#** In order to get the 10 box filled correctly I made a new line after the 35 box, counted 17 bits into the new line, and then made another new line.  I then took the first occurrence of the 3rd line that matched the -10 box sequence.  This obviously works to find the correct sequence, however it breaks up the entire sequence into 3 lines, so at the end I will have to remedy this.

#** In order to get the 10 box filled correctly I made a new line after the 35 box, counted 17 bits into the new line, and then made another new line.  I then took the first occurrence of the 3rd line that matched the -10 box sequence.  This obviously works to find the correct sequence, however it breaks up the entire sequence into 3 lines, so at the end I will have to remedy this.

  cat infA-E.coli-K12.txt | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box>\n/1" | sed -r "2s/^.{17}/&\n/g" | sed -r "3s/[ct]at[at]at/<minus10box>&<\/minus10box>/1"

  cat infA-E.coli-K12.txt | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box>\n/1" | sed -r "2s/^.{17}/&\n/g" | sed -r "3s/[ct]at[at]at/<minus10box>&<\/minus10box>/1"