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Arabidopsis thaliana vs Selaginella moellendorffii LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Selaginella moellendorffii (Selaginella moellendorffii, v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 90. Arabidopsis thaliana 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

ParameterArabidopsis thalianaSelaginella moellendorffii
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 102,032 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 100,375,332 out of 119,667,750
Covered: 19,292,418 out of 119,667,750

Uncovered: 19,641,818 out of 33,775,569
Matches: 8,810,372 out of 33,775,569
Mismatches: 4,921,811 out of 33,775,569
Insertions: 401,568 out of 33,775,569
Identity over aligned base-pairs: 62.3%

Selaginella moellendorffii

Uncovered: 183,883,906 out of 212,645,483
Covered: 28,761,577 out of 212,645,483

Uncovered: 22,828,761 out of 41,155,148
Matches: 11,457,830 out of 41,155,148
Mismatches: 6,481,703 out of 41,155,148
Insertions: 386,854 out of 41,155,148
Identity over aligned base-pairs: 62.5%

Block size distribution

Size range All 102,032 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
664
3.9 kb
10 bp - 100 bp
14,662
997.2 kb
3,066
219.0 kb
100 bp - 1 kb
78,620
28.4 Mb
25,787
11.5 Mb
1 kb - 10 kb
8,086
11.7 Mb
15,529
29.1 Mb
10 kb - 100 kb
15
192.6 kb