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: 53.200


Aligning:
Query:	4QCN_A:30-31_500-510_521-535
Target:	1S72_0:27-28_480-490_502-516

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

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

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

	-GC.GUGAAAAGAAC.GAGUGAAAUAGAGCC
	 ||. |* *|** *|. *| *|*||***|* 
	UGC.-UGCAAAGUAC.AGGCGAAAUAGAGCA

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

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

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



Alignment Score: 61.600


Aligning:
Query:	4QCN_A:500-510_521-535_30-31
Target:	4IOA_X:485-495_506-520_30-31

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

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

iso	..*...**+....+..*....*...*....
edge	..s...hWS....W..s....h...W....
struc	..(...)((....)..(....)...)....

	GUGAAAAGAAC.GAGUGAAAUAGAGCC.GC
	||*|*|**++|.|+||*|*| *** *|.||
	GUGAAAAGAAC.GAGUGAAAGAGAACC.GC

struc	..(...)((....)..(....)...)....
edge	..s...hWs....w..s....h...W....
iso	..*...**+....+..*....*...*....

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

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



Alignment Score: 61.600


Aligning:
Query:	4QCN_A:500-510_521-535_30-31
Target:	2QBG_B:474-484_496-510_30-31

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

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

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

	GUGAAAAGAAC.GAGUGAAAUAGAGCC.GC
	| *|*|****|.|*||*|*| *** *|.||
	GCGAAAAGAAC.GAGUGAAAAAGAACC.GC

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

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

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