Search: for a Sequence String

string search

Oligo's search for string is not just a plain 'Find' function commonly implemented in most editing software. It allows searching for mismatches and for ambiguous bases. In this example BRCA sequence was searched for PmeI restriction site GTTTAAAC, an 8-cutter. Oligo finds 3 strings, shown below:

string search results

The results are shown in the "Selected Bases" window (available from the Search menu), holding also automatic search results for hairpin loops, stems and palindromes, all displayed in the Sequence window. When you click on any position number displayed in this window Oligo automatically moves its Current Oligo to this position. In this example it was position 64259. The image below shows the relevant part of the Sequence window:

sequence window

The yellow rectangle, indicated by arrow, is the string search result (5'-end of the PmeI site), above this yellow mark you can see the entire palindrome marked in green. It is 10 bp long (see the Upper Oligo - top letters in red- selected just to show the sequence of the entire palindrome). The Current Oligo is the sequence in the grey backgroubd box.