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Medicago truncatula vs Juglans regia LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Juglans regia (Juglans regia, Walnut_2.0) 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 truncatulaJuglans regia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 221,740 alignment blocks

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

Uncovered: 374,635,466 out of 429,196,467
Covered: 54,561,001 out of 429,196,467

Uncovered: 14,057,705 out of 45,081,035
Matches: 21,881,046 out of 45,081,035
Mismatches: 8,540,465 out of 45,081,035
Insertions: 601,819 out of 45,081,035
Identity over aligned base-pairs: 70.5%

Juglans regia

Uncovered: 509,665,146 out of 572,786,133
Covered: 63,120,987 out of 572,786,133

Uncovered: 12,466,107 out of 40,412,433
Matches: 19,806,591 out of 40,412,433
Mismatches: 7,423,822 out of 40,412,433
Insertions: 715,913 out of 40,412,433
Identity over aligned base-pairs: 70.9%

Block size distribution

Size range All 221,740 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,199
11.3 kb
10 bp - 100 bp
32,583
2.1 Mb
9,486
676.0 kb
100 bp - 1 kb
168,499
58.8 Mb
51,839
18.9 Mb
1 kb - 10 kb
18,458
28.4 Mb
23,429
55.1 Mb
10 kb - 100 kb
1
10.3 kb
608
12.4 Mb
100 kb - 1 Mb
13
2.3 Mb