Picture from Fay, Samuel F. et al. MicroPubl Biol

Figure 1. Summary of CRISPRcruncher: (A) Example CRISPRcruncher output displaying options for introducing restriction sites (>6 bp) within the first 33 coding nucleotides of CELE_F54B11.2. For simplicity, only 17/65 lines of output are shown. Red letters indicate changes from the input sequence; bold letters indicate the newly introduced endonuclease recognition site. 'Strand' column indicates whether the top (shown) or bottom strand contains the recognition motif; both indicates that the motif is an inverted repeat (a.k.a. palindrome). (B-G) Analyses of site frequencies for five randomly selected genes on the X chromosome. The first 99 coding nucleotides within the first exon of each gene were examined either as a contiguous sequence (B,C) or as three nonoverlapping 33-bp segments (D-G). 'Total Reported REs' indicates the complete set of REs, including isoschizomers and other categories of related motifs, capable of cleaving at the identified new sites. 'Distinct Sequences' indicates the total number of distinct new 33-bp or 99-bp sequences identified by CRISPRcruncher. Parameters were set to identify new restriction sites of 4 bp or greater (>4 cutter; red circles) or 6 bp or greater (>6 cutter; blue circles). (H) Percent of palindromic versus non-palindromic restriction motifs for the five 99-bp sequences. For supporting information, see Extended Data.