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Arabidopsis thaliana vs Cucumis melo LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cucumis melo (Cucumis melo, Melonv4) 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 thalianaCucumis melo
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 123,091 alignment blocks

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

Uncovered: 85,871,551 out of 119,667,750
Covered: 33,796,199 out of 119,667,750

Uncovered: 9,517,873 out of 33,775,569
Matches: 16,391,268 out of 33,775,569
Mismatches: 7,353,695 out of 33,775,569
Insertions: 512,733 out of 33,775,569
Identity over aligned base-pairs: 67.6%

Cucumis melo

Uncovered: 324,670,055 out of 357,857,370
Covered: 33,187,315 out of 357,857,370

Uncovered: 8,025,206 out of 27,459,425
Matches: 13,039,335 out of 27,459,425
Mismatches: 5,859,188 out of 27,459,425
Insertions: 535,696 out of 27,459,425
Identity over aligned base-pairs: 67.1%

Block size distribution

Size range All 123,091 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,128
6.0 kb
10 bp - 100 bp
18,894
1.3 Mb
4,572
319.5 kb
100 bp - 1 kb
94,417
32.2 Mb
24,011
9.2 Mb
1 kb - 10 kb
8,652
12.9 Mb
14,069
32.8 Mb
10 kb - 100 kb
250
4.1 Mb