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: 13.200


Aligning:
Query:	1FJG_A:732-734_672-673_717-725
Target:	3U5F_6:943-945_883-884_928-936

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

	CAG.UG.CGCCGAUGG
	|* .  .   | *  |
	CAU.CA.UAACUACUG

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



Alignment Score: 12.400


Aligning:
Query:	4BPP_A:921-923_861-862_906-914
Target:	1FJG_A:717-725_732-734_672-673

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

	C----AU.UA.UAACUAAUG
	|    *|.  .   | * ||
	CGCCGAU.--.-GGC-AGUG

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



Alignment Score: 13.000


Aligning:
Query:	3J7A_A:1012-1015_951-953_997-1005
Target:	1FJG_A:717-725_732-734_672-673

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

	C----AUU.UUC.GAACAACUG
	|    *| .   .|  | * ||
	CGCCGAU-.---.GG-C-AGUG

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