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Arabidopsis thaliana vs Gossypium raimondii LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Gossypium raimondii (Gossypium raimondii, Graimondii2_0_v6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 102. 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 thalianaGossypium raimondii
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 218,886 alignment blocks

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

Uncovered: 80,582,285 out of 119,667,750
Covered: 39,085,465 out of 119,667,750

Uncovered: 7,297,473 out of 33,775,569
Matches: 17,974,664 out of 33,775,569
Mismatches: 7,877,883 out of 33,775,569
Insertions: 625,549 out of 33,775,569
Identity over aligned base-pairs: 67.9%

Gossypium raimondii

Uncovered: 705,124,485 out of 761,405,269
Covered: 56,280,784 out of 761,405,269

Uncovered: 10,485,863 out of 45,523,048
Matches: 23,790,321 out of 45,523,048
Mismatches: 10,257,322 out of 45,523,048
Insertions: 989,542 out of 45,523,048
Identity over aligned base-pairs: 67.9%

Block size distribution

Size range All 218,886 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,425
13.3 kb
10 bp - 100 bp
32,849
2.1 Mb
5,316
389.5 kb
100 bp - 1 kb
163,146
58.7 Mb
32,330
12.5 Mb
1 kb - 10 kb
20,460
31.2 Mb
22,722
62.1 Mb
10 kb - 100 kb
6
78.7 kb
1,006
16.9 Mb
100 kb - 1 Mb
2
293.9 kb