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Medicago truncatula vs Ficus carica LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Ficus carica (Ficus carica, UNIPI_FiCari_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 105. Medicago truncatula 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

ParameterMedicago truncatulaFicus carica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 161,113 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 361,441,862 out of 412,800,391
Covered: 51,358,529 out of 412,800,391

Uncovered: 18,080,096 out of 50,132,764
Matches: 22,044,424 out of 50,132,764
Mismatches: 9,362,921 out of 50,132,764
Insertions: 645,323 out of 50,132,764
Identity over aligned base-pairs: 68.8%

Ficus carica

Uncovered: 291,479,528 out of 333,439,967
Covered: 41,960,439 out of 333,439,967

Uncovered: 12,844,811 out of 35,811,513
Matches: 15,762,847 out of 35,811,513
Mismatches: 6,573,089 out of 35,811,513
Insertions: 630,766 out of 35,811,513
Identity over aligned base-pairs: 68.6%

Block size distribution

Size range All 161,113 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,458
7.8 kb
10 bp - 100 bp
21,872
1.4 Mb
5,115
367.9 kb
100 bp - 1 kb
124,600
44.1 Mb
31,464
11.7 Mb
1 kb - 10 kb
13,156
20.4 Mb
16,348
40.0 Mb
10 kb - 100 kb
27
944.1 kb
591
13.1 Mb
100 kb - 1 Mb
13
1.8 Mb