One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/05/18/peak-motifs.2026-05-18.122218_2026-05-18.122218_kgALDz/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/2026/05/18/peak-motifs.2026-05-18.122218_2026-05-18.122218_kgALDz/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=5; ncol=20; -----hwAGCTAGCTAAgww ; Alignment reference a 0 0 0 0 0 132 120 400 42 12 37 424 56 22 38 381 333 84 152 238 c 0 0 0 0 0 121 50 11 8 391 9 3 8 416 3 32 20 94 50 35 g 0 0 0 0 0 44 46 19 369 21 8 7 376 7 10 12 59 215 38 42 t 0 0 0 0 0 163 244 30 41 36 406 26 20 15 409 35 48 67 220 145

oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=5; score= 1; -----hwAGCTAGCTAAgww ; cor=; Ncor= a 0 0 0 0 0 132 120 400 42 12 37 424 56 22 38 381 333 84 152 238 c 0 0 0 0 0 121 50 11 8 391 9 3 8 416 3 32 20 94 50 35 g 0 0 0 0 0 44 46 19 369 21 8 7 376 7 10 12 59 215 38 42 t 0 0 0 0 0 163 244 30 41 36 406 26 20 15 409 35 48 67 220 145

oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=2/3; ncol2=19; w=-2; offset=-2; strand=D; shift=3; score=0.678535; ---adcwAgCwAGCWAacwA ; cor=; Ncor= a 0 0 0 360 218 95 189 536 109 19 379 547 121 22 149 550 365 81 341 478 c 0 0 0 43 44 333 18 17 12 539 9 9 6 537 9 14 27 398 22 29 g 0 0 0 49 151 27 17 10 397 5 9 11 424 8 5 9 113 23 13 24 t 0 0 0 138 177 135 366 27 72 27 193 23 39 23 427 17 85 88 214 59

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/3; ncol2=22; w=-5; offset=-5; strand=R; shift=0; score=0.636876; dwTwryTAGCTAGCTArcwA ; cor=; Ncor= a 179 136 72 256 114 64 31 428 61 23 37 403 77 24 19 408 249 80 161 342 c 31 90 14 11 18 126 9 4 4 350 8 5 5 366 2 5 15 243 25 25 g 128 38 25 25 240 15 5 2 363 5 5 8 347 4 4 9 125 18 11 14 t 115 189 342 161 81 248 408 19 25 75 403 37 24 59 428 31 64 112 256 72

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=17; shift=3; ncol=20; ---haAACAAACAAAaAAaw ; Alignment reference a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331

oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---haAACAAACAAAaAAaw ; cor=; Ncor= a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331

oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/5; ncol2=16; w=0; offset=1; strand=D; shift=4; score=0.927477; ----waACAAACAAAaAaww ; cor=; Ncor= a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309

oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=3/5; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.810389; ---wwATCAATCAAAAAaww ; cor=; Ncor= a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277

oligos_6nt_test_vs_ctrl_m5_rc_shift2 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=4/5; ncol2=21; w=-1; offset=-1; strand=R; shift=2; score=0.70505; --ahwAACAAACAArCAArC ; cor=; Ncor= a 0 0 236 103 259 365 301 24 361 384 303 18 355 381 176 30 342 369 162 41 c 0 0 20 163 18 14 2 323 3 4 5 351 7 9 9 341 5 9 5 312 g 0 0 59 29 17 9 55 15 4 5 65 5 4 4 176 8 7 8 194 11 t 0 0 91 111 112 18 48 44 38 13 33 32 40 12 45 27 52 20 45 42

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=5/5; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.690541; wwAAAATCAATCAAAAAAww ; cor=; Ncor= a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift2 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=14; shift=2; ncol=16; --wwArTGAATGAAwd ; Alignment reference a 0 0 249 269 558 254 41 26 652 595 42 25 636 608 228 258 c 0 0 64 65 16 32 14 7 14 14 12 8 13 20 56 60 g 0 0 81 174 35 295 14 662 14 43 22 661 20 35 77 186 t 0 0 321 207 106 134 646 20 35 63 639 21 46 52 354 211

oligos_7nt_test_vs_ctrl_m4_shift2 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --wwArTGAATGAAwd ; cor=; Ncor= a 0 0 249 269 558 254 41 26 652 595 42 25 636 608 228 258 c 0 0 64 65 16 32 14 7 14 14 12 8 13 20 56 60 g 0 0 81 174 35 295 14 662 14 43 22 661 20 35 77 186 t 0 0 321 207 106 134 646 20 35 63 639 21 46 52 354 211

