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: 10.600


Aligning:
Query:	3U5H_5:3135-3136_3010-3012_3042-3043_3098-3099
Target:	4A1B_1:3124-3125_2999-3001_3031-3032_3087-3088

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

	UG.UAA.UC.GC
	||.|*|.|*.| 
	UG.UAA.UC.GU

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



Alignment Score: 11.200


Aligning:
Query:	3U5H_5:3042-3043_3098-3099_3135-3136_3010-3012
Target:	4W21_5:4620-4621_4676-4678_4712-4715_4587-4590

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

	UC.G----C.UG.UAA
	|*.|    |. |.|*|
	UC.GUGCGC.CG.UAA

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



Alignment Score: 10.600


Aligning:
Query:	3U5H_5:3135-3136_3010-3012_3042-3043_3098-3099
Target:	1VX6_A:3520-3521_3396-3398_3428-3429_3482-3483

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

	UG.UAA.UC.GC
	||.|*|.|*.| 
	UG.UAA.UC.GU

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



Alignment Score: 13.400


Aligning:
Query:	3U5H_5:3042-3043_3098-3099_3135-3136_3010-3012
Target:	3IVK_C:85-86_105-106_54-55_69-72

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

	UC.G--C.UG.UAA
	 *.|  |. |. * 
	CC.GUAC.-G.CAG

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