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Triticum turgidum vs Aegilops tauschii LastZ results

Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Triticum turgidum 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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

ParameterTriticum turgidumAegilops tauschii
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 6,372,569 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum turgidum

Uncovered: 6,435,490,103 out of 10,463,058,104
Covered: 4,027,568,001 out of 10,463,058,104

Uncovered: 1,792,371 out of 88,577,667
Matches: 81,744,423 out of 88,577,667
Mismatches: 4,548,803 out of 88,577,667
Insertions: 492,070 out of 88,577,667
Identity over aligned base-pairs: 94.2%

Aegilops tauschii

Uncovered: 3,030,781,202 out of 4,224,915,394
Covered: 1,194,134,192 out of 4,224,915,394

Uncovered: 946,080 out of 53,210,770
Matches: 49,063,749 out of 53,210,770
Mismatches: 2,784,060 out of 53,210,770
Insertions: 416,881 out of 53,210,770
Identity over aligned base-pairs: 93.9%

Block size distribution

Size range All 6,372,569 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
108,047
577.0 kb
10 bp - 100 bp
1,513,291
83.6 Mb
591,887
35.6 Mb
100 bp - 1 kb
3,330,969
1.3 Gb
1,376,990
533.1 Mb
1 kb - 10 kb
1,412,555
3.2 Gb
895,427
2.8 Gb
10 kb - 100 kb
7,681
131.0 Mb
57,657
879.3 Mb
100 kb - 1 Mb
26
3.4 Mb
296
63.6 Mb
1 Mb - 10 Mb
16
60.3 Mb
10 Mb - 100 Mb
13
374.1 Mb