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: 15.800 Aligning: Query: 4GXY_A:49-57 Target: 2QBG_B:305-312 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC ** ** CUGGAAAG- struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 4FRG_B:28-36 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |** ** || GUGAAAUUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 17.600 Aligning: Query: 4GXY_A:49-57 Target: 3OVA_C:12-20 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|**||| GUUCAAGUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 17.600 Aligning: Query: 4GXY_A:49-57 Target: 2BTE_E:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|**||| GUUCAAGUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 3ADD_C:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUUCAAUUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 17.600 Aligning: Query: 4GXY_A:49-57 Target: 2BTE_B:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|**||| GUUCAAGUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 15.800 Aligning: Query: 4GXY_A:49-57 Target: 4BPP_A:1523-1532 iso .**.**.... edge .ws.hh.... struc .((.)).... GUGCAAGUC- ** ** | UUGGAAUUGU struc .((.)).... edge .ws.hh.... iso .**.**.... Alignment Score: 17.600 Aligning: Query: 4GXY_A:49-57 Target: 4P5J_A:46-54 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUGCAACUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 2ZZN_C:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUUCAAAUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 3ADC_C:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUUCAAUUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 15.800 Aligning: Query: 4GXY_A:49-57 Target: 2QBG_B:1281-1289 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |** ** | GUGAAAAGC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 15.200 Aligning: Query: 4GXY_A:49-57 Target: 3U5F_6:1550-1561 iso ..**.**..... edge ..ws.hh..... struc ..((.))..... G-UGCAAGUC-- ** ** | AUUGUAAUUAUU struc ..((.))..... edge ..ws.hh..... iso ..**.**..... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 2ZUF_B:953-961 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUUCAAAUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 2ZNI_C:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |** ** || GUGAAACUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 3WQY_C:1653-1661 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUUCAAAUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 4FRN_A:28-36 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |** ** || GUGUAAUUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 3F4G_X:17-25 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |** ** || GUGAAAUUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 3F4G_Y:68-76 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |** ** || GUGAAAUUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 3RG5_A:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUUCAAUUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 15.800 Aligning: Query: 4GXY_A:49-57 Target: 1S72_0:312-319 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC ** ** UUGGAACA- struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 15.800 Aligning: Query: 4GXY_A:49-57 Target: 3U5H_5:194-201 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC ** ** UUGGAACA- struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 1J1U_B:554-562 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUUCAAAUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 17.200 Aligning: Query: 4GXY_A:49-57 Target: 1FJG_A:1314-1323 iso .**.**.... edge .ws.hh.... struc .((.)).... GUGCAAGUC- **|** | CUGCAACCCG struc .((.)).... edge .ws.hh.... iso .**.**.... Alignment Score: 17.600 Aligning: Query: 4GXY_A:49-57 Target: 4AQ7_B:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|**||| GUUCAAGUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 16.200 Aligning: Query: 4GXY_A:49-57 Target: 2ZZM_B:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|** || GUUCAAAUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 17.600 Aligning: Query: 4GXY_A:49-57 Target: 1QU2_T:53-61 iso .**.**... edge .ws.hh... struc .((.))... GUGCAAGUC |**|**||| GUUCAAGUC struc .((.))... edge .ws.hh... iso .**.**... Alignment Score: 17.200 Aligning: Query: 4GXY_A:49-57 Target: 2AW7_A:1314-1323 iso .**.**.... edge .ws.hh.... struc .((.)).... GUGCAAGUC- **|** || CUGCAACUCG struc .((.)).... edge .ws.hh.... iso .**.**.... Alignment Score: 16.600 Aligning: Query: 4GXY_A:49-57 Target: 3J7A_A:1847-1858 iso ..**.**..... edge ..ws.hh..... struc ..((.))..... G-UGCAAGUC-- **|** | AUUGCAAUUAUU struc ..((.))..... edge ..ws.hh..... iso ..**.**.....