In this section

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

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) 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 109. 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 303,662 alignment blocks

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

Uncovered: 309,951,813 out of 412,800,391
Covered: 102,848,578 out of 412,800,391

Uncovered: 10,342,914 out of 50,132,764
Matches: 30,576,116 out of 50,132,764
Mismatches: 8,327,057 out of 50,132,764
Insertions: 886,677 out of 50,132,764
Identity over aligned base-pairs: 76.8%

Cajanus cajan (pigeon pea) - GCA_000340665.1

Uncovered: 495,175,951 out of 592,816,859
Covered: 97,640,908 out of 592,816,859

Uncovered: 16,613,365 out of 46,457,444
Matches: 23,439,260 out of 46,457,444
Mismatches: 5,874,517 out of 46,457,444
Insertions: 530,302 out of 46,457,444
Identity over aligned base-pairs: 78.5%

Block size distribution

Size range All 303,662 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,876
23.2 kb
10 bp - 100 bp
46,194
2.9 Mb
15,984
1.1 Mb
100 bp - 1 kb
221,832
82.9 Mb
82,260
27.7 Mb
1 kb - 10 kb
31,663
51.8 Mb
20,554
50.8 Mb
10 kb - 100 kb
97
2.3 Mb
1,250
34.3 Mb
100 kb - 1 Mb
114
23.7 Mb
1 Mb - 10 Mb
2
2.3 Mb