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Trypanosoma brucei vs Giardia lamblia LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Giardia lamblia (Giardia lamblia, GL2) 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 bruceiGiardia lamblia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,049 alignment blocks

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

Uncovered: 25,368,825 out of 25,789,186
Covered: 420,361 out of 25,789,186

Uncovered: 12,760,812 out of 13,171,744
Matches: 240,402 out of 13,171,744
Mismatches: 157,277 out of 13,171,744
Insertions: 13,253 out of 13,171,744
Identity over aligned base-pairs: 58.5%

Giardia lamblia

Uncovered: 10,874,490 out of 11,192,215
Covered: 317,725 out of 11,192,215

Uncovered: 9,012,065 out of 9,322,001
Matches: 177,161 out of 9,322,001
Mismatches: 116,646 out of 9,322,001
Insertions: 16,129 out of 9,322,001
Identity over aligned base-pairs: 57.2%

Block size distribution

Size range All 1,049 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
120
8.7 kb
77
6.0 kb
100 bp - 1 kb
822
333.9 kb
540
246.2 kb
1 kb - 10 kb
105
153.5 kb
122
243.9 kb