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Arabidopsis thaliana vs Vigna angularis LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Vigna angularis (Vigna angularis, Vigan1.1) 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 thalianaVigna angularis
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 144,816 alignment blocks

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

Uncovered: 85,295,260 out of 119,667,750
Covered: 34,372,490 out of 119,667,750

Uncovered: 9,180,667 out of 33,775,569
Matches: 16,530,954 out of 33,775,569
Mismatches: 7,495,942 out of 33,775,569
Insertions: 568,006 out of 33,775,569
Identity over aligned base-pairs: 67.2%

Vigna angularis

Uncovered: 425,879,610 out of 466,744,453
Covered: 40,864,843 out of 466,744,453

Uncovered: 13,689,796 out of 37,822,470
Matches: 16,178,761 out of 37,822,470
Mismatches: 7,345,848 out of 37,822,470
Insertions: 608,065 out of 37,822,470
Identity over aligned base-pairs: 67.0%

Block size distribution

Size range All 144,816 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,302
7.0 kb
10 bp - 100 bp
22,280
1.5 Mb
5,535
391.3 kb
100 bp - 1 kb
111,272
38.1 Mb
30,401
11.8 Mb
1 kb - 10 kb
9,962
14.8 Mb
16,815
38.6 Mb
10 kb - 100 kb
246
3.6 Mb