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Arabidopsis thaliana vs Cannabis sativa female LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cannabis sativa female (Cannabis sativa, cs10) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 thalianaCannabis sativa female
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 125,811 alignment blocks

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

Uncovered: 83,414,847 out of 119,667,750
Covered: 36,252,903 out of 119,667,750

Uncovered: 8,926,447 out of 33,775,569
Matches: 16,761,332 out of 33,775,569
Mismatches: 7,572,625 out of 33,775,569
Insertions: 515,165 out of 33,775,569
Identity over aligned base-pairs: 67.5%

Cannabis sativa female

Uncovered: 836,074,529 out of 875,732,045
Covered: 39,657,516 out of 875,732,045

Uncovered: 13,689,392 out of 33,180,649
Matches: 13,116,019 out of 33,180,649
Mismatches: 5,811,261 out of 33,180,649
Insertions: 563,977 out of 33,180,649
Identity over aligned base-pairs: 67.3%

Block size distribution

Size range All 125,811 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
991
5.6 kb
10 bp - 100 bp
19,063
1.2 Mb
5,165
364.8 kb
100 bp - 1 kb
93,623
34.0 Mb
25,105
9.9 Mb
1 kb - 10 kb
12,113
18.5 Mb
17,445
40.3 Mb
10 kb - 100 kb
18
356.4 kb
224
3.4 Mb
100 kb - 1 Mb
3
402.2 kb
4
565.7 kb