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Solanum lycopersicum vs Sesamum indicum LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Sesamum indicum (Sesamum indicum, S_indicum_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 104. Solanum lycopersicum was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterSolanum lycopersicumSesamum indicum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 161,772 alignment blocks

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

Uncovered: 778,666,900 out of 827,747,456
Covered: 49,080,556 out of 827,747,456

Uncovered: 9,430,387 out of 36,416,191
Matches: 18,980,509 out of 36,416,191
Mismatches: 7,481,172 out of 36,416,191
Insertions: 524,123 out of 36,416,191
Identity over aligned base-pairs: 70.3%

Sesamum indicum

Uncovered: 232,447,613 out of 274,906,174
Covered: 42,458,561 out of 274,906,174

Uncovered: 7,574,831 out of 30,374,283
Matches: 16,066,752 out of 30,374,283
Mismatches: 6,246,568 out of 30,374,283
Insertions: 486,132 out of 30,374,283
Identity over aligned base-pairs: 70.5%

Block size distribution

Size range All 161,772 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,607
8.1 kb
10 bp - 100 bp
24,036
1.6 Mb
7,173
513.6 kb
100 bp - 1 kb
123,348
42.6 Mb
34,715
12.6 Mb
1 kb - 10 kb
12,776
19.8 Mb
14,576
34.2 Mb
10 kb - 100 kb
5
52.8 kb
473
10.7 Mb
100 kb - 1 Mb
26
6.0 Mb