One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/08/peak-motifs.2026-01-08.111926_2026-01-08.111926_ViZhty/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/2026/01/08/peak-motifs.2026-01-08.111926_2026-01-08.111926_ViZhty/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 2 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=14; shift=0; ncol=14; sstGGCCGCCtGss ; Alignment reference a 398 356 228 66 63 79 88 130 66 71 364 90 357 408 c 974 877 608 231 153 2290 2189 52 2288 2163 374 384 912 679 g 743 1041 401 2180 2251 116 166 2273 118 217 474 1911 921 966 t 419 260 1297 57 67 49 91 79 62 83 1322 149 344 481

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=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; sstGGCCGCCtGss ; cor=; Ncor= a 398 356 228 66 63 79 88 130 66 71 364 90 357 408 c 974 877 608 231 153 2290 2189 52 2288 2163 374 384 912 679 g 743 1041 401 2180 2251 116 166 2273 118 217 474 1911 921 966 t 419 260 1297 57 67 49 91 79 62 83 1322 149 344 481

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=23; shift=0; ncol=23; CrsCAGaGGGCGCCccaGcCCcg ; Alignment reference a 56 399 39 54 666 14 589 24 33 20 56 73 27 41 135 56 452 67 90 100 73 158 201 c 643 118 252 657 106 29 70 46 57 77 774 29 763 603 549 546 185 102 544 616 663 383 209 g 138 267 566 93 74 829 207 749 784 767 39 764 60 124 161 203 149 667 192 93 74 193 377 t 50 103 30 83 41 15 21 68 13 23 18 21 37 119 42 82 101 51 61 78 77 153 100

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/2; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; CrsCAGaGGGCGCCccaGcCCcg ; cor=; Ncor= a 56 399 39 54 666 14 589 24 33 20 56 73 27 41 135 56 452 67 90 100 73 158 201 c 643 118 252 657 106 29 70 46 57 77 774 29 763 603 549 546 185 102 544 616 663 383 209 g 138 267 566 93 74 829 207 749 784 767 39 764 60 124 161 203 149 667 192 93 74 193 377 t 50 103 30 83 41 15 21 68 13 23 18 21 37 119 42 82 101 51 61 78 77 153 100

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=2/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.771946; crgcaGaGGGCGCCCtCtgcyg- ; cor=; Ncor= a 134 322 48 85 528 55 564 38 73 14 43 50 32 25 81 25 43 85 75 63 127 101 0 c 434 97 176 588 171 89 131 59 83 60 784 14 783 707 711 168 701 105 142 603 346 221 0 g 221 344 603 142 105 702 169 711 709 783 14 782 60 83 59 132 90 174 587 175 97 432 0 t 100 126 62 74 85 43 25 81 24 32 48 43 14 74 38 564 55 525 85 48 319 135 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=1; ncol=25; -ssGCCCCGCmGCGCCCCmGCCCss ; Alignment reference a 0 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 15 34 60 62 c 0 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 365 344 189 193 g 0 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 75 63 184 180 t 0 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22 32 46 54 52

oligos_6nt_test_vs_ctrl_m3_shift1 (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=1; score= 1; -ssGCCCCGCmGCGCCCCmGCCCss ; cor=; Ncor= a 0 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 15 34 60 62 c 0 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 365 344 189 193 g 0 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 75 63 184 180 t 0 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22 32 46 54 52

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=2/4; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.702142; ssCGCCCCGCaGCGCCCyGCGGss- ; cor=; Ncor= a 61 46 32 20 23 15 23 31 19 8 188 12 19 15 12 19 11 32 13 23 33 18 67 42 0 c 196 169 306 53 324 317 299 309 64 374 105 64 352 52 326 336 333 128 91 327 76 96 182 150 0 g 125 159 58 323 60 65 79 58 322 32 86 341 38 333 66 58 65 92 306 40 293 292 126 166 0 t 46 54 32 32 21 31 27 30 23 14 49 11 19 28 24 15 19 176 18 38 26 22 53 70 0

oligos_7nt_test_vs_ctrl_m2_shift6 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=3/4; ncol2=15; w=0; offset=5; strand=D; shift=6; score=0.487891; ------ssGCAGCGCCaCCys---- ; cor=; Ncor= a 0 0 0 0 0 0 581 709 446 83 2732 65 115 172 120 71 1718 171 223 546 626 0 0 0 0 c 0 0 0 0 0 0 1570 1095 481 3191 330 266 3146 173 3145 3229 780 2445 2616 948 1078 0 0 0 0 g 0 0 0 0 0 0 944 1138 2447 198 406 3165 139 3099 214 211 762 558 496 879 1334 0 0 0 0 t 0 0 0 0 0 0 487 640 208 110 114 86 182 138 103 71 322 408 247 1209 544 0 0 0 0

oligos_7nt_test_vs_ctrl_m5_shift10 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=4/4; ncol2=15; w=0; offset=9; strand=D; shift=10; score=0.446143; ----------ssaGCCCTGGCCCss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 377 346 1165 97 77 64 70 142 39 74 89 70 170 381 355 c 0 0 0 0 0 0 0 0 0 0 746 922 440 117 1832 1915 1954 251 155 188 1906 1902 1579 757 683 g 0 0 0 0 0 0 0 0 0 0 739 657 388 1893 173 129 103 212 1925 1838 129 129 238 625 810 t 0 0 0 0 0 0 0 0 0 0 328 265 197 83 108 82 63 1585 71 90 66 89 203 427 342

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 3 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=22; shift=0; ncol=22; crgcaGaGGGCGCCCtCtgcyg ; Alignment reference a 134 322 48 85 528 55 564 38 73 14 43 50 32 25 81 25 43 85 75 63 127 101 c 434 97 176 588 171 89 131 59 83 60 784 14 783 707 711 168 701 105 142 603 346 221 g 221 344 603 142 105 702 169 711 709 783 14 782 60 83 59 132 90 174 587 175 97 432 t 100 126 62 74 85 43 25 81 24 32 48 43 14 74 38 564 55 525 85 48 319 135

