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: 63.800


Aligning:
Query:	3U5F_6:1407-1415_1336-1338_1386-1391
Target:	1FJG_A:1116-1118_1155-1160_1176-1184

iso	..............+...........+..
edge	..............W...........W..
struc	..............(...........)..

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

	-------U--GGAAGUUU.AAC.GGACUA
	       |  +*|*+   .   .   +  
	CGCGGACUGAGGAAG---.---.---GAG

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

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



Alignment Score: 55.000


Aligning:
Query:	2AW7_A:1176-1184_1116-1118_1155-1160
Target:	1FJG_A:1116-1118_1155-1160_1176-1184

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

	---------AG---GAAGGUG.UAU.AGACUG
	         ||   +      .   .  +  |
	CGCGGACUGAGGAAG------.---.--GA-G

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



Alignment Score: 55.000


Aligning:
Query:	4BPP_A:1378-1386_1308-1310_1356-1361
Target:	1FJG_A:1116-1118_1155-1160_1176-1184

iso	..............+...........+..
edge	..............W...........W..
struc	..............(...........)..

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

	-------U--GGAAGUUU.AAC.GGACUA
	       |  +|||+   .   .   +  
	CGCGGACUGAGGAAG---.---.---GAG

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

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



Alignment Score: 61.400


Aligning:
Query:	3J7A_A:1653-1661_1438-1439_1633-1637
Target:	1FJG_A:1116-1118_1155-1160_1176-1184

iso	..............+.........+..
edge	..............W.........W..
struc	..............(.........)..

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

	---------AGGAAGUUU.AA.AACAU
	         |+*|*+   .  .  +| 
	CGCGGACUGAGGAAG---.--.--GAG

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

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