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: 9.400


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	1KOG_J:96-100_74-76

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

	GCACU.AAAC
	 *|||.*   
	CCACU.AUG-

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



Alignment Score: 9.400


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	1S72_0:1425-1429_1437-1439

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

	GCACU.AAAC
	|*|||.*  |
	GCACU.AG-C

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



Alignment Score: 9.400


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	2QBG_B:2680-2684_2725-2727

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

	GCACU.AAAC
	 *|||.*|| 
	UCACU.AAA-

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



Alignment Score: 8.000


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	3U5F_6:1617-1621_1157-1160

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

	GCACU.AAAC
	 * ||.*   
	UCCCU.ACCA

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



Alignment Score: 10.200


Aligning:
Query:	4QCN_A:955-958_911-915
Target:	1S72_0:1005-1008_958-963

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

	AAAC.GC-ACU
	|||+.*| *+ 
	AAAC.GCGACC

struc	...(.(..)).
edge	...S.s..wW.
iso	...+.*..*+.



Alignment Score: 8.000


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	4W23_2:1681-1685_1214-1217

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

	GCACU.AAAC
	 * ||.*   
	UCCCU.ACCA

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



Alignment Score: 10.000


Aligning:
Query:	4QCN_A:955-958_911-915
Target:	4A1B_1:1072-1075_1025-1030

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

	AAAC.GC-ACU
	*|||.|* | |
	AAAC.GCGAAU

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



Alignment Score: 10.000


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	2QBG_B:864-868_909-912

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

	GCACU.AAAC
	|||*|.|||*
	GCACU.AAAC

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



Alignment Score: 8.000


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	4BPP_A:1589-1593_1130-1132

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

	GCACU.AAAC
	 * ||.* | 
	UCCCU.ACA-

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



Alignment Score: 7.600


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	3J7A_A:1914-1918_1258-1261

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

	GCACU.AAAC
	 * ||.*   
	UCCCU.ACCA

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



Alignment Score: 17.200


Aligning:
Query:	4QCN_A:955-958_911-915
Target:	4IOA_X:921-924_877-881

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

	AAAC.GCACU
	|||*.*|**|
	AAAC.GCACU

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



Alignment Score: 7.600


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	4QCN_A:1365-1369_1377-1379

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

	GCACU.AAAC
	|*| |.*  |
	GCAAU.AG-C

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



Alignment Score: 8.600


Aligning:
Query:	4QCN_A:955-958_911-915
Target:	1VW3_A:835-838_787-791

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

	AAAC.GCACU
	*| |.|*| |
	AAUC.GCAAU

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



Alignment Score: 9.400


Aligning:
Query:	4QCN_A:911-915_955-958
Target:	1S72_0:2717-2721_2761-2763

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

	GCACU.AAAC-
	 *|||.*  | 
	CCACU.A--CG

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



Alignment Score: 10.000


Aligning:
Query:	4QCN_A:955-958_911-915
Target:	3U5H_5:1046-1049_999-1004

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

	AAAC.GC-ACU
	*|||.|* | |
	AAAC.GCGAAU

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