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Arabidopsis thaliana vs Phaseolus vulgaris LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Phaseolus vulgaris (Phaseolus vulgaris, PhaVulg1_0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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.


Number of alignment blocks: 137,058

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 84,897,697 out of 119,667,750
Covered: 34,770,053 out of 119,667,750

Uncovered: 9,163,754 out of 33,775,569
Matches: 16,478,477 out of 33,775,569
Mismatches: 7,569,924 out of 33,775,569
Insertions: 563,414 out of 33,775,569

Phaseolus vulgaris

Uncovered: 481,726,169 out of 521,076,696
Covered: 39,350,527 out of 521,076,696

Uncovered: 9,023,437 out of 34,663,348
Matches: 17,191,069 out of 34,663,348
Mismatches: 7,807,657 out of 34,663,348
Insertions: 641,185 out of 34,663,348

Configuration parameters

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)
     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

Arabidopsis thaliana Phaseolus vulgaris
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}