how to align a sequence with a pair of sequence DNA?

Question

[midox]

how to align a short reads (paired-end) over a sequence. while the short reads file is in two files ie two sequences which represent the short reads?

example:

sequence: AGTGGTAGCTGCCTG
short read: GGTAGCT
            ||||  | |
            CCATCGA

in Computer science how alignment?

was a string (sequence) with two chianes of chars (short reads)

thank you