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: 11.200


Aligning:
Query:	4QCN_A:1340-1341_1692-1695_2031-2032_1316-1322
Target:	1VW3_A:1303-1308_1325-1326_1597-1600_1909-1910

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

	U---C.GCGC.GG.CGAUAA-A----
	    +.    .  .  || + |    
	CGAAA.----.--.--AU-CGAAUAG

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



Alignment Score: 11.800


Aligning:
Query:	4QCN_A:1316-1322_1340-1341_1692-1695_2031-2032
Target:	2QBG_B:1270-1276_1294-1295_1645-1648_2009-2010

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

	CGAUAAA.UC.GCGC.GG
	|||||*|.|*.||  . |
	CGAUAAA.UC.GCUU.AG

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