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Medicago truncatula vs Cannabis sativa female LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Cannabis sativa female (Cannabis sativa, cs10) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 112. Medicago truncatula 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

ParameterMedicago truncatulaCannabis sativa female
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 231,876 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 372,471,892 out of 429,196,467
Covered: 56,724,575 out of 429,196,467

Uncovered: 15,165,991 out of 45,081,035
Matches: 20,587,015 out of 45,081,035
Mismatches: 8,690,833 out of 45,081,035
Insertions: 637,196 out of 45,081,035
Identity over aligned base-pairs: 68.8%

Cannabis sativa female

Uncovered: 801,699,665 out of 875,732,045
Covered: 74,032,380 out of 875,732,045

Uncovered: 10,029,529 out of 33,180,649
Matches: 15,674,057 out of 33,180,649
Mismatches: 6,787,211 out of 33,180,649
Insertions: 689,852 out of 33,180,649
Identity over aligned base-pairs: 67.7%

Block size distribution

Size range All 231,876 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,641
8.7 kb
10 bp - 100 bp
37,288
2.4 Mb
17,656
1.2 Mb
100 bp - 1 kb
169,276
60.8 Mb
65,562
24.3 Mb
1 kb - 10 kb
23,601
37.8 Mb
30,463
69.8 Mb
10 kb - 100 kb
57
1.7 Mb
366
6.7 Mb
100 kb - 1 Mb
13
1.6 Mb
19
2.4 Mb