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Arabidopsis thaliana vs Citrus clementina LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Citrus clementina (Citrus clementina, Citrus_clementina_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 thalianaCitrus clementina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 131,953 alignment blocks

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

Uncovered: 82,513,056 out of 119,667,750
Covered: 37,154,694 out of 119,667,750

Uncovered: 7,647,160 out of 33,775,569
Matches: 17,886,179 out of 33,775,569
Mismatches: 7,693,617 out of 33,775,569
Insertions: 548,613 out of 33,775,569
Identity over aligned base-pairs: 68.5%

Citrus clementina

Uncovered: 260,001,091 out of 301,364,702
Covered: 41,363,611 out of 301,364,702

Uncovered: 6,665,809 out of 30,721,724
Matches: 16,190,513 out of 30,721,724
Mismatches: 7,160,683 out of 30,721,724
Insertions: 704,719 out of 30,721,724
Identity over aligned base-pairs: 67.3%

Block size distribution

Size range All 131,953 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,249
6.9 kb
10 bp - 100 bp
18,566
1.2 Mb
3,943
275.0 kb
100 bp - 1 kb
100,069
36.0 Mb
22,967
9.0 Mb
1 kb - 10 kb
12,066
18.5 Mb
14,920
36.0 Mb
10 kb - 100 kb
3
31.1 kb
479
9.4 Mb
100 kb - 1 Mb
6
1.1 Mb