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: 28.600


Aligning:
Query:	3U5F_6:1293-1294_1303-1308_1317-1322
Target:	4BPP_A:1265-1266_1275-1280_1289-1294

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

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

	UG.UGUCUG.CGAUAA
	|*.|||**|.|* |*|
	UG.UGUCUG.CGUUAA

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

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



Alignment Score: 15.800


Aligning:
Query:	3U5F_6:1293-1294_1303-1308_1317-1322
Target:	3J7A_A:1394-1395_1405-1410_1419-1424

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

	UG.UGUCUG.CGAUAA
	|+.|||*||.|*||+|
	UG.UGUCUG.CGAUAA

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