One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/11/peak-motifs.2026-01-11.234142_2026-01-11.234142_53Rg2T/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/11/peak-motifs.2026-01-11.234142_2026-01-11.234142_53Rg2T/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; wwtAgTAATAcAww ; Alignment reference a 543 475 200 1318 307 263 1284 1329 96 1329 225 1182 566 572 c 238 354 144 33 86 61 66 45 81 31 1000 100 212 243 g 272 254 144 58 966 70 64 43 68 57 104 58 299 253 t 443 413 1008 87 137 1102 82 79 1251 79 167 156 419 428

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wwtAgTAATAcAww ; cor=; Ncor= a 543 475 200 1318 307 263 1284 1329 96 1329 225 1182 566 572 c 238 354 144 33 86 61 66 45 81 31 1000 100 212 243 g 272 254 144 58 966 70 64 43 68 57 104 58 299 253 t 443 413 1008 87 137 1102 82 79 1251 79 167 156 419 428

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; wwAAAAtAATTTTAAAAAATgAww ; Alignment reference a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAAtAATTTTAAAAAATgAww ; cor=; Ncor= a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/4; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.861575; -wwAAAtAATTTTAAAAAATTAtw ; cor=; Ncor= a 0 98 110 203 211 221 57 214 202 53 48 47 42 201 221 224 220 217 227 46 45 207 44 84 c 0 37 41 16 23 16 17 11 19 10 11 9 15 19 15 16 12 6 15 20 21 19 34 56 g 0 52 47 19 16 17 22 25 12 7 11 18 20 17 13 10 16 15 11 13 20 17 28 32 t 0 92 81 41 29 25 183 29 46 209 209 205 202 42 30 29 31 41 26 200 193 36 173 107

oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/4; ncol2=20; w=0; offset=4; strand=D; shift=4; score=0.689617; ----wwTcATTTTTAAAAATgAww ; cor=; Ncor= a 0 0 0 0 107 101 29 43 265 26 36 26 29 37 264 265 273 260 275 33 72 248 107 116 c 0 0 0 0 47 56 29 189 21 15 15 18 20 12 19 18 14 20 15 14 26 25 68 62 g 0 0 0 0 62 67 25 27 13 15 20 14 18 19 12 20 18 15 16 21 191 29 56 47 t 0 0 0 0 116 108 249 73 33 276 261 274 265 264 37 29 27 37 26 264 43 30 101 107

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=4/4; ncol2=24; w=0; offset=3; strand=D; shift=3; score=0.613579; ---wwAtAATTTTAAAAmAAAAAA ; cor=; Ncor= a 0 0 0 72 91 162 41 179 163 34 31 34 45 180 192 183 196 80 177 187 184 183 189 185 c 0 0 0 31 33 21 20 7 21 11 8 6 10 16 16 7 9 88 11 8 16 7 13 9 g 0 0 0 38 36 16 20 10 13 7 18 17 16 10 6 10 7 22 14 12 8 10 12 9 t 0 0 0 88 69 30 148 33 32 177 172 172 158 23 15 29 17 39 27 22 21 29 15 26

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=1; ncol=25; -wwAAAtAATTTTAAAAAATTAtww ; Alignment reference a 0 98 110 203 211 221 57 214 202 53 48 47 42 201 221 224 220 217 227 46 45 207 44 84 80 c 0 37 41 16 23 16 17 11 19 10 11 9 15 19 15 16 12 6 15 20 21 19 34 56 58 g 0 52 47 19 16 17 22 25 12 7 11 18 20 17 13 10 16 15 11 13 20 17 28 32 41 t 0 92 81 41 29 25 183 29 46 209 209 205 202 42 30 29 31 41 26 200 193 36 173 107 100

