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Arabidopsis thaliana vs Prunus dulcis LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Prunus dulcis (Prunus dulcis, ALMONDv2) 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 thalianaPrunus dulcis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 127,490 alignment blocks

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

Uncovered: 83,164,320 out of 119,667,750
Covered: 36,503,430 out of 119,667,750

Uncovered: 7,989,733 out of 33,775,569
Matches: 17,572,928 out of 33,775,569
Mismatches: 7,681,499 out of 33,775,569
Insertions: 531,409 out of 33,775,569
Identity over aligned base-pairs: 68.1%

Prunus dulcis

Uncovered: 188,425,367 out of 227,498,357
Covered: 39,072,990 out of 227,498,357

Uncovered: 9,826,657 out of 33,980,404
Matches: 16,248,809 out of 33,980,404
Mismatches: 7,201,956 out of 33,980,404
Insertions: 702,982 out of 33,980,404
Identity over aligned base-pairs: 67.3%

Block size distribution

Size range All 127,490 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,170
6.6 kb
10 bp - 100 bp
18,625
1.2 Mb
3,686
258.9 kb
100 bp - 1 kb
96,273
34.4 Mb
21,329
8.4 Mb
1 kb - 10 kb
11,416
17.4 Mb
14,005
34.2 Mb
10 kb - 100 kb
6
83.2 kb
508
9.6 Mb
100 kb - 1 Mb
4
713.5 kb