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Medicago truncatula vs Sphenostylis stenocarpa LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Sphenostylis stenocarpa (Sphenostylis stenocarpa, hybrid_with_Hi_C) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 114. 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 truncatulaSphenostylis stenocarpa
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 255,098 alignment blocks

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

Uncovered: 333,960,597 out of 429,196,467
Covered: 95,235,870 out of 429,196,467

Uncovered: 7,758,909 out of 45,081,035
Matches: 28,720,796 out of 45,081,035
Mismatches: 7,814,704 out of 45,081,035
Insertions: 786,626 out of 45,081,035
Identity over aligned base-pairs: 77.0%

Sphenostylis stenocarpa

Uncovered: 566,911,799 out of 649,801,261
Covered: 82,889,462 out of 649,801,261

Uncovered: 4,343,331 out of 34,594,766
Matches: 23,577,724 out of 34,594,766
Mismatches: 6,009,622 out of 34,594,766
Insertions: 664,089 out of 34,594,766
Identity over aligned base-pairs: 77.9%

Block size distribution

Size range All 255,098 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,018
18.2 kb
10 bp - 100 bp
38,832
2.4 Mb
13,043
928.2 kb
100 bp - 1 kb
183,015
70.4 Mb
60,054
20.3 Mb
1 kb - 10 kb
30,225
49.0 Mb
16,972
40.9 Mb
10 kb - 100 kb
8
117.4 kb
579
13.0 Mb
100 kb - 1 Mb
61
20.0 Mb
1 Mb - 10 Mb
13
26.8 Mb