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=2/2; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.767297; wwwGArTGAATGAww- ; cor=; Ncor= a 413 342 308 131 668 242 59 35 703 562 51 61 666 332 245 0 c 47 60 44 28 7 32 16 8 8 29 8 10 18 69 54 0 g 90 112 53 513 26 327 15 677 11 57 25 640 18 114 71 0 t 197 233 342 75 46 146 657 27 25 99 663 36 45 232 377 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=3; ncol=20; ---wwATCAATCAAAAAaww ; Alignment reference a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277

oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/4; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---wwATCAATCAAAAAaww ; cor=; Ncor= a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=2/4; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.817326; wwAAAATCAATCAAAAAAww ; cor=; Ncor= a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143

oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=3/4; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.810389; ---haAACAAACAAAaAAaw ; cor=; Ncor= a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331

oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=4/4; ncol2=16; w=0; offset=1; strand=D; shift=4; score=0.775527; ----waACAAACAAAaAaww ; cor=; Ncor= a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=19; shift=3; ncol=22; ---adcwAgCwAGCWAacwAwh ; Alignment reference a 0 0 0 360 218 95 189 536 109 19 379 547 121 22 149 550 365 81 341 478 287 165 c 0 0 0 43 44 333 18 17 12 539 9 9 6 537 9 14 27 398 22 29 45 207 g 0 0 0 49 151 27 17 10 397 5 9 11 424 8 5 9 113 23 13 24 104 43 t 0 0 0 138 177 135 366 27 72 27 193 23 39 23 427 17 85 88 214 59 154 175

oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=3; score= 1; ---adcwAgCwAGCWAacwAwh ; cor=; Ncor= a 0 0 0 360 218 95 189 536 109 19 379 547 121 22 149 550 365 81 341 478 287 165 c 0 0 0 43 44 333 18 17 12 539 9 9 6 537 9 14 27 398 22 29 45 207 g 0 0 0 49 151 27 17 10 397 5 9 11 424 8 5 9 113 23 13 24 104 43 t 0 0 0 138 177 135 366 27 72 27 193 23 39 23 427 17 85 88 214 59 154 175

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=2/4; ncol2=22; w=-3; offset=-3; strand=R; shift=0; score=0.766021; dwTwryTAGCTAGCTArcwAwh ; cor=; Ncor= a 179 136 72 256 114 64 31 428 61 23 37 403 77 24 19 408 249 80 161 342 190 114 c 31 90 14 11 18 126 9 4 4 350 8 5 5 366 2 5 15 243 25 25 36 130 g 128 38 25 25 240 15 5 2 363 5 5 8 347 4 4 9 125 18 11 14 90 32 t 115 189 342 161 81 248 408 19 25 75 403 37 24 59 428 31 64 112 256 72 137 177

oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=3/4; ncol2=15; w=0; offset=2; strand=D; shift=5; score=0.678535; -----hwAGCTAGCTAAgww-- ; cor=; Ncor= a 0 0 0 0 0 132 120 400 42 12 37 424 56 22 38 381 333 84 152 238 0 0 c 0 0 0 0 0 121 50 11 8 391 9 3 8 416 3 32 20 94 50 35 0 0 g 0 0 0 0 0 44 46 19 369 21 8 7 376 7 10 12 59 215 38 42 0 0 t 0 0 0 0 0 163 244 30 41 36 406 26 20 15 409 35 48 67 220 145 0 0

oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=4/4; ncol2=21; w=-3; offset=-3; strand=R; shift=0; score=0.653025; ahwAACAAACAArCAArCwAa- ; cor=; Ncor= a 236 103 259 365 301 24 361 384 303 18 355 381 176 30 342 369 162 41 201 285 202 0 c 20 163 18 14 2 323 3 4 5 351 7 9 9 341 5 9 5 312 10 29 26 0 g 59 29 17 9 55 15 4 5 65 5 4 4 176 8 7 8 194 11 8 19 83 0 t 91 111 112 18 48 44 38 13 33 32 40 12 45 27 52 20 45 42 187 73 95 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 5 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=20; shift=0; ncol=20; wwAAAATCAATCAAAAAAww ; Alignment reference a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143

