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Arabidopsis thaliana vs Corchorus capsularis LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Corchorus capsularis (Corchorus capsularis, CCACVL1_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 thalianaCorchorus capsularis
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 118,607 alignment blocks

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

Uncovered: 82,227,722 out of 119,667,750
Covered: 37,440,028 out of 119,667,750

Uncovered: 7,786,763 out of 33,775,569
Matches: 17,871,759 out of 33,775,569
Mismatches: 7,565,227 out of 33,775,569
Insertions: 551,820 out of 33,775,569
Identity over aligned base-pairs: 68.8%

Corchorus capsularis

Uncovered: 279,948,606 out of 317,178,409
Covered: 37,229,803 out of 317,178,409

Uncovered: 9,338,364 out of 30,371,305
Matches: 14,346,709 out of 30,371,305
Mismatches: 6,085,711 out of 30,371,305
Insertions: 600,521 out of 30,371,305
Identity over aligned base-pairs: 68.2%

Block size distribution

Size range All 118,607 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,094
6.2 kb
10 bp - 100 bp
16,517
1.1 Mb
3,291
236.8 kb
100 bp - 1 kb
89,296
32.6 Mb
20,075
7.9 Mb
1 kb - 10 kb
11,700
17.9 Mb
15,606
39.4 Mb
10 kb - 100 kb
292
4.0 Mb