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Medicago truncatula vs Cannabis sativa female LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Cannabis sativa female (Cannabis sativa, cs10) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 223,448 alignment blocks

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

Uncovered: 356,121,537 out of 412,800,391
Covered: 56,678,854 out of 412,800,391

Uncovered: 16,852,301 out of 50,132,764
Matches: 22,885,907 out of 50,132,764
Mismatches: 9,689,821 out of 50,132,764
Insertions: 704,735 out of 50,132,764
Identity over aligned base-pairs: 68.8%

Cannabis sativa female

Uncovered: 818,058,700 out of 875,732,045
Covered: 57,673,345 out of 875,732,045

Uncovered: 11,275,822 out of 33,180,649
Matches: 15,048,766 out of 33,180,649
Mismatches: 6,258,054 out of 33,180,649
Insertions: 598,007 out of 33,180,649
Identity over aligned base-pairs: 68.7%

Block size distribution

Size range All 223,448 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,739
9.6 kb
10 bp - 100 bp
33,012
2.2 Mb
9,770
705.8 kb
100 bp - 1 kb
168,898
59.7 Mb
52,853
19.1 Mb
1 kb - 10 kb
19,708
31.0 Mb
24,346
60.5 Mb
10 kb - 100 kb
81
2.8 Mb
706
13.6 Mb
100 kb - 1 Mb
10
1.3 Mb
19
3.0 Mb