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=1/4; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAATCAATCAAAAAAww ; cor=; Ncor= a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143

oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=2/4; ncol2=17; w=0; offset=3; strand=D; shift=3; score=0.817326; ---wwATCAATCAAAAAaww ; cor=; Ncor= a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277

oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=3/4; ncol2=17; w=0; offset=3; strand=D; shift=3; score=0.690541; ---haAACAAACAAAaAAaw ; cor=; Ncor= a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331

oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=4/4; ncol2=16; w=0; offset=4; strand=D; shift=4; score=0.656805; ----waACAAACAAAaAaww ; cor=; Ncor= a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=21; shift=1; ncol=22; -tTwGyTTGyTTGTTTGTTwdt ; Alignment reference a 0 95 73 187 42 45 20 52 27 45 12 40 32 33 13 38 44 48 18 112 111 91 c 0 83 19 8 11 194 8 7 8 176 4 4 5 65 5 4 15 55 9 17 29 59 g 0 26 29 10 312 5 9 5 341 9 9 7 351 5 4 3 323 2 14 18 163 20 t 0 202 285 201 41 162 369 342 30 176 381 355 18 303 384 361 24 301 365 259 103 236

oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/4; ncol2=21; w=0; offset=0; strand=D; shift=1; score= 1; -tTwGyTTGyTTGTTTGTTwdt ; cor=; Ncor= a 0 95 73 187 42 45 20 52 27 45 12 40 32 33 13 38 44 48 18 112 111 91 c 0 83 19 8 11 194 8 7 8 176 4 4 5 65 5 4 15 55 9 17 29 59 g 0 26 29 10 312 5 9 5 341 9 9 7 351 5 4 3 323 2 14 18 163 20 t 0 202 285 201 41 162 369 342 30 176 381 355 18 303 384 361 24 301 365 259 103 236

oligos_7nt_test_vs_ctrl_m1_rc_shift4 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/4; ncol2=17; w=0; offset=3; strand=R; shift=4; score=0.70505; ----wtTTtTTTGTTTGTTtd- ; cor=; Ncor= a 0 0 0 0 331 262 102 115 179 73 30 71 90 57 38 74 86 95 79 258 298 0 c 0 0 0 0 95 109 29 29 50 36 11 9 30 23 10 9 33 47 25 51 92 0 g 0 0 0 0 242 104 55 41 232 19 31 18 849 10 25 8 838 24 43 83 294 0 t 0 0 0 0 421 614 903 904 628 961 1017 991 120 999 1016 998 132 923 942 697 405 0

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3_rc; m=3/4; ncol2=19; w=-1; offset=-1; strand=R; shift=0; score=0.653025; dwTwgtTWGCTwGcTwght--- ; cor=; Ncor= a 175 154 59 214 88 85 17 427 23 39 23 193 27 72 27 366 135 177 138 0 0 0 c 43 104 24 13 23 113 9 5 8 424 11 9 5 397 10 17 27 151 49 0 0 0 g 207 45 29 22 398 27 14 9 537 6 9 9 539 12 17 18 333 44 43 0 0 0 t 165 287 478 341 81 365 550 149 22 121 547 379 19 109 536 189 95 218 360 0 0 0

