Medicago truncatula vs Trifolium pratense LastZ Results

Back to all analyses

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Trifolium pratense (Trifolium pratense, Trpr) 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: 739,673

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

Uncovered: 208,983,438 out of 412,800,391
Covered: 203,816,953 out of 412,800,391

Uncovered: 5,658,898 out of 50,132,764
Matches: 35,519,085 out of 50,132,764
Mismatches: 8,257,427 out of 50,132,764
Insertions: 697,354 out of 50,132,764

Trifolium pratense

Uncovered: 124,275,960 out of 304,842,038
Covered: 180,566,078 out of 304,842,038

Uncovered: 3,234,756 out of 41,242,947
Matches: 31,706,763 out of 41,242,947
Mismatches: 5,667,129 out of 41,242,947
Insertions: 634,299 out of 41,242,947

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 Trifolium pratense
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}