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Medicago truncatula vs Vigna radiata LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Vigna radiata (Vigna radiata var. radiata, Vradiata_ver6) 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 radiata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 301,593 alignment blocks

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

Uncovered: 330,847,250 out of 429,196,467
Covered: 98,349,217 out of 429,196,467

Uncovered: 7,953,844 out of 45,081,035
Matches: 28,043,990 out of 45,081,035
Mismatches: 8,270,653 out of 45,081,035
Insertions: 812,548 out of 45,081,035
Identity over aligned base-pairs: 75.5%

Vigna radiata

Uncovered: 368,870,934 out of 463,085,359
Covered: 94,214,425 out of 463,085,359

Uncovered: 2,568,984 out of 28,307,530
Matches: 20,086,712 out of 28,307,530
Mismatches: 5,150,366 out of 28,307,530
Insertions: 501,468 out of 28,307,530
Identity over aligned base-pairs: 78.0%

Block size distribution

Size range All 301,593 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,195
19.2 kb
10 bp - 100 bp
51,174
3.2 Mb
23,436
1.6 Mb
100 bp - 1 kb
214,632
79.4 Mb
87,370
29.7 Mb
1 kb - 10 kb
32,577
55.3 Mb
21,948
53.3 Mb
10 kb - 100 kb
15
170.6 kb
619
14.0 Mb
100 kb - 1 Mb
76
20.0 Mb
1 Mb - 10 Mb
10
19.4 Mb