I have a large BAM file containing reads from a single human genome. I'd like a visual map of the locations of a specific 120bp nucleotide sequence. I've been using the IGV browser which allows you to find and display motifs in the hg18 reference sequence, but I can't find how to search for them in the sequence indicated by the BAM reads.
I'd also like to do the same for the HuRef (Craig Venter) and Jim Watson sequences, to illustrate individual-level polymorphism for a lecture. Can anyone point me to suitable software?