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: 40.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4A1B_1:44-51_29-35 iso ....*.......*... edge ....w.......h... struc ....(.......)... iso .*****.....*.**. edge .shSHh.....s.hh. struc .((()(.....).)). UGAGUAA--.UGAAAU |*****| .|****| UCAGUAAGC.UGAACU struc .((()(.....).)). edge .shSHh.....s.hh. iso .*****.....*.**. struc ....(.......)... edge ....w.......h... iso ....*.......*... Alignment Score: 42.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3U5F_6:1111-1118_1129-1134 iso ....*......*... edge ....w......h... struc ....(......)... iso .*****....*.**. edge .shSHh....s.hh. struc .((()(....).)). UGAGUAA-.UGAAAU ***** .|**** GGAGUAUG.UGAAAC struc .((()(....).)). edge .shSHh....s.hh. iso .*****....*.**. struc ....(......)... edge ....w......h... iso ....*......*... Alignment Score: 33.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4MGN_C:13-23_81-92 iso .........*.....*......... edge .........w.....h......... struc .........(.....)......... iso .......****...*.*........ edge .......hSHh...s.h........ struc .......(()(...).)........ -----UGAGUAA.UGAAA------U | **** .|***| | AUCAAU-AGUAG.UGAAACGGCAGU struc .......(()(...).)........ edge .......hSHh...s.h........ iso .......****...*.*........ struc .........(.....)......... edge .........w.....h......... iso .........*.....*......... Alignment Score: 33.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4TZZ_C:16-23_83-90 iso .....*.....*...... edge .....w.....h...... struc .....(.....)...... iso ...****...*.*..... edge ...hSHh...s.h..... struc ...(()(...).)..... U-GAGUAA.UGAA---AU |**** . *** | AAGAGUAU.AGAAGGCA- struc ...(()(...).)..... edge ...hSHh...s.h..... iso ...****...*.*..... struc .....(.....)...... edge .....w.....h...... iso .....*.....*...... Alignment Score: 26.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1S72_0:356-361_291-295 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso ...***...*.... edge ...SHh...s.... struc ...()(...).... UGAGUAA.UGAAAU |*** . ** C-AGUAC.CGACC- struc ...()(...).... edge ...SHh...s.... iso ...***...*.... struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 22.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1VX6_A:46-52_32-37 iso ..*.**...***.. edge ..h.wh...shh.. struc ..(.((...))).. UGAGUAA.UGAAAU | * **|. *** | UAAUUAA.CGAAUU struc ..(.((...))).. edge ..h.wh...shh.. iso ..*.**...***.. Alignment Score: 35.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4IOA_X:1276-1282_1994-1999 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*.***...*..*. edge .s.SHh...s..h. struc .(.()(...)..). UGAGUAA.UGAAAU |*|***|.|**|*| UGAGUAA.UGAAAU struc .(.()(...)..). edge .s.SHh...s..h. iso .*.***...*..*. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 40.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4IOA_X:179-185_165-170 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |***** . ****| UCAGUAC.GGAACU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 41.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3U5H_5:1444-1450_2354-2359 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU ***** . **** GUAGUAG.CGAAAC struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 42.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4W23_2:1168-1175_1186-1191 iso ....*......*... edge ....w......h... struc ....(......)... iso .*****....*.**. edge .shSHh....s.hh. struc .((()(....).)). UGAGUAA-.UGAAAU ***** .|**** GGAGUAUG.UGAAAC struc .((()(....).)). edge .shSHh....s.hh. iso .*****....*.**. struc ....(......)... edge ....w......h... iso ....*......*... Alignment Score: 43.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3J7Y_A:2307-2313_2674-2679 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |*****|.|****| UAAGUAA.UGAAAU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 40.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 2QBG_B:202-208_188-193 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |***** . ****| UAAGUAC.GGAACU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 40.000 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 2QBG_B:239-245_253-258 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU ***** . **** CCAGUAG.CGAACG struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 33.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1S72_0:172-178_158-163 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso ..****...*.*.. edge ..hSHh...s.h.. struc ..(()(...).).. UGAGUAA.UGAAAU | **** . *** | UCAGUAU.AGAACU struc ..(()(...).).. edge ..hSHh...s.h.. iso ..****...*.*.. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 36.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4FAW_A:296-303_316-321 iso .....*.....*... edge .....w.....h... struc .....(.....)... iso ..+****...*.*+. edge ..shSHh...s.hh. struc ..((()(...).)). U-GAGUAA.UGAAAU +**** . ***+ CAUAGUAC.GGAAGG struc ..((()(...).)). edge ..WhSHh...s.hW. iso ..