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Medicago truncatula vs Vigna angularis LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Vigna angularis (Vigna angularis, Vigan1.1) 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 truncatulaVigna angularis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 295,729 alignment blocks

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

Uncovered: 334,535,227 out of 429,196,467
Covered: 94,661,240 out of 429,196,467

Uncovered: 7,909,754 out of 45,081,035
Matches: 28,275,838 out of 45,081,035
Mismatches: 8,085,099 out of 45,081,035
Insertions: 810,344 out of 45,081,035
Identity over aligned base-pairs: 76.1%

Vigna angularis

Uncovered: 374,570,363 out of 466,744,453
Covered: 92,174,090 out of 466,744,453

Uncovered: 8,353,412 out of 37,822,470
Matches: 22,774,878 out of 37,822,470
Mismatches: 6,095,011 out of 37,822,470
Insertions: 599,169 out of 37,822,470
Identity over aligned base-pairs: 77.3%

Block size distribution

Size range All 295,729 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,193
19.2 kb
10 bp - 100 bp
49,786
3.1 Mb
22,346
1.5 Mb
100 bp - 1 kb
211,805
78.6 Mb
84,057
28.3 Mb
1 kb - 10 kb
30,928
50.4 Mb
20,390
48.3 Mb
10 kb - 100 kb
17
236.9 kb
694
17.0 Mb
100 kb - 1 Mb
99
24.7 Mb
1 Mb - 10 Mb
8
12.5 Mb