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Arabidopsis thaliana vs Triticum dicoccoides LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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 dicoccoides
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 359,368 alignment blocks

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

Uncovered: 91,559,711 out of 119,667,750
Covered: 28,108,039 out of 119,667,750

Uncovered: 13,622,876 out of 33,775,569
Matches: 12,879,126 out of 33,775,569
Mismatches: 6,825,785 out of 33,775,569
Insertions: 447,782 out of 33,775,569
Identity over aligned base-pairs: 63.9%

Triticum dicoccoides

Uncovered: 9,963,479,210 out of 10,079,039,394
Covered: 115,560,184 out of 10,079,039,394

Uncovered: 35,941,884 out of 81,268,905
Matches: 28,904,563 out of 81,268,905
Mismatches: 15,259,258 out of 81,268,905
Insertions: 1,163,200 out of 81,268,905
Identity over aligned base-pairs: 63.8%

Block size distribution

Size range All 359,368 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,832
9.4 kb
10 bp - 100 bp
56,449
3.9 Mb
22,910
1.6 Mb
100 bp - 1 kb
281,634
97.3 Mb
136,672
53.4 Mb
1 kb - 10 kb
19,453
28.8 Mb
38,350
74.3 Mb
10 kb - 100 kb
57
696.6 kb