Ensembl resources are currently in reduced functionality mode. Please see our blog post for the latest information and our Twitter feed

Solanum lycopersicum vs Ipomoea triloba LastZ Results

Back to all analyses

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Ipomoea triloba (Ipomoea triloba, ASM357664v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Solanum lycopersicum 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: 249,773

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum

Uncovered: 759,433,395 out of 827,747,456
Covered: 68,314,061 out of 827,747,456

Uncovered: 6,660,989 out of 36,416,191
Matches: 21,375,571 out of 36,416,191
Mismatches: 7,802,112 out of 36,416,191
Insertions: 577,519 out of 36,416,191

Ipomoea triloba

Uncovered: 387,616,713 out of 461,827,428
Covered: 74,210,715 out of 461,827,428

Uncovered: 5,543,317 out of 39,533,495
Matches: 24,321,750 out of 39,533,495
Mismatches: 8,937,967 out of 39,533,495
Insertions: 730,461 out of 39,533,495

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

Solanum lycopersicum Ipomoea triloba
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}