In this section

Triticum dicoccoides vs Triticum turgidum LastZ results

Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Triticum dicoccoides 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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

ParameterTriticum dicoccoidesTriticum turgidum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 1,996,754 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum dicoccoides

Uncovered: 2,243,046,094 out of 10,079,039,394
Covered: 7,835,993,300 out of 10,079,039,394

Uncovered: 13,105,125 out of 81,268,905
Matches: 66,926,635 out of 81,268,905
Mismatches: 1,110,814 out of 81,268,905
Insertions: 126,331 out of 81,268,905
Identity over aligned base-pairs: 98.2%

Triticum turgidum

Uncovered: 2,415,799,529 out of 10,463,058,104
Covered: 8,047,258,575 out of 10,463,058,104

Uncovered: 16,093,563 out of 88,577,667
Matches: 71,072,689 out of 88,577,667
Mismatches: 1,278,176 out of 88,577,667
Insertions: 133,239 out of 88,577,667
Identity over aligned base-pairs: 98.1%

Block size distribution

Size range All 1,996,754 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
25,332
143.7 kb
10 bp - 100 bp
402,045
21.7 Mb
179,952
10.5 Mb
100 bp - 1 kb
813,165
312.0 Mb
395,257
144.3 Mb
1 kb - 10 kb
524,939
1.8 Gb
204,761
634.5 Mb
10 kb - 100 kb
229,029
6.0 Gb
12,799
207.5 Mb
100 kb - 1 Mb
2,244
276.6 Mb
788
301.1 Mb
1 Mb - 10 Mb
161
522.1 Mb
10 Mb - 100 Mb
29
480.0 Mb
100 Mb - 1 Gb
14
6.2 Gb