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=1/2; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; crgcaGaGGGCGCCCtCtgcyg ; cor=; Ncor= a 134 322 48 85 528 55 564 38 73 14 43 50 32 25 81 25 43 85 75 63 127 101 c 434 97 176 588 171 89 131 59 83 60 784 14 783 707 711 168 701 105 142 603 346 221 g 221 344 603 142 105 702 169 711 709 783 14 782 60 83 59 132 90 174 587 175 97 432 t 100 126 62 74 85 43 25 81 24 32 48 43 14 74 38 564 55 525 85 48 319 135

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=2/2; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.771946; CrsCAGaGGGCGCCccaGcCCc ; cor=; Ncor= a 56 399 39 54 666 14 589 24 33 20 56 73 27 41 135 56 452 67 90 100 73 158 c 643 118 252 657 106 29 70 46 57 77 774 29 763 603 549 546 185 102 544 616 663 383 g 138 267 566 93 74 829 207 749 784 767 39 764 60 124 161 203 149 667 192 93 74 193 t 50 103 30 83 41 15 21 68 13 23 18 21 37 119 42 82 101 51 61 78 77 153

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift7 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=7; ncol=31; -------ssCGCCCCGCaGCGCCCyGCGGss ; Alignment reference a 0 0 0 0 0 0 0 61 46 32 20 23 15 23 31 19 8 188 12 19 15 12 19 11 32 13 23 33 18 67 42 c 0 0 0 0 0 0 0 196 169 306 53 324 317 299 309 64 374 105 64 352 52 326 336 333 128 91 327 76 96 182 150 g 0 0 0 0 0 0 0 125 159 58 323 60 65 79 58 322 32 86 341 38 333 66 58 65 92 306 40 293 292 126 166 t 0 0 0 0 0 0 0 46 54 32 32 21 31 27 30 23 14 49 11 19 28 24 15 19 176 18 38 26 22 53 70

oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=7; score= 1; -------ssCGCCCCGCaGCGCCCyGCGGss ; cor=; Ncor= a 0 0 0 0 0 0 0 61 46 32 20 23 15 23 31 19 8 188 12 19 15 12 19 11 32 13 23 33 18 67 42 c 0 0 0 0 0 0 0 196 169 306 53 324 317 299 309 64 374 105 64 352 52 326 336 333 128 91 327 76 96 182 150 g 0 0 0 0 0 0 0 125 159 58 323 60 65 79 58 322 32 86 341 38 333 66 58 65 92 306 40 293 292 126 166 t 0 0 0 0 0 0 0 46 54 32 32 21 31 27 30 23 14 49 11 19 28 24 15 19 176 18 38 26 22 53 70

oligos_6nt_test_vs_ctrl_m4_rc_shift7 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=2/5; ncol2=24; w=0; offset=0; strand=R; shift=7; score=0.785637; -------ssgGCCtGGCCCCGCCCyGCGGss ; cor=; Ncor= a 0 0 0 0 0 0 0 37 51 24 12 5 9 18 14 12 7 13 13 15 21 13 8 11 20 7 14 23 14 34 43 c 0 0 0 0 0 0 0 114 120 57 43 249 231 70 45 16 234 213 218 216 27 227 218 234 76 43 229 50 63 125 90 g 0 0 0 0 0 0 0 98 89 186 218 24 32 62 220 243 32 41 42 35 218 41 50 30 44 228 32 199 197 89 110 t 0 0 0 0 0 0 0 39 28 21 15 10 16 138 9 17 15 21 15 22 22 7 12 13 148 10 13 16 14 40 45

oligos_6nt_test_vs_ctrl_m3_shift8 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=3/5; ncol2=24; w=0; offset=1; strand=D; shift=8; score=0.702142; --------ssGCCCCGCmGCGCCCCmGCCCs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 15 34 60 c 0 0 0 0 0 0 0 0 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 365 344 189 g 0 0 0 0 0 0 0 0 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 75 63 184 t 0 0 0 0 0 0 0 0 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22 32 46 54

oligos_7nt_test_vs_ctrl_m2_shift13 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=4/5; ncol2=15; w=0; offset=6; strand=D; shift=13; score=0.465989; -------------ssGCAGCGCCaCCys--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 581 709 446 83 2732 65 115 172 120 71 1718 171 223 546 626 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 1570 1095 481 3191 330 266 3146 173 3145 3229 780 2445 2616 948 1078 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 944 1138 2447 198 406 3165 139 3099 214 211 762 558 496 879 1334 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 487 640 208 110 114 86 182 138 103 71 322 408 247 1209 544 0 0 0

oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=5/5; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.42277; ssGyGGCCCCGCCCtGCggGGCss------- ; cor=; Ncor= a 29 33 5 24 9 13 5 9 17 12 5 8 4 3 23 4 6 13 7 11 20 25 34 33 0 0 0 0 0 0 0 c 100 90 33 66 28 20 183 170 162 186 14 185 175 197 57 31 190 43 51 38 25 163 87 98 0 0 0 0 0 0 0 g 72 79 190 43 196 189 35 36 41 22 208 27 50 24 48 193 20 160 159 175 176 32 80 73 0 0 0 0 0 0 0 t 35 34 8 103 3 14 13 21 16 16 9 16 7 12 108 8 20 20 19 12 15 16 35 32 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---ssCCGCaGsGCGGCCcCGCCCtss ; Alignment reference a 0 0 0 53 53 26 32 40 23 226 25 30 14 31 33 21 26 22 26 25 20 16 21 23 33 41 47 c 0 0 0 189 154 310 337 59 351 101 77 119 80 375 67 55 354 339 298 358 32 346 321 345 104 173 173 g 0 0 0 147 173 88 61 322 64 86 320 277 339 25 328 345 57 73 89 43 371 62 81 57 99 187 157 t 0 0 0 61 70 26 20 29 12 37 28 24 17 19 22 29 13 16 37 24 27 26 27 25 214 49 73

oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCCGCaGsGCGGCCcCGCCCtss ; cor=; Ncor= a 0 0 0 53 53 26 32 40 23 226 25 30 14 31 33 21 26 22 26 25 20 16 21 23 33 41 47 c 0 0 0 189 154 310 337 59 351 101 77 119 80 375 67 55 354 339 298 358 32 346 321 345 104 173 173 g 0 0 0 147 173 88 61 322 64 86 320 277 339 25 328 345 57 73 89 43 371 62 81 57 99 187 157 t 0 0 0 61 70 26 20 29 12 37 28 24 17 19 22 29 13 16 37 24 27 26 27 25 214 49 73

