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Medicago truncatula vs Trifolium pratense LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Trifolium pratense (Trifolium pratense, Trpr) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 truncatulaTrifolium pratense
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 739,673 alignment blocks

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

Uncovered: 208,983,438 out of 412,800,391
Covered: 203,816,953 out of 412,800,391

Uncovered: 5,658,898 out of 50,132,764
Matches: 35,519,085 out of 50,132,764
Mismatches: 8,257,427 out of 50,132,764
Insertions: 697,354 out of 50,132,764
Identity over aligned base-pairs: 79.9%

Trifolium pratense

Uncovered: 124,275,960 out of 304,842,038
Covered: 180,566,078 out of 304,842,038

Uncovered: 3,234,756 out of 41,242,947
Matches: 31,706,763 out of 41,242,947
Mismatches: 5,667,129 out of 41,242,947
Insertions: 634,299 out of 41,242,947
Identity over aligned base-pairs: 83.4%

Block size distribution

Size range All 739,673 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,304
43.0 kb
10 bp - 100 bp
158,579
10.2 Mb
88,266
6.1 Mb
100 bp - 1 kb
514,381
166.3 Mb
302,209
94.5 Mb
1 kb - 10 kb
58,839
106.7 Mb
38,828
88.5 Mb
10 kb - 100 kb
565
8.7 Mb
2,069
58.1 Mb
100 kb - 1 Mb
5
501.5 kb
186
41.9 Mb
1 Mb - 10 Mb
3
3.4 Mb