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -wwAAAtAATTTTAAAAAATTAtww ; cor=; Ncor= a 0 98 110 203 211 221 57 214 202 53 48 47 42 201 221 224 220 217 227 46 45 207 44 84 80 c 0 37 41 16 23 16 17 11 19 10 11 9 15 19 15 16 12 6 15 20 21 19 34 56 58 g 0 52 47 19 16 17 22 25 12 7 11 18 20 17 13 10 16 15 11 13 20 17 28 32 41 t 0 92 81 41 29 25 183 29 46 209 209 205 202 42 30 29 31 41 26 200 193 36 173 107 100

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/4; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.861575; wwAAAAtAATTTTAAAAAATgAww- ; cor=; Ncor= a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 0 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 0 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 0 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94 0

oligos_7nt_test_vs_ctrl_m4_rc_shift4 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/4; ncol2=20; w=0; offset=3; strand=R; shift=4; score=0.637894; ----wwTcATTTTTAAAAATgAww- ; cor=; Ncor= a 0 0 0 0 107 101 30 43 264 26 37 27 29 37 264 265 274 261 276 33 73 249 108 116 0 c 0 0 0 0 47 56 29 191 21 16 15 18 20 12 19 18 14 20 15 13 27 25 67 62 0 g 0 0 0 0 62 68 25 26 14 15 20 14 18 19 12 20 18 15 15 21 189 29 56 47 0 t 0 0 0 0 116 107 248 72 33 275 260 273 265 264 37 29 26 36 26 265 43 29 101 107 0

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/4; ncol2=24; w=0; offset=2; strand=D; shift=3; score=0.625156; ---wwAtAATTTTAAAAmAAAAAAw ; cor=; Ncor= a 0 0 0 72 91 162 41 179 163 34 31 34 45 180 192 183 196 80 177 187 184 183 189 185 65 c 0 0 0 31 33 21 20 7 21 11 8 6 10 16 16 7 9 88 11 8 16 7 13 9 8 g 0 0 0 38 36 16 20 10 13 7 18 17 16 10 6 10 7 22 14 12 8 10 12 9 17 t 0 0 0 88 69 30 148 33 32 177 172 172 158 23 15 29 17 39 27 22 21 29 15 26 139

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; wdaTAaTTTTyTTwTTTTTTaaww ; Alignment reference a 113 110 173 38 237 231 35 33 28 26 50 31 26 200 24 36 19 30 23 41 222 231 121 114 c 51 45 58 21 20 20 20 15 20 10 127 10 11 12 15 6 9 9 9 5 26 17 36 50 g 73 90 31 18 26 17 15 14 14 22 24 31 19 22 14 14 17 11 17 18 29 25 68 69 t 110 102 85 270 64 79 277 285 285 289 146 275 291 113 294 291 302 297 298 283 70 74 122 114

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/2; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wdaTAaTTTTyTTwTTTTTTaaww ; cor=; Ncor= a 113 110 173 38 237 231 35 33 28 26 50 31 26 200 24 36 19 30 23 41 222 231 121 114 c 51 45 58 21 20 20 20 15 20 10 127 10 11 12 15 6 9 9 9 5 26 17 36 50 g 73 90 31 18 26 17 15 14 14 22 24 31 19 22 14 14 17 11 17 18 29 25 68 69 t 110 102 85 270 64 79 277 285 285 289 146 275 291 113 294 291 302 297 298 283 70 74 122 114

oligos_6nt_test_vs_ctrl_m3_rc_shift4 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/2; ncol2=24; w=0; offset=4; strand=R; shift=4; score=0.517227; ----wwwTTTTTTkTTTTAAAATT ; cor=; Ncor= a 0 0 0 0 64 67 139 26 15 29 21 22 27 39 17 29 15 23 158 172 172 177 32 33 c 0 0 0 0 32 38 17 9 12 10 8 12 14 22 7 10 6 10 16 17 18 7 13 10 g 0 0 0 0 32 36 8 9 13 7 16 8 11 88 9 7 16 16 10 6 8 11 21 7 t 0 0 0 0 101 88 65 185 189 183 184 187 177 80 196 183 192 180 45 34 31 34 163 179

