I am trying to extract the sequences of hairpin forming regions from a list of oligonucleotide sequences between 23-100 bases in length. The sequences are in table format consisting of coordinates (sequence ID) and sequence columns.
In my output, I would like to get the sequence ID, hairpin-forming sequence, length of stem, and length of loop within the oligonucleotide.
So far, I have tried using the eInverted and palindrome tools from EMBOSS, which give me the inverted repeats but the output is not in the format I desire.
Any help is greatly appreciated.