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Medicago truncatula vs Cucumis sativus LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Cucumis sativus (Cucumis sativus, ASM407v2) 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 truncatulaCucumis sativus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 147,816 alignment blocks

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

Uncovered: 383,244,775 out of 429,196,467
Covered: 45,951,692 out of 429,196,467

Uncovered: 16,639,993 out of 45,081,035
Matches: 19,473,998 out of 45,081,035
Mismatches: 8,364,169 out of 45,081,035
Insertions: 602,875 out of 45,081,035
Identity over aligned base-pairs: 68.5%

Cucumis sativus

Uncovered: 159,086,980 out of 193,829,320
Covered: 34,742,340 out of 193,829,320

Uncovered: 5,482,316 out of 26,192,424
Matches: 14,216,894 out of 26,192,424
Mismatches: 5,985,045 out of 26,192,424
Insertions: 508,169 out of 26,192,424
Identity over aligned base-pairs: 68.6%

Block size distribution

Size range All 147,816 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,236
6.3 kb
10 bp - 100 bp
21,270
1.4 Mb
5,805
407.1 kb
100 bp - 1 kb
114,951
39.5 Mb
31,787
12.0 Mb
1 kb - 10 kb
10,359
15.7 Mb
16,177
38.4 Mb
10 kb - 100 kb
333
5.8 Mb