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: 11.600


Aligning:
Query:	4QCN_A:2692-2696_2738-2740
Target:	3U5F_6:443-448_458-461

iso	.+.+........
edge	.W.H........
struc	.(.)........

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

	CCUCU---.AUG
	|+ +|   .+ |
	CCAAUCGG.A-G

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

struc	.(.)........
edge	.W.H........
iso	.+.+........



Alignment Score: 33.200


Aligning:
Query:	4QCN_A:2738-2740_2692-2696
Target:	4JRC_B:73-75_29-33

iso	***....*.
edge	ssS....W.
struc	()(....).

iso	+.+..*.*.
edge	s.h..W.H.
struc	(.)..(.).

	AUG.CCUCU
	+++.|+|+|
	ACG.CCUCU

struc	(.)..(.).
edge	s.h..W.H.
iso	+.+..*.*.

struc	()(....).
edge	ssS....W.
iso	***....*.



Alignment Score: 12.200


Aligning:
Query:	4QCN_A:2692-2696_2738-2740
Target:	3J7Y_A:3148-3152_3161-3163

iso	.+.+.....
edge	.W.H.....
struc	.(.).....

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

	CCUCU.AUG
	|+|+ .+ |
	CCUAC.GCG

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

struc	.(.).....
edge	.S.W.....
iso	.+.+.....