In this section

Medicago truncatula vs Vicia faba LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Vicia faba (Vicia faba, Hedin2_genome_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 truncatulaVicia faba
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 761,446 alignment blocks

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

Uncovered: 284,748,086 out of 429,196,467
Covered: 144,448,381 out of 429,196,467

Uncovered: 9,449,641 out of 45,081,035
Matches: 28,726,330 out of 45,081,035
Mismatches: 6,193,252 out of 45,081,035
Insertions: 711,812 out of 45,081,035
Identity over aligned base-pairs: 80.6%

Vicia faba

Uncovered: 11,688,572,905 out of 11,914,498,746
Covered: 225,925,841 out of 11,914,498,746

Uncovered: 11,892,705 out of 38,745,029
Matches: 22,278,905 out of 38,745,029
Mismatches: 4,133,969 out of 38,745,029
Insertions: 439,450 out of 38,745,029
Identity over aligned base-pairs: 83.0%

Block size distribution

Size range All 761,446 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6,287
36.3 kb
10 bp - 100 bp
131,123
8.6 Mb
71,029
5.0 Mb
100 bp - 1 kb
551,231
190.7 Mb
343,444
120.0 Mb
1 kb - 10 kb
72,791
122.6 Mb
78,448
179.8 Mb
10 kb - 100 kb
14
188.6 kb
1,133
17.4 Mb