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Medicago truncatula vs Quercus suber LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Quercus suber (Quercus suber, CorkOak1.0) 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 truncatulaQuercus suber
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 294,283 alignment blocks

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

Uncovered: 368,299,341 out of 429,196,467
Covered: 60,897,126 out of 429,196,467

Uncovered: 12,733,346 out of 45,081,035
Matches: 22,765,488 out of 45,081,035
Mismatches: 8,892,308 out of 45,081,035
Insertions: 689,893 out of 45,081,035
Identity over aligned base-pairs: 70.4%

Quercus suber

Uncovered: 868,326,296 out of 953,298,670
Covered: 84,972,374 out of 953,298,670

Uncovered: 19,366,605 out of 50,527,809
Matches: 21,852,431 out of 50,527,809
Mismatches: 8,488,343 out of 50,527,809
Insertions: 820,430 out of 50,527,809
Identity over aligned base-pairs: 70.1%

Block size distribution

Size range All 294,283 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,178
11.2 kb
10 bp - 100 bp
44,139
2.9 Mb
19,738
1.4 Mb
100 bp - 1 kb
224,227
76.4 Mb
95,420
33.4 Mb
1 kb - 10 kb
23,724
37.1 Mb
33,293
75.9 Mb
10 kb - 100 kb
15
205.2 kb
415
6.0 Mb