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Arabidopsis thaliana vs Cyanidioschyzon merolae LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cyanidioschyzon merolae (Cyanidioschyzon merolae strain 10D, ASM9120v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 66. 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Statistics over 6,297 alignment blocks

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

Uncovered: 118,271,128 out of 119,667,750
Covered: 1,396,622 out of 119,667,750

Uncovered: 32,479,085 out of 33,775,569
Matches: 806,221 out of 33,775,569
Mismatches: 459,755 out of 33,775,569
Insertions: 30,508 out of 33,775,569
Identity over aligned base-pairs: 62.2%

Cyanidioschyzon merolae

Uncovered: 16,066,082 out of 16,728,945
Covered: 662,863 out of 16,728,945

Uncovered: 6,843,905 out of 7,493,795
Matches: 402,788 out of 7,493,795
Mismatches: 233,199 out of 7,493,795
Insertions: 13,903 out of 7,493,795
Identity over aligned base-pairs: 62.0%

Block size distribution

Size range All 6,297 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
25
152.0 bp
10 bp - 100 bp
1,647
121.6 kb
241
17.8 kb
100 bp - 1 kb
4,496
1.1 Mb
1,853
791.2 kb
1 kb - 10 kb
129
168.4 kb
423
613.4 kb