Medicago truncatula vs Vigna radiata LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Vigna radiata (Vigna radiata var. radiata, Vradiata_ver6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Medicago truncatula was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 347,033

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

Uncovered: 314,483,266 out of 412,800,391
Covered: 98,317,125 out of 412,800,391

Uncovered: 10,304,323 out of 50,132,764
Matches: 29,866,271 out of 50,132,764
Mismatches: 9,092,013 out of 50,132,764
Insertions: 870,157 out of 50,132,764

Vigna radiata var. radiata

Uncovered: 346,917,182 out of 463,085,359
Covered: 116,168,177 out of 463,085,359

Uncovered: 2,519,836 out of 36,130,572
Matches: 25,676,798 out of 36,130,572
Mismatches: 7,264,417 out of 36,130,572
Insertions: 669,521 out of 36,130,572

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Medicago truncatula Vigna radiata
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}