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Tetrahymena thermophila vs Giardia lamblia LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Giardia lamblia (Giardia lamblia, GL2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Tetrahymena thermophila 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

ParameterTetrahymena thermophilaGiardia lamblia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,946 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,546,391 out of 103,014,375
Covered: 467,984 out of 103,014,375

Uncovered: 47,766,747 out of 48,193,658
Matches: 249,484 out of 48,193,658
Mismatches: 165,416 out of 48,193,658
Insertions: 12,011 out of 48,193,658
Identity over aligned base-pairs: 58.4%

Giardia lamblia

Uncovered: 10,935,260 out of 11,192,215
Covered: 256,955 out of 11,192,215

Uncovered: 9,073,117 out of 9,322,001
Matches: 144,470 out of 9,322,001
Mismatches: 95,392 out of 9,322,001
Insertions: 9,022 out of 9,322,001
Identity over aligned base-pairs: 58.0%

Block size distribution

Size range All 1,946 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
28.0 bp
10 bp - 100 bp
547
39.9 kb
377
28.8 kb
100 bp - 1 kb
1,337
405.7 kb
672
246.4 kb
1 kb - 10 kb
57
80.3 kb
126
250.7 kb