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: 55.400


Aligning:
Query:	4IOA_X:2725-2739
Target:	4QCN_A:2758-2772

iso	...........*.*.
edge	...........W.H.
struc	...........(.).

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

iso	.*.***.***...*.
edge	.w.hhs.www...w.
struc	.(.(((.)))...).

	CUGAAAGCAUCUAAG
	|*|***|***|*|*|
	CUGAAAGCAUCUAAG

struc	.(.(((.)))...).
edge	.w.hhs.www...w.
iso	.*.***.***...*.

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

struc	...........(.).
edge	...........W.H.
iso	...........*.*.



Alignment Score: 32.600


Aligning:
Query:	4IOA_X:2725-2739
Target:	4W21_5:4688-4702

iso	...........*.*.
edge	...........W.H.
struc	...........(.).

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

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

	CUGAAAGCAUCUAAG
	|*|*| || *|*|*|
	CUGAACGCCUCUAAG

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

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

struc	...........(.).
edge	...........W.H.
iso	...........*.*.



Alignment Score: 27.800


Aligning:
Query:	4IOA_X:2725-2739
Target:	4A1B_1:3099-3113

iso	...........*.*.
edge	...........W.H.
struc	...........(.).

iso	.*.*+...+*.*...
edge	.w.hh...ww.h...
struc	.(.((...)).)...

	CUGAAAGCAUCUAAG
	|*|*+ ||+*|*|*|
	CUGAAGGCCUCUAAG

struc	.(.((...)).)...
edge	.w.hh...ww.h...
iso	.*.*+...+*.*...

struc	...........(.).
edge	...........W.H.
iso	...........*.*.



Alignment Score: 39.600


Aligning:
Query:	4IOA_X:2725-2739
Target:	1S72_0:2780-2794

iso	...........*.*.
edge	...........W.H.
struc	...........(.).

iso	.*.**+.+**.*...
edge	.w.hhs.www.h...
struc	.(.(((.))).)...

	CUGAAAGCAUCUAAG
	|*|**+|+**|*|*|
	CUGAACGCAUCUAAG

struc	.(.(((.))).)...
edge	.w.hhS.Hww.h...
iso	.*.**+.+**.*...

struc	...........(.).
edge	...........W.H.
iso	...........*.*.



Alignment Score: 46.200


Aligning:
Query:	4IOA_X:2725-2739
Target:	3U5H_5:3110-3124

iso	...........*.*.
edge	...........W.H.
struc	...........(.).

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

iso	.*.*++.++*...*.
edge	.w.hhs.www...w.
struc	.(.(((.)))...).

	CUGAAAGCAUCUAAG
	|*|*++|++*|*|*|
	CUGAACGCCUCUAAG

struc	.(.(((.)))...).
edge	.w.hhS.Www...w.
iso	.*.*++.++*...*.

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

struc	...........(.).
edge	...........W.H.
iso	...........*.*.



Alignment Score: 53.000


Aligning:
Query:	4IOA_X:2725-2739
Target:	2QBG_B:2745-2759

iso	...........*.*.
edge	...........W.H.
struc	...........(.).

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

iso	.*.***.***...*.
edge	.w.hhs.www...w.
struc	.(.(((.)))...).

	CUGAAAGCAUCUAAG
	|*|***|***|*|*|
	CUGAAAGCAUCUAAG

struc	.(.(((.)))...).
edge	.w.hhs.www...w.
iso	.*.***.***...*.

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

struc	...........(.).
edge	...........W.H.
iso	...........*.*.