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: 43.800


Aligning:
Query:	3U5F_6:1136-1140_14-21_604-614_1107-1109
Target:	4BPP_A:1109-1113_14-21_598-608_1079-1081

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

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

	UAAAG.CUGCCAGU.AAAGUUGUUGC.GGG
	||**|.|**|||||.||||||*||||.|**
	UAAAG.CUGCCAGU.AAAGUUGUUGC.GGG

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

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



Alignment Score: 35.000


Aligning:
Query:	3U5F_6:14-21_604-614_1107-1109_1136-1140
Target:	3J7A_A:15-21_611-621_1208-1210_1237-1240

iso	....................+..........................+.
edge	....................w..........................w.
struc	....................(..........................).

	--C-----------------UGCCAGU.AAAGUUGUUGC.GGG.UAAAG
	  |                 +      .    |      .   .  |+ 
	UGCCAGUAAAAUUGUUGCGGG------.----U------.---.--AAA

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