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Medicago truncatula vs Prunus persica LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) 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 truncatulaPrunus persica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 177,972 alignment blocks

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

Uncovered: 374,265,620 out of 429,196,467
Covered: 54,930,847 out of 429,196,467

Uncovered: 13,159,864 out of 45,081,035
Matches: 22,400,482 out of 45,081,035
Mismatches: 8,884,393 out of 45,081,035
Insertions: 636,296 out of 45,081,035
Identity over aligned base-pairs: 70.2%

Prunus persica

Uncovered: 180,733,056 out of 227,411,381
Covered: 46,678,325 out of 227,411,381

Uncovered: 6,880,984 out of 33,236,255
Matches: 18,297,276 out of 33,236,255
Mismatches: 7,343,671 out of 33,236,255
Insertions: 714,324 out of 33,236,255
Identity over aligned base-pairs: 69.4%

Block size distribution

Size range All 177,972 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,518
8.3 kb
10 bp - 100 bp
25,982
1.7 Mb
7,912
560.9 kb
100 bp - 1 kb
135,175
47.8 Mb
39,023
13.9 Mb
1 kb - 10 kb
15,294
23.7 Mb
16,428
38.9 Mb
10 kb - 100 kb
3
30.3 kb
469
10.8 Mb
100 kb - 1 Mb
45
9.2 Mb