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=20; shift=4; ncol=24; ----wwTcATTTTTAAAAATgAww ; Alignment reference a 0 0 0 0 107 101 29 43 265 26 36 26 29 37 264 265 273 260 275 33 72 248 107 116 c 0 0 0 0 47 56 29 189 21 15 15 18 20 12 19 18 14 20 15 14 26 25 68 62 g 0 0 0 0 62 67 25 27 13 15 20 14 18 19 12 20 18 15 16 21 191 29 56 47 t 0 0 0 0 116 108 249 73 33 276 261 274 265 264 37 29 27 37 26 264 43 30 101 107

oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=4; score= 1; ----wwTcATTTTTAAAAATgAww ; cor=; Ncor= a 0 0 0 0 107 101 29 43 265 26 36 26 29 37 264 265 273 260 275 33 72 248 107 116 c 0 0 0 0 47 56 29 189 21 15 15 18 20 12 19 18 14 20 15 14 26 25 68 62 g 0 0 0 0 62 67 25 27 13 15 20 14 18 19 12 20 18 15 16 21 191 29 56 47 t 0 0 0 0 116 108 249 73 33 276 261 274 265 264 37 29 27 37 26 264 43 30 101 107

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=2/3; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.689617; wwAAAAtAATTTTAAAAAATgAww ; cor=; Ncor= a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94

oligos_6nt_test_vs_ctrl_m1_rc_shift3 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/3; ncol2=24; w=-1; offset=-1; strand=R; shift=3; score=0.637894; ---wwaTAATTTTTTAAAATTaTT ; cor=; Ncor= a 0 0 0 100 107 173 36 193 200 26 41 31 29 30 42 202 205 209 209 46 29 183 25 29 c 0 0 0 41 32 28 17 20 13 11 15 16 10 13 17 20 18 11 7 12 25 22 17 16 g 0 0 0 58 56 34 19 21 20 15 6 12 16 15 19 15 9 11 10 19 11 17 16 23 t 0 0 0 80 84 44 207 45 46 227 217 220 224 221 201 42 47 48 53 202 214 57 221 211

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwATAACTCww ; Alignment reference a 1047 1018 2616 66 2524 2485 215 127 162 1142 806 c 516 685 85 58 126 173 2383 87 2372 702 706 g 594 501 102 52 146 139 101 16 196 249 607 t 805 758 159 2786 166 165 263 2732 232 869 843

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwATAACTCww ; cor=; Ncor= a 1047 1018 2616 66 2524 2485 215 127 162 1142 806 c 516 685 85 58 126 173 2383 87 2372 702 706 g 594 501 102 52 146 139 101 16 196 249 607 t 805 758 159 2786 166 165 263 2732 232 869 843

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; dyAGCTTACww ; Alignment reference a 602 481 1780 142 134 93 78 1828 70 758 498 c 325 505 23 101 1589 48 100 66 1690 367 451 g 504 427 63 1591 102 24 87 42 77 269 483 t 554 572 119 151 160 1820 1720 49 148 591 553

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; dyAGCTTACww ; cor=; Ncor= a 602 481 1780 142 134 93 78 1828 70 758 498 c 325 505 23 101 1589 48 100 66 1690 367 451 g 504 427 63 1591 102 24 87 42 77 269 483 t 554 572 119 151 160 1820 1720 49 148 591 553

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; kcmAGGACCTggr ; Alignment reference a 673 734 1667 2934 63 41 2526 87 105 45 361 703 961 c 527 1066 940 56 36 47 114 2924 2868 149 249 630 726 g 977 625 238 88 2957 2967 53 55 90 52 1933 1099 781 t 940 692 272 39 61 62 424 51 54 2871 574 685 649

