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: 46.000


Aligning:
Query:	3UMY_B:2124-2127_2161-2174
Target:	1MZP_B:20-23_32-45

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

iso	.*........***.****.
edge	.s........wws.hhhh.
struc	.(........(((.)))).

	GGAG.CGCCGGUGAAAUAC
	|*|*.|||||***|****|
	GGAG.CGCCGGUGAAAUAC

struc	.(........(((.)))).
edge	.s........wws.hhhh.
iso	.*........***.****.

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



Alignment Score: 15.600


Aligning:
Query:	3UMY_B:2161-2174_2124-2127
Target:	2QBG_B:97-104_82-85

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

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

	CGCCGGUGAAAUAC.GGAG
	||    | |  |* . *|*
	CG----UUA--UAA.UAAG

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

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



Alignment Score: 24.400


Aligning:
Query:	3UMY_B:2161-2174_2124-2127
Target:	2HW8_B:22-29_10-13

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

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

	CGCCGGUGAAAUAC.GGAG
	|||    *|*  *|.|*|*
	CGC----GAA--AC.GGAG

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

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