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Medicago truncatula vs Arachis hypogaea LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Arachis hypogaea (Arachis hypogaea, arahy.Tifrunner.gnm2.J5K5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. 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 truncatulaArachis hypogaea
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 495,015 alignment blocks

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

Uncovered: 340,177,249 out of 429,196,467
Covered: 89,019,218 out of 429,196,467

Uncovered: 8,097,041 out of 45,081,035
Matches: 27,723,629 out of 45,081,035
Mismatches: 8,419,325 out of 45,081,035
Insertions: 841,040 out of 45,081,035
Identity over aligned base-pairs: 75.0%

Arachis hypogaea

Uncovered: 2,376,330,882 out of 2,557,413,415
Covered: 181,082,533 out of 2,557,413,415

Uncovered: 24,462,646 out of 87,135,882
Matches: 47,516,382 out of 87,135,882
Mismatches: 13,579,091 out of 87,135,882
Insertions: 1,577,763 out of 87,135,882
Identity over aligned base-pairs: 75.8%

Block size distribution

Size range All 495,015 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6,181
35.7 kb
10 bp - 100 bp
74,209
4.5 Mb
21,947
1.6 Mb
100 bp - 1 kb
360,675
135.9 Mb
127,231
47.0 Mb
1 kb - 10 kb
53,937
86.8 Mb
45,380
109.8 Mb
10 kb - 100 kb
13
160.2 kb
1,211
25.3 Mb
100 kb - 1 Mb
112
35.9 Mb
1 Mb - 10 Mb
6
7.7 Mb