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: 13.600


Aligning:
Query:	4A1B_1:2286-2296
Target:	4V19_A:943-949

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

	AUCUAAUUAGU
	  |*|**|*  
	--CCAAAUA--

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



Alignment Score: 22.600


Aligning:
Query:	4A1B_1:2286-2296
Target:	3U5H_5:2292-2300

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

iso	..+*.*..+..
edge	..Ws.h..W..
struc	..((.)..)..

	AUCUAAUUAGU
	 |+*|*+|+| 
	-UCUAAUUAG-

struc	..((.)..)..
edge	..ws.h..w..
iso	..+*.*..+..

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



Alignment Score: 14.400


Aligning:
Query:	4A1B_1:2286-2296
Target:	4W23_2:1054-1064

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

iso	.+++.+..++.
edge	.WWs.h..WW.
struc	.(((.)..)).

	AUCUAAUUAGU
	 +++|++|++ 
	GAUCAGAUACC

struc	.(((.)..)).
edge	.wws.h..hh.
iso	.+++.+..++.

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



Alignment Score: 15.000


Aligning:
Query:	4A1B_1:2286-2296
Target:	3J7Y_A:2613-2619

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

	AUCUAAUUAGU
	 | *|**|*  
	-U-UAAAUA--

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



Alignment Score: 16.400


Aligning:
Query:	4A1B_1:2286-2296
Target:	1VX6_A:2586-2592

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

	AUCUAAUUAGU
	  |*|**|*  
	--CUAAUUA--

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