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=2/3; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score= 0.5968; ssGCCccGCaGGGCGGGGCCrCss--- ; cor=; Ncor= a 32 35 16 15 12 19 20 20 8 108 12 7 16 9 16 16 21 13 14 3 103 8 34 35 0 0 0 c 73 80 32 176 175 159 160 20 193 48 24 50 27 208 22 41 36 35 189 196 43 190 79 72 0 0 0 g 98 87 163 25 38 51 43 190 31 57 197 175 185 14 186 162 170 183 20 28 66 33 90 100 0 0 0 t 33 34 25 20 11 7 13 6 4 23 3 4 8 5 12 17 9 5 13 9 24 5 33 29 0 0 0

oligos_6nt_test_vs_ctrl_m4_rc_shift7 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4_rc; m=3/3; ncol2=24; w=0; offset=4; strand=R; shift=7; score=0.521554; -------ssgGCCtGGCCCCGCCCyGC ; cor=; Ncor= a 0 0 0 0 0 0 0 37 51 24 12 5 9 18 14 12 7 13 13 15 21 13 8 11 20 7 14 c 0 0 0 0 0 0 0 114 120 57 43 249 231 70 45 16 234 213 218 216 27 227 218 234 76 43 229 g 0 0 0 0 0 0 0 98 89 186 218 24 32 62 220 243 32 41 42 35 218 41 50 30 44 228 32 t 0 0 0 0 0 0 0 39 28 21 15 10 16 138 9 17 15 21 15 22 22 7 12 13 148 10 13

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---ssCCGCrGGGCGGGGCCaGGCcss ; Alignment reference a 0 0 0 45 40 14 16 13 10 148 13 12 7 22 22 15 21 15 17 9 138 16 10 15 21 28 39 c 0 0 0 110 89 197 199 32 228 44 30 50 41 218 35 42 41 32 243 220 62 32 24 218 186 89 98 g 0 0 0 90 125 63 50 229 43 76 234 218 227 27 216 218 213 234 16 45 70 231 249 43 57 120 114 t 0 0 0 43 34 14 23 14 7 20 11 8 13 21 15 13 13 7 12 14 18 9 5 12 24 51 37

oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCCGCrGGGCGGGGCCaGGCcss ; cor=; Ncor= a 0 0 0 45 40 14 16 13 10 148 13 12 7 22 22 15 21 15 17 9 138 16 10 15 21 28 39 c 0 0 0 110 89 197 199 32 228 44 30 50 41 218 35 42 41 32 243 220 62 32 24 218 186 89 98 g 0 0 0 90 125 63 50 229 43 76 234 218 227 27 216 218 213 234 16 45 70 231 249 43 57 120 114 t 0 0 0 43 34 14 23 14 7 20 11 8 13 21 15 13 13 7 12 14 18 9 5 12 24 51 37

oligos_6nt_test_vs_ctrl_m2_rc_shift3 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/5; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.785637; ---ssCCGCrGGGCGCtGCGGGGCGss ; cor=; Ncor= a 0 0 0 70 53 22 26 38 18 176 19 15 24 28 19 11 49 14 23 30 27 31 21 32 32 54 46 c 0 0 0 166 126 292 293 40 306 92 65 58 66 333 38 341 86 32 322 58 79 65 60 323 58 159 125 g 0 0 0 150 182 96 76 327 91 128 333 336 326 52 352 64 105 374 64 309 299 317 324 53 306 169 196 t 0 0 0 42 67 18 33 23 13 32 11 19 12 15 19 12 188 8 19 31 23 15 23 20 32 46 61

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=3/5; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.656549; ssGCCccGCaGGGCGGGGCCrCss--- ; cor=; Ncor= a 32 35 16 15 12 19 20 20 8 108 12 7 16 9 16 16 21 13 14 3 103 8 34 35 0 0 0 c 73 80 32 176 175 159 160 20 193 48 24 50 27 208 22 41 36 35 189 196 43 190 79 72 0 0 0 g 98 87 163 25 38 51 43 190 31 57 197 175 185 14 186 162 170 183 20 28 66 33 90 100 0 0 0 t 33 34 25 20 11 7 13 6 4 23 3 4 8 5 12 17 9 5 13 9 24 5 33 29 0 0 0

oligos_6nt_test_vs_ctrl_m1_rc_shift7 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=4/5; ncol2=24; w=0; offset=4; strand=R; shift=7; score=0.521554; -------ssaGGGCGgGGCCGCsCtGC ; cor=; Ncor= a 0 0 0 0 0 0 0 73 49 214 25 27 26 27 24 37 16 13 29 22 19 17 24 28 37 12 29 c 0 0 0 0 0 0 0 157 187 99 57 81 62 371 43 89 73 57 345 328 25 339 277 320 86 64 322 g 0 0 0 0 0 0 0 173 173 104 345 321 346 32 358 298 339 354 55 67 375 80 119 77 101 351 59 t 0 0 0 0 0 0 0 47 41 33 23 21 16 20 25 26 22 26 21 33 31 14 30 25 226 23 40

oligos_7nt_test_vs_ctrl_m5_rc_shift13 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=5/5; ncol2=15; w=0; offset=10; strand=R; shift=13; score=0.451485; -------------ssGGGCCAGGGCts ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 342 427 203 89 66 90 71 1585 63 82 108 83 197 265 c 0 0 0 0 0 0 0 0 0 0 0 0 0 810 625 238 129 129 1838 1925 212 103 129 173 1893 388 657 g 0 0 0 0 0 0 0 0 0 0 0 0 0 683 757 1579 1902 1906 188 155 251 1954 1915 1832 117 440 922 t 0 0 0 0 0 0 0 0 0 0 0 0 0 355 381 170 70 89 74 39 142 70 64 77 97 1165 346

