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Medicago truncatula vs Prunus avium LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Prunus avium (Prunus avium, PAV_r1.0) 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 truncatulaPrunus avium
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 173,802 alignment blocks

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

Uncovered: 374,594,707 out of 429,196,467
Covered: 54,601,760 out of 429,196,467

Uncovered: 13,593,605 out of 45,081,035
Matches: 22,069,312 out of 45,081,035
Mismatches: 8,793,584 out of 45,081,035
Insertions: 624,534 out of 45,081,035
Identity over aligned base-pairs: 70.1%

Prunus avium

Uncovered: 226,625,329 out of 272,361,615
Covered: 45,736,286 out of 272,361,615

Uncovered: 15,991,091 out of 38,693,511
Matches: 15,741,394 out of 38,693,511
Mismatches: 6,312,875 out of 38,693,511
Insertions: 648,151 out of 38,693,511
Identity over aligned base-pairs: 69.3%

Block size distribution

Size range All 173,802 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,542
8.3 kb
10 bp - 100 bp
23,999
1.5 Mb
6,325
457.6 kb
100 bp - 1 kb
133,432
47.4 Mb
38,314
14.2 Mb
1 kb - 10 kb
14,820
23.0 Mb
17,318
41.1 Mb
10 kb - 100 kb
9
100.9 kb
648
14.9 Mb
100 kb - 1 Mb
11
1.4 Mb