oligos_6nt_test_vs_ctrl_m1_rc_shift4 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1_rc; m=4/4; ncol2=16; w=0; offset=3; strand=R; shift=4; score=0.64212; ----wwtTtTTTGTTTGTtw-- ; cor=; Ncor= a 0 0 0 0 309 250 188 84 144 51 46 50 75 68 50 68 61 120 241 256 0 0 c 0 0 0 0 85 107 57 19 26 24 13 12 15 31 10 7 14 65 61 51 0 0 g 0 0 0 0 206 96 88 26 176 25 31 14 853 11 33 14 829 22 113 66 0 0 t 0 0 0 0 387 534 654 858 641 887 897 911 44 877 894 898 83 780 572 614 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift4 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=4; ncol=20; ----waACAAACAAAaAaww ; Alignment reference a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309

oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=4; score= 1; ----waACAAACAAAaAaww ; cor=; Ncor= a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309

oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=2/5; ncol2=17; w=-1; offset=-1; strand=D; shift=3; score=0.927477; ---haAACAAACAAAaAAaw ; cor=; Ncor= a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331

oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=3/5; ncol2=17; w=-1; offset=-1; strand=D; shift=3; score=0.775527; ---wwATCAATCAAAAAaww ; cor=; Ncor= a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=4/5; ncol2=20; w=-4; offset=-4; strand=D; shift=0; score=0.656805; wwAAAATCAATCAAAAAAww ; cor=; Ncor= a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143

oligos_6nt_test_vs_ctrl_m5_rc_shift2 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=5/5; ncol2=21; w=-2; offset=-2; strand=R; shift=2; score=0.64212; --ahwAACAAACAArCAArC ; cor=; Ncor= a 0 0 236 103 259 365 301 24 361 384 303 18 355 381 176 30 342 369 162 41 c 0 0 20 163 18 14 2 323 3 4 5 351 7 9 9 341 5 9 5 312 g 0 0 59 29 17 9 55 15 4 5 65 5 4 4 176 8 7 8 194 11 t 0 0 91 111 112 18 48 44 38 13 33 32 40 12 45 27 52 20 45 42

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 4 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=22; shift=0; ncol=22; dwTwgyTAGCTAGCTArywAwh ; Alignment reference a 177 137 72 256 112 64 31 428 59 24 37 403 75 25 19 408 248 81 161 342 189 115 c 32 90 14 11 18 125 9 4 4 347 8 5 5 363 2 5 15 240 25 25 38 128 g 130 36 25 25 243 15 5 2 366 5 5 8 350 4 4 9 126 18 11 14 90 31 t 114 190 342 161 80 249 408 19 24 77 403 37 23 61 428 31 64 114 256 72 136 179

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=1/3; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; dwTwgyTAGCTAGCTArywAwh ; cor=; Ncor= a 177 137 72 256 112 64 31 428 59 24 37 403 75 25 19 408 248 81 161 342 189 115 c 32 90 14 11 18 125 9 4 4 347 8 5 5 363 2 5 15 240 25 25 38 128 g 130 36 25 25 243 15 5 2 366 5 5 8 350 4 4 9 126 18 11 14 90 31 t 114 190 342 161 80 249 408 19 24 77 403 37 23 61 428 31 64 114 256 72 136 179

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/3; ncol2=19; w=0; offset=0; strand=R; shift=0; score=0.766021; dwTwgtTWGCTwGcTwght--- ; cor=; Ncor= a 175 154 59 214 88 85 17 427 23 39 23 193 27 72 27 366 135 177 138 0 0 0 c 43 104 24 13 23 113 9 5 8 424 11 9 5 397 10 17 27 151 49 0 0 0 g 207 45 29 22 398 27 14 9 537 6 9 9 539 12 17 18 333 44 43 0 0 0 t 165 287 478 341 81 365 550 149 22 121 547 379 19 109 536 189 95 218 360 0 0 0

oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/3; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.636876; --wwcTTAGCTAGCTwd----- ; cor=; Ncor= a 0 0 145 220 67 48 35 409 15 20 26 406 36 41 30 244 163 0 0 0 0 0 c 0 0 42 38 215 59 12 10 7 376 7 8 21 369 19 46 44 0 0 0 0 0 g 0 0 35 50 94 20 32 3 416 8 3 9 391 8 11 50 121 0 0 0 0 0 t 0 0 238 152 84 333 381 38 22 56 424 37 12 42 400 120 132 0 0 0 0 0