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift6 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift6 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=6; ncol=21; ------ssGCAGCGCCaCCys ; Alignment reference a 0 0 0 0 0 0 581 709 446 83 2732 65 115 172 120 71 1718 171 223 546 626 c 0 0 0 0 0 0 1570 1095 481 3191 330 266 3146 173 3145 3229 780 2445 2616 948 1078 g 0 0 0 0 0 0 944 1138 2447 198 406 3165 139 3099 214 211 762 558 496 879 1334 t 0 0 0 0 0 0 487 640 208 110 114 86 182 138 103 71 322 408 247 1209 544

oligos_7nt_test_vs_ctrl_m2_shift6 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=6; score= 1; ------ssGCAGCGCCaCCys ; cor=; Ncor= a 0 0 0 0 0 0 581 709 446 83 2732 65 115 172 120 71 1718 171 223 546 626 c 0 0 0 0 0 0 1570 1095 481 3191 330 266 3146 173 3145 3229 780 2445 2616 948 1078 g 0 0 0 0 0 0 944 1138 2447 198 406 3165 139 3099 214 211 762 558 496 879 1334 t 0 0 0 0 0 0 487 640 208 110 114 86 182 138 103 71 322 408 247 1209 544

oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/3; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.487891; -ssGCCCCGCmGCGCCCCmGC ; cor=; Ncor= a 0 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 c 0 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 g 0 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 t 0 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=3/3; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.465989; ssCGCCCCGCaGCGCCCyGCG ; cor=; Ncor= a 61 46 32 20 23 15 23 31 19 8 188 12 19 15 12 19 11 32 13 23 33 c 196 169 306 53 324 317 299 309 64 374 105 64 352 52 326 336 333 128 91 327 76 g 125 159 58 323 60 65 79 58 322 32 86 341 38 333 66 58 65 92 306 40 293 t 46 54 32 32 21 31 27 30 23 14 49 11 19 28 24 15 19 176 18 38 26

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift7 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=24; shift=7; ncol=31; -------ssGCCccGCaGGGCGGGGCCrCss ; Alignment reference a 0 0 0 0 0 0 0 32 35 16 15 12 19 20 20 8 108 12 7 16 9 16 16 21 13 14 3 103 8 34 35 c 0 0 0 0 0 0 0 73 80 32 176 175 159 160 20 193 48 24 50 27 208 22 41 36 35 189 196 43 190 79 72 g 0 0 0 0 0 0 0 98 87 163 25 38 51 43 190 31 57 197 175 185 14 186 162 170 183 20 28 66 33 90 100 t 0 0 0 0 0 0 0 33 34 25 20 11 7 13 6 4 23 3 4 8 5 12 17 9 5 13 9 24 5 33 29

oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=7; score= 1; -------ssGCCccGCaGGGCGGGGCCrCss ; cor=; Ncor= a 0 0 0 0 0 0 0 32 35 16 15 12 19 20 20 8 108 12 7 16 9 16 16 21 13 14 3 103 8 34 35 c 0 0 0 0 0 0 0 73 80 32 176 175 159 160 20 193 48 24 50 27 208 22 41 36 35 189 196 43 190 79 72 g 0 0 0 0 0 0 0 98 87 163 25 38 51 43 190 31 57 197 175 185 14 186 162 170 183 20 28 66 33 90 100 t 0 0 0 0 0 0 0 33 34 25 20 11 7 13 6 4 23 3 4 8 5 12 17 9 5 13 9 24 5 33 29

oligos_6nt_test_vs_ctrl_m4_shift10 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=2/4; ncol2=24; w=0; offset=3; strand=D; shift=10; score=0.656549; ----------ssCCGCrGGGCGGGGCCaGGC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 45 40 14 16 13 10 148 13 12 7 22 22 15 21 15 17 9 138 16 10 15 c 0 0 0 0 0 0 0 0 0 0 110 89 197 199 32 228 44 30 50 41 218 35 42 41 32 243 220 62 32 24 218 g 0 0 0 0 0 0 0 0 0 0 90 125 63 50 229 43 76 234 218 227 27 216 218 213 234 16 45 70 231 249 43 t 0 0 0 0 0 0 0 0 0 0 43 34 14 23 14 7 20 11 8 13 21 15 13 13 7 12 14 18 9 5 12

oligos_6nt_test_vs_ctrl_m1_shift10 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=24; w=0; offset=3; strand=D; shift=10; score= 0.5968; ----------ssCCGCaGsGCGGCCcCGCCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 53 53 26 32 40 23 226 25 30 14 31 33 21 26 22 26 25 20 16 21 23 c 0 0 0 0 0 0 0 0 0 0 189 154 310 337 59 351 101 77 119 80 375 67 55 354 339 298 358 32 346 321 345 g 0 0 0 0 0 0 0 0 0 0 147 173 88 61 322 64 86 320 277 339 25 328 345 57 73 89 43 371 62 81 57 t 0 0 0 0 0 0 0 0 0 0 61 70 26 20 29 12 37 28 24 17 19 22 29 13 16 37 24 27 26 27 25

