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: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 1I9V_A:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*| | GUUCGAUCC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 4MGN_D:52-60 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAGUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 2D6F_F:953-961 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGACUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 1U0B_A:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGACUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 12.600 Aligning: Query: 3AM1_B:59-67 Target: 1S72_0:623-632 iso .*+.+*.... edge .ws.hh.... struc .((.)).... GUUCGAUUC- *+ +* UUUUGAAAAA struc .((.)).... edge .ws.hh.... iso .*+.+*.... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 4TZZ_E:52-60 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAAUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 2AKE_B:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAAUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 3VJR_D:13-21 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*| | GUUCGAUCC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 15.800 Aligning: Query: 3AM1_B:59-67 Target: 3WFS_A:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*||| GUUCGAUUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 15.800 Aligning: Query: 3AM1_B:59-67 Target: 3Q1Q_C:63-71 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*||| GUUCGAUUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 2DU3_D:952-960 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAAUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 4TZZ_B:52-60 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAAUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 15.800 Aligning: Query: 3AM1_B:59-67 Target: 2DR8_B:12-20 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*||| GUUCGAUUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 15.800 Aligning: Query: 3AM1_B:59-67 Target: 2ZM5_C:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*||| GUUCGAUUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 2AZX_C:553-561 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAAUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 3AL0_E:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAGUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 3AMU_B:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAAUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 3VJR_B:13-21 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*| | GUUCGAUCC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 3A2K_C:54-62 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAGUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 15.800 Aligning: Query: 3AM1_B:59-67 Target: 2CV1_D:553-561 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*||| GUUCGAUUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 1WZ2_D:965-973 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAAUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 3EPH_E:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*| | GUUCGAUCC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.000 Aligning: Query: 3AM1_B:59-67 Target: 4GCW_B:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* | GUUCGAGCC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 1QRS_B:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAAUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 15.800 Aligning: Query: 3AM1_B:59-67 Target: 3W3S_B:53-61 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+*||| GUUCGAUUC struc .((.))... edge .ws.hh... iso .*+.+*... Alignment Score: 14.400 Aligning: Query: 3AM1_B:59-67 Target: 4MGM_B:52-60 iso .*+.+*... edge .ws.hh... struc .((.))... GUUCGAUUC |*+|+* || GUUCGAGUC struc .((.))... edge .ws.hh... iso .*+.+*...