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Medicago truncatula vs Corchorus capsularis LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Corchorus capsularis (Corchorus capsularis, CCACVL1_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 truncatulaCorchorus capsularis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 170,692 alignment blocks

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

Uncovered: 357,523,835 out of 412,800,391
Covered: 55,276,556 out of 412,800,391

Uncovered: 15,862,541 out of 50,132,764
Matches: 23,729,346 out of 50,132,764
Mismatches: 9,808,005 out of 50,132,764
Insertions: 732,872 out of 50,132,764
Identity over aligned base-pairs: 69.2%

Corchorus capsularis

Uncovered: 273,602,529 out of 317,178,409
Covered: 43,575,880 out of 317,178,409

Uncovered: 7,793,285 out of 30,371,305
Matches: 15,685,961 out of 30,371,305
Mismatches: 6,317,075 out of 30,371,305
Insertions: 574,984 out of 30,371,305
Identity over aligned base-pairs: 69.5%

Block size distribution

Size range All 170,692 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,422
7.9 kb
10 bp - 100 bp
23,583
1.5 Mb
6,370
462.3 kb
100 bp - 1 kb
130,740
46.3 Mb
37,476
13.7 Mb
1 kb - 10 kb
14,933
23.2 Mb
19,437
48.2 Mb
10 kb - 100 kb
14
317.7 kb
584
9.0 Mb