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=15; shift=0; ncol=15; wwwGArTGAATGAww ; Alignment reference a 413 342 308 131 668 242 59 35 703 562 51 61 666 332 245 c 47 60 44 28 7 32 16 8 8 29 8 10 18 69 54 g 90 112 53 513 26 327 15 677 11 57 25 640 18 114 71 t 197 233 342 75 46 146 657 27 25 99 663 36 45 232 377

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=15; w=0; offset=0; strand=D; shift=0; score= 1; wwwGArTGAATGAww ; cor=; Ncor= a 413 342 308 131 668 242 59 35 703 562 51 61 666 332 245 c 47 60 44 28 7 32 16 8 8 29 8 10 18 69 54 g 90 112 53 513 26 327 15 677 11 57 25 640 18 114 71 t 197 233 342 75 46 146 657 27 25 99 663 36 45 232 377

oligos_7nt_test_vs_ctrl_m4_shift2 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=2/2; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.767297; --wwArTGAATGAAw ; cor=; Ncor= a 0 0 249 269 558 254 41 26 652 595 42 25 636 608 228 c 0 0 64 65 16 32 14 7 14 14 12 8 13 20 56 g 0 0 81 174 35 295 14 662 14 43 22 661 20 35 77 t 0 0 321 207 106 134 646 20 35 63 639 21 46 52 354

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=5; ncol=20; -----hwAGCTAGCTAAgww ; Alignment reference a 0 0 0 0 0 132 120 400 42 12 37 424 56 22 38 381 333 84 152 238 c 0 0 0 0 0 121 50 11 8 391 9 3 8 416 3 32 20 94 50 35 g 0 0 0 0 0 44 46 19 369 21 8 7 376 7 10 12 59 215 38 42 t 0 0 0 0 0 163 244 30 41 36 406 26 20 15 409 35 48 67 220 145
oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=5; score= 1; -----hwAGCTAGCTAAgww ; cor=; Ncor= a 0 0 0 0 0 132 120 400 42 12 37 424 56 22 38 381 333 84 152 238 c 0 0 0 0 0 121 50 11 8 391 9 3 8 416 3 32 20 94 50 35 g 0 0 0 0 0 44 46 19 369 21 8 7 376 7 10 12 59 215 38 42 t 0 0 0 0 0 163 244 30 41 36 406 26 20 15 409 35 48 67 220 145
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=2/3; ncol2=19; w=-2; offset=-2; strand=D; shift=3; score=0.678535; ---adcwAgCwAGCWAacwA ; cor=; Ncor= a 0 0 0 360 218 95 189 536 109 19 379 547 121 22 149 550 365 81 341 478 c 0 0 0 43 44 333 18 17 12 539 9 9 6 537 9 14 27 398 22 29 g 0 0 0 49 151 27 17 10 397 5 9 11 424 8 5 9 113 23 13 24 t 0 0 0 138 177 135 366 27 72 27 193 23 39 23 427 17 85 88 214 59
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/3; ncol2=22; w=-5; offset=-5; strand=R; shift=0; score=0.636876; dwTwryTAGCTAGCTArcwA ; cor=; Ncor= a 179 136 72 256 114 64 31 428 61 23 37 403 77 24 19 408 249 80 161 342 c 31 90 14 11 18 126 9 4 4 350 8 5 5 366 2 5 15 243 25 25 g 128 38 25 25 240 15 5 2 363 5 5 8 347 4 4 9 125 18 11 14 t 115 189 342 161 81 248 408 19 25 75 403 37 24 59 428 31 64 112 256 72