+****...*.*+. struc .....(.....)... edge .....w.....h... iso .....*.....*... Alignment Score: 37.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1VX6_A:82-89_97-103 iso .....*.....*.... edge .....w.....h.... struc .....(.....).... iso ..+****...*.*+.. edge ..shSHh...s.hh.. struc ..((()(...).)).. U-GAGUAA.UGAAAU- | +****|.|***+ UUUAGUAA.UGAACAA struc ..((()(...).)).. edge ..shSHh...s.hw.. iso ..+****...*.*+.. struc .....(.....).... edge .....w.....h.... iso .....*.....*.... Alignment Score: 42.000 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4V19_A:73-79_87-92 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU ***** . ****| AAAGUAU.AGAAAU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 42.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1FJG_A:887-894_905-910 iso ....*......*... edge ....w......h... struc ....(......)... iso .*****....*.**. edge .shSHh....s.hh. struc .((()(....).)). UGAGUAA-.UGAAAU ***** .|**** GGAGUACG.UGAAAC struc .((()(....).)). edge .shSHh....s.hh. iso .*****....*.**. struc ....(......)... edge ....w......h... iso ....*......*... Alignment Score: 44.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1VW3_A:1296-1302_1911-1916 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |*****|.|****| UGAGUAA.UGAAAU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 40.000 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1VX6_B:72-78_98-103 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU ***** . **** CUAGUAC.GGAACA struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 26.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1S72_0:586-594_563-571 iso ....*............*... edge ....w............h... struc ....(............)... iso ...***..........*.... edge ...SHh..........s.... struc ...()(..........).... UGAGUAA-------.UGAAAU |***| .|** C-AGUAAGACCGAA.UGACC- struc ...()(..........).... edge ...SHh..........s.... iso ...***..........*.... struc ....(............)... edge ....w............h... iso ....*............*... Alignment Score: 42.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1S72_9:75-81_101-106 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU ***** . **** GGAGUAC.GGAAAC struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 38.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1VW3_A:242-248_228-233 iso ....+.....+... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |**++*|.|*+**| UAAGUAA.UGAACU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....w... iso ....+.....+... Alignment Score: 40.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1S72_0:1367-1373_2052-2057 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU ***** .|****| AUAGUAG.UGAACU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 16.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4W21_5:45-52_30-36 iso ..*.*+.....+**.. edge ..h.wh.....shh.. struc ..(.((.....))).. UGAGUAA--.UGAAAU | *|*+| .|+** | UUAGUCAGC.UGAAUU struc ..(.((.....))).. edge ..h.wh.....shh.. iso ..*.*+.....+**.. Alignment Score: 41.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1S72_0:210-216_224-229 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |*****|.|**** UUAGUAA.UGAACG struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 31.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3J7A_A:1212-1219_1230-1235 iso .**.**....****. edge .sh.wh....shhh. struc .((.((....)))). UGAGUAA.U-GAAAU **|** .| **** CGAGUAU.UAGAAAG struc .((.((....)))). edge .sh.wh....shhh. iso .**.**....****. Alignment Score: 35.000 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3U5H_5:82-89_97-103 iso .....*.....*.... edge .....w.....h.... struc .....(.....).... iso ...****...*.*... edge ...hSHh...s.h... struc ...(()(...).)... -UGAGUAA.UGAAAU- | ****|.|*** CUUAGUAA.UGAAGCG struc ...(()(...).)... edge ...hSHh...s.h... iso ...****...*.*... struc .....(.....).... edge .....w.....h.... iso .....*.....*.... Alignment Score: 41.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1NBS_B:165-171_138-143 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |***** . **** UGAGUAU.AAAAAA struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 42.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3D0U_A:20-27_60-66 iso .....*.....*.... edge .....w.....h.... struc .....(.....).... iso ..*****...*.**.. edge ..shSHh...s.hh.. struc ..((()(...).)).. -UGAGUAA.UGAAAU- |***** .|**** AUGAGUAG.UGAAAGG struc ..((()(...).)).. edge ..shSHh...s.hh.. iso ..*****...*.**.. struc .....(.....).... edge .....w.....h.... iso .....*.....*.... Alignment Score: 41.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1VX6_A:1593-1599_2647-2652 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU ***** . **** GAAGUAG.CGAAAC struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 42.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4QCN_A:228-234_242-247 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |***** . **** UGAGUAG.CGAAAG struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 40.