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: 28.400


Aligning:
Query:	3U5H_5:2156-2161_2173-2180
Target:	4W21_5:3660-3665_3677-3684

iso	.**.*...*.**...
edge	.sw.w...w.ws...
struc	.((.(...).))...

	CGAUGG.UGUUGACG
	|** *|.|*|**|||
	CGAAGG.UGUUGACG

struc	.((.(...).))...
edge	.sw.w...w.ws...
iso	.**.*...*.**...



Alignment Score: 16.400


Aligning:
Query:	3U5H_5:2156-2161_2173-2180
Target:	1VX6_A:2449-2455_2466-2473

iso	.+*..*...*.*+...
edge	.sw..w...w.ws...
struc	.((..(...).))...

	CGAU-GG.UGUUGACG
	 +*  *|.|*|*+|| 
	UGAAAAG.UAUUAACA

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



Alignment Score: 25.600


Aligning:
Query:	3U5H_5:2156-2161_2173-2180
Target:	4A1B_1:2152-2157_2168-2175

iso	.**.*...*.**...
edge	.sw.w...w.ws...
struc	.((.(...).))...

	CGAUGG.UGUUGACG
	 ** *|.|* **|| 
	UGACGG.UGAUGACA

struc	.((.(...).))...
edge	.sw.w...w.ws...
iso	.**.*...*.**...