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Arabidopsis thaliana vs Ipomoea triloba LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Ipomoea triloba (Ipomoea triloba, ASM357664v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 thalianaIpomoea triloba
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 151,803 alignment blocks

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

Uncovered: 84,807,217 out of 119,667,750
Covered: 34,860,533 out of 119,667,750

Uncovered: 9,343,071 out of 33,775,569
Matches: 16,252,093 out of 33,775,569
Mismatches: 7,630,877 out of 33,775,569
Insertions: 549,528 out of 33,775,569
Identity over aligned base-pairs: 66.5%

Ipomoea triloba

Uncovered: 416,608,013 out of 461,827,428
Covered: 45,219,415 out of 461,827,428

Uncovered: 11,888,605 out of 39,533,495
Matches: 18,379,559 out of 39,533,495
Mismatches: 8,536,069 out of 39,533,495
Insertions: 729,262 out of 39,533,495
Identity over aligned base-pairs: 66.5%

Block size distribution

Size range All 151,803 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,528
8.2 kb
10 bp - 100 bp
23,272
1.5 Mb
5,657
399.5 kb
100 bp - 1 kb
115,591
39.9 Mb
29,537
11.5 Mb
1 kb - 10 kb
11,394
17.3 Mb
18,268
42.6 Mb
10 kb - 100 kb
18
376.3 kb
279
4.5 Mb