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Medicago truncatula vs Lablab purpureus Natoba LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Lablab purpureus Natoba (Lablab purpureus, ILRI_Lpur) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 115. 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 truncatulaLablab purpureus Natoba
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 253,337 alignment blocks

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

Uncovered: 332,762,342 out of 429,196,467
Covered: 96,434,125 out of 429,196,467

Uncovered: 7,799,493 out of 45,081,035
Matches: 28,723,186 out of 45,081,035
Mismatches: 7,777,061 out of 45,081,035
Insertions: 781,295 out of 45,081,035
Identity over aligned base-pairs: 77.0%

Lablab purpureus Natoba

Uncovered: 344,859,826 out of 426,257,348
Covered: 81,397,522 out of 426,257,348

Uncovered: 3,136,993 out of 32,180,237
Matches: 22,886,515 out of 32,180,237
Mismatches: 5,607,263 out of 32,180,237
Insertions: 549,466 out of 32,180,237
Identity over aligned base-pairs: 78.8%

Block size distribution

Size range All 253,337 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,163
19.3 kb
10 bp - 100 bp
38,317
2.3 Mb
13,343
952.4 kb
100 bp - 1 kb
182,241
70.0 Mb
59,858
20.0 Mb
1 kb - 10 kb
29,612
48.0 Mb
16,009
38.2 Mb
10 kb - 100 kb
4
56.7 kb
517
11.4 Mb
100 kb - 1 Mb
59
21.2 Mb
1 Mb - 10 Mb
14
28.6 Mb