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=4/4; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.42277; ssCCGCrGGGCGCtGCGGGGCGss------- ; cor=; Ncor= a 70 53 22 26 38 18 176 19 15 24 28 19 11 49 14 23 30 27 31 21 32 32 54 46 0 0 0 0 0 0 0 c 166 126 292 293 40 306 92 65 58 66 333 38 341 86 32 322 58 79 65 60 323 58 159 125 0 0 0 0 0 0 0 g 150 182 96 76 327 91 128 333 336 326 52 352 64 105 374 64 309 299 317 324 53 306 169 196 0 0 0 0 0 0 0 t 42 67 18 33 23 13 32 11 19 12 15 19 12 188 8 19 31 23 15 23 20 32 46 61 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift9 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift9 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------ssaGCCCTGGCCCss ; Alignment reference a 0 0 0 0 0 0 0 0 0 377 346 1165 97 77 64 70 142 39 74 89 70 170 381 355 c 0 0 0 0 0 0 0 0 0 746 922 440 117 1832 1915 1954 251 155 188 1906 1902 1579 757 683 g 0 0 0 0 0 0 0 0 0 739 657 388 1893 173 129 103 212 1925 1838 129 129 238 625 810 t 0 0 0 0 0 0 0 0 0 328 265 197 83 108 82 63 1585 71 90 66 89 203 427 342

oligos_7nt_test_vs_ctrl_m5_shift9 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=9; score= 1; ---------ssaGCCCTGGCCCss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 377 346 1165 97 77 64 70 142 39 74 89 70 170 381 355 c 0 0 0 0 0 0 0 0 0 746 922 440 117 1832 1915 1954 251 155 188 1906 1902 1579 757 683 g 0 0 0 0 0 0 0 0 0 739 657 388 1893 173 129 103 212 1925 1838 129 129 238 625 810 t 0 0 0 0 0 0 0 0 0 328 265 197 83 108 82 63 1585 71 90 66 89 203 427 342

oligos_6nt_test_vs_ctrl_m4_rc_shift10 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=2/3; ncol2=24; w=0; offset=1; strand=R; shift=10; score=0.451485; ----------ssgGCCtGGCCCCG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 37 51 24 12 5 9 18 14 12 7 13 13 15 21 c 0 0 0 0 0 0 0 0 0 0 114 120 57 43 249 231 70 45 16 234 213 218 216 27 g 0 0 0 0 0 0 0 0 0 0 98 89 186 218 24 32 62 220 243 32 41 42 35 218 t 0 0 0 0 0 0 0 0 0 0 39 28 21 15 10 16 138 9 17 15 21 15 22 22

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=3/3; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.446143; ssGCCCCGCmGCGCCCCmGCCCss ; cor=; Ncor= a 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 15 34 60 62 c 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 365 344 189 193 g 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 75 63 184 180 t 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22 32 46 54 52

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=1; ncol=25; -ssGCCCCGCmGCGCCCCmGCCCss ; Alignment reference a 0 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 15 34 60 62 c 0 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 365 344 189 193 g 0 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 75 63 184 180 t 0 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22 32 46 54 52
oligos_6nt_test_vs_ctrl_m3_shift1 (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=1; score= 1; -ssGCCCCGCmGCGCCCCmGCCCss ; cor=; Ncor= a 0 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 15 34 60 62 c 0 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 365 344 189 193 g 0 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 75 63 184 180 t 0 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22 32 46 54 52
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=2/4; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.702142; ssCGCCCCGCaGCGCCCyGCGGss- ; cor=; Ncor= a 61 46 32 20 23 15 23 31 19 8 188 12 19 15 12 19 11 32 13 23 33 18 67 42 0 c 196 169 306 53 324 317 299 309 64 374 105 64 352 52 326 336 333 128 91 327 76 96 182 150 0 g 125 159 58 323 60 65 79 58 322 32 86 341 38 333 66 58 65 92 306 40 293 292 126 166 0 t 46 54 32 32 21 31 27 30 23 14 49 11 19 28 24 15 19 176 18 38 26 22 53 70 0
oligos_7nt_test_vs_ctrl_m2_shift6 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=3/4; ncol2=15; w=0; offset=5; strand=D; shift=6; score=0.487891; ------ssGCAGCGCCaCCys---- ; cor=; Ncor= a 0 0 0 0 0 0 581 709 446 83 2732 65 115 172 120 71 1718 171 223 546 626 0 0 0 0 c 0 0 0 0 0 0 1570 1095 481 3191 330 266 3146 173 3145 3229 780 2445 2616 948 1078 0 0 0 0 g 0 0 0 0 0 0 944 1138 2447 198 406 3165 139 3099 214 211 762 558 496 879 1334 0 0 0 0 t 0 0 0 0 0 0 487 640 208 110 114 86 182 138 103 71 322 408 247 1209 544 0 0 0 0
oligos_7nt_test_vs_ctrl_m5_shift10 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=4/4; ncol2=15; w=0; offset=9; strand=D; shift=10; score=0.446143; ----------ssaGCCCTGGCCCss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 377 346 1165 97 77 64 70 142 39 74 89 70 170 381 355 c 0 0 0 0 0 0 0 0 0 0 746 922 440 117 1832 1915 1954 251 155 188 1906 1902 1579 757 683 g 0 0 0 0 0 0 0 0 0 0 739 657 388 1893 173 129 103 212 1925 1838 129 129 238 625 810 t 0 0 0 0 0 0 0 0 0 0 328 265 197 83 108 82 63 1585 71 90 66 89 203 427 342

