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Arabidopsis thaliana vs Triticum turgidum LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. Arabidopsis thaliana 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

ParameterArabidopsis thalianaTriticum turgidum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 299,840 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 91,784,354 out of 119,667,750
Covered: 27,883,396 out of 119,667,750

Uncovered: 13,713,327 out of 33,775,569
Matches: 12,831,436 out of 33,775,569
Mismatches: 6,784,861 out of 33,775,569
Insertions: 445,945 out of 33,775,569
Identity over aligned base-pairs: 64.0%

Triticum turgidum

Uncovered: 10,369,576,299 out of 10,463,058,104
Covered: 93,481,805 out of 10,463,058,104

Uncovered: 43,419,594 out of 88,577,667
Matches: 28,803,563 out of 88,577,667
Mismatches: 15,237,698 out of 88,577,667
Insertions: 1,116,812 out of 88,577,667
Identity over aligned base-pairs: 63.8%

Block size distribution

Size range All 299,840 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,801
9.2 kb
10 bp - 100 bp
47,432
3.3 Mb
13,975
1.0 Mb
100 bp - 1 kb
232,859
78.1 Mb
91,490
35.8 Mb
1 kb - 10 kb
17,748
26.2 Mb
36,091
70.0 Mb
10 kb - 100 kb
59
715.2 kb