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=17; shift=3; ncol=20; ---haAACAAACAAAaAAaw ; Alignment reference a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/5; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---haAACAAACAAAaAAaw ; cor=; Ncor= a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/5; ncol2=16; w=0; offset=1; strand=D; shift=4; score=0.927477; ----waACAAACAAAaAaww ; cor=; Ncor= a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=3/5; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.810389; ---wwATCAATCAAAAAaww ; cor=; Ncor= a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277
oligos_6nt_test_vs_ctrl_m5_rc_shift2 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=4/5; ncol2=21; w=-1; offset=-1; strand=R; shift=2; score=0.70505; --ahwAACAAACAArCAArC ; cor=; Ncor= a 0 0 236 103 259 365 301 24 361 384 303 18 355 381 176 30 342 369 162 41 c 0 0 20 163 18 14 2 323 3 4 5 351 7 9 9 341 5 9 5 312 g 0 0 59 29 17 9 55 15 4 5 65 5 4 4 176 8 7 8 194 11 t 0 0 91 111 112 18 48 44 38 13 33 32 40 12 45 27 52 20 45 42
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=5/5; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.690541; wwAAAATCAATCAAAAAAww ; cor=; Ncor= a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=3; ncol=20; ---wwATCAATCAAAAAaww ; Alignment reference a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/4; ncol2=17; w=0; offset=0; strand=D; shift=3; score= 1; ---wwATCAATCAAAAAaww ; cor=; Ncor= a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=2/4; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.817326; wwAAAATCAATCAAAAAAww ; cor=; Ncor= a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=3/4; ncol2=17; w=0; offset=0; strand=D; shift=3; score=0.810389; ---haAACAAACAAAaAAaw ; cor=; Ncor= a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=4/4; ncol2=16; w=0; offset=1; strand=D; shift=4; score=0.775527; ----waACAAACAAAaAaww ; cor=; Ncor= a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=19; shift=3; ncol=22; ---adcwAgCwAGCWAacwAwh ; Alignment reference a 0 0 0 360 218 95 189 536 109 19 379 547 121 22 149 550 365 81 341 478 287 165 c 0 0 0 43 44 333 18 17 12 539 9 9 6 537 9 14 27 398 22 29 45 207 g 0 0 0 49 151 27 17 10 397 5 9 11 424 8 5 9 113 23 13 24 104 43 t 0 0 0 138 177 135 366 27 72 27 193 23 39 23 427 17 85 88 214 59 154 175
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=3; score= 1; ---adcwAgCwAGCWAacwAwh ; cor=; Ncor= a 0 0 0 360 218 95 189 536 109 19 379 547 121 22 149 550 365 81 341 478 287 165 c 0 0 0 43 44 333 18 17 12 539 9 9 6 537 9 14 27 398 22 29 45 207 g 0 0 0 49 151 27 17 10 397 5 9 11 424 8 5 9 113 23 13 24 104 43 t 0 0 0 138 177 135 366 27 72 27 193 23 39 23 427 17 85 88 214 59 154 175
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=2/4; ncol2=22; w=-3; offset=-3; strand=R; shift=0; score=0.766021; dwTwryTAGCTAGCTArcwAwh ; cor=; Ncor= a 179 136 72 256 114 64 31 428 61 23 37 403 77 24 19 408 249 80 161 342 190 114 c 31 90 14 11 18 126 9 4 4 350 8 5 5 366 2 5 15 243 25 25 36 130 g 128 38 25 25 240 15 5 2 363 5 5 8 347 4 4 9 125 18 11 14 90 32 t 115 189 342 161 81 248 408 19 25 75 403 37 24 59 428 31 64 112 256 72 137 177
oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=3/4; ncol2=15; w=0; offset=2; strand=D; shift=5; score=0.678535; -----hwAGCTAGCTAAgww-- ; cor=; Ncor= a 0 0 0 0 0 132 120 400 42 12 37 424 56 22 38 381 333 84 152 238 0 0 c 0 0 0 0 0 121 50 11 8 391 9 3 8 416 3 32 20 94 50 35 0 0 g 0 0 0 0 0 44 46 19 369 21 8 7 376 7 10 12 59 215 38 42 0 0 t 0 0 0 0 0 163 244 30 41 36 406 26 20 15 409 35 48 67 220 145 0 0
oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=4/4; ncol2=21; w=-3; offset=-3; strand=R; shift=0; score=0.653025; ahwAACAAACAArCAArCwAa- ; cor=; Ncor= a 236 103 259 365 301 24 361 384 303 18 355 381 176 30 342 369 162 41 201 285 202 0 c 20 163 18 14 2 323 3 4 5 351 7 9 9 341 5 9 5 312 10 29 26 0 g 59 29 17 9 55 15 4 5 65 5 4 4 176 8 7 8 194 11 8 19 83 0 t 91 111 112 18 48 44 38 13 33 32 40 12 45 27 52 20 45 42 187 73 95 0

