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: 24.600


Aligning:
Query:	4QCN_A:721-725_846-853
Target:	4IOA_X:687-691_812-819

iso	.*+*...*.+*...
edge	.hhw...w.ww...
struc	.(((...).))...

	GAAAC.GAGAUAGC
	|*+*|.|*|+*|||
	GAAAC.GAGAUAGC

struc	.(((...).))...
edge	.hww...w.ww...
iso	.*+*...*.+*...



Alignment Score: 23.200


Aligning:
Query:	4QCN_A:721-725_846-853
Target:	3J7Y_A:1906-1910_2009-2016

iso	.**+...+.**...
edge	.hhw...w.ww...
struc	.(((...).))...

	GAAAC.GAGAUAGC
	|**+|.|+|**|||
	GAAAC.GUGAUAGC

struc	.(((...).))...
edge	.hhw...w.ww...
iso	.**+...+.**...



Alignment Score: 27.800


Aligning:
Query:	4QCN_A:721-725_846-853
Target:	2QBG_B:674-678_799-806

iso	.***...*.**...
edge	.hhw...w.ww...
struc	.(((...).))...

	GAAAC.GAGAUAGC
	|***|.|*|**|||
	GAAAC.GAGAUAGC

struc	.(((...).))...
edge	.hhw...w.ww...
iso	.***...*.**...



Alignment Score: 20.800


Aligning:
Query:	4QCN_A:721-725_846-853
Target:	4V19_A:239-245_345-354

iso	...**+...+.**.....
edge	...hhw...w.ww.....
struc	...(((...).)).....

	--GAAAC.GAGAUAGC--
	  |**+|.|+|**|||  
	CCGAAAC.GUGAUAGCUG

struc	...(((...).)).....
edge	...hhw...w.ww.....
iso	...**+...+.**.....



Alignment Score: 27.200


Aligning:
Query:	4QCN_A:846-853_721-725
Target:	1VW3_A:690-697_583-587

iso	.*.**.....***.
edge	.w.ww.....hhw.
struc	.(.((.....))).

	GAGAUAGC.GAAAC
	 *|**|||.|*** 
	CAGAUAGC.GAAAG

struc	.(.((.....))).
edge	.w.ww.....hhw.
iso	.*.**.....***.