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3U5H_7:72-80_100-106 iso ......*.....*.... edge ......w.....h.... struc ......(.....).... iso ...*****...*.**.. edge ...shSHh...s.hh.. struc ...((()(...).)).. U--GAGUAA.UGAAA-U ***** . **** | ACCGAGUAG.CGAAACU struc ...((()(...).)).. edge ...shSHh...s.hh.. iso ...*****...*.**.. struc ......(.....).... edge ......w.....h.... iso ......*.....*.... Alignment Score: 39.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4IOA_X:215-222_230-236 iso .....*.....*.... edge .....w.....h.... struc .....(.....).... iso ..*****...*.**.. edge ..shSHh...s.hh.. struc ..((()(...).)).. -UGAGUAA.UGAAAU- |***** . **** GUUAGUAG.CGAACCC struc ..((()(...).)).. edge ..shSHh...s.hh.. iso ..*****...*.**.. struc .....(.....).... edge .....w.....h.... iso .....*.....*.... Alignment Score: 42.000 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3J7Y_A:1739-1745_1753-1758 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU ***** . ****| AAAGUAU.AGAAAU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 29.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3U5H_5:46-53_31-37 iso .**.**.....****. edge .sh.wh.....shhh. struc .((.((.....)))). UGAGUAA--.UGAAAU |** **| .|****| UCAAUAAGC.UGAACU struc .((.((.....)))). edge .sh.wh.....shhh. iso .**.**.....****. Alignment Score: 33.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 1UN6_F:73-78_98-102 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso ..****...*.*.. edge ..hSHh...s.h.. struc ..(()(...).).. UGAGUAA.UGAAAU | **** . *** | U-AGUAC.GGAA-U struc ..(()(...).).. edge ..hSHh...s.h.. iso ..****...*.*.. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 42.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3DIR_A:23-30_63-69 iso .....*.....*.... edge .....w.....h.... struc .....(.....).... iso ..*****...*.**.. edge ..shSHh...s.hh.. struc ..((()(...).)).. -UGAGUAA.UGAAAU- |***** .|**** AUGAGUAG.UGAAAGG struc ..((()(...).)).. edge ..shSHh...s.hh.. iso ..*****...*.**.. struc .....(.....).... edge .....w.....h.... iso .....*.....*.... Alignment Score: 23.200 Aligning: Query: 4V19_A:1004-1009_639-645 Target: 4A1B_1:2349-2354_1470-1476 iso .***.....*.**. edge .shh.....h.wh. struc .(((.....).)). UGAAAU.UGAGUAA *** . *|** CGAACC.GUAGUAG struc .(((.....).)). edge .shh.....h.wh. iso .***.....*.**. Alignment Score: 40.600 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4QCN_A:191-197_177-182 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |***** . ****| UCAGUAC.GGAACU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 30.000 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4A1B_1:81-87_95-100 iso .**.**...****. edge .sh.wh...shhh. struc .((.((...)))). UGAGUAA.UGAAAU **|**|.|**** CCAGUAA.UGAACA struc .((.((...)))). edge .sh.wh...shhh. iso .**.**...****. Alignment Score: 36.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4W21_7:71-78_98-104 iso .....*.....*.... edge .....w.....h.... struc .....(.....).... iso ..+****...*.*+.. edge ..shSHh...s.hh.. struc ..((()(...).)).. -UGAGUAA.UGAAAU- |+**** . ***+ GUUAGUAC.GGAAUAC struc ..((()(...).)).. edge ..whSHh...s.hh.. iso ..+****...*.*+.. struc .....(.....).... edge .....w.....h.... iso .....*.....*.... Alignment Score: 43.200 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 2QBG_B:1263-1269_2011-2016 iso ....*.....*... edge ....w.....h... struc ....(.....)... iso .*****...*.**. edge .shSHh...s.hh. struc .((()(...).)). UGAGUAA.UGAAAU |*****|.|****| UAAGUAA.UGAAAU struc .((()(...).)). edge .shSHh...s.hh. iso .*****...*.**. struc ....(.....)... edge ....w.....h... iso ....*.....*... Alignment Score: 41.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 4BPP_A:1083-1090_1102-1107 iso ....*......*... edge ....w......h... struc ....(......)... iso .*****....*.**. edge .shSHh....s.hh. struc .((()(....).)). UGAGUAA-.UGAAAU ***** .|**** GAAGUAUG.UGAAAC struc .((()(....).)). edge .shSHh....s.hh. iso .*****....*.**. struc ....(......)... edge ....w......h... iso ....*......*... Alignment Score: 41.400 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 2AW7_A:887-894_905-910 iso ....*......*... edge ....w......h... struc ....(......)... iso .*****....*.**. edge .shSHh....s.hh. struc .((()(....).)). UGAGUAA-.UGAAAU ***** .|**** GGAGUACG.UAAAAC struc .((()(....).)). edge .shSHh....s.hh. iso .*****....*.**. struc ....(......)... edge ....w......h... iso ....*......*... Alignment Score: 24.800 Aligning: Query: 4V19_A:639-645_1004-1009 Target: 3U5H_5:992-998_1050-1057 iso ....*........*... edge ....w........h... struc ....(........)... iso ...***......*.... edge ...SHh......s.... struc ...()(......).... UGAGUAA---.UGAAAU | ***| .|**| AG-GUAAAUU.UAAAUA struc ...()(......).... edge ...SHh......s.... iso ...***......*.... struc ....(........)... edge ....w........h... iso ....*........*...