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Arabidopsis thaliana vs Panicum hallii HAL2 LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Panicum hallii HAL2 (Panicum hallii var. hallii str. HAL2, PhalliiHAL_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.


Number of alignment blocks: 77,573

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

Uncovered: 93,815,542 out of 119,667,750
Covered: 25,852,208 out of 119,667,750

Uncovered: 14,369,921 out of 33,775,569
Matches: 12,637,197 out of 33,775,569
Mismatches: 6,401,110 out of 33,775,569
Insertions: 367,341 out of 33,775,569

Panicum hallii var. hallii str. HAL2

Uncovered: 468,814,870 out of 487,473,734
Covered: 18,658,864 out of 487,473,734

Uncovered: 24,490,237 out of 37,739,336
Matches: 8,599,142 out of 37,739,336
Mismatches: 4,345,113 out of 37,739,336
Insertions: 304,844 out of 37,739,336

Configuration parameters

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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Arabidopsis thaliana Panicum hallii HAL2
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}