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Tetrahymena thermophila vs Bigelowiella natans LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Tetrahymena thermophila 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

ParameterTetrahymena thermophilaBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,317 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,089,825 out of 103,014,375
Covered: 924,550 out of 103,014,375

Uncovered: 47,332,945 out of 48,193,658
Matches: 513,826 out of 48,193,658
Mismatches: 319,732 out of 48,193,658
Insertions: 27,155 out of 48,193,658
Identity over aligned base-pairs: 59.7%

Bigelowiella natans

Uncovered: 94,031,444 out of 94,701,163
Covered: 669,719 out of 94,701,163

Uncovered: 28,207,965 out of 28,817,508
Matches: 371,269 out of 28,817,508
Mismatches: 222,188 out of 28,817,508
Insertions: 16,086 out of 28,817,508
Identity over aligned base-pairs: 60.9%

Block size distribution

Size range All 4,317 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
66.0 bp
10 bp - 100 bp
1,089
77.7 kb
286
21.0 kb
100 bp - 1 kb
3,088
864.4 kb
1,473
558.8 kb
1 kb - 10 kb
125
183.3 kb
251
535.7 kb
10 kb - 100 kb
1
10.0 kb