601 sequence original (non-barcode section 12 repeats including the generic restriction site (RS)):
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTTGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
601 sequence unique (barcode section 13 individual sequences)*:

                                                                                                    |vary|
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTTGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG (copy of original)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTATGTACAGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGACGTCGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAACCGGTGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAAGATCTGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAACGCGTGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGCCGGCGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGGTACCGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGATATCGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAATGCATGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAAAGCTTGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGGATCCGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAAGCGCTGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTATCGCGAGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
                                                                                                    |vary|
                                                                                                    
*Each 601 sequence has a unique restriction site after 100bp, indicated in rainbow colors in visual guide

So the general 601 sequence with Ns at varied sites is:
                                                                                                    |vary|
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTANNNNNNGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

For bisulfite calling, only columns with C or G in the generic version any Ts or As in the varied versions (first: conversion on plus, second: conversion on minus) are problematic, 
since these are both mapped with a "50M" cigar string in bisulfite mapping). After alignment to the generic version, the sequence to use the analysis is:

ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTANNNNNNGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG



Generic linker sequence original section: (coming after 601 sequence)
GGCGGCCGCGTATAGGGTCCATCCCCGAGAGGTCGCTGTTCAATACATGC
Unique linker sequences (linking the respective 601 sequence to the next)*:

                       |vary|
GGCGGCCGCGTATAGGGTCCATCCCCGAGAGGTCGCTGTTCAATACATGC (copy of generic version)
GGCGGCCGCGTATAGGGTCCATCAACGTTAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCCCGCGGAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCCGATCGAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCCTTAAGAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCCCATGGAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCGAGCTCAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCCATATGAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCCTGCAGAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCTGCGCAAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCCACGAGAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCTTTAAAAGGTCGCTGTTCAATACATGC
GGCGGCCGCGTATAGGGTCCATCTCATGAAGGTCGCTGTTCAATACATGC
                       |vary|
                       
So the general linker with Ns at varied sites is:

                       |vary|
GGCGGCCGCGTATAGGGTCCATCNNNNNNAGGTCGCTGTTCAATACATGC

For bisulfite calling, only columns with C or G in the generic version any Ts or As in the varied versions (first: conversion on plus, second: conversion on minus) are problematic, 
since these are both mapped with a "50M" cigar string in bisulfite mapping). After alignment to the generic version, the sequence to use the analysis is:

                       |vary|
GGCGGCCGCGTATAGGGTCCATCNNNNANAGGTCGCTGTTCAATACATGC
