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: 19.600


Aligning:
Query:	1FJG_A:242-247_277-284
Target:	3J7A_A:317-322_354-361

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

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

	CAUCAG.CGACGACG
	 *||*|.|*| **||
	UAUCAG.CUAUGACG

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

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



Alignment Score: 14.600


Aligning:
Query:	1FJG_A:277-284_242-247
Target:	1VX6_A:153-159_118-124

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

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

	CGACGACG.CAUCAG-
	 *  * ||.  | *  
	AAUUGUCG.G-UUAAU

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

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



Alignment Score: 18.600


Aligning:
Query:	1FJG_A:242-247_277-284
Target:	3U5F_6:311-316_348-355

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

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

	CAUCAG.CGACGACG
	 *||* . * |**||
	UAUCAA.UUUCAACG

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

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



Alignment Score: 24.000


Aligning:
Query:	1FJG_A:242-247_277-284
Target:	2AW7_A:242-247_277-284

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

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

	CAUCAG.CGACGACG
	 *| *|.|*||**  
	GAUUAG.CGACGAUC

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

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



Alignment Score: 20.600


Aligning:
Query:	1FJG_A:242-247_277-284
Target:	3RW6_H:11-18_43-50

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

iso	.....**......*.*.
edge	.....Wh......s.W.
struc	.....((......).).

	CAU--CAG.CGACGACG
	 |   **|.|*| *|*|
	UAAGACAG.CAAUGACG

struc	.....((......).).
edge	.....Wh......s.W.
iso	.....**......*.*.

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



Alignment Score: 14.600


Aligning:
Query:	1FJG_A:277-284_242-247
Target:	4W23_2:967-975_951-956

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

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

	CGACGAC-G.CAUCAG
	|*  *|| |.|   *|
	CUUGGACCG.CGCUAG

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

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



Alignment Score: 24.000


Aligning:
Query:	1FJG_A:277-284_242-247
Target:	4BPP_A:888-895_873-877

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

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

	CGACGAC-G.CAUCAG
	|*  **  |.  ||*|
	CUUGGAUUG.--UCAG

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

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