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: 10.400


Aligning:
Query:	4A1B_1:2828-2836
Target:	3J7Y_A:2958-2966

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

	AGUUCAUAU
	|*| |||*|
	AGUCCAUAU

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



Alignment Score: 10.400


Aligning:
Query:	4A1B_1:2828-2836
Target:	4IOA_X:2450-2458

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

	AGUUCAUAU
	|*| |||*|
	AGUCCAUAU

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



Alignment Score: 11.200


Aligning:
Query:	4A1B_1:2828-2836
Target:	3U5H_5:2840-2848

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

	AGUUCAUAU
	 *|||||* 
	CGUUCAUAG

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



Alignment Score: 11.800


Aligning:
Query:	4A1B_1:2828-2836
Target:	2QBG_B:2471-2479

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

	AGUUCAUAU
	|*|||||*|
	AGUUCAUAU

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



Alignment Score: 10.600


Aligning:
Query:	4A1B_1:2828-2836
Target:	4W21_5:4412-4430

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

	--A---GUUCAUAU-----
	  |   *|||||*      
	CCAAGCGUUCAUAGCGACG

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