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: 49.600


Aligning:
Query:	4QCN_A:649-653_660-663_675-691_699-703_624-627
Target:	3U5H_5:675-678_702-706_713-721_749-751_782-787

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

	C-GUAG.CGAG.CGCAAGCGGGCCGCACG.CAAAG.CGA--------------------G
	| +   .   |.|                .     .  +                    |
	CGA---.---G.C----------------.-----.--GUAAUGAACGUAGCGAUAAGAG

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



Alignment Score: 56.200


Aligning:
Query:	4QCN_A:660-663_675-691_699-703_624-627_649-653
Target:	4A1B_1:727-731_738-747_773-774_808-812_699-702

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

	C--------------------GAG.CGCAAGCGGGCCGCACG.CAAAG.CGAG.CGUAG
	|                    *  .           ||    .     .    .   *|
	CGAAAUGAGUACAAGCAAAGAG--.-----------CG----.-----.----.---AG

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