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: 24.800


Aligning:
Query:	4A1B_1:1751-1757_1735-1741
Target:	4A1B_1:1245-1253_1310-1314

iso	.............**...
edge	.............sh...
struc	.............()...

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

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

	-AGAGAUA.UG--AAAUU
	 *  *| |. |  **|  
	UACGGACA.-GCCGAA--

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

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

struc	.............()...
edge	.............sh...
iso	.............**...



Alignment Score: 24.800


Aligning:
Query:	4A1B_1:1735-1741_1751-1757
Target:	4W21_5:2656-2662_2672-2678

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

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

iso	..**...........
edge	..sh...........
struc	..()...........

	UGAAAUU.AGAGAUA
	||**|| .*||*| |
	UGGAAUG.CGAGAGA

struc	..()...........
edge	..sh...........
iso	..**...........

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

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