Medicago truncatula vs Corchorus capsularis LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Corchorus capsularis (Corchorus capsularis, CCACVL1_1.0) 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: 170,692

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

Uncovered: 357,523,835 out of 412,800,391
Covered: 55,276,556 out of 412,800,391

Uncovered: 15,862,541 out of 50,132,764
Matches: 23,729,346 out of 50,132,764
Mismatches: 9,808,005 out of 50,132,764
Insertions: 732,872 out of 50,132,764

Corchorus capsularis

Uncovered: 273,602,529 out of 317,178,409
Covered: 43,575,880 out of 317,178,409

Uncovered: 7,793,285 out of 30,371,305
Matches: 15,685,961 out of 30,371,305
Mismatches: 6,317,075 out of 30,371,305
Insertions: 574,984 out of 30,371,305

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 Corchorus capsularis
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}