In this section

Arabidopsis thaliana vs Arabis alpina LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Arabis alpina (Arabis alpina, A_alpina_V4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 thalianaArabis alpina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 144,847 alignment blocks

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

Uncovered: 45,497,573 out of 119,667,750
Covered: 74,170,177 out of 119,667,750

Uncovered: 2,335,477 out of 33,775,569
Matches: 26,323,441 out of 33,775,569
Mismatches: 4,533,184 out of 33,775,569
Insertions: 583,467 out of 33,775,569
Identity over aligned base-pairs: 83.7%

Arabis alpina

Uncovered: 223,112,372 out of 308,032,609
Covered: 84,920,237 out of 308,032,609

Uncovered: 4,307,794 out of 25,084,253
Matches: 17,778,418 out of 25,084,253
Mismatches: 2,735,311 out of 25,084,253
Insertions: 262,730 out of 25,084,253
Identity over aligned base-pairs: 85.6%

Block size distribution

Size range All 144,847 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,689
10.5 kb
10 bp - 100 bp
24,623
1.5 Mb
8,829
609.0 kb
100 bp - 1 kb
89,497
34.3 Mb
36,236
12.7 Mb
1 kb - 10 kb
28,959
63.6 Mb
8,921
20.8 Mb
10 kb - 100 kb
79
925.4 kb
546
12.1 Mb
100 kb - 1 Mb
12
3.8 Mb
1 Mb - 10 Mb
12
50.3 Mb