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: 32.000 Aligning: Query: 1S72_0:93-100_77-81 Target: 4B5R_A:31-38_17-21 iso ....+......+.. edge ....s......w.. struc ....(......).. iso ....***...***. edge ....shh...ssh. struc ....(((...))). CGAAGAAC.GGGAG ||||++*|.|*++| CGAAGAAC.GGGAG struc ....(((...))). edge ....shh...ssh. iso ....***...***. struc ....(......).. edge ....s......w.. iso ....+......+.. Alignment Score: 28.600 Aligning: Query: 1S72_0:93-100_77-81 Target: 4C4W_D:26-33_3-7 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...*+...+**. edge .s...hh...ssw. struc .(...((...))). CGAAGAAC.GGGAG *| **+|.|+**| UGAUGACC.GCAAG struc .(...((...))). edge .s...hh...wsw. iso .*...*+...+**. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 21.400 Aligning: Query: 1S72_0:93-100_77-81 Target: 3NVI_E:15-21_5-8 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...*.....**. edge .s...h.....sw. struc .(...(.....)). CGAAGAAC.GGGAG * ** . ** GCGUGAUU.--GAC struc .(...(.....)). edge .s...h.....sw. iso .*...*.....**. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 21.400 Aligning: Query: 1S72_0:93-100_77-81 Target: 1RLG_D:15-21_5-8 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...*.....**. edge .s...h.....sw. struc .(...(.....)). CGAAGAAC.GGGAG * ** . ** GCGUGAUU.--GAC struc .(...(.....)). edge .s...h.....sw. iso .*...*.....**. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 38.600 Aligning: Query: 1S72_0:93-100_77-81 Target: 1S72_0:1312-1319_1338-1342 iso ....**.....**. edge ....sh.....sh. struc ....((.....)). iso .*..+.*...*+*. edge .s..s.h...sww. struc .(..(.(...))). CGAAGAAC.GGGAG * ++* . *++ GAUGGAAG.UGGAC struc .(..(.(...))). edge .s..s.h...sww. iso .*..+.*...*+*. struc ....((.....)). edge ....sh.....sh. iso ....**.....**. Alignment Score: 33.400 Aligning: Query: 1S72_0:93-100_77-81 Target: 4IOA_X:1221-1228_1247-1251 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...**...***. edge .s...hh...ssw. struc .(...((...))). CGAAGAAC.GGGAG |* |*** . ***| CGGAGAAG.UGGAG struc .(...((...))). edge .s...hh...ssw. iso .*...**...***. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 30.200 Aligning: Query: 1S72_0:93-100_77-81 Target: 1S72_0:1147-1155_1212-1216 iso ....**.......**. edge ....sh.......sh. struc ....((.......)). iso .*..+........+*. edge .s..s........ww. struc .(..(........)). CGAAGAAC.GG--GAG |* |++ |. | ++| CCUAGA-C.AGCCGAG struc .(..(........)). edge .s..s........ww. iso .*..+........+*. struc ....((.......)). edge ....sh.......sh. iso ....**.......**. Alignment Score: 22.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 3Q3Z_A:16-22_55-58 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...*.....**. edge .s...h.....sw. struc .(...(.....)). CGAAGAAC.GGGAG |*| ** . **| CAAUGAUU.--GAG struc .(...(.....)). edge .s...h.....sw. iso .*...*.....**. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 22.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 3Q3Z_V:16-22_55-58 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...*.....**. edge .s...h.....sw. struc .(...(.....)). CGAAGAAC.GGGAG |*| ** . **| CAAUGAUU.--GAG struc .(...(.....)). edge .s...h.....sw. iso .*...*.....**. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 30.200 Aligning: Query: 1S72_0:93-100_77-81 Target: 3U5H_5:1218-1225_1284-1287 iso ....**......**. edge ....sh......sh. struc ....((......)). iso .*..+.......+*. edge .s..s.......ww. struc .(..(.......)). CGAAGA-AC.GGGAG * |++ ||. ++ UCUAGACAC.--GAA struc .(..(.......)). edge .s..s.......ww. iso .*..+.......+*. struc ....((......)). edge ....sh......sh. iso ....**......**. Alignment Score: 32.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 1VX6_A:1884-1890_1868-1874 iso ....*.......*... edge ....s.......h... struc ....(.......)... iso .*...**...***... edge .s...hh...ssw... struc .(...((...)))... CGAAGAAC.GGGAG-- * |*** . *** -GGAGAAG.UGGAAUC struc .(...((...)))... edge .s...hh...ssw... iso .*...**...***... struc ....(.......)... edge ....s.......h... iso ....*.......*... Alignment Score: 31.400 Aligning: Query: 1S72_0:93-100_77-81 Target: 1S72_0:1602-1608_1587-1592 iso ....*.......*.. edge ....s.......h.. struc ....(.......).. iso .*...**...***.. edge .s...hh...ssw.. struc .(...((...))).. CGAAGAAC.GGGA-G *| *** . *** | -CAGGAAG.UGGAAG struc .(...((...))).. edge .s...hh...ssw.. iso .*...**...***.. struc ....(.......).. edge ....s.......h.. iso ....*.......*.. Alignment Score: 22.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 1E7K_D:28-34_42-45 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...