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: 14.800


Aligning:
Query:	3U5F_6:760-763_773-775_785-790
Target:	3J7A_A:810-813_823-825_848-853

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

	AGAG.CAG.UCGAAU
	|*||.|+ .|+||*|
	AGAG.CAA.UUGAAU

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



Alignment Score: 11.800


Aligning:
Query:	3U5F_6:785-790_760-763_773-775
Target:	4BPP_A:768-773_744-747_757-759

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

	UCGAAU.AGAG.CAG
	 |||*|.|*||.|||
	CCGAAU.AGAG.CAG

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