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: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	3U5H_5:1462-1470

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  **|**| |  
	A-UGAGAA-CU-

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 15.200


Aligning:
Query:	3U5F_6:393-404
Target:	4MGN_C:51-63

iso	......**.**.....
edge	......ws.hh.....
struc	......((.)).....

	C--C--UGAGAAACGG
	   |  ** **   | 
	GGGCGGUGGGA---GC

struc	......((.)).....
edge	......ws.hh.....
iso	......**.**.....



Alignment Score: 15.200


Aligning:
Query:	3U5F_6:393-404
Target:	4QCN_A:329-336

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  ** **|   |
	U-UGGGAA---G

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 15.200


Aligning:
Query:	3U5F_6:393-404
Target:	4JRC_B:51-63

iso	......**.**.....
edge	......ws.hh.....
struc	......((.)).....

	C--C--UGAGAAACGG
	   |  ** **   | 
	GGGCGGUGGGA---GC

struc	......((.)).....
edge	......ws.hh.....
iso	......**.**.....



Alignment Score: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	4FAW_A:30-38

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  **|**  |  
	G-UGAGAGUC--

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	4GMA_Z:58-66

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  **|**| |  
	G-UGAGAAUC--

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	4A1B_1:1488-1496

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  **|**| |  
	A-UGAGAA-CU-

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 30.800


Aligning:
Query:	3U5F_6:393-404
Target:	3J7A_A:399-410

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

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

	CCUGAGAAACGG
	|+**|**|+  +
	CCUGAGAAAUAG

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

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



Alignment Score: 31.600


Aligning:
Query:	3U5F_6:393-404
Target:	2AW7_A:321-332

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

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

	CCUGAGAAACGG
	 +**|** +||+
	ACUGAGACACGG

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

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



Alignment Score: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	1S72_0:1387-1395

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  **|**| |  
	G-UGAGAACC--

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	4IOA_X:1294-1302

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  **|**| |  
	G-UGAGAAUC--

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	4QCN_A:1327-1335

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  **|**| |  
	G-UGAGAAUC--

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	1VX6_A:1611-1619

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	  **|**| |  
	A-UGAGAA-CU-

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....



Alignment Score: 16.600


Aligning:
Query:	3U5F_6:393-404
Target:	3DHS_A:69-76

iso	..**.**.....
edge	..ws.hh.....
struc	..((.)).....

	CCUGAGAAACGG
	| **|**    |
	C-UGAGAU---G

struc	..((.)).....
edge	..ws.hh.....
iso	..**.**.....