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: 158.800 Aligning: Query: 1S72_0:1889-1891_1946-1947_1965-1986_2002-2013 Target: 4V19_A:874-876_899-900_917-938_954-965 iso ............+.....................................+................... edge ............W.....................................H................... struc ............(.....................................)................... C-----------UG.CG.CUUAAGGUAGCGUAGUACCUUG.CUUGCAUGAA------------------- | + . . . + CUGCCGCAAAGGU-.--.----------------------.---------AGCAUAAUCACUUGCUUGUA struc ............(.....................................)................... edge ............s.....................................h................... iso ............+.....................................+................... iso ...... edge ...... struc ...... ----UG || UGAAUG struc ...... edge ...... iso ...... Alignment Score: 157.800 Aligning: Query: 1S72_0:1965-1986_2002-2013_1889-1891_1946-1947 Target: 1VW3_A:1861-1872_1741-1743_1806-1807_1824-1845 iso ...................+..++...................................+.......... edge ...................W..Hs...................................h.......... struc ...................(..)(...................................).......... C-----U------------UA-AGGUAGCGUAGUACCUUG.CUUGCAUGAAUG.CUG.CG---------- | | +| ++ . . . + CCCGCAUGAAUGCUGCAUAUAAUG----------------.------------.---.-UAGCGAAAUUC struc ...................(..)(...................................).......... edge ...................w..wS...................................H.......... iso ...................+..++...................................+.......... iso .... edge .... struc .... ---- CUUG struc .... edge .... iso .... Alignment Score: 159.200 Aligning: Query: 1S72_0:1965-1986_2002-2013_1889-1891_1946-1947 Target: 4QCN_A:1864-1866_1927-1928_1946-1967_1983-1994 iso .......+.+.+...................................+...................... edge .......W.H.s...................................h...................... struc .......(.).(...................................)...................... CU-----UAA-GGUAGCGUAGUACCUUG.CUUGCAUGAAUG.CUG.CG---------------------- | +|+ + . . . + UUGCGCCUAAGG----------------.------------.---.-UAGCGAAAUUCCUUGCCUGCACG struc .......(.).(...................................)...................... edge .......s.h.S...................................H...................... iso .......+.+.+...................................+...................... iso .... edge .... struc .... ---- AAAA struc .... edge .... iso .... Alignment Score: 143.200 Aligning: Query: 4A1B_1:2187-2189_2243-2244_2262-2283_2299-2310 Target: 1S72_0:1889-1891_1946-1947_1965-1986_2002-2013 iso ...........+.....................................+.................... edge ...........W.....................................H.................... struc ...........(.....................................).................... C----------UG.CG.CUUAAGGUAGCCAAAUGCCUCG.CGCGCAUGAA-------------------- | + . . . + CUGCGCUUAAGG-.--.----------------------.---------UAGCGUAGUACCUUGCUUGCA struc ...........(.....................................).................... edge ...........S.....................................H.................... iso ...........+.....................................+.................... iso ...... edge ...... struc ...... ----UG || UGAAUG struc ...... edge ...... iso ...... Alignment Score: 156.000 Aligning: Query: 1S72_0:1889-1891_1946-1947_1965-1986_2002-2013 Target: 4IOA_X:1825-1827_1888-1928_1944-1955 iso ............................+.....................................+... edge ............................W.....................................H... struc ............................(.....................................)... C---------------------------UG.CG.CUUAAGGUAGCGUAGUACCUUG.CUUGCAUGAA--- | + . . . + CUGCGGCCGUAACUAUAACGGUCCUAAGG-.--.----------------------.---------UAGC struc ............................(.....................................)... edge ............................S.....................................H... iso ............................+.....................................+... iso ....................... edge ....................... struc ....................... ----U-----------------G | | GAAAUUCCUUGCCUGCACGAAAG struc ....................... edge ....................... iso ....................... Alignment Score: 157.400 Aligning: Query: 1S72_0:1965-1986_2002-2013_1889-1891_1946-1947 Target: 3U5H_5:2192-2194_2248-2249_2267-2288_2304-2315 iso ......+...++...................................+...................... edge ......W...Hs...................................h...................... struc ......(...)(...................................)...................... CU----U--AAGGUAGCGUAGUACCUUG.CUUGCAUGAAUG.CUG.CG---------------------- || + |++ . . . + CUGCGCUUAAGG----------------.------------.---.-UAGCCAAAUGCCUCGCGCGCAUG struc ......(...)(...................................)...................... edge ......w...wS...................................H...................... iso ......+...++...................................+...................... iso .... edge .... struc .... ---- AAUG struc .... edge .... iso .... Alignment Score: 146.400 Aligning: Query: 2QBG_B:1833-1835_1905-1906_1924-1945_1961-1972 Target: 1S72_0:1889-1891_1946-1947_1965-1986_2002-2013 iso ...........+.....................................+.................... edge ...........W.....................................H.................... struc ...........(.....................................).................... C----------UG.CG.CCUAAGGUAGCGAAAUUCCUUG.CCUGCACGAA-------------------- | + . . . + CUGCGCUUAAGG-.--.----------------------.---------UAGCGUAGUACCUUGCUUGCA struc ...........(.....................................).................... edge ...........S.....................................H.................... iso ...........+.....................................+.................... iso ...... edge ...... struc ...... ----UG || UGAAUG struc ...... edge ...... iso ...... Alignment Score: 157.400 Aligning: Query: 1S72_0:1889-1891_1946-1947_1965-1986_2002-2013 Target: 3J7Y_A:2544-2546_2569-2570_2587-2608_2624-2635 iso ........+.....................................+....................... edge ........W.....................................H....................... struc ........(.....................................)....................... C-------UG.CG.CUUAAGGUAGCGUAGUACCUUG.CUUGCAUGAA----------------------- | + . . . + CUGCCGCAA-.--.----------------------.---------AGGUAGCAUAAUCACUUGCCUGUA struc ........(.....................................)....................... edge ........s.....................................h....................... iso ........+.....................................+....................... iso ...... edge ...... struc ...... ----UG || UGAAUG struc ...... edge ...... iso ...... Alignment Score: 157.400 Aligning: Query: 1S72_0:1889-1891_1946-1947_1965-1986_2002-2013 Target: 4W21_5:3696-3698_3752-3755_3769-3794_3806-3819 iso ............+.....................................+................... edge ............W.....................................H................... struc ............(.....................................)................... C-----------UG.CG.CUUAAGGUAGCGUAGUACCUUG.CUUGCAUGAA------------------- | + . . . + CUGCGGGCUCUUA-.--.----------------------.---------AGGUAGCCAAAUGCCUCGUC struc ............(.....................................)................... edge ............s.....................................s................... iso ............+.....................................+................... iso .............. edge .............. struc .............. ------------UG || GACGCGCAUGAAUG struc .............. edge .............. iso .............. Alignment Score: 159.200 Aligning: Query: 1S72_0:1965-1986_2002-2013_1889-1891_1946-1947 Target: 1VX6_A:2485-2487_2541-2542_2560-2581_2597-2608 iso .......+.+.+...................................+...................... edge .......W.H.s...................................h...................... struc .......(.).(...................................)...................... CU-----UAA-GGUAGCGUAGUACCUUG.CUUGCAUGAAUG.CUG.CG---------------------- || +|+ + . . . + CUGCGCUUAAGG----------------.------------.---.-UAGCCAAAUGCCUCGCGCGCAUG struc .......(.).(...................................)...................... edge .......s.h.S...................................H...................... iso .......+.+.+...................................+...................... iso .... edge .... struc .... ---- AAUG struc .... edge .... iso ....