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Albugo laibachii vs Tetrahymena thermophila LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Albugo laibachii 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

ParameterAlbugo laibachiiTetrahymena thermophila
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,612 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 31,763,634 out of 32,766,811
Covered: 1,003,177 out of 32,766,811

Uncovered: 14,982,326 out of 15,902,867
Matches: 549,683 out of 15,902,867
Mismatches: 339,072 out of 15,902,867
Insertions: 31,786 out of 15,902,867
Identity over aligned base-pairs: 59.7%

Tetrahymena thermophila

Uncovered: 101,682,762 out of 103,014,375
Covered: 1,331,613 out of 103,014,375

Uncovered: 46,998,859 out of 48,193,658
Matches: 712,991 out of 48,193,658
Mismatches: 439,709 out of 48,193,658
Insertions: 42,099 out of 48,193,658
Identity over aligned base-pairs: 59.7%

Block size distribution

Size range All 5,612 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
23
137.0 bp
10 bp - 100 bp
970
71.3 kb
345
28.2 kb
100 bp - 1 kb
4,436
1.3 Mb
2,181
813.8 kb
1 kb - 10 kb
183
270.8 kb
409
769.2 kb
10 kb - 100 kb
4
44.7 kb