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Medicago truncatula vs Vigna unguiculata LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Vigna unguiculata (Vigna unguiculata, ASM411807v1) 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 truncatulaVigna unguiculata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 257,272 alignment blocks

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

Uncovered: 337,010,196 out of 429,196,467
Covered: 92,186,271 out of 429,196,467

Uncovered: 7,930,488 out of 45,081,035
Matches: 28,355,372 out of 45,081,035
Mismatches: 7,976,268 out of 45,081,035
Insertions: 818,907 out of 45,081,035
Identity over aligned base-pairs: 76.3%

Vigna unguiculata

Uncovered: 435,902,545 out of 519,066,764
Covered: 83,164,219 out of 519,066,764

Uncovered: 6,331,872 out of 38,844,626
Matches: 25,134,600 out of 38,844,626
Mismatches: 6,721,427 out of 38,844,626
Insertions: 656,727 out of 38,844,626
Identity over aligned base-pairs: 77.3%

Block size distribution

Size range All 257,272 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,108
19.0 kb
10 bp - 100 bp
39,303
2.4 Mb
13,556
969.0 kb
100 bp - 1 kb
185,463
70.2 Mb
63,739
21.4 Mb
1 kb - 10 kb
29,385
48.1 Mb
17,543
42.5 Mb
10 kb - 100 kb
13
203.4 kb
477
10.4 Mb
100 kb - 1 Mb
39
14.9 Mb
1 Mb - 10 Mb
15
30.9 Mb