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: 16.600 Aligning: Query: 3U5F_6:186-189_196-199 Target: 3J7A_A:1966-1969_2021-2024 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG ** . ** UGAA.UAAA struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.600 Aligning: Query: 3U5F_6:186-189_196-199 Target: 3U5F_6:1669-1672_1729-1732 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG ** . ** UGAG.CAAA struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:186-189_196-199 Target: 1GID_B:205-208_112-116 iso .**...**.. edge .sh...sh.. struc .((...)).. CGAC.GAA-G **|.|** | UAAC.GAAAG struc .((...)).. edge .sh...sh.. iso .**...**.. Alignment Score: 16.600 Aligning: Query: 3U5F_6:186-189_196-199 Target: 4FAW_A:172-175_190-194 iso .**...**.. edge .sh...sh.. struc .((...)).. CGAC.GAA-G ** . ** | UGAG.CAAAG struc .((...)).. edge .sh...sh.. iso .**...**.. Alignment Score: 16.600 Aligning: Query: 3U5F_6:186-189_196-199 Target: 4BPP_A:1697-1700_1625-1628 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG ** . ** GGAA.UAAC struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.600 Aligning: Query: 3U5F_6:186-189_196-199 Target: 4BPP_A:1640-1643_1682-1685 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG ** . ** UGAA.UAAA struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 3DIR_A:19-22_70-73 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|** CGAG.CGAG struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:186-189_196-199 Target: 1U6B_B:85-88_56-59 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG |**|.|** CAAC.GAAA struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 4W23_2:1733-1736_1798-1801 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|** UGAG.CGAA struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 18.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 1S72_0:2502-2505_2515-2518 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|**| CAAG.CGAC struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 18.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 4A1B_1:2824-2827_2837-2840 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|**| CAAG.CGAC struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 3D0U_A:16-19_67-70 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|** CGAG.CGAG struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 4QCN_A:2362-2365_2376-2379 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|** CGAG.CGAG struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 17.000 Aligning: Query: 3U5F_6:186-189_196-199 Target: 1FJG_A:1481-1484_1416-1419 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG **|.|**| UGAC.GGAG struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:186-189_196-199 Target: 1VW3_A:2617-2620_2631-2634 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG **|.|** UAAC.GAAA struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 18.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 2QBG_B:2467-2470_2480-2483 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|**| CAAG.CGAC struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 17.000 Aligning: Query: 3U5F_6:186-189_196-199 Target: 2QBG_B:554-557_536-539 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG **|.|**| UGAC.GGAG struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 17.000 Aligning: Query: 3U5F_6:186-189_196-199 Target: 2AW7_A:1481-1484_1416-1419 iso .**...**. edge .sh...sh. struc .((...)). CGAC.GAAG **|.|**| UGAC.GGAG struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 4W21_5:1431-1434_1450-1453 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|** CGAG.CGAG struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 16.400 Aligning: Query: 3U5F_6:196-199_186-189 Target: 2QBG_B:2350-2353_2364-2367 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|** CGAG.CGAG struc .((...)). edge .sh...sh. iso .**...**. Alignment Score: 17.000 Aligning: Query: 3U5F_6:196-199_186-189 Target: 4WFL_A:73-76_91-94 iso .**...**. edge .sh...sh. struc .((...)). GAAG.CGAC **|.|**| CGAG.CGAC struc .((...)). edge .sh...sh. iso .**...**.