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Arabidopsis thaliana vs Eutrema salsugineum LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Eutrema salsugineum (Eutrema salsugineum, Eutsalg1_0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 107. 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 thalianaEutrema salsugineum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 116,103 alignment blocks

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

Uncovered: 44,497,894 out of 119,667,750
Covered: 75,169,856 out of 119,667,750

Uncovered: 2,450,299 out of 33,775,569
Matches: 26,886,210 out of 33,775,569
Mismatches: 4,029,252 out of 33,775,569
Insertions: 409,808 out of 33,775,569
Identity over aligned base-pairs: 85.8%

Eutrema salsugineum

Uncovered: 163,776,393 out of 243,110,105
Covered: 79,333,712 out of 243,110,105

Uncovered: 2,368,426 out of 32,250,823
Matches: 25,781,706 out of 32,250,823
Mismatches: 3,683,430 out of 32,250,823
Insertions: 417,261 out of 32,250,823
Identity over aligned base-pairs: 86.3%

Block size distribution

Size range All 116,103 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,563
10.0 kb
10 bp - 100 bp
20,773
1.2 Mb
6,022
411.8 kb
100 bp - 1 kb
65,703
26.1 Mb
21,795
7.6 Mb
1 kb - 10 kb
27,993
64.9 Mb
6,017
13.4 Mb
10 kb - 100 kb
71
864.2 kb
144
3.5 Mb
100 kb - 1 Mb
24
10.0 Mb
1 Mb - 10 Mb
17
58.1 Mb