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Arabidopsis thaliana vs Daucus carota LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Daucus carota (Daucus carota subsp. sativus, ASM162521v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 thalianaDaucus carota
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 155,802 alignment blocks

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

Uncovered: 85,951,759 out of 119,667,750
Covered: 33,715,991 out of 119,667,750

Uncovered: 9,477,353 out of 33,775,569
Matches: 16,227,530 out of 33,775,569
Mismatches: 7,510,755 out of 33,775,569
Insertions: 559,931 out of 33,775,569
Identity over aligned base-pairs: 66.8%

Daucus carota

Uncovered: 376,465,506 out of 421,502,825
Covered: 45,037,319 out of 421,502,825

Uncovered: 12,107,747 out of 38,118,360
Matches: 17,330,738 out of 38,118,360
Mismatches: 8,038,034 out of 38,118,360
Insertions: 641,841 out of 38,118,360
Identity over aligned base-pairs: 66.6%

Block size distribution

Size range All 155,802 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,384
7.3 kb
10 bp - 100 bp
23,898
1.6 Mb
5,752
403.2 kb
100 bp - 1 kb
119,749
40.6 Mb
31,221
12.1 Mb
1 kb - 10 kb
10,768
16.0 Mb
18,469
42.5 Mb
10 kb - 100 kb
3
49.1 kb
231
3.2 Mb
100 kb - 1 Mb
1
114.9 kb