...and delete those positions in seq2

What exactly do you mean by "delete"? Cut out the chars at those positions, or somehow tag them as "invalid" (e.g. by also putting "-" in those places), or even something else?  I.e., is the result supposed to be

1-in:  --TAGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC-
2-in:  -ATTGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC-
       ====================================================
2-out: TTGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC
[download]

or

1-in:  --TAGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC-
2-in:  -ATTGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC-
       ====================================================
2-out: --TTGAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC-
[download]

I'm not much of a biologist, but keeping the sequences aligned (the latter variant) somehow seems to make more sense... (?)