*.....**. edge .s...h.....sw. struc .(...(.....)). CGAAGAAC.GGGAG |*| ** |. **| CAAUGAGC.--GAG struc .(...(.....)). edge .s...h.....sw. iso .*...*.....**. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 38.600 Aligning: Query: 1S72_0:93-100_77-81 Target: 2QBG_B:1208-1215_1234-1238 iso ....**.....**. edge ....sh.....sh. struc ....((.....)). iso .*..+.*...*+*. edge .s..s.h...sww. struc .(..(.(...))). CGAAGAAC.GGGAG |* ++* . *++| CUGCGAAG.UGGAG struc .(..(.(...))). edge .s..s.h...sww. iso .*..+.*...*+*. struc ....((.....)). edge ....sh.....sh. iso ....**.....**. Alignment Score: 37.600 Aligning: Query: 1S72_0:93-100_77-81 Target: 4GMA_Z:138-150_93-103 iso .........**.....**....... edge .........sh.....sh....... struc .........((.....))....... iso ......*..+.+...++*....... edge ......s..s.h...sww....... struc ......(..(.(...)))....... C-----GAAGAAC.GGGA-G----- *| +++ . +++ | GUGGAGGAUGAGU.AGGACGAAGCC struc ......(..(.(...)))....... edge ......s..s.h...sww....... iso ......*..+.+...++*....... struc .........((.....))....... edge .........sh.....sh....... iso .........**.....**....... Alignment Score: 39.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 3UMY_B:2129-2136_2155-2159 iso ....**.....**. edge ....sh.....sh. struc ....((.....)). iso .*..+.*...*+*. edge .s..s.h...sww. struc .(..(.(...))). CGAAGAAC.GGGAG |* ++*|.|*++| CUGUGAAC.GGGAG struc .(..(.(...))). edge .s..s.h...sww. iso .*..+.*...*+*. struc ....((.....)). edge ....sh.....sh. iso ....**.....**. Alignment Score: 39.600 Aligning: Query: 1S72_0:77-81_93-100 Target: 4A1B_1:1441-1445_1414-1421 iso ..+*...*..+... edge ..ww...s..s... struc ..((...)..)... iso .***......***. edge .ssh......shh. struc .(((......))). GGGAG.CGAAGAAC *++|.|+ |++* UGGAG.CCUAGAAG struc .(((......))). edge .ssh......shh. iso .***......***. struc ..((...)..)... edge ..ww...s..s... iso ..+*...*..+... Alignment Score: 22.600 Aligning: Query: 1S72_0:93-100_77-81 Target: 1S72_0:1026-1033_937-940 iso .....*.......*. edge .....s.......h. struc .....(.......). iso .*....*.....**. edge .s....h.....sw. struc .(....(.....)). CGAA-GAAC.GGGAG |* ** |. **| CGUUUGACC.--GAG struc .(....(.....)). edge .s....h.....sw. iso .*....*.....**. struc .....(.......). edge .....s.......h. iso .....*.......*. Alignment Score: 39.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 3U5H_5:1388-1395_1415-1419 iso ....**.....**. edge ....sh.....sh. struc ....((.....)). iso .*..+.*...*+*. edge .s..s.h...sww. struc .(..(.(...))). CGAAGAAC.GGGAG *| ++* . *++ UGACGAAG.UCGAA struc .(..(.(...))). edge .s..s.h...sww. iso .*..+.*...*+*. struc ....((.....)). edge ....sh.....sh. iso ....**.....**. Alignment Score: 41.200 Aligning: Query: 1S72_0:93-100_77-81 Target: 4QCN_A:1253-1260_1280-1284 iso ....**.....**. edge ....sh.....sh. struc ....((.....)). iso .*..+.*...*+*. edge .s..s.h...sww. struc .(..(.(...))). CGAAGAAC.GGGAG |*| ++* . *++| CGAUGAAG.UGGAG struc .(..(.(...))). edge .s..s.h...sww. iso .*..+.*...*+*. struc ....((.....)). edge ....sh.....sh. iso ....**.....**. Alignment Score: 22.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 2OZB_C:28-34_42-45 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...*.....**. edge .s...h.....sw. struc .(...(.....)). CGAAGAAC.GGGAG |*| ** |. **| CAAUGAGC.--GAG struc .(...(.....)). edge .s...h.....sw. iso .*...*.....**. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 22.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 3SIU_C:33-39_47-50 iso ....*.......*. edge ....s.......h. struc ....(.......). iso .*...*.....**. edge .s...h.....sw. struc .(...(.....)). CGAAGAAC.GGGAG |*| ** .| **| CAAUGA--.GUGAG struc .(...(.....)). edge .s...h.....sw. iso .*...*.....**. struc ....(.......). edge ....s.......h. iso ....*.......*. Alignment Score: 30.800 Aligning: Query: 1S72_0:93-100_77-81 Target: 3GX5_A:31-38_17-21 iso ....+......+.. edge ....s......w.. struc ....(......).. iso ....***...***. edge ....shh...ssh. struc ....(((...))). CGAAGAAC.GGGAG ||| ++* . *++| CGACGAAA.UGGAG struc ....(((...))). edge ....shh...ssh. iso ....***...***. struc ....(......).. edge ....s......w.. iso ....+......+.. Alignment Score: 36.200 Aligning: Query: 1S72_0:93-100_77-81 Target: 3U5H_5:1727-1733_1711-1717 iso ....**.....**... edge ....sh.....sh... struc ....((.....))... iso .*..+.+...++*... edge .s..s.h...sww... struc .(..(.(...)))... CGAAGAAC.GGGAG-- * |+++ . +++ -GGAGAUG.CGGAAUU struc .(..(.(...)))... edge .s..s.h...sww... iso .*..+.+...++*... struc ....((.....))... edge ....sh.....sh... iso ....**.....**...