Alignment represention:
-> The line labled 'iso' is the isostericity base-pair indication. A Star '*' represents the matched location in the seqeunce is a of part a matched isosteric base-pair.A plus symbol '+' represents the matched location is a part of matched non-isosteric base-pair.
-> The line labeled 'edge' is the interacting edges. 'W' is for Watson-Crick, 'H' is for Hoogsteen, and 'S' is for sugar edge.Upper case letters are for 'cis' orientation base-pairs while lower case letters are for 'trans' orientation base-pairs.
-> The line labeled 'struc' represents the base-pair locations. A pair of '(' and ')' represent the base-pair that was identified in the first stage,while '<' and '>' represent the base-pair that was identified in the second stage.
-> A dot in the sequence represents the breakage location of the original sequence due to presentation of multiple strands in the query motif.An '-' symbol represents a gap in the sequence.
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Alignment Score: 25.800


Aligning:
Query:	3J7A_A:1106-1108_1180-1184_1191-1195
Target:	4BPP_A:1015-1017_1051-1055_1062-1066

iso	............+.+
edge	............s.h
struc	............(.)

iso	.*...*.....**..
edge	.w...w.....hw..
struc	.(...(.....))..

	CUA.UUAUG.CAAAG
	|+ . *|||.|*+|+
	CUC.GUAUG.CAAAG

struc	.(...(.....))..
edge	.w...w.....hw..
iso	.*...*.....**..

struc	............(.)
edge	............s.h
iso	............+.+