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=7; ncol=31; -------ssCGCCCCGCaGCGCCCyGCGGss ; Alignment reference a 0 0 0 0 0 0 0 61 46 32 20 23 15 23 31 19 8 188 12 19 15 12 19 11 32 13 23 33 18 67 42 c 0 0 0 0 0 0 0 196 169 306 53 324 317 299 309 64 374 105 64 352 52 326 336 333 128 91 327 76 96 182 150 g 0 0 0 0 0 0 0 125 159 58 323 60 65 79 58 322 32 86 341 38 333 66 58 65 92 306 40 293 292 126 166 t 0 0 0 0 0 0 0 46 54 32 32 21 31 27 30 23 14 49 11 19 28 24 15 19 176 18 38 26 22 53 70
oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=7; score= 1; -------ssCGCCCCGCaGCGCCCyGCGGss ; cor=; Ncor= a 0 0 0 0 0 0 0 61 46 32 20 23 15 23 31 19 8 188 12 19 15 12 19 11 32 13 23 33 18 67 42 c 0 0 0 0 0 0 0 196 169 306 53 324 317 299 309 64 374 105 64 352 52 326 336 333 128 91 327 76 96 182 150 g 0 0 0 0 0 0 0 125 159 58 323 60 65 79 58 322 32 86 341 38 333 66 58 65 92 306 40 293 292 126 166 t 0 0 0 0 0 0 0 46 54 32 32 21 31 27 30 23 14 49 11 19 28 24 15 19 176 18 38 26 22 53 70
oligos_6nt_test_vs_ctrl_m4_rc_shift7 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=2/5; ncol2=24; w=0; offset=0; strand=R; shift=7; score=0.785637; -------ssgGCCtGGCCCCGCCCyGCGGss ; cor=; Ncor= a 0 0 0 0 0 0 0 37 51 24 12 5 9 18 14 12 7 13 13 15 21 13 8 11 20 7 14 23 14 34 43 c 0 0 0 0 0 0 0 114 120 57 43 249 231 70 45 16 234 213 218 216 27 227 218 234 76 43 229 50 63 125 90 g 0 0 0 0 0 0 0 98 89 186 218 24 32 62 220 243 32 41 42 35 218 41 50 30 44 228 32 199 197 89 110 t 0 0 0 0 0 0 0 39 28 21 15 10 16 138 9 17 15 21 15 22 22 7 12 13 148 10 13 16 14 40 45
oligos_6nt_test_vs_ctrl_m3_shift8 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=3/5; ncol2=24; w=0; offset=1; strand=D; shift=8; score=0.702142; --------ssGCCCCGCmGCGCCCCmGCCCs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 15 34 60 c 0 0 0 0 0 0 0 0 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 365 344 189 g 0 0 0 0 0 0 0 0 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 75 63 184 t 0 0 0 0 0 0 0 0 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22 32 46 54
oligos_7nt_test_vs_ctrl_m2_shift13 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=4/5; ncol2=15; w=0; offset=6; strand=D; shift=13; score=0.465989; -------------ssGCAGCGCCaCCys--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 581 709 446 83 2732 65 115 172 120 71 1718 171 223 546 626 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 1570 1095 481 3191 330 266 3146 173 3145 3229 780 2445 2616 948 1078 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 944 1138 2447 198 406 3165 139 3099 214 211 762 558 496 879 1334 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 487 640 208 110 114 86 182 138 103 71 322 408 247 1209 544 0 0 0
oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=5/5; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.42277; ssGyGGCCCCGCCCtGCggGGCss------- ; cor=; Ncor= a 29 33 5 24 9 13 5 9 17 12 5 8 4 3 23 4 6 13 7 11 20 25 34 33 0 0 0 0 0 0 0 c 100 90 33 66 28 20 183 170 162 186 14 185 175 197 57 31 190 43 51 38 25 163 87 98 0 0 0 0 0 0 0 g 72 79 190 43 196 189 35 36 41 22 208 27 50 24 48 193 20 160 159 175 176 32 80 73 0 0 0 0 0 0 0 t 35 34 8 103 3 14 13 21 16 16 9 16 7 12 108 8 20 20 19 12 15 16 35 32 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---ssCCGCaGsGCGGCCcCGCCCtss ; Alignment reference a 0 0 0 53 53 26 32 40 23 226 25 30 14 31 33 21 26 22 26 25 20 16 21 23 33 41 47 c 0 0 0 189 154 310 337 59 351 101 77 119 80 375 67 55 354 339 298 358 32 346 321 345 104 173 173 g 0 0 0 147 173 88 61 322 64 86 320 277 339 25 328 345 57 73 89 43 371 62 81 57 99 187 157 t 0 0 0 61 70 26 20 29 12 37 28 24 17 19 22 29 13 16 37 24 27 26 27 25 214 49 73
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCCGCaGsGCGGCCcCGCCCtss ; cor=; Ncor= a 0 0 0 53 53 26 32 40 23 226 25 30 14 31 33 21 26 22 26 25 20 16 21 23 33 41 47 c 0 0 0 189 154 310 337 59 351 101 77 119 80 375 67 55 354 339 298 358 32 346 321 345 104 173 173 g 0 0 0 147 173 88 61 322 64 86 320 277 339 25 328 345 57 73 89 43 371 62 81 57 99 187 157 t 0 0 0 61 70 26 20 29 12 37 28 24 17 19 22 29 13 16 37 24 27 26 27 25 214 49 73
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=2/3; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score= 0.5968; ssGCCccGCaGGGCGGGGCCrCss--- ; cor=; Ncor= a 32 35 16 15 12 19 20 20 8 108 12 7 16 9 16 16 21 13 14 3 103 8 34 35 0 0 0 c 73 80 32 176 175 159 160 20 193 48 24 50 27 208 22 41 36 35 189 196 43 190 79 72 0 0 0 g 98 87 163 25 38 51 43 190 31 57 197 175 185 14 186 162 170 183 20 28 66 33 90 100 0 0 0 t 33 34 25 20 11 7 13 6 4 23 3 4 8 5 12 17 9 5 13 9 24 5 33 29 0 0 0
oligos_6nt_test_vs_ctrl_m4_rc_shift7 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4_rc; m=3/3; ncol2=24; w=0; offset=4; strand=R; shift=7; score=0.521554; -------ssgGCCtGGCCCCGCCCyGC ; cor=; Ncor= a 0 0 0 0 0 0 0 37 51 24 12 5 9 18 14 12 7 13 13 15 21 13 8 11 20 7 14 c 0 0 0 0 0 0 0 114 120 57 43 249 231 70 45 16 234 213 218 216 27 227 218 234 76 43 229 g 0 0 0 0 0 0 0 98 89 186 218 24 32 62 220 243 32 41 42 35 218 41 50 30 44 228 32 t 0 0 0 0 0 0 0 39 28 21 15 10 16 138 9 17 15 21 15 22 22 7 12 13 148 10 13

