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.
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


Alignment Score: 9.800


Aligning:
Query:	3J7A_A:64-68_84-88
Target:	4A1B_1:3043-3048_3073-3077

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

	UAUAU.A-GAAA
	|| *|.| *|| 
	UAAAU.AUGAAG

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



Alignment Score: 11.800


Aligning:
Query:	3J7A_A:84-88_64-68
Target:	3U5F_6:82-86_64-69

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

	AGAAA.UAUAU-
	 *|||.|||*  
	UGAAA.UAUAAG

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