Covered: 705,459 out of 103,014,375

Uncovered: 47,549,364 out of 48,193,658
Matches: 379,289 out of 48,193,658
Mismatches: 246,022 out of 48,193,658
Insertions: 18,983 out of 48,193,658
Identity over aligned base-pairs: 58.9%

Block size distribution

Size range All 3,106 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
14
69.0 bp
10 bp - 100 bp
708
52.5 kb
406
32.3 kb
100 bp - 1 kb
2,294
685.3 kb
1,174
444.6 kb
1 kb - 10 kb
90
133.0 kb
194
383.1 kb
10 kb - 100 kb
1
10.8 kb