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Arabidopsis thaliana vs Theobroma cacao Matina 1-6 LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Theobroma cacao Matina 1-6 (Theobroma cacao, Theobroma_cacao_20110822) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Arabidopsis thaliana 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

ParameterArabidopsis thalianaTheobroma cacao Matina 1-6
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 119,635 alignment blocks

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

Uncovered: 82,225,495 out of 119,667,750
Covered: 37,442,255 out of 119,667,750

Uncovered: 7,358,838 out of 33,775,569
Matches: 18,170,165 out of 33,775,569
Mismatches: 7,703,371 out of 33,775,569
Insertions: 543,195 out of 33,775,569
Identity over aligned base-pairs: 68.8%

Theobroma cacao Matina 1-6

Uncovered: 309,743,692 out of 345,993,675
Covered: 36,249,983 out of 345,993,675

Uncovered: 10,800,894 out of 34,800,751
Matches: 16,277,388 out of 34,800,751
Mismatches: 7,040,720 out of 34,800,751
Insertions: 681,749 out of 34,800,751
Identity over aligned base-pairs: 67.8%

Block size distribution

Size range All 119,635 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,234
6.9 kb
10 bp - 100 bp
16,813
1.1 Mb
2,988
208.7 kb
100 bp - 1 kb
90,799
32.6 Mb
17,198
6.8 Mb
1 kb - 10 kb
10,782
16.4 Mb
12,553
30.9 Mb
10 kb - 100 kb
7
71.7 kb
474
10.1 Mb
100 kb - 1 Mb
14
2.2 Mb