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: 61.200


Aligning:
Query:	3DIR_A:38-55
Target:	3D0U_A:35-52

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

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

iso	.*.***...*..**..*.
edge	.S.HhW...H..ws..s.
struc	.(.)((...)..)(..).

	CAUCAGGGGAGGAAUCGG
	|*|***|***||**||*|
	CAUCAGGGGAGGAAUCGG

struc	.(.)((...)..)(..).
edge	.S.HhW...H..ws..s.
iso	.*.***...*..**..*.

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

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