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; kcmAGGACCTggr ; cor=; Ncor= a 673 734 1667 2934 63 41 2526 87 105 45 361 703 961 c 527 1066 940 56 36 47 114 2924 2868 149 249 630 726 g 977 625 238 88 2957 2967 53 55 90 52 1933 1099 781 t 940 692 272 39 61 62 424 51 54 2871 574 685 649

oligos_6nt_test_vs_ctrl_m5_rc_shift1 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/2; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.794351; -ccAGGACCTtar ; cor=; Ncor= a 0 401 392 1626 31 22 1605 28 54 26 187 891 481 c 0 641 777 39 30 16 23 1662 1621 78 152 205 406 g 0 334 233 71 1644 1676 29 27 51 69 299 351 482 t 0 385 359 25 56 47 104 44 35 1588 1123 314 392

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wwAtAATTTTAAAAmAAAAAAwww ; Alignment reference a 0 0 0 72 91 162 41 179 163 34 31 34 45 180 192 183 196 80 177 187 184 183 189 185 65 88 101 c 0 0 0 31 33 21 20 7 21 11 8 6 10 16 16 7 9 88 11 8 16 7 13 9 8 36 32 g 0 0 0 38 36 16 20 10 13 7 18 17 16 10 6 10 7 22 14 12 8 10 12 9 17 38 32 t 0 0 0 88 69 30 148 33 32 177 172 172 158 23 15 29 17 39 27 22 21 29 15 26 139 67 64

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wwAtAATTTTAAAAmAAAAAAwww ; cor=; Ncor= a 0 0 0 72 91 162 41 179 163 34 31 34 45 180 192 183 196 80 177 187 184 183 189 185 65 88 101 c 0 0 0 31 33 21 20 7 21 11 8 6 10 16 16 7 9 88 11 8 16 7 13 9 8 36 32 g 0 0 0 38 36 16 20 10 13 7 18 17 16 10 6 10 7 22 14 12 8 10 12 9 17 38 32 t 0 0 0 88 69 30 148 33 32 177 172 172 158 23 15 29 17 39 27 22 21 29 15 26 139 67 64

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=2/4; ncol2=24; w=-2; offset=-2; strand=D; shift=1; score=0.625156; -wwAAAtAATTTTAAAAAATTAtww-- ; cor=; Ncor= a 0 98 110 203 211 221 57 214 202 53 48 47 42 201 221 224 220 217 227 46 45 207 44 84 80 0 0 c 0 37 41 16 23 16 17 11 19 10 11 9 15 19 15 16 12 6 15 20 21 19 34 56 58 0 0 g 0 52 47 19 16 17 22 25 12 7 11 18 20 17 13 10 16 15 11 13 20 17 28 32 41 0 0 t 0 92 81 41 29 25 183 29 46 209 209 205 202 42 30 29 31 41 26 200 193 36 173 107 100 0 0

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=3/4; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.613579; wwAAAAtAATTTTAAAAAATgAww--- ; cor=; Ncor= a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 0 0 0 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 0 0 0 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 0 0 0 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94 0 0 0

oligos_6nt_test_vs_ctrl_m4_rc_shift7 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/4; ncol2=24; w=0; offset=4; strand=R; shift=7; score=0.517227; -------wwttAAAAAAwAArAAAAtT ; cor=; Ncor= a 0 0 0 0 0 0 0 114 122 74 70 283 298 297 302 291 294 113 291 275 146 289 285 285 277 79 64 c 0 0 0 0 0 0 0 69 68 25 29 18 17 11 17 14 14 22 19 31 24 22 14 14 15 17 26 g 0 0 0 0 0 0 0 50 36 17 26 5 9 9 9 6 15 12 11 10 127 10 20 15 20 20 20 t 0 0 0 0 0 0 0 114 121 231 222 41 23 30 19 36 24 200 26 31 50 26 28 33 35 231 237

