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: 30.200


Aligning:
Query:	3U5H_5:1857-1859_1871-1874_1479-1485
Target:	1VX6_A:2124-2126_2138-2141_1628-1634

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

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

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

	CAA.UCUA.UGAAGUG
	|||.||* .|*||*||
	CAA.UCUG.UGAAGUG

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

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

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



Alignment Score: 20.600


Aligning:
Query:	1FJG_A:751-755_586-588_651-655
Target:	3U5H_5:1479-1485_1857-1859_1871-1874

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

	U---GACG.CGG.CUAG------A
	|   *   .   . | *      |
	UGAAG---.---.-U-GCAAUCUA

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



Alignment Score: 30.200


Aligning:
Query:	3U5H_5:1857-1859_1871-1874_1479-1485
Target:	4A1B_1:1881-1883_1895-1898_1505-1511

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

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

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

	CAA.UCUA.UGAAGUG
	|||.||* . *||*||
	CAA.UCUG.CGAAGUG

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

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

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



Alignment Score: 20.400


Aligning:
Query:	3U5H_5:1479-1485_1857-1859_1871-1874
Target:	1F7Y_B:4-6_15-19_50-54

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

iso	......+..+...........
edge	......S..S...........
struc	......(..)...........

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

	----U-GAAGUG.CAA.UCUA
	    | +| +  . | .  + 
	CGGCUAGAUG--.-A-.--CG

struc	......(............).
edge	......W............W.
iso	......+............+.

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

struc	.........(.........).
edge	.........S.........H.
iso	.........+.........+.



Alignment Score: 17.600


Aligning:
Query:	3U5H_5:1479-1485_1857-1859_1871-1874
Target:	2QBG_B:1625-1627_1639-1642_1298-1303

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

iso	.....+..+............
edge	.....S..S............
struc	.....(..)............

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

	U----GAAGUG.CAA.UCUA-
	     +  + |.   .  +| 
	CAGCAAGCG-G.---.--AAG

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

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

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