In this section

Triticum turgidum vs Triticum aestivum LastZ results

Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) and Triticum aestivum (Triticum aestivum, IWGSC) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Triticum turgidum 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 turgidumTriticum aestivum
Chunk size10,100,00010,100,000
Overlap100,000100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,616,606 alignment blocks

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

Uncovered: 1,755,766,743 out of 10,463,058,104
Covered: 8,707,291,361 out of 10,463,058,104

Uncovered: 20,694,181 out of 88,577,667
Matches: 66,594,061 out of 88,577,667
Mismatches: 1,173,737 out of 88,577,667
Insertions: 115,688 out of 88,577,667
Identity over aligned base-pairs: 98.1%

Triticum aestivum

Uncovered: 5,947,469,820 out of 14,547,261,565
Covered: 8,599,791,745 out of 14,547,261,565

Uncovered: 64,059,838 out of 133,674,966
Matches: 68,139,580 out of 133,674,966
Mismatches: 1,339,353 out of 133,674,966
Insertions: 136,195 out of 133,674,966
Identity over aligned base-pairs: 97.9%

Block size distribution

Size range All 1,616,606 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
18,000
104.6 kb
10 bp - 100 bp
294,809
16.1 Mb
128,381
7.6 Mb
100 bp - 1 kb
654,762
251.0 Mb
324,581
120.8 Mb
1 kb - 10 kb
416,992
1.5 Gb
159,418
461.4 Mb
10 kb - 100 kb
226,761
6.6 Gb
8,257
141.7 Mb
100 kb - 1 Mb
5,282
671.1 Mb
677
287.8 Mb
1 Mb - 10 Mb
132
460.0 Mb
10 Mb - 100 Mb
28
488.5 Mb
100 Mb - 1 Gb
14
7.1 Gb