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; yytaAGGTCCTgg ; Alignment reference a 392 392 314 1123 1588 35 44 104 47 56 25 359 385 c 448 482 351 299 69 51 27 29 1676 1644 71 233 334 g 380 406 205 152 78 1621 1662 23 16 30 39 777 641 t 541 481 891 187 26 54 28 1605 22 31 1626 392 401

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; yytaAGGTCCTgg ; cor=; Ncor= a 392 392 314 1123 1588 35 44 104 47 56 25 359 385 c 448 482 351 299 69 51 27 29 1676 1644 71 233 334 g 380 406 205 152 78 1621 1662 23 16 30 39 777 641 t 541 481 891 187 26 54 28 1605 22 31 1626 392 401

oligos_7nt_test_vs_ctrl_m1_rc_shift1 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/2; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.794351; -yccAGGTCCTkg ; cor=; Ncor= a 0 649 685 574 2871 54 51 424 62 61 39 272 692 c 0 781 1099 1933 52 90 55 53 2967 2957 88 238 625 g 0 726 630 249 149 2868 2924 114 47 36 56 940 1066 t 0 961 703 361 45 105 87 2526 41 63 2934 1667 734

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; wwAAAAtAATTTTAAAAAATgAww ; Alignment reference a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAAtAATTTTAAAAAATgAww ; cor=; Ncor= a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/4; ncol2=24; w=0; offset=1; strand=D; shift=1; score=0.861575; -wwAAAtAATTTTAAAAAATTAtw ; cor=; Ncor= a 0 98 110 203 211 221 57 214 202 53 48 47 42 201 221 224 220 217 227 46 45 207 44 84 c 0 37 41 16 23 16 17 11 19 10 11 9 15 19 15 16 12 6 15 20 21 19 34 56 g 0 52 47 19 16 17 22 25 12 7 11 18 20 17 13 10 16 15 11 13 20 17 28 32 t 0 92 81 41 29 25 183 29 46 209 209 205 202 42 30 29 31 41 26 200 193 36 173 107
oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/4; ncol2=20; w=0; offset=4; strand=D; shift=4; score=0.689617; ----wwTcATTTTTAAAAATgAww ; cor=; Ncor= a 0 0 0 0 107 101 29 43 265 26 36 26 29 37 264 265 273 260 275 33 72 248 107 116 c 0 0 0 0 47 56 29 189 21 15 15 18 20 12 19 18 14 20 15 14 26 25 68 62 g 0 0 0 0 62 67 25 27 13 15 20 14 18 19 12 20 18 15 16 21 191 29 56 47 t 0 0 0 0 116 108 249 73 33 276 261 274 265 264 37 29 27 37 26 264 43 30 101 107
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=4/4; ncol2=24; w=0; offset=3; strand=D; shift=3; score=0.613579; ---wwAtAATTTTAAAAmAAAAAA ; cor=; Ncor= a 0 0 0 72 91 162 41 179 163 34 31 34 45 180 192 183 196 80 177 187 184 183 189 185 c 0 0 0 31 33 21 20 7 21 11 8 6 10 16 16 7 9 88 11 8 16 7 13 9 g 0 0 0 38 36 16 20 10 13 7 18 17 16 10 6 10 7 22 14 12 8 10 12 9 t 0 0 0 88 69 30 148 33 32 177 172 172 158 23 15 29 17 39 27 22 21 29 15 26