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---ssCCGCrGGGCGGGGCCaGGCcss ; Alignment reference a 0 0 0 45 40 14 16 13 10 148 13 12 7 22 22 15 21 15 17 9 138 16 10 15 21 28 39 c 0 0 0 110 89 197 199 32 228 44 30 50 41 218 35 42 41 32 243 220 62 32 24 218 186 89 98 g 0 0 0 90 125 63 50 229 43 76 234 218 227 27 216 218 213 234 16 45 70 231 249 43 57 120 114 t 0 0 0 43 34 14 23 14 7 20 11 8 13 21 15 13 13 7 12 14 18 9 5 12 24 51 37
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCCGCrGGGCGGGGCCaGGCcss ; cor=; Ncor= a 0 0 0 45 40 14 16 13 10 148 13 12 7 22 22 15 21 15 17 9 138 16 10 15 21 28 39 c 0 0 0 110 89 197 199 32 228 44 30 50 41 218 35 42 41 32 243 220 62 32 24 218 186 89 98 g 0 0 0 90 125 63 50 229 43 76 234 218 227 27 216 218 213 234 16 45 70 231 249 43 57 120 114 t 0 0 0 43 34 14 23 14 7 20 11 8 13 21 15 13 13 7 12 14 18 9 5 12 24 51 37
oligos_6nt_test_vs_ctrl_m2_rc_shift3 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/5; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.785637; ---ssCCGCrGGGCGCtGCGGGGCGss ; cor=; Ncor= a 0 0 0 70 53 22 26 38 18 176 19 15 24 28 19 11 49 14 23 30 27 31 21 32 32 54 46 c 0 0 0 166 126 292 293 40 306 92 65 58 66 333 38 341 86 32 322 58 79 65 60 323 58 159 125 g 0 0 0 150 182 96 76 327 91 128 333 336 326 52 352 64 105 374 64 309 299 317 324 53 306 169 196 t 0 0 0 42 67 18 33 23 13 32 11 19 12 15 19 12 188 8 19 31 23 15 23 20 32 46 61
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=3/5; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.656549; ssGCCccGCaGGGCGGGGCCrCss--- ; cor=; Ncor= a 32 35 16 15 12 19 20 20 8 108 12 7 16 9 16 16 21 13 14 3 103 8 34 35 0 0 0 c 73 80 32 176 175 159 160 20 193 48 24 50 27 208 22 41 36 35 189 196 43 190 79 72 0 0 0 g 98 87 163 25 38 51 43 190 31 57 197 175 185 14 186 162 170 183 20 28 66 33 90 100 0 0 0 t 33 34 25 20 11 7 13 6 4 23 3 4 8 5 12 17 9 5 13 9 24 5 33 29 0 0 0
oligos_6nt_test_vs_ctrl_m1_rc_shift7 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=4/5; ncol2=24; w=0; offset=4; strand=R; shift=7; score=0.521554; -------ssaGGGCGgGGCCGCsCtGC ; cor=; Ncor= a 0 0 0 0 0 0 0 73 49 214 25 27 26 27 24 37 16 13 29 22 19 17 24 28 37 12 29 c 0 0 0 0 0 0 0 157 187 99 57 81 62 371 43 89 73 57 345 328 25 339 277 320 86 64 322 g 0 0 0 0 0 0 0 173 173 104 345 321 346 32 358 298 339 354 55 67 375 80 119 77 101 351 59 t 0 0 0 0 0 0 0 47 41 33 23 21 16 20 25 26 22 26 21 33 31 14 30 25 226 23 40
oligos_7nt_test_vs_ctrl_m5_rc_shift13 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=5/5; ncol2=15; w=0; offset=10; strand=R; shift=13; score=0.451485; -------------ssGGGCCAGGGCts ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 342 427 203 89 66 90 71 1585 63 82 108 83 197 265 c 0 0 0 0 0 0 0 0 0 0 0 0 0 810 625 238 129 129 1838 1925 212 103 129 173 1893 388 657 g 0 0 0 0 0 0 0 0 0 0 0 0 0 683 757 1579 1902 1906 188 155 251 1954 1915 1832 117 440 922 t 0 0 0 0 0 0 0 0 0 0 0 0 0 355 381 170 70 89 74 39 142 70 64 77 97 1165 346

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift6 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=6; ncol=21; ------ssGCAGCGCCaCCys ; Alignment reference a 0 0 0 0 0 0 581 709 446 83 2732 65 115 172 120 71 1718 171 223 546 626 c 0 0 0 0 0 0 1570 1095 481 3191 330 266 3146 173 3145 3229 780 2445 2616 948 1078 g 0 0 0 0 0 0 944 1138 2447 198 406 3165 139 3099 214 211 762 558 496 879 1334 t 0 0 0 0 0 0 487 640 208 110 114 86 182 138 103 71 322 408 247 1209 544
oligos_7nt_test_vs_ctrl_m2_shift6 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=6; score= 1; ------ssGCAGCGCCaCCys ; cor=; Ncor= a 0 0 0 0 0 0 581 709 446 83 2732 65 115 172 120 71 1718 171 223 546 626 c 0 0 0 0 0 0 1570 1095 481 3191 330 266 3146 173 3145 3229 780 2445 2616 948 1078 g 0 0 0 0 0 0 944 1138 2447 198 406 3165 139 3099 214 211 762 558 496 879 1334 t 0 0 0 0 0 0 487 640 208 110 114 86 182 138 103 71 322 408 247 1209 544
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/3; ncol2=24; w=-5; offset=-5; strand=D; shift=1; score=0.487891; -ssGCCCCGCmGCGCCCCmGC ; cor=; Ncor= a 0 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 c 0 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 g 0 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 t 0 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=3/3; ncol2=24; w=-6; offset=-6; strand=D; shift=0; score=0.465989; ssCGCCCCGCaGCGCCCyGCG ; cor=; Ncor= a 61 46 32 20 23 15 23 31 19 8 188 12 19 15 12 19 11 32 13 23 33 c 196 169 306 53 324 317 299 309 64 374 105 64 352 52 326 336 333 128 91 327 76 g 125 159 58 323 60 65 79 58 322 32 86 341 38 333 66 58 65 92 306 40 293 t 46 54 32 32 21 31 27 30 23 14 49 11 19 28 24 15 19 176 18 38 26

