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Arabidopsis thaliana vs Corymbia citriodora LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Corymbia citriodora (Corymbia citriodora subsp. variegata, Ccitriodora_v2_1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. 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 thalianaCorymbia citriodora
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 129,987 alignment blocks

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

Uncovered: 89,617,088 out of 119,667,750
Covered: 30,050,662 out of 119,667,750

Uncovered: 11,598,496 out of 33,775,569
Matches: 14,920,746 out of 33,775,569
Mismatches: 6,821,921 out of 33,775,569
Insertions: 434,406 out of 33,775,569
Identity over aligned base-pairs: 67.3%

Corymbia citriodora

Uncovered: 508,234,777 out of 544,191,601
Covered: 35,956,824 out of 544,191,601

Uncovered: 22,225,801 out of 44,291,432
Matches: 14,716,248 out of 44,291,432
Mismatches: 6,787,875 out of 44,291,432
Insertions: 561,508 out of 44,291,432
Identity over aligned base-pairs: 66.7%

Block size distribution

Size range All 129,987 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,329
7.0 kb
10 bp - 100 bp
19,925
1.3 Mb
3,576
260.1 kb
100 bp - 1 kb
101,019
33.9 Mb
24,948
10.2 Mb
1 kb - 10 kb
7,710
11.4 Mb
14,997
33.7 Mb
10 kb - 100 kb
4
41.7 kb
176
2.5 Mb