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Arabidopsis thaliana vs Eragrostis curvula LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Eragrostis curvula (Eragrostis curvula, CERZOS_E.curvula1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 thalianaEragrostis curvula
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 156,373 alignment blocks

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

Uncovered: 92,708,001 out of 119,667,750
Covered: 26,959,749 out of 119,667,750

Uncovered: 13,995,225 out of 33,775,569
Matches: 12,765,970 out of 33,775,569
Mismatches: 6,597,675 out of 33,775,569
Insertions: 416,699 out of 33,775,569
Identity over aligned base-pairs: 64.5%

Eragrostis curvula

Uncovered: 558,772,205 out of 603,072,269
Covered: 44,300,064 out of 603,072,269

Uncovered: 35,284,662 out of 62,628,176
Matches: 17,516,068 out of 62,628,176
Mismatches: 9,175,824 out of 62,628,176
Insertions: 651,622 out of 62,628,176
Identity over aligned base-pairs: 64.1%

Block size distribution

Size range All 156,373 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,192
6.4 kb
10 bp - 100 bp
23,621
1.6 Mb
4,554
322.7 kb
100 bp - 1 kb
122,146
41.1 Mb
32,602
13.8 Mb
1 kb - 10 kb
9,414
13.6 Mb
20,545
41.8 Mb
10 kb - 100 kb
38
454.4 kb