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: 55.600


Aligning:
Query:	4A1B_1:1942-1958
Target:	1S72_0:1764-1780

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

iso	.******..****.**.
edge	.sshhWw..wWsh.hh.
struc	.((((((..)))).)).

	CGUAACUUCGGGAUAAG
	|*****++|+*** **|
	CGUACCUUCGGAAGAAG

struc	.((((((..)))).)).
edge	.sshhWw..wWsh.hh.
iso	.******..****.**.

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



Alignment Score: 58.400


Aligning:
Query:	4A1B_1:1942-1958
Target:	1VX6_A:2186-2202

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

iso	.******..****.**.
edge	.sshhWw..wWsh.hh.
struc	.((((((..)))).)).

	CGUAACUUCGGGAUAAG
	|*****++|+*** **|
	CGUAACUUCGGGAAAAG

struc	.((((((..)))).)).
edge	.sshhWw..wWsh.hh.
iso	.******..****.**.

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



Alignment Score: 44.000


Aligning:
Query:	4A1B_1:1942-1958
Target:	4QCN_A:1733-1749

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

iso	.**.**+..+**..**.
edge	.ss.hWw..wWs..hh.
struc	.((.(((..)))..)).

	CGUAACUUCGGGAUAAG
	|**|**++|+**| **|
	CGUAACUUCGGGAGAAG

struc	.((.(((..)))..)).
edge	.ss.hWs..wWs..hh.
iso	.**.**+..+**..**.

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



Alignment Score: 56.600


Aligning:
Query:	4A1B_1:1942-1958
Target:	3U5H_5:1918-1934

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

iso	.*****+..+***.**.
edge	.sshhWw..wWsh.hh.
struc	.((((((..)))).)).

	CGUAACUUCGGGAUAAG
	|*****++|+***|**|
	CGUAACUUCGGGAUAAG

struc	.((((((..)))).)).
edge	.sshhWs..wWsh.hh.
iso	.*****+..+***.**.

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



Alignment Score: 39.000


Aligning:
Query:	4A1B_1:1942-1958
Target:	4W21_5:2867-2883

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

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

	CGUAACUUCGGGAUAAG
	|*||**++|+**|||*|
	CGUAACUUCGGGAUAAG

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

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



Alignment Score: 57.000


Aligning:
Query:	4A1B_1:1942-1958
Target:	4IOA_X:1703-1719

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

iso	.******..****.**.
edge	.sshhWw..wWsh.hh.
struc	.((((((..)))).)).

	CGUAACUUCGGGAUAAG
	|*****++|+*** **|
	CGUAACUUCGGAAGAAG

struc	.((((((..)))).)).
edge	.sshhWw..wWsh.hh.
iso	.******..****.**.

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



Alignment Score: 45.600


Aligning:
Query:	4A1B_1:1942-1958
Target:	2QBG_B:1686-1702

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

iso	.*.***+..+***..*.
edge	.s.hhWw..wWsh..h.
struc	.(.((((..))))..).

	CGUAACUUCGGGAUAAG
	|*|***++|+*** |*|
	CGUAACUUCGGGAGAAG

struc	.(.((((..))))..).
edge	.s.hhWs..wWsh..h.
iso	.*.***+..+***..*.

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



Alignment Score: 20.600


Aligning:
Query:	4A1B_1:1942-1958
Target:	3J7Y_A:3120-3136

iso	....+**+..+**+....
edge	....hhWw..wWsh....
struc	....((((..))))....

	CGU-AACUUCGGGAUAAG
	| | +**+  +**+ || 
	CCUGUACGAAAGGACAA-

struc	....((((..))))....
edge	....whWs..hWsh....
iso	....+**+..+**+....



Alignment Score: 20.600


Aligning:
Query:	4A1B_1:1942-1958
Target:	4V19_A:1453-1469

iso	....+**+..+**+....
edge	....hhWw..wWsh....
struc	....((((..))))....

	CGU-AACUUCGGGAUAAG
	|   +**+  +**+ || 
	CCAGUACGAAAGGACAA-

struc	....((((..))))....
edge	....whWs..hWsh....
iso	....+**+..+**+....



Alignment Score: 20.600


Aligning:
Query:	4A1B_1:1942-1958
Target:	1VW3_A:2920-2934

iso	...+**+..+**+....
edge	...hhWw..wWsh....
struc	...((((..))))....

	CGUAACUUCGGGAUAAG
	   +**+  +**+    
	UAGUACGCAAGGACC--

struc	...((((..))))....
edge	...whWs..hWsh....
iso	...+**+..+**+....



Alignment Score: 12.600


Aligning:
Query:	4A1B_1:1942-1958
Target:	1JBS_D:7-23

iso	....+**....**+....
edge	....hhW....Wsh....
struc	....(((....)))....

	-CGUAACUUCGGGAUAAG
	 |  +**    **+ |  
	UCAGUACGAUAGGA-ACC

struc	....(((....)))....
edge	....whW....Wsh....
iso	....+**....**+....