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Medicago truncatula vs Manihot esculenta LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Manihot esculenta (Manihot esculenta, M.esculenta_v8) 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 truncatulaManihot esculenta
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 231,510 alignment blocks

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

Uncovered: 372,910,347 out of 429,196,467
Covered: 56,286,120 out of 429,196,467

Uncovered: 13,516,542 out of 45,081,035
Matches: 21,901,053 out of 45,081,035
Mismatches: 8,965,561 out of 45,081,035
Insertions: 697,879 out of 45,081,035
Identity over aligned base-pairs: 69.4%

Manihot esculenta

Uncovered: 570,136,387 out of 639,586,700
Covered: 69,450,313 out of 639,586,700

Uncovered: 9,906,197 out of 41,320,091
Matches: 21,806,123 out of 41,320,091
Mismatches: 8,804,580 out of 41,320,091
Insertions: 803,191 out of 41,320,091
Identity over aligned base-pairs: 69.4%

Block size distribution

Size range All 231,510 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,445
12.4 kb
10 bp - 100 bp
32,887
2.1 Mb
10,146
704.6 kb
100 bp - 1 kb
174,800
62.3 Mb
56,500
21.3 Mb
1 kb - 10 kb
21,376
33.2 Mb
26,461
61.8 Mb
10 kb - 100 kb
2
32.7 kb
576
12.1 Mb
100 kb - 1 Mb
12
1.7 Mb