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Medicago truncatula vs Citrullus lanatus LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Citrullus lanatus (Citrullus lanatus, Cla97_v1) 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 truncatulaCitrullus lanatus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 144,631 alignment blocks

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

Uncovered: 383,902,929 out of 429,196,467
Covered: 45,293,538 out of 429,196,467

Uncovered: 17,613,040 out of 45,081,035
Matches: 18,878,600 out of 45,081,035
Mismatches: 8,027,024 out of 45,081,035
Insertions: 562,371 out of 45,081,035
Identity over aligned base-pairs: 68.7%

Citrullus lanatus

Uncovered: 331,710,318 out of 365,450,462
Covered: 33,740,144 out of 365,450,462

Uncovered: 6,822,544 out of 26,302,942
Matches: 13,475,647 out of 26,302,942
Mismatches: 5,548,031 out of 26,302,942
Insertions: 456,720 out of 26,302,942
Identity over aligned base-pairs: 69.2%

Block size distribution

Size range All 144,631 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,232
6.4 kb
10 bp - 100 bp
20,846
1.4 Mb
6,537
456.3 kb
100 bp - 1 kb
112,465
38.4 Mb
32,656
12.2 Mb
1 kb - 10 kb
10,058
15.3 Mb
16,148
37.9 Mb
10 kb - 100 kb
30
471.5 kb
302
5.0 Mb