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: 14.400


Aligning:
Query:	4QCN_B:34-48
Target:	4W21_7:32-45

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

iso	...+*.....*...+
edge	...WW.....W...S
struc	...((.....)...)

	UUCCCAUUCCGAACA
	 ||+* | | *| *+
	AUCUCGU-CUGAUCU

struc	...((.....)...)
edge	...WW.....W...S
iso	...+*.....*...+

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



Alignment Score: 16.400


Aligning:
Query:	4QCN_B:34-48
Target:	4IOA_Y:36-50

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

iso	...+*.....*...+
edge	...WW.....W...S
struc	...((.....)...)

	UUCCCAUUCCGAACA
	  |+*|| ||*||*+
	ACCCCAUGCCGAACU

struc	...((.....)...)
edge	...wW.....W...s
iso	...+*.....*...+

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



Alignment Score: 19.600


Aligning:
Query:	4QCN_B:34-48
Target:	1MJI_C:34-48

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

iso	...**.....*...*
edge	...WW.....W...S
struc	...((.....)...)

	UUCCCAUUCCGAACA
	  |**|| ||*||**
	ACCCCAUGCCGAACU

struc	...((.....)...)
edge	...WW.....W...S
iso	...**.....*...*

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



Alignment Score: 15.200


Aligning:
Query:	4QCN_B:34-48
Target:	4A1C_3:32-45

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

iso	...+*.....*...+
edge	...WW.....W...S
struc	...((.....)...)

	UUCCCAUUCCGAACA
	 ||+*|||| *||*+
	AUCCCAUUC-GAACU

struc	...((.....)...)
edge	...wW.....W...s
iso	...+*.....*...+

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



Alignment Score: 17.000


Aligning:
Query:	4QCN_B:34-48
Target:	3U5H_7:32-45

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

iso	...**.....*...*
edge	...WW.....W...S
struc	...((.....)...)

	UUCCCAUUCCGAACA
	|||** | ||*| **
	UUCCCGU-CCGAUCA

struc	...((.....)...)
edge	...WW.....W...S
iso	...**.....*...*

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



Alignment Score: 21.000


Aligning:
Query:	4QCN_B:34-48
Target:	1S72_9:33-47

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

iso	...**.....*...*
edge	...WW.....W...S
struc	...((.....)...)

	UUCCCAUUCCGAACA
	| |**|| ||*||**
	UACCCAUCCCGAACA

struc	...((.....)...)
edge	...WW.....W...S
iso	...**.....*...*

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



Alignment Score: 16.400


Aligning:
Query:	4QCN_B:34-48
Target:	2QBG_A:34-48

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

iso	...+*.....*...+
edge	...WW.....W...S
struc	...((.....)...)

	UUCCCAUUCCGAACA
	  |+*|| ||*||*+
	ACCCCAUGCCGAACU

struc	...((.....)...)
edge	...wW.....W...s
iso	...+*.....*...+

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