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Medicago truncatula vs Corylus avellana LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Corylus avellana (Corylus avellana, CavTom2PMs-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. 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 truncatulaCorylus avellana
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 167,923 alignment blocks

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

Uncovered: 360,219,717 out of 412,800,391
Covered: 52,580,674 out of 412,800,391

Uncovered: 18,174,302 out of 50,132,764
Matches: 22,517,076 out of 50,132,764
Mismatches: 8,792,841 out of 50,132,764
Insertions: 648,545 out of 50,132,764
Identity over aligned base-pairs: 70.5%

Corylus avellana

Uncovered: 325,622,274 out of 369,779,143
Covered: 44,156,869 out of 369,779,143

Uncovered: 10,630,074 out of 31,083,732
Matches: 14,452,154 out of 31,083,732
Mismatches: 5,504,629 out of 31,083,732
Insertions: 496,875 out of 31,083,732
Identity over aligned base-pairs: 70.7%

Block size distribution

Size range All 167,923 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,489
8.2 kb
10 bp - 100 bp
22,129
1.4 Mb
5,931
428.8 kb
100 bp - 1 kb
131,264
46.4 Mb
36,971
13.6 Mb
1 kb - 10 kb
13,014
19.9 Mb
16,226
39.1 Mb
10 kb - 100 kb
27
738.9 kb
561
12.7 Mb
100 kb - 1 Mb
16
2.6 Mb