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: 9.000 Aligning: Query: 4IOA_X:1029-1041_1135-1155 Target: 4W21_5:1934-1944_2038-2052 iso ..................**..................+..+....... edge ..................SH..................w..h....... struc ..................()..................(..)....... --CUCA------------GUGGUUAAG.CGAAAAUGAUCGGGGCUCAAG | || ** | . +||+| ACCCCAGAAAAUGAAAAUGG----A--.----------UGGCG------ struc ..................()..................(..)....... edge ..................SH..................H..H....... iso ..................**..................+..+....... Alignment Score: 20.600 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 4A1B_1:1326-1340_1222-1232 iso .**.......+..+..................**. edge .sh.......w..h..................hh. struc .((.......(..)..................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG **||||| +||+| | | .| || ** UGAAAAUGGAUGGCGAU--AC.CACA------AAA struc .((.......(..)..................)). edge .sh.......H..H..................hh. iso .**.......+..+..................**. Alignment Score: 19.000 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 3U5H_5:1299-1313_1195-1205 iso .**.......+..+...................**. edge .sh.......w..h...................hh. struc .((.......(..)...................)). CGAAAAUGAUCGGGG-CUCAAG.CUCAGUGGUUAAG **||||| +||+| | | .| || ** UGAAAAUGGAUGGCGACAC---.CACA------AAA struc .((.......(..)...................)). edge .sh.......H..H...................hh. iso .**.......+..+...................**. Alignment Score: 20.800 Aligning: Query: 4IOA_X:1029-1041_1135-1155 Target: 1VW3_A:950-957_1091-1105 iso ..........**...**........*..*....... edge ..........hh...sh........w..h....... struc ..........((...))........(..)....... CUCAGUGGUUAAG.CGAAAAUGAU-CGGGGCUCAAG | | ** . ** ||| || *||* | --AAAUA---AAU.AGAUAAU-AUACGGA--U---- struc ..........((...))........(..)....... edge ..........hh...sh........w..h....... iso ..........**...**........*..*....... Alignment Score: 17.200 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 2QBG_B:1520-1524_1468-1471 iso .**.............................**. edge .sh.............................hh. struc .((.............................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG ** || . |**| UGA---UG-------------.---------UAAG struc .((.............................)). edge .sh.............................hh. iso .**.............................**. Alignment Score: 16.600 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 3U5H_5:1654-1658_1791-1801 iso .**.............................**. edge .sh.............................hh. struc .((.............................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG ** | |.| | ||| ** AGA--------------C--G.CCC-GUGAA-AAU struc .((.............................)). edge .sh.............................hh. iso .**.............................**. Alignment Score: 17.200 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 1S72_0:1531-1535_1650-1660 iso .**.............................**. edge .sh.............................hh. struc .((.............................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG ** | |.| || || **| UGA--------------C--G.CCCA-UGAA-AAG struc .((.............................)). edge .sh.............................hh. iso .**.............................**. Alignment Score: 16.600 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 4A1B_1:1678-1682_1817-1827 iso .**.............................**. edge .sh.............................hh. struc .((.............................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG ** | |.| | | | ** AGA--------------C--G.CCC--UUGAAAAU struc .((.............................)). edge .sh.............................hh. iso .**.............................**. Alignment Score: 17.200 Aligning: Query: 4IOA_X:1029-1041_1135-1155 Target: 1S72_0:1521-1529_1662-1665 iso ..........**...**.................. edge ..........hh...sh.................. struc ..........((...)).................. CUCAGUGGUUAAG.CGAAAAUGAUCGGGGCUCAAG ||||| **|.|** | --CAGUGA--AAG.CGA-----------------G struc ..........((...)).................. edge ..........hh...sh.................. iso ..........**...**.................. Alignment Score: 68.800 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 4QCN_A:1170-1190_1064-1076 iso .......................*.*......... edge .......................S.W......... struc .......................(.)......... iso .