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: 14.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4QCN_A:235-241 iso .......*..*....... edge .......s..h....... struc .......(..)....... iso .......*...*...... edge .......s...h...... struc .......(...)...... UUAGUACGA-GAGGAACA |* **| ------CGGCGAG----- struc .......(...)...... edge .......s...h...... iso .......*...*...... struc .......(..)....... edge .......s..h....... iso .......*..*....... Alignment Score: 17.600 Aligning: Query: 3U5H_5:3019-3035 Target: 1FJG_A:296-301 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | *|**| U------GAGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 17.600 Aligning: Query: 3U5H_5:3019-3035 Target: 4L81_A:57-62 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | *|** | ---G---GAGA----C- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4QCN_A:513-518 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGGGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 14.200 Aligning: Query: 3U5H_5:3019-3035 Target: 2QBG_B:246-252 iso .......*..*....... edge .......s..h....... struc .......(..)....... iso .......*...*...... edge .......s...h...... struc .......(...)...... UUAGUACGA-GAGGAACA |* **| ------CGGCGAG----- struc .......(...)...... edge .......s...h...... iso .......*...*...... struc .......(..)....... edge .......s..h....... iso .......*..*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 2QBG_B:2856-2861 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | * ** --A----GCGAU----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1S72_0:468-473 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | * ** | U------GUGA-----A struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4QCN_A:2606-2611 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 55.400 Aligning: Query: 3U5H_5:3019-3035 Target: 4IOA_X:2632-2646 iso ....*..*.*...*... edge ....w..s.h...h... struc ....(..(.)...)... iso ...*****..***.... edge ...SHhWs..hWs.... struc ...()(((..))).... UUAGUACGAGAGGAACA | |*****|***** | U-AGUACGAGAGGA-CC struc ...()(((..))).... edge ...SHhWs..hWs.... iso ...*****..***.... struc ....(..(.)...)... edge ....w..s.h...h... iso ....*..*.*...*... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1VX6_A:1551-1556 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 55.400 Aligning: Query: 3U5H_5:3019-3035 Target: 4NLF_A:2652-2668 iso ....*..*.*...*... edge ....w..s.h...h... struc ....(..(.)...)... iso ...*****..***.... edge ...SHhWs..hWs.... struc ...()(((..))).... UUAGUACGAGAGGAACA ||*****|***** | CUAGUACGAGAGGACCG struc ...()(((..))).... edge ...SHhWs..hWs.... iso ...*****..***.... struc ....(..(.)...)... edge ....w..s.h...h... iso ....*..*.*...*... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4A1C_3:86-91 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | * ** | ---G---GGGA----C- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 14.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1VX6_A:90-96 iso .......*..*....... edge .......s..h....... struc .......(..)....... iso .......*...*...... edge .......s...h...... struc .......(...)...... UUAGUACGA-GAGGAACA |* **| ------CGGCGAG----- struc .......(...)...... edge .......s...h...... iso .......*...*...... struc .......(..)....... edge .......s..h....... iso .......*..*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 2QBG_B:462-467 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 56.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4W21_5:4597-4613 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .**.****..******. edge .sh.whWs..hWshhh. struc .((.((((..)))))). UUAGUACGAGAGGAACA |**|****|******* UCAGUACGAGAGGAACC struc .((.((((..)))))). edge .sh.whWs..hWshhh. iso .**.****..******. struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 55.400 Aligning: Query: 3U5H_5:3019-3035 Target: 1VX6_A:3406-3420 iso ....*..*.*...*... edge ....w..s.h...h... struc ....(..(.)...)... iso ...*****..***.... edge ...SHhWs..hWs.... struc ...()(((..))).... UUAGUACGAGAGGAACA | *****|***** UG-GUACGAGAGGAUU- struc ...()(((..))).... edge ...SHhWs..hWs.... iso ...*****..***.... struc ....(..(.)...)... edge ....w..s.h...h... iso ....*..*.*...*... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4IOA_X:473-478 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 67.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1Q96_A:6-24 iso .....*..*.*...*.... edge .....w..s.h...h.... struc .....(..(.)...).... iso ..*******..***.**.. edge ..shSHhWs..hWs.hh.. struc ..((()(((..))).)).. -UUAGUACGAGAGGAACA- |*******|******* CUCAGUAUGAGAAGAACCG struc ..((()(((..))).)).. edge ..shSHhWs..hWs.hh.. iso ..*******..***.**.. struc .....(..(.)...).... edge .....w..s.h...h.... iso .....*..*.*...*.... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 3U5H_5:2963-2968 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 67.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1Q96_C:6-24 iso .....*..*.*...*.... edge .....w..s.h...h.... struc .....(..(.)...).... iso ..*******..***.**.. edge ..shSHhWs..hWs.hh.. struc ..((()(((..))).)).. -UUAGUACGAGAGGAACA- |*******|******* CUCAGUAUGAGAAGAACCG struc ..((()(((..))).)).. edge ..shSHhWs..hWs.hh.. iso ..*******..***.**.. struc .....(..(.)...).... edge .....w..s.h...h.... iso .....*..*.*...*.... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 3U5H_7:88-93 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | * ** | ---G---GUGA----C- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 58.400 Aligning: Query: 3U5H_5:3019-3035 Target: 2QBG_B:2653-2667 iso ....