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: 19.800


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	1FJG_A:779-783_799-803

iso	.*+*.....*+*.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	 *+* |.| *+* 
	CAAA-C.G-GUAG

struc	.(((.....))).
edge	.shh.....swh.
iso	.*+*.....*+*.



Alignment Score: 19.800


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	4BPP_A:946-950_621-625

iso	.*+*.....*+*.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	|*+* |.  *+* 
	UCAAGC.--GUAG

struc	.(((.....))).
edge	.shh.....swh.
iso	.*+*.....*+*.



Alignment Score: 19.800


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	4BPP_A:968-972_988-992

iso	.*+*.....*+*.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	 *+* |.  *+* 
	CAAAGC.--GUAG

struc	.(((.....))).
edge	.shh.....swh.
iso	.*+*.....*+*.



Alignment Score: 19.800


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	3U5F_6:968-972_627-631

iso	.*+*.....*+*.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	|*+* |.  *+* 
	UCAAGC.--GUAG

struc	.(((.....))).
edge	.shh.....swh.
iso	.*+*.....*+*.



Alignment Score: 19.800


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	3J7A_A:1037-1041_634-638

iso	.*+*.....*+*.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	|*+* |.  *+* 
	UCAAGC.--GUAG

struc	.(((.....))).
edge	.shh.....swh.
iso	.*+*.....*+*.



Alignment Score: 18.400


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	1S72_0:1639-1643_1542-1546

iso	.*+*.....*+*.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	|*+* |.| *+* 
	UCAA-C.G-GUCG

struc	.(((.....))).
edge	.shh.....swh.
iso	.*+*.....*+*.



Alignment Score: 19.800


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	4W23_2:1025-1029_676-680

iso	.*+*.....*+*.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	|*+* |.  *+* 
	UCAAGC.--GUAG

struc	.(((.....))).
edge	.shh.....swh.
iso	.*+*.....*+*.



Alignment Score: 19.800


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	2AW7_A:779-783_799-803

iso	.*+*.....*+*.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	 *+* |.| *+* 
	CAAA-C.G-GUAG

struc	.(((.....))).
edge	.shh.....swh.
iso	.*+*.....*+*.



Alignment Score: 25.800


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	4QCN_A:1904-1908_1887-1891

iso	.***.....***.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	 *** |.| *** 
	CGAA-C.G-GGAG

struc	.(((.....))).
edge	.shh.....ssh.
iso	.***.....***.



Alignment Score: 18.400


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	3J7Y_A:2872-2876_2856-2860

iso	.**+.....+**.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	 **+ |.  +** 
	CAAAGC.--UAAG

struc	.(((.....))).
edge	.shw.....wsh.
iso	.**+.....+**.



Alignment Score: 25.200


Aligning:
Query:	4IOA_X:24-29_521-526
Target:	2QBG_B:702-707_724-730

iso	.+*+*...*+*+..
edge	.wssh...shhh..
struc	.((((...))))..

	GUGGAU.UGAAAC-
	 +*+* .|*+*+  
	UUGAAG.UGGAGGA

struc	.((((...))))..
edge	.Wshh...sshW..
iso	.+*+*...*+*+..



Alignment Score: 22.600


Aligning:
Query:	4IOA_X:521-526_24-29
Target:	4UYK_R:86-90_111-115

iso	.**+.....+**.
edge	.shh.....ssh.
struc	.(((.....))).

	UGAAAC.GUGGAU
	 **+  .||+** 
	CGAA--.GUGGAG

struc	.(((.....))).
edge	.shw.....ssh.
iso	.**+.....+**.



Alignment Score: 27.600


Aligning:
Query:	4IOA_X:24-29_521-526
Target:	2QBG_B:24-29_511-516

iso	..***...***..
edge	..ssh...shh..
struc	..(((...)))..

	GUGGAU.UGAAAC
	||***|.|***||
	GUGGAU.UGAAAC

struc	..(((...)))..
edge	..ssh...shh..
iso	..***...***..



Alignment Score: 27.600


Aligning:
Query:	4IOA_X:24-29_521-526
Target:	4QCN_A:24-29_536-541

iso	..***...***..
edge	..ssh...shh..
struc	..(((...)))..

	GUGGAU.UGAAAC
	||***|.|***||
	GUGGAU.UGAAAC

struc	..(((...)))..
edge	..ssh...shh..
iso	..***...***..



Alignment Score: 37.000


Aligning:
Query:	4IOA_X:24-29_521-526
Target:	1S72_0:21-26_517-522

iso	.****...****.
edge	.wssh...shhh.
struc	.((((...)))).

	GUGGAU.UGAAAC
	|****|.|**** 
	GUGGAU.UGAAAU

struc	.((((...)))).
edge	.wssh...shhh.
iso	.****...****.