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Medicago truncatula vs Corylus avellana LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Corylus avellana (Corylus avellana, CavTom2PMs-1.0) 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 truncatulaCorylus avellana
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 167,801 alignment blocks

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

Uncovered: 377,164,403 out of 429,196,467
Covered: 52,032,064 out of 429,196,467

Uncovered: 14,971,874 out of 45,081,035
Matches: 21,358,406 out of 45,081,035
Mismatches: 8,151,970 out of 45,081,035
Insertions: 598,785 out of 45,081,035
Identity over aligned base-pairs: 70.9%

Corylus avellana

Uncovered: 324,601,576 out of 369,779,143
Covered: 45,177,567 out of 369,779,143

Uncovered: 10,839,022 out of 31,083,732
Matches: 14,377,317 out of 31,083,732
Mismatches: 5,372,388 out of 31,083,732
Insertions: 495,005 out of 31,083,732
Identity over aligned base-pairs: 71.0%

Block size distribution

Size range All 167,801 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,459
7.9 kb
10 bp - 100 bp
21,697
1.4 Mb
5,909
424.6 kb
100 bp - 1 kb
130,868
46.6 Mb
37,428
13.8 Mb
1 kb - 10 kb
13,777
21.1 Mb
16,813
40.6 Mb
10 kb - 100 kb
533
11.8 Mb
100 kb - 1 Mb
15
2.5 Mb