#State transitions for detecting sequences of 2 repetitions separated by any nt (A?A, C?C, G?G, T?T) and start in the next NT							
#State -1 means a correct finding a uses the current position to start							
#State -22 means a failing pattern. Will restart the search by increasing 1 position relative to the start state.							
# Hash # mark optional Comments, as many lines as needed
# Then key start in the next NT
# FILE CONTENT FORMAT:
# # ...
# Extension: 4 letters (not used as only 1 file is now in index)
# MAX_LEN_NO_PATTERN : integer (supposed to be short, around 24)
# isSymmetric : 0=no, 1=yes
# guideLen : size of the guide in nucleotides, integer. All guideLen-combinations are expected
# # Optional Comments, as many lines as needed
# # ...
# State	A	C	G	T	N	X	Comment
#
# State : number
# A : Transition state when finding an A
# C,G,T : Equivalent to A
# N : when literally finding an N
# X : when finding any other letter
# Comment : comment
# Next lines start with extension, maxlennopatrn, issym, guidelen
XyXs
24
1
3
#St	A	C	G	T	N	X	Comment
0	10	20	30	40	0	0	A,C,G,T ?
1	-1	-1	-1	-1	-1	-1	Set the position, and finish
10	11	11	11	11	0	0	A->An
11	1	-22	-22	-22	0	0	An->AnA
20	21	21	21	21	0	0	C->Cn
21	-22	1	-22	-22	0	0	Cn->CnC
30	31	31	31	31	0	0	G->Gn
31	-22	-22	1	-22	0	0	Gn->GnG
40	41	41	41	41	0	0	T->Tn
41	-22	-22	-22	1	0	0	Tn->TnT
