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: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4A1B_1:1194-1198_1355-1359 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|*|.|** AUAAG.CGAUA struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4QCN_A:2751-2755_2775-2779 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|* . **|| AUAAC.GGAAG struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4BPP_A:63-67_78-82 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG * *|.|**| UUCAG.CGAAA struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1S72_0:1456-1460_1483-1489 iso .*.*...**.... edge .w.h...sh.... struc .(.(...)).... CUAAG.CGAA--G |*|*|.|**| | CUAAG.CGAAAUG struc .(.(...)).... edge .w.h...sh.... iso .*.*...**.... Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 2QBG_B:2738-2742_2762-2766 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|*|.|**| AUAAG.CGAAA struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1S72_0:1095-1099_1257-1261 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|*|.|** UUAAG.CGAGA struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1S72_0:2773-2777_2797-2801 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|*|.|**| GUAAG.CGAAA struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 16.400 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1VX6_A:3487-3491_3512-3516 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|* . **| AUAAU.AGAAA struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 16.400 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4A1B_1:3092-3096_3116-3120 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG * * . **| AUUAU.AGAAU struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 2XXA_G:62-66_31-37 iso .*.*...**.... edge .w.h...sh.... struc .(.(...)).... CUAAG.CGAAG-- *|*|.|**| AUAAG.CGAACCU struc .(.(...)).... edge .w.h...sh.... iso .*.*...**.... Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4IOA_X:2718-2722_2742-2746 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|* . **|| AUAAC.GGAAG struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 3U5H_5:1532-1536_1585-1590 iso .*.*...**... edge .w.h...sh... struc .(.(...))... CUAAG.CGAA-G |*|*|.|**| | CUAAG.CGAAAG struc .(.(...))... edge .w.h...sh... iso .*.*...**... Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1VW3_A:3074-3078_3099-3103 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|* . **|| AUAAA.UGAAG struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 16.400 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1VW3_A:924-928_1173-1177 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|* . **| AUAAA.UGAAU struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 16.400 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4W21_5:4681-4685_4705-4709 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG * * . **| AUUAU.AGAAU struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 16.400 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 3U5H_5:3103-3107_3127-3131 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG * * . **| AUUAU.AGAAU struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 18.800 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 2QBG_B:1577-1581_1417-1421 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG |*|*|.|**|| CUAAG.CGAAG struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 16.400 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1S72_0:2672-2676_2809-2817 iso .*.*...**...... edge .w.h...sh...... struc .(.(...))...... CUAAG.CGAA----G |* * . **| | CUGAC.GGAAAAGAG struc .(.(...))...... edge .w.h...sh...... iso .*.*...**...... Alignment Score: 18.800 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 2QBG_B:998-1002_1153-1157 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG |*|*|.|**|| CUAAG.CGAAG struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 18.800 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4QCN_A:1044-1048_1199-1203 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG |*|*|.|**|| CUAAG.CGAAG struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 16.200 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1VX6_A:1681-1685_1728-1733 iso .*.*...**... edge .w.h...sh... struc .(.(...))... CUAAG.CGAA-G |*|*|.|**| | CUAAG.CAAAAG struc .(.(...))... edge .w.h...sh... iso .*.*...**... Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4W21_5:2446-2450_2509-2514 iso .*.*...**... edge .w.h...sh... struc .(.(...))... CUAAG.CGAA-G |* *|.|**| | CUGAG.CGAAAG struc .(.(...))... edge .w.h...sh... iso .*.*...**... Alignment Score: 13.600 Aligning: Query: 4IOA_X:1164-1168_1009-1013 Target: 4FAW_A:113-117_70-74 iso .*+....+.*. edge .sh....w.h. struc .((....).). CGAAG.CUAAG *+ |.|+|* GGACG.CUAAC struc .((....).). edge .ss....w.h. iso .*+....+.*. Alignment Score: 17.600 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 1VX6_A:1295-1299_1456-1460 iso .*.*...**.. edge .w.h...sh.. struc .(.(...)).. CUAAG.CGAAG *|*|.|** AUAAG.CGAUA struc .(.(...)).. edge .w.h...sh.. iso .*.*...**.. Alignment Score: 16.200 Aligning: Query: 4IOA_X:1009-1013_1164-1168 Target: 4A1B_1:1558-1562_1610-1615 iso .*.*...**... edge .w.h...sh... struc .(.(...))... CUAAG.CGAA-G |*|*|.|**| | CUAAG.CAAAAG struc .(.(...))... edge .w.h...sh... iso .*.*...**...