bwt-algorithm/repeat_notrim.tab at main · wyim-pgl/bwt-algorithm · GitHub

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BWT-based Tandem Repeat Finder
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Reference:    test.fa
Output:       repeat.tab (strfinder format)
Tiers:        Tier 1 + Tier 2 (short + medium repeats)
Parallelism:  4 CPU cores

Detection Parameters:
  Tier 1 motif length: 1-9 bp
  Tier 2 period range: 10-1000 bp
  Min copies required: 3
  Min entropy (bits):  1.0
  Mismatch tolerance:  Enabled (10% of full sequence)
  SA sampling rate:    32
  Flank trimming:      0 bp from each end

Building BWT indices...
[░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 0.0% Building index for 0 (35 bp) - 0s[████████░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 20.0% Building index for 1 (84 bp) - 0s[████████████████░░░░░░░░░░░░░░░░░░░░░░░░] 40.0% Building index for 2 (1,225 bp) - 0s[████████████████████████░░░░░░░░░░░░░░░░] 60.0% Building index for 3 (350 bp) - 0s[████████████████████████████████░░░░░░░░] 80.0% Building index for 4 (77 bp) - 0s[████████████████████████████████████████] 100.0% BWT indices built for 5 chromosome(s) - 0s

Parallel mode: Using 4 CPU cores for 5 chromosomes

Processing 5 chromosome(s)...

[████████░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░] 20.0% (1/5) chromosomes completed - 0s[████████████████░░░░░░░░░░░░░░░░░░░░░░░░] 40.0% (2/5) chromosomes completed - 0s[████████████████████████░░░░░░░░░░░░░░░░] 60.0% (3/5) chromosomes completed - 0s[████████████████████████████████░░░░░░░░] 80.0% (4/5) chromosomes completed - 0s[████████████████████████████████████████] 100.0% (5/5) chromosomes completed - 1s[DEBUG] Seq 1: n=84, min_copies=3, max_possible_unit=28
[DEBUG] Seq 1: Starting scan for unit_len=12
[DEBUG] Seq 1: Testing position i=0
[DEBUG] Seq 1: Found repeat at i=0, count=7, motif=ACCCCTCAGGGT


Nested call suppression: 169 -> 38 repeats
Analysis complete! Found 26 unique repeats (deduplicated 136).

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Completed! Found 26 total tandem repeats.
Average mismatch rate: 0.002
Imperfect repeats: 1 (3.8%)
Results saved to repeat.tab