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: 23.000


Aligning:
Query:	1U6B_B:61-65_80-83
Target:	4R0D_A:532-536_518-521

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

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

	CUAAG.UAUG
	|+**|.|+|+
	CUAAG.UAUG

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

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



Alignment Score: 23.000


Aligning:
Query:	1U6B_B:61-65_80-83
Target:	4K27_U:19-23_34-37

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

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

	CUAAG.UAUG
	|+**|.|+|+
	CUAAG.UAUG

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

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



Alignment Score: 23.000


Aligning:
Query:	1U6B_B:61-65_80-83
Target:	4FAW_A:346-350_332-335

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

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

	CUAAG.UAUG
	|+**|.|+|+
	CUAAG.UAUG

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

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



Alignment Score: 32.200


Aligning:
Query:	1U6B_B:61-65_80-83
Target:	4R0D_A:306-311_163-167

iso	.........**.
edge	.........ss.
struc	.........().

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

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

	CUAA-G-.UAUG
	|+** | .|+++
	CUAAAGC.UAUG

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

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

struc	.........().
edge	.........ss.
iso	.........**.