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: 9.400


Aligning:
Query:	3U5F_6:550-559_586-588
Target:	4QCN_A:1050-1059_1195-1197

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

	AGGGCAAGUC.GCU
	    |||*||.|* 
	CCCCCAAGUC.GCG

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



Alignment Score: 9.400


Aligning:
Query:	3U5F_6:550-559_586-588
Target:	2QBG_B:1004-1013_1149-1151

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

	AGGGCAAGUC.GCU
	     ||*||.|* 
	UCCCAAAGUC.GCA

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



Alignment Score: 7.600


Aligning:
Query:	3U5F_6:550-559_586-588
Target:	4W21_5:2062-2065_1911-1922

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

	AGGGCAAG---------UC.GCU-
	    |  *         | .|*  
	----C--GGGCGCCCGAU-.GCCG

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



Alignment Score: 8.200


Aligning:
Query:	3U5F_6:586-588_550-559
Target:	1S72_0:1253-1255_1101-1110

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

	GCU.AGGGCAAGUC
	 * .    |||*| 
	CCA.UCCCCAAGUG

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



Alignment Score: 12.400


Aligning:
Query:	3U5F_6:550-559_586-588
Target:	4BPP_A:543-554_579-582

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

	AGGGCAAGUC---.GCU
	|||||||*||   .|*|
	AGGGCAAGUCAUA.GCU

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



Alignment Score: 12.600


Aligning:
Query:	3U5F_6:550-559_586-588
Target:	3J7A_A:557-566_593-595

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

	AGGGCAAGUC.GCU
	|||||||*||.|*|
	AGGGCAAGUC.GCU

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