*..*.*...*... edge ....w..s.h...h... struc ....(..(.)...)... iso ..+*****..***.+.. edge ..hSHhWs..hWs.h.. struc ..(()(((..))).).. UUAGUACGAGAGGAACA | +*****|*****+| U-AGUACGAGAGGACC- struc ..(()(((..))).).. edge ..hSHhWs..hWs.w.. iso ..+*****..***.+.. struc ....(..(.)...)... edge ....w..s.h...h... iso ....*..*.*...*... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1VW3_A:2861-2866 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | * ** | U------GUGA-----A struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 2NZ4_R:108-113 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | * ** | ---G---GUGA----C- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 17.600 Aligning: Query: 3U5H_5:3019-3035 Target: 3AM1_B:45-50 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |*|**| ------CGAGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1S72_0:2248-2253 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGGGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 14.200 Aligning: Query: 3U5H_5:3019-3035 Target: 2QBG_B:487-493 iso .......*..*....... edge .......s..h....... struc .......(..)....... iso .......*...*...... edge .......s...h...... struc .......(...)...... UUAGUACGA-GAGGAACA |* **| ------CGGCGAG----- struc .......(...)...... edge .......s...h...... iso .......*...*...... struc .......(..)....... edge .......s..h....... iso .......*..*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1VX6_A:3322-3327 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 17.600 Aligning: Query: 3U5H_5:3019-3035 Target: 1VX6_B:86-91 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | *|** | ---G---GAGA----C- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 11.800 Aligning: Query: 3U5H_5:3019-3035 Target: 3J7Y_A:1746-1752 iso .......*..*....... edge .......s..h....... struc .......(..)....... iso .......*...*...... edge .......s...h...... struc .......(...)...... UUAGUACGA-GAGGAACA | * ** --A----GGCGAU----- struc .......(...)...... edge .......s...h...... iso .......*...*...... struc .......(..)....... edge .......s..h....... iso .......*..*....... Alignment Score: 45.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4QCN_A:2665-2679 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso ....****..****... edge ....whWs..hWsh... struc ....((((..))))... UUAGUACGAGAGGAACA | ||****|***** | U-AGUACGAGAGGA-CC struc ....((((..))))... edge ....whWs..hWsh... iso ....****..****... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 14.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4IOA_X:223-229 iso .......*..*....... edge .......s..h....... struc .......(..)....... iso .......*...*...... edge .......s...h...... struc .......(...)...... UUAGUACGA-GAGGAACA |* **| ------CGGCGAG----- struc .......(...)...... edge .......s...h...... iso .......*...*...... struc .......(..)....... edge .......s..h....... iso .......*..*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4IOA_X:498-503 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGGGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4W21_5:4540-4545 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4QCN_A:488-493 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 17.600 Aligning: Query: 3U5H_5:3019-3035 Target: 4L81_A:13-18 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | *|** | ---G---GAGA----C- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4IOA_X:2573-2578 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 9.600 Aligning: Query: 3U5H_5:3019-3035 Target: 1S72_0:217-223 iso .......+..+....... edge .......s..h....... struc .......(..)....... iso .......*...*...... edge .......s...h...... struc .......(...)...... UUAGUACGA-GAGGAACA |+ ++| ------CCGCGAG----- struc .......(...)...... edge .......s...h...... iso .......*...*...... struc .......(..)....... edge .......s..h....... iso .......+..+....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1VX6_A:365-370 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGUGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 17.600 Aligning: Query: 3U5H_5:3019-3035 Target: 4LVZ_A:58-63 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |*|**| ------CGAGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 4A1B_1:356-361 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | * ** | U------GCGA-----A struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 3U5H_5:357-362 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA | * ** --A----GUGAU----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 16.200 Aligning: Query: 3U5H_5:3019-3035 Target: 1S72_9:89-94 iso .......*.*....... edge .......s.h....... struc .......(.)....... iso .......*..*...... edge .......s..h...... struc .......(..)...... UUAGUACGAGAGGAACA |* **| ------CGCGAG----- struc .......(..)...... edge .......s..h...... iso .......*..*...... struc .......(.)....... edge .......s.h....... iso .......*.*....... Alignment Score: 14.200 Aligning: Query: 3U5H_5:3019-3035 Target: 3U5H_5:90-96 iso .......*..*....... edge .......s..h....... struc .......(..)....... iso .......*...*...... edge .......s...h...... struc .......(...)...... UUAGUACGA-GAGGAACA |* **| ------CGGCGAG----- struc .......(...)...... edge .......s...h...... iso .......*...*...... struc .......(..)....... edge .......s..h....... iso .......*..*.......