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Medicago truncatula vs Lupinus angustifolius LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_v1.0) 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 truncatulaLupinus angustifolius
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 494,718 alignment blocks

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

Uncovered: 328,295,304 out of 429,196,467
Covered: 100,901,163 out of 429,196,467

Uncovered: 8,276,117 out of 45,081,035
Matches: 28,161,513 out of 45,081,035
Mismatches: 7,821,886 out of 45,081,035
Insertions: 821,519 out of 45,081,035
Identity over aligned base-pairs: 76.5%

Lupinus angustifolius

Uncovered: 460,790,050 out of 609,203,021
Covered: 148,412,971 out of 609,203,021

Uncovered: 5,291,630 out of 42,631,353
Matches: 29,362,582 out of 42,631,353
Mismatches: 7,166,457 out of 42,631,353
Insertions: 810,684 out of 42,631,353
Identity over aligned base-pairs: 78.6%

Block size distribution

Size range All 494,718 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6,392
36.1 kb
10 bp - 100 bp
103,115
6.3 Mb
46,966
3.2 Mb
100 bp - 1 kb
341,407
120.1 Mb
146,716
47.2 Mb
1 kb - 10 kb
43,797
73.0 Mb
34,247
86.9 Mb
10 kb - 100 kb
7
99.9 kb
972
20.7 Mb
100 kb - 1 Mb
109
33.5 Mb
1 Mb - 10 Mb
7
8.0 Mb