**.......*..***..*....*..****..**. edge .sh.......w..hwW..w....w..SHWw..hh. struc .((.......(..)((..(....)..()))..)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG |**|||||||*||***| *||.|* *****| **| CGAAAAUGAUCGGGGCUUAAG.CUAAGUGGUAAAG struc .((.......(..)((..(....)..()))..)). edge .sh.......w..hwW..w....w..SHWw..hh. iso .**.......*..***..*....*..****..**. struc .......................(.)......... edge .......................S.W......... iso .......................*.*......... Alignment Score: 19.000 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 1VX6_A:1427-1441_1323-1333 iso .**.......+..+..................**. edge .sh.......w..h..................hh. struc .((.......(..)..................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG **||||| +||+| || .| || | ** UGAAAAUGGAUGGCGAUC---.C-CA----UAAAA struc .((.......(..)..................)). edge .sh.......H..H..................hh. iso .**.......+..+..................**. Alignment Score: 16.000 Aligning: Query: 4IOA_X:1029-1041_1135-1155 Target: 2QBG_B:1564-1574_1424-1429 iso ..........**.....**.................. edge ..........hh.....sh.................. struc ..........((.....)).................. CUCAGUGGUUAAG.C--GAAAAUGAUCGGGGCUCAAG | ||| | **|.| ** || C-CAG--GAAAAG.CGGGA-------CG--------- struc ..........((.....)).................. edge ..........hh.....sh.................. iso ..........**.....**.................. Alignment Score: 15.200 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 1VX6_A:1809-1813_2013-2023 iso .**.............................**. edge .sh.............................hh. struc .((.............................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG ** | || || . | | ** UUACA----UC----CU----.-UGAA-----AAA struc .((.............................)). edge .sh.............................hh. iso .**.............................**. Alignment Score: 27.200 Aligning: Query: 4IOA_X:1029-1041_1135-1155 Target: 1S72_0:1122-1134_1228-1242 iso ...............**...**.......*..*....... edge ...............hh...sh.......w..h....... struc ...............((...)).......(..)....... -----CUCAGUGGUUAAG.CGAAAAUGAUCGGGGCUCAAG ||| || **|.|**|||||||*||* | UAAUCCUC--UG---AAG.CCAAAAUGAUCGGG----A-- struc ...............((...)).......(..)....... edge ...............hh...sh.......w..h....... iso ...............**...**.......*..*....... Alignment Score: 47.600 Aligning: Query: 4IOA_X:1029-1041_1135-1155 Target: 2QBG_B:1018-1030_1124-1144 iso .+.+.............................+.+ edge .S.W.............................s.h struc .(.).............................(.) iso .+..****..**...**............**..+.. edge .w..SHWw..hh...sh............wW..w.. struc .(..()((..((...))............))..).. CUCAGUGGUUAAG.CGAAAAUG-AUCGGGGCUCAAG + +**** ** . **| ||| | ||||**| +|+ UUAAGUGGGAAAC.GGAAGAUGUAACGGGGCU-AAA struc .(..()((..((...))............))..).. edge .w..SHWw..hh...sh............wW..h.. iso .+..****..**...**............**..+.. struc .(.).............................(.) edge .s.w.............................s.h iso .+.+.............................+.+ Alignment Score: 16.600 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 4QCN_A:1844-1852_1829-1835 iso .**.............................**. edge .sh.............................hh. struc .((.............................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG ** || | | |.| | ** GGA---------GGUAU-AUG.C-----G---AAC struc .((.............................)). edge .sh.............................hh. iso .**.............................**. Alignment Score: 16.600 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 4IOA_X:1805-1813_1789-1795 iso .**.............................**. edge .sh.............................hh. struc .((.............................)). CGAAAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG ** || | | |.| | ** GGA-------CGU--AU-AUG.C-C-------AAC struc .((.............................)). edge .sh.............................hh. iso .**.............................**. Alignment Score: 16.600 Aligning: Query: 4IOA_X:1135-1155_1029-1041 Target: 2QBG_B:1813-1821_1798-1804 iso .**................................**. edge .sh................................hh. struc .((................................)). CGA---AAAUGAUCGGGGCUCAAG.CUCAGUGGUUAAG ** | ||| || . ** GGACGUAUAUG---------CA--.----------AAC struc .((................................)). edge .sh................................hh. iso .**................................**.