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Medicago truncatula vs Cajanus cajan (pigeon pea) - GCA_000340665.1 LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Cajanus cajan (pigeon pea) - GCA_000340665.1 (Cajanus cajan, C.cajan_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 truncatulaCajanus cajan (pigeon pea) - GCA_000340665.1
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 335,724 alignment blocks

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

Uncovered: 318,422,190 out of 429,196,467
Covered: 110,774,277 out of 429,196,467

Uncovered: 7,039,263 out of 45,081,035
Matches: 29,399,043 out of 45,081,035
Mismatches: 7,805,205 out of 45,081,035
Insertions: 837,524 out of 45,081,035
Identity over aligned base-pairs: 77.3%

Cajanus cajan (pigeon pea) - GCA_000340665.1

Uncovered: 493,182,759 out of 592,816,859
Covered: 99,634,100 out of 592,816,859

Uncovered: 16,188,623 out of 46,457,444
Matches: 23,820,815 out of 46,457,444
Mismatches: 5,901,197 out of 46,457,444
Insertions: 546,809 out of 46,457,444
Identity over aligned base-pairs: 78.7%

Block size distribution

Size range All 335,724 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,953
23.6 kb
10 bp - 100 bp
51,440
3.2 Mb
20,045
1.4 Mb
100 bp - 1 kb
246,116
91.3 Mb
101,109
34.3 Mb
1 kb - 10 kb
34,211
55.4 Mb
23,317
56.0 Mb
10 kb - 100 kb
4
46.6 kb
1,160
31.8 Mb
100 kb - 1 Mb
114
24.1 Mb
1 Mb - 10 Mb
2
2.3 Mb