In this section

Arabidopsis thaliana vs Chondrus crispus LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Chondrus crispus (Chondrus crispus, ASM35022v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 thalianaChondrus crispus
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 7,927 alignment blocks

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

Uncovered: 118,049,190 out of 119,667,750
Covered: 1,618,560 out of 119,667,750

Uncovered: 32,274,028 out of 33,775,569
Matches: 934,225 out of 33,775,569
Mismatches: 527,523 out of 33,775,569
Insertions: 39,793 out of 33,775,569
Identity over aligned base-pairs: 62.2%

Chondrus crispus

Uncovered: 104,028,320 out of 104,980,420
Covered: 952,100 out of 104,980,420

Uncovered: 9,419,718 out of 10,311,317
Matches: 551,095 out of 10,311,317
Mismatches: 319,216 out of 10,311,317
Insertions: 21,288 out of 10,311,317
Identity over aligned base-pairs: 61.8%

Block size distribution

Size range All 7,927 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
25
147.0 bp
10 bp - 100 bp
2,163
158.1 kb
242
18.3 kb
100 bp - 1 kb
5,556
1.4 Mb
2,210
949.9 kb
1 kb - 10 kb
183
252.2 kb
532
820.8 kb