Scheme 3:
Sequence design strategy. In the upper left, an example of A, B, and C sequence blocks with a length of 10 nt each, composed into the ABCAC string. The theoretical reads generated from sequencing by hybridization using pentamers are shown below the string. The table at the right provides the architecture (‘Block structure’) of pairs of sequences which yield the same theoretical SBH reads as the ABCAC string. The ‘Binding Pattern’ gives the design of fluorescently-labelled three-block sequences that when hybridized to the array will distinguish the 14 array features from one another. Subscript ‘C’ indicates complementarity to the sequence of the given block structure (‘ABCC’ is the complement of sequence ABC). Yellow denotes hybridization signal will be observed, blue indicates no hybridization signal will be observed.