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=1; ncol=25; -wwAAAtAATTTTAAAAAATTAtww ; Alignment reference a 0 98 110 203 211 221 57 214 202 53 48 47 42 201 221 224 220 217 227 46 45 207 44 84 80 c 0 37 41 16 23 16 17 11 19 10 11 9 15 19 15 16 12 6 15 20 21 19 34 56 58 g 0 52 47 19 16 17 22 25 12 7 11 18 20 17 13 10 16 15 11 13 20 17 28 32 41 t 0 92 81 41 29 25 183 29 46 209 209 205 202 42 30 29 31 41 26 200 193 36 173 107 100
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -wwAAAtAATTTTAAAAAATTAtww ; cor=; Ncor= a 0 98 110 203 211 221 57 214 202 53 48 47 42 201 221 224 220 217 227 46 45 207 44 84 80 c 0 37 41 16 23 16 17 11 19 10 11 9 15 19 15 16 12 6 15 20 21 19 34 56 58 g 0 52 47 19 16 17 22 25 12 7 11 18 20 17 13 10 16 15 11 13 20 17 28 32 41 t 0 92 81 41 29 25 183 29 46 209 209 205 202 42 30 29 31 41 26 200 193 36 173 107 100
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/4; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.861575; wwAAAAtAATTTTAAAAAATgAww- ; cor=; Ncor= a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 0 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 0 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 0 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94 0
oligos_7nt_test_vs_ctrl_m4_rc_shift4 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/4; ncol2=20; w=0; offset=3; strand=R; shift=4; score=0.637894; ----wwTcATTTTTAAAAATgAww- ; cor=; Ncor= a 0 0 0 0 107 101 30 43 264 26 37 27 29 37 264 265 274 261 276 33 73 249 108 116 0 c 0 0 0 0 47 56 29 191 21 16 15 18 20 12 19 18 14 20 15 13 27 25 67 62 0 g 0 0 0 0 62 68 25 26 14 15 20 14 18 19 12 20 18 15 15 21 189 29 56 47 0 t 0 0 0 0 116 107 248 72 33 275 260 273 265 264 37 29 26 36 26 265 43 29 101 107 0
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/4; ncol2=24; w=0; offset=2; strand=D; shift=3; score=0.625156; ---wwAtAATTTTAAAAmAAAAAAw ; cor=; Ncor= a 0 0 0 72 91 162 41 179 163 34 31 34 45 180 192 183 196 80 177 187 184 183 189 185 65 c 0 0 0 31 33 21 20 7 21 11 8 6 10 16 16 7 9 88 11 8 16 7 13 9 8 g 0 0 0 38 36 16 20 10 13 7 18 17 16 10 6 10 7 22 14 12 8 10 12 9 17 t 0 0 0 88 69 30 148 33 32 177 172 172 158 23 15 29 17 39 27 22 21 29 15 26 139

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=20; shift=4; ncol=24; ----wwTcATTTTTAAAAATgAww ; Alignment reference a 0 0 0 0 107 101 29 43 265 26 36 26 29 37 264 265 273 260 275 33 72 248 107 116 c 0 0 0 0 47 56 29 189 21 15 15 18 20 12 19 18 14 20 15 14 26 25 68 62 g 0 0 0 0 62 67 25 27 13 15 20 14 18 19 12 20 18 15 16 21 191 29 56 47 t 0 0 0 0 116 108 249 73 33 276 261 274 265 264 37 29 27 37 26 264 43 30 101 107
oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=4; score= 1; ----wwTcATTTTTAAAAATgAww ; cor=; Ncor= a 0 0 0 0 107 101 29 43 265 26 36 26 29 37 264 265 273 260 275 33 72 248 107 116 c 0 0 0 0 47 56 29 189 21 15 15 18 20 12 19 18 14 20 15 14 26 25 68 62 g 0 0 0 0 62 67 25 27 13 15 20 14 18 19 12 20 18 15 16 21 191 29 56 47 t 0 0 0 0 116 108 249 73 33 276 261 274 265 264 37 29 27 37 26 264 43 30 101 107
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=2/3; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.689617; wwAAAAtAATTTTAAAAAATgAww ; cor=; Ncor= a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94
oligos_6nt_test_vs_ctrl_m1_rc_shift3 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/3; ncol2=24; w=-1; offset=-1; strand=R; shift=3; score=0.637894; ---wwaTAATTTTTTAAAATTaTT ; cor=; Ncor= a 0 0 0 100 107 173 36 193 200 26 41 31 29 30 42 202 205 209 209 46 29 183 25 29 c 0 0 0 41 32 28 17 20 13 11 15 16 10 13 17 20 18 11 7 12 25 22 17 16 g 0 0 0 58 56 34 19 21 20 15 6 12 16 15 19 15 9 11 10 19 11 17 16 23 t 0 0 0 80 84 44 207 45 46 227 217 220 224 221 201 42 47 48 53 202 214 57 221 211

