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: 18.400


Aligning:
Query:	3J7A_A:1384-1389_1429-1434_1665-1670
Target:	3U5F_6:1327-1332_1419-1424_1283-1288

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

	U---------UUUAG.CGAGAU.GCAAC--A-
	          *    .    ||.    *  | 
	CGAGACGCAAU----.----AU.----CUUAG

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