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Arabidopsis thaliana vs Kalanchoe fedtschenkoi LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Kalanchoe fedtschenkoi (Kalanchoe fedtschenkoi, K_fedtschenkoi_M2_v1) 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 thalianaKalanchoe fedtschenkoi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 118,257 alignment blocks

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

Uncovered: 88,197,000 out of 119,667,750
Covered: 31,470,750 out of 119,667,750

Uncovered: 12,114,058 out of 33,775,569
Matches: 14,076,686 out of 33,775,569
Mismatches: 7,114,455 out of 33,775,569
Insertions: 470,370 out of 33,775,569
Identity over aligned base-pairs: 65.0%

Kalanchoe fedtschenkoi

Uncovered: 219,761,982 out of 256,351,415
Covered: 36,589,433 out of 256,351,415

Uncovered: 11,963,379 out of 35,074,438
Matches: 15,384,164 out of 35,074,438
Mismatches: 7,170,071 out of 35,074,438
Insertions: 556,824 out of 35,074,438
Identity over aligned base-pairs: 66.6%

Block size distribution

Size range All 118,257 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,240
6.5 kb
10 bp - 100 bp
17,971
1.2 Mb
2,565
189.3 kb
100 bp - 1 kb
88,388
31.3 Mb
20,965
8.9 Mb
1 kb - 10 kb
10,655
16.3 Mb
16,210
37.4 Mb
10 kb - 100 kb
3
31.9 kb
173
2.3 Mb