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Arabidopsis thaliana vs Eucalyptus grandis LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Eucalyptus grandis (Eucalyptus grandis, Egrandis1_0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 103. 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 thalianaEucalyptus grandis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 173,293 alignment blocks

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

Uncovered: 87,985,260 out of 119,667,750
Covered: 31,682,490 out of 119,667,750

Uncovered: 11,089,550 out of 33,775,569
Matches: 14,900,936 out of 33,775,569
Mismatches: 7,348,047 out of 33,775,569
Insertions: 437,036 out of 33,775,569
Identity over aligned base-pairs: 65.7%

Eucalyptus grandis

Uncovered: 640,060,734 out of 691,269,672
Covered: 51,208,938 out of 691,269,672

Uncovered: 16,551,065 out of 41,838,270
Matches: 16,717,592 out of 41,838,270
Mismatches: 7,913,240 out of 41,838,270
Insertions: 656,373 out of 41,838,270
Identity over aligned base-pairs: 66.1%

Block size distribution

Size range All 173,293 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,509
8.1 kb
10 bp - 100 bp
25,886
1.8 Mb
5,865
427.8 kb
100 bp - 1 kb
135,905
45.4 Mb
40,200
16.1 Mb
1 kb - 10 kb
9,940
14.9 Mb
20,065
42.6 Mb
10 kb - 100 kb
51
1.0 Mb
237
3.8 Mb
100 kb - 1 Mb
2
273.7 kb
2
402.8 kb