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Medicago truncatula vs Cucumis melo LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Cucumis melo (Cucumis melo, Melonv4) 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 truncatulaCucumis melo
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 148,735 alignment blocks

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

Uncovered: 384,267,677 out of 429,196,467
Covered: 44,928,790 out of 429,196,467

Uncovered: 17,325,317 out of 45,081,035
Matches: 19,074,398 out of 45,081,035
Mismatches: 8,104,090 out of 45,081,035
Insertions: 577,230 out of 45,081,035
Identity over aligned base-pairs: 68.7%

Cucumis melo

Uncovered: 322,874,041 out of 357,857,370
Covered: 34,983,329 out of 357,857,370

Uncovered: 8,398,056 out of 27,459,425
Matches: 13,128,158 out of 27,459,425
Mismatches: 5,461,869 out of 27,459,425
Insertions: 471,342 out of 27,459,425
Identity over aligned base-pairs: 68.9%

Block size distribution

Size range All 148,735 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,201
6.2 kb
10 bp - 100 bp
21,299
1.4 Mb
5,948
426.4 kb
100 bp - 1 kb
116,075
39.6 Mb
34,495
13.0 Mb
1 kb - 10 kb
10,158
15.4 Mb
16,185
38.3 Mb
10 kb - 100 kb
2
30.7 kb
288
4.7 Mb