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Arabidopsis thaliana vs Citrullus lanatus LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Citrullus lanatus (Citrullus lanatus, Cla97_v1) 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 thalianaCitrullus lanatus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 114,497 alignment blocks

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

Uncovered: 85,866,320 out of 119,667,750
Covered: 33,801,430 out of 119,667,750

Uncovered: 9,548,003 out of 33,775,569
Matches: 16,344,255 out of 33,775,569
Mismatches: 7,382,852 out of 33,775,569
Insertions: 500,459 out of 33,775,569
Identity over aligned base-pairs: 67.5%

Citrullus lanatus

Uncovered: 334,774,786 out of 365,450,462
Covered: 30,675,676 out of 365,450,462

Uncovered: 6,273,267 out of 26,302,942
Matches: 13,489,041 out of 26,302,942
Mismatches: 6,016,688 out of 26,302,942
Insertions: 523,946 out of 26,302,942
Identity over aligned base-pairs: 67.3%

Block size distribution

Size range All 114,497 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,078
5.8 kb
10 bp - 100 bp
17,252
1.1 Mb
3,850
264.5 kb
100 bp - 1 kb
88,146
30.3 Mb
18,894
7.5 Mb
1 kb - 10 kb
8,010
12.0 Mb
13,624
32.1 Mb
10 kb - 100 kb
10
174.3 kb
231
3.7 Mb
100 kb - 1 Mb
1
135.7 kb
1
135.7 kb