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Medicago truncatula vs Trifolium pratense LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Trifolium pratense (Trifolium pratense, Trpr) 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 truncatulaTrifolium pratense
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 874,944 alignment blocks

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

Uncovered: 194,766,403 out of 429,196,467
Covered: 234,430,064 out of 429,196,467

Uncovered: 2,737,435 out of 45,081,035
Matches: 34,207,745 out of 45,081,035
Mismatches: 7,492,351 out of 45,081,035
Insertions: 643,504 out of 45,081,035
Identity over aligned base-pairs: 80.8%

Trifolium pratense

Uncovered: 123,185,520 out of 304,842,038
Covered: 181,656,518 out of 304,842,038

Uncovered: 3,864,099 out of 41,242,947
Matches: 31,665,749 out of 41,242,947
Mismatches: 5,068,748 out of 41,242,947
Insertions: 644,351 out of 41,242,947
Identity over aligned base-pairs: 84.7%

Block size distribution

Size range All 874,944 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8,392
47.9 kb
10 bp - 100 bp
193,740
12.5 Mb
115,223
7.9 Mb
100 bp - 1 kb
608,549
193.9 Mb
379,892
119.5 Mb
1 kb - 10 kb
63,937
113.9 Mb
45,749
98.9 Mb
10 kb - 100 kb
326
3.4 Mb
1,786
51.6 Mb
100 kb - 1 Mb
189
42.5 Mb
1 Mb - 10 Mb
3
3.5 Mb