**#With the addition of these two commands, my command sequence was as follows:

**#With the addition of these two commands, my command sequence was as follows:

   sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^.     

   sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^.     

   {17}/&<minus10box>/g" | sed "s/<minus10box>....../&<\/minus10box/g"

   {17}/&<minus10box>/g" | sed "s/<minus10box>....../&<\/minus10box>/g"

*'''tss'''

*'''tss'''

**Because the transcription start site is located 12 nucleotides from the beginning of the 6 nucleotide long minus 10 box, I reasoned that it would be simplest to calculate its location as 6 characters after the <code></minus10box></code> tag. This means that there are 5 characters between that tag before the <code><tss></code> tag should be inserted. Subsequently, the <code></tss><code> end tag should be placed one character after the tss start tag.

**Because the transcription start site is located 12 nucleotides from the beginning of the 6 nucleotide long minus 10 box, I reasoned that it would be simplest to calculate its location as 6 characters after the <code></minus10box></code> tag. This means that there are 5 characters between that tag before the <code><tss></code> tag should be inserted. Subsequently, the <code></tss></code> end tag should be placed one character after the tss start tag.

**#To accomplish this, I strung together two sed commands using a semicolon to both insert the start and end tags at the right locations.

**#To accomplish this, I strung together two sed commands using a semicolon to both insert the start and end tags at the right locations.

**#I piped this command to the growing sequence:

**#I piped this command to the growing sequence:

   sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^.     

   sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^.