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=24; shift=7; ncol=31; -------ssGCCccGCaGGGCGGGGCCrCss ; Alignment reference a 0 0 0 0 0 0 0 32 35 16 15 12 19 20 20 8 108 12 7 16 9 16 16 21 13 14 3 103 8 34 35 c 0 0 0 0 0 0 0 73 80 32 176 175 159 160 20 193 48 24 50 27 208 22 41 36 35 189 196 43 190 79 72 g 0 0 0 0 0 0 0 98 87 163 25 38 51 43 190 31 57 197 175 185 14 186 162 170 183 20 28 66 33 90 100 t 0 0 0 0 0 0 0 33 34 25 20 11 7 13 6 4 23 3 4 8 5 12 17 9 5 13 9 24 5 33 29
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=7; score= 1; -------ssGCCccGCaGGGCGGGGCCrCss ; cor=; Ncor= a 0 0 0 0 0 0 0 32 35 16 15 12 19 20 20 8 108 12 7 16 9 16 16 21 13 14 3 103 8 34 35 c 0 0 0 0 0 0 0 73 80 32 176 175 159 160 20 193 48 24 50 27 208 22 41 36 35 189 196 43 190 79 72 g 0 0 0 0 0 0 0 98 87 163 25 38 51 43 190 31 57 197 175 185 14 186 162 170 183 20 28 66 33 90 100 t 0 0 0 0 0 0 0 33 34 25 20 11 7 13 6 4 23 3 4 8 5 12 17 9 5 13 9 24 5 33 29
oligos_6nt_test_vs_ctrl_m4_shift10 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=2/4; ncol2=24; w=0; offset=3; strand=D; shift=10; score=0.656549; ----------ssCCGCrGGGCGGGGCCaGGC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 45 40 14 16 13 10 148 13 12 7 22 22 15 21 15 17 9 138 16 10 15 c 0 0 0 0 0 0 0 0 0 0 110 89 197 199 32 228 44 30 50 41 218 35 42 41 32 243 220 62 32 24 218 g 0 0 0 0 0 0 0 0 0 0 90 125 63 50 229 43 76 234 218 227 27 216 218 213 234 16 45 70 231 249 43 t 0 0 0 0 0 0 0 0 0 0 43 34 14 23 14 7 20 11 8 13 21 15 13 13 7 12 14 18 9 5 12
oligos_6nt_test_vs_ctrl_m1_shift10 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=24; w=0; offset=3; strand=D; shift=10; score= 0.5968; ----------ssCCGCaGsGCGGCCcCGCCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 53 53 26 32 40 23 226 25 30 14 31 33 21 26 22 26 25 20 16 21 23 c 0 0 0 0 0 0 0 0 0 0 189 154 310 337 59 351 101 77 119 80 375 67 55 354 339 298 358 32 346 321 345 g 0 0 0 0 0 0 0 0 0 0 147 173 88 61 322 64 86 320 277 339 25 328 345 57 73 89 43 371 62 81 57 t 0 0 0 0 0 0 0 0 0 0 61 70 26 20 29 12 37 28 24 17 19 22 29 13 16 37 24 27 26 27 25
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=4/4; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.42277; ssCCGCrGGGCGCtGCGGGGCGss------- ; cor=; Ncor= a 70 53 22 26 38 18 176 19 15 24 28 19 11 49 14 23 30 27 31 21 32 32 54 46 0 0 0 0 0 0 0 c 166 126 292 293 40 306 92 65 58 66 333 38 341 86 32 322 58 79 65 60 323 58 159 125 0 0 0 0 0 0 0 g 150 182 96 76 327 91 128 333 336 326 52 352 64 105 374 64 309 299 317 324 53 306 169 196 0 0 0 0 0 0 0 t 42 67 18 33 23 13 32 11 19 12 15 19 12 188 8 19 31 23 15 23 20 32 46 61 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift9 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------ssaGCCCTGGCCCss ; Alignment reference a 0 0 0 0 0 0 0 0 0 377 346 1165 97 77 64 70 142 39 74 89 70 170 381 355 c 0 0 0 0 0 0 0 0 0 746 922 440 117 1832 1915 1954 251 155 188 1906 1902 1579 757 683 g 0 0 0 0 0 0 0 0 0 739 657 388 1893 173 129 103 212 1925 1838 129 129 238 625 810 t 0 0 0 0 0 0 0 0 0 328 265 197 83 108 82 63 1585 71 90 66 89 203 427 342
oligos_7nt_test_vs_ctrl_m5_shift9 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=9; score= 1; ---------ssaGCCCTGGCCCss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 377 346 1165 97 77 64 70 142 39 74 89 70 170 381 355 c 0 0 0 0 0 0 0 0 0 746 922 440 117 1832 1915 1954 251 155 188 1906 1902 1579 757 683 g 0 0 0 0 0 0 0 0 0 739 657 388 1893 173 129 103 212 1925 1838 129 129 238 625 810 t 0 0 0 0 0 0 0 0 0 328 265 197 83 108 82 63 1585 71 90 66 89 203 427 342
oligos_6nt_test_vs_ctrl_m4_rc_shift10 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4_rc; m=2/3; ncol2=24; w=0; offset=1; strand=R; shift=10; score=0.451485; ----------ssgGCCtGGCCCCG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 37 51 24 12 5 9 18 14 12 7 13 13 15 21 c 0 0 0 0 0 0 0 0 0 0 114 120 57 43 249 231 70 45 16 234 213 218 216 27 g 0 0 0 0 0 0 0 0 0 0 98 89 186 218 24 32 62 220 243 32 41 42 35 218 t 0 0 0 0 0 0 0 0 0 0 39 28 21 15 10 16 138 9 17 15 21 15 22 22
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=3/3; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.446143; ssGCCCCGCmGCGCCCCmGCCCss ; cor=; Ncor= a 62 68 33 23 29 22 28 24 21 212 10 31 17 13 14 19 15 203 20 17 15 34 60 62 c 220 196 65 380 354 358 358 57 416 156 115 399 67 401 398 376 385 151 61 389 365 344 189 193 g 142 165 344 61 68 79 64 388 40 74 342 36 379 47 45 74 64 98 356 59 75 63 184 180 t 63 58 45 23 36 28 37 18 10 45 20 21 24 26 30 18 23 35 50 22 32 46 54 52