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: 113.200


Aligning:
Query:	4BPP_A:1000-1010_1075-1077_610-618_953-957
Target:	4W23_2:1079-1089_1160-1162_665-673_1032-1036

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

	UAUAAACUAUA.UUC.GUUAAAAAG.CGAAA----------------------
	 +         .   .         . +|||                      
	CA---------.---.---------.-UAAACGAUGUUCGUUAAAAAGCGAAA

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



Alignment Score: 111.600


Aligning:
Query:	3U5F_6:616-624_975-979_1022-1032_1103-1105
Target:	4W23_2:665-673_1032-1036_1079-1089_1160-1162

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

	GUUAAA---------AAG.CGAAA.CAUAAACUAUG.UU----------C
	||||||         +  .     .           . +          |
	GUUAAAAAGCGAAACA--.-----.-----------.-UAAACGAUGUUC

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



Alignment Score: 111.600


Aligning:
Query:	3J7A_A:623-631_1044-1048_1091-1101_1204-1206
Target:	4W23_2:665-673_1032-1036_1079-1089_1160-1162

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

	GUUAAA---------ACG.CGAAA.CAUAAACUAUG.UU----------C
	||||||         +  .     .           . +          |
	GUUAAAAAGCGAAACA--.-----.-----------.-UAAACGAUGUUC

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