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: 81.200


Aligning:
Query:	3U5H_5:1898-1914_1938-1939_2109-2122_2331-2337
Target:	1VW3_A:1618-1636_1658-1672_1887-1894

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

	G----GAAGUCGGCAAAAUAG.UG.UGGUACGGACAAGG.CACUGU------------------------
	|    +       |       .  .              .     +                        
	GGAACU-------C-------.--.--------------.-----GGCAAAGAUAGCGUAAUAAGAACAA

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

iso	..........
edge	..........
struc	..........

	---------C
	         |
	AGCAACUGUC

struc	..........
edge	..........
iso	..........



Alignment Score: 162.200


Aligning:
Query:	3U5H_5:1898-1914_1938-1939_2109-2122_2331-2337
Target:	4W21_5:2847-2863_2887-2888_3613-3626_3835-3841

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

	G-----------GAAGUCGGCAAAAUAG.UG.UGGUACGGACAAGG.CACUGUC----------------
	|           +               .  .              .     +|                
	GGAAGUCGGCAAG---------------.--.--------------.-----CCGGUGUGGUGCGGACCA

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

iso	.........
edge	.........
struc	.........

	---------
	         
	GGCACUGUC

struc	.........
edge	.........
iso	.........