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Table 1 Run times for 20-mer queries

From: “Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs

QUERY

PAM

Time (in seconds)

Number of retrieved potential off-targets (≤5 mismatches)

ATTCGCGGCAAAGGAGGAGA

NNGRRT

0.723

259

ATTCGCGGCAAAGGAGGAGA

NNNNACA

0.718

326

AACTCCTGACCTCAGCAAAA

NNGRRT

0.773

677

CATCATCAAAGACCAAAAGT

NNGRRT

0.801

705

AACTCCTGACCTCAGAAAAA

NNGRRT

0.768

894

ATTCGCGGCAAAGGAGGAGA

NGG

0.729

1,223

CATCATCAAAGACCAAAAGT

NNNNACA

0.765

1,485

ATTCGCGGCAAAGGAGGAGA

NAG

0.735

1,554

AACTCCTGACCTCAGCAAAA

NNNNACA

0.775

2,077

CATCATCAAAGACCAAAAGT

NGG

0.802

2,350

AACTCCTGACCTCAGAAAAA

NNNNACA

0.790

2,407

AACTCCTGACCTCAGCAAAA

NGG

0.778

3,612

AACTCCTGACCTCAGAAAAA

NGG

0.773

4,087

CATCATCAAAGACCAAAAGT

NAG

0.769

4,947

AACTCCTGACCTCAGCAAAA

NAG

0.791

5,406

CTTTGGGAGGCTGAGGTGGG

NNNNACA

0.986

5,907

AACTCCTGACCTCAGAAAAA

NAG

0.813

7,334

CTTTGGGAGGCTGAGGTGGG

NNGRRT

0.898

10,347

AAAAAAAAAAAAAAAAAAAA

NNGRRT

2.401

220,857

CTTTGGGAGGCTGAGGTGGG

NAG

1.682

241,707

TTTTTTTTTTTTTTTTTTTT

NNNNACA

2.945

458,847

TTTTTTTTTTTTTTTTTTTT

NGG

3.172

549,466

TTTTTTTTTTTTTTTTTTTT

NNGRRT

3.991

554,972

AAAAAAAAAAAAAAAAAAAA

NNNNACA

3.637

614,732

AAAAAAAAAAAAAAAAAAAA

NGG

3.320

617,790

CTTTGGGAGGCTGAGGTGGG

NGG

3.828

708,125

TTTTTTTTTTTTTTTTTTTT

NAG

15.143

1,807,996

AAAAAAAAAAAAAAAAAAAA

NAG

12.092

1,902,731

  1. The chosen 20-mers are meant to sample the whole gamut of potential off-targets that a candidate gRNA may generate. The entries also demonstrate how impactful the chosen PAM can be on the number of potential off-targets. The times shown do not include annotation reports. We note here that the number of results of AACTCCTGACCTCAGAAAAA shown in this Table are not expected to agree with the number of results for AACTCCTGACCTCAGAAAAA that are shown in Figure 4: this Table shows all potential targets of AACTCCTGACCTCAGAAAAA for a specific PAM with up to 5 mismatches and an unspecified seed whereas Figure 4 shows the number of all 20-mers that have the form AACTCCTGACCTCAGANNNN, where N = {A,C,G,T} and are followed by any of the PAMs that we have implemented.