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wwAtAATTTTAAAAmAAAAAAwww ; Alignment reference a 0 0 0 72 91 162 41 179 163 34 31 34 45 180 192 183 196 80 177 187 184 183 189 185 65 88 101 c 0 0 0 31 33 21 20 7 21 11 8 6 10 16 16 7 9 88 11 8 16 7 13 9 8 36 32 g 0 0 0 38 36 16 20 10 13 7 18 17 16 10 6 10 7 22 14 12 8 10 12 9 17 38 32 t 0 0 0 88 69 30 148 33 32 177 172 172 158 23 15 29 17 39 27 22 21 29 15 26 139 67 64
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wwAtAATTTTAAAAmAAAAAAwww ; cor=; Ncor= a 0 0 0 72 91 162 41 179 163 34 31 34 45 180 192 183 196 80 177 187 184 183 189 185 65 88 101 c 0 0 0 31 33 21 20 7 21 11 8 6 10 16 16 7 9 88 11 8 16 7 13 9 8 36 32 g 0 0 0 38 36 16 20 10 13 7 18 17 16 10 6 10 7 22 14 12 8 10 12 9 17 38 32 t 0 0 0 88 69 30 148 33 32 177 172 172 158 23 15 29 17 39 27 22 21 29 15 26 139 67 64
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=2/4; ncol2=24; w=-2; offset=-2; strand=D; shift=1; score=0.625156; -wwAAAtAATTTTAAAAAATTAtww-- ; cor=; Ncor= a 0 98 110 203 211 221 57 214 202 53 48 47 42 201 221 224 220 217 227 46 45 207 44 84 80 0 0 c 0 37 41 16 23 16 17 11 19 10 11 9 15 19 15 16 12 6 15 20 21 19 34 56 58 0 0 g 0 52 47 19 16 17 22 25 12 7 11 18 20 17 13 10 16 15 11 13 20 17 28 32 41 0 0 t 0 92 81 41 29 25 183 29 46 209 209 205 202 42 30 29 31 41 26 200 193 36 173 107 100 0 0
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=3/4; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.613579; wwAAAAtAATTTTAAAAAATgAww--- ; cor=; Ncor= a 106 115 210 219 216 228 51 223 216 45 35 38 27 217 239 238 248 241 225 43 63 211 114 115 0 0 0 c 44 39 25 20 18 14 26 14 15 20 19 8 35 24 16 14 9 15 25 15 26 26 48 49 0 0 0 g 63 52 18 16 27 16 21 22 15 16 11 19 18 16 13 13 17 15 14 13 159 25 49 39 0 0 0 t 84 91 44 42 36 39 199 38 51 216 232 232 217 40 29 32 23 26 33 226 49 35 86 94 0 0 0
oligos_6nt_test_vs_ctrl_m4_rc_shift7 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/4; ncol2=24; w=0; offset=4; strand=R; shift=7; score=0.517227; -------wwttAAAAAAwAArAAAAtT ; cor=; Ncor= a 0 0 0 0 0 0 0 114 122 74 70 283 298 297 302 291 294 113 291 275 146 289 285 285 277 79 64 c 0 0 0 0 0 0 0 69 68 25 29 18 17 11 17 14 14 22 19 31 24 22 14 14 15 17 26 g 0 0 0 0 0 0 0 50 36 17 26 5 9 9 9 6 15 12 11 10 127 10 20 15 20 20 20 t 0 0 0 0 0 0 0 114 121 231 222 41 23 30 19 36 24 200 26 31 50 26 28 33 35 231 237