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Medicago truncatula vs Ficus carica LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Ficus carica (Ficus carica, UNIPI_FiCari_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 112. 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 157,199 alignment blocks

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

Uncovered: 379,160,079 out of 429,196,467
Covered: 50,036,388 out of 429,196,467

Uncovered: 15,369,170 out of 45,081,035
Matches: 20,586,330 out of 45,081,035
Mismatches: 8,542,318 out of 45,081,035
Insertions: 583,217 out of 45,081,035
Identity over aligned base-pairs: 69.3%

Ficus carica

Uncovered: 292,444,496 out of 333,439,967
Covered: 40,995,471 out of 333,439,967

Uncovered: 13,175,778 out of 35,811,513
Matches: 15,612,218 out of 35,811,513
Mismatches: 6,399,087 out of 35,811,513
Insertions: 624,430 out of 35,811,513
Identity over aligned base-pairs: 69.0%

Block size distribution

Size range All 157,199 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,361
7.3 kb
10 bp - 100 bp
20,936
1.3 Mb
4,945
355.7 kb
100 bp - 1 kb
121,889
43.4 Mb
31,044
11.6 Mb
1 kb - 10 kb
13,005
20.0 Mb
16,015
39.2 Mb
10 kb - 100 kb
8
126.9 kb
582
12.3 Mb
100 kb - 1 Mb
10
1.3 Mb