In this section

Triticum aestivum vs Hordeum vulgare LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, MorexV3_pseudomolecules_assembly) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. Triticum aestivum 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 aestivumHordeum vulgare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,695,703 alignment blocks

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

Uncovered: 13,431,949,576 out of 14,547,261,565
Covered: 1,115,311,989 out of 14,547,261,565

Uncovered: 11,783,171 out of 133,674,966
Matches: 111,646,673 out of 133,674,966
Mismatches: 9,219,004 out of 133,674,966
Insertions: 1,026,118 out of 133,674,966
Identity over aligned base-pairs: 91.6%

Hordeum vulgare

Uncovered: 3,732,624,518 out of 4,225,577,519
Covered: 492,953,001 out of 4,225,577,519

Uncovered: 4,867,447 out of 42,301,356
Matches: 34,457,332 out of 42,301,356
Mismatches: 2,668,210 out of 42,301,356
Insertions: 308,367 out of 42,301,356
Identity over aligned base-pairs: 92.0%

Block size distribution

Size range All 2,695,703 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
36,218
206.7 kb
10 bp - 100 bp
486,079
28.9 Mb
175,800
11.3 Mb
100 bp - 1 kb
1,793,559
680.0 Mb
796,281
321.3 Mb
1 kb - 10 kb
379,694
715.0 Mb
302,383
711.9 Mb
10 kb - 100 kb
151
2.0 Mb
8,583
164.5 Mb
100 kb - 1 Mb
2
242.5 kb
307
76.3 Mb
1 Mb - 10 Mb
40
117.7 Mb
10 Mb - 100 Mb
2
23.5 Mb