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Oryza sativa Japonica Group vs Theobroma cacao Matina 1-6 LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Theobroma cacao Matina 1-6 (Theobroma cacao, Theobroma_cacao_20110822) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Oryza sativa Japonica Group 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

ParameterOryza sativa Japonica GroupTheobroma cacao Matina 1-6
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 125,076 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 342,335,946 out of 375,049,285
Covered: 32,713,339 out of 375,049,285

Uncovered: 14,196,290 out of 34,424,450
Matches: 13,132,084 out of 34,424,450
Mismatches: 6,646,377 out of 34,424,450
Insertions: 449,699 out of 34,424,450
Identity over aligned base-pairs: 64.9%

Theobroma cacao Matina 1-6

Uncovered: 317,425,740 out of 345,993,675
Covered: 28,567,935 out of 345,993,675

Uncovered: 14,916,118 out of 34,800,751
Matches: 12,950,388 out of 34,800,751
Mismatches: 6,503,828 out of 34,800,751
Insertions: 430,417 out of 34,800,751
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 125,076 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
939
4.7 kb
10 bp - 100 bp
18,816
1.3 Mb
3,380
241.5 kb
100 bp - 1 kb
98,277
32.1 Mb
24,359
10.0 Mb
1 kb - 10 kb
7,036
10.5 Mb
15,227
33.0 Mb
10 kb - 100 kb
8
87.1 kb
61
803.0 kb