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=20; shift=0; ncol=20; wwAAAATCAATCAAAAAAww ; Alignment reference a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143
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=1/4; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAATCAATCAAAAAAww ; cor=; Ncor= a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=2/4; ncol2=17; w=0; offset=3; strand=D; shift=3; score=0.817326; ---wwATCAATCAAAAAaww ; cor=; Ncor= a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=3/4; ncol2=17; w=0; offset=3; strand=D; shift=3; score=0.690541; ---haAACAAACAAAaAAaw ; cor=; Ncor= a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=4/4; ncol2=16; w=0; offset=4; strand=D; shift=4; score=0.656805; ----waACAAACAAAaAaww ; cor=; Ncor= a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=21; shift=1; ncol=22; -tTwGyTTGyTTGTTTGTTwdt ; Alignment reference a 0 95 73 187 42 45 20 52 27 45 12 40 32 33 13 38 44 48 18 112 111 91 c 0 83 19 8 11 194 8 7 8 176 4 4 5 65 5 4 15 55 9 17 29 59 g 0 26 29 10 312 5 9 5 341 9 9 7 351 5 4 3 323 2 14 18 163 20 t 0 202 285 201 41 162 369 342 30 176 381 355 18 303 384 361 24 301 365 259 103 236
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/4; ncol2=21; w=0; offset=0; strand=D; shift=1; score= 1; -tTwGyTTGyTTGTTTGTTwdt ; cor=; Ncor= a 0 95 73 187 42 45 20 52 27 45 12 40 32 33 13 38 44 48 18 112 111 91 c 0 83 19 8 11 194 8 7 8 176 4 4 5 65 5 4 15 55 9 17 29 59 g 0 26 29 10 312 5 9 5 341 9 9 7 351 5 4 3 323 2 14 18 163 20 t 0 202 285 201 41 162 369 342 30 176 381 355 18 303 384 361 24 301 365 259 103 236
oligos_7nt_test_vs_ctrl_m1_rc_shift4 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/4; ncol2=17; w=0; offset=3; strand=R; shift=4; score=0.70505; ----wtTTtTTTGTTTGTTtd- ; cor=; Ncor= a 0 0 0 0 331 262 102 115 179 73 30 71 90 57 38 74 86 95 79 258 298 0 c 0 0 0 0 95 109 29 29 50 36 11 9 30 23 10 9 33 47 25 51 92 0 g 0 0 0 0 242 104 55 41 232 19 31 18 849 10 25 8 838 24 43 83 294 0 t 0 0 0 0 421 614 903 904 628 961 1017 991 120 999 1016 998 132 923 942 697 405 0
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3_rc; m=3/4; ncol2=19; w=-1; offset=-1; strand=R; shift=0; score=0.653025; dwTwgtTWGCTwGcTwght--- ; cor=; Ncor= a 175 154 59 214 88 85 17 427 23 39 23 193 27 72 27 366 135 177 138 0 0 0 c 43 104 24 13 23 113 9 5 8 424 11 9 5 397 10 17 27 151 49 0 0 0 g 207 45 29 22 398 27 14 9 537 6 9 9 539 12 17 18 333 44 43 0 0 0 t 165 287 478 341 81 365 550 149 22 121 547 379 19 109 536 189 95 218 360 0 0 0
oligos_6nt_test_vs_ctrl_m1_rc_shift4 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1_rc; m=4/4; ncol2=16; w=0; offset=3; strand=R; shift=4; score=0.64212; ----wwtTtTTTGTTTGTtw-- ; cor=; Ncor= a 0 0 0 0 309 250 188 84 144 51 46 50 75 68 50 68 61 120 241 256 0 0 c 0 0 0 0 85 107 57 19 26 24 13 12 15 31 10 7 14 65 61 51 0 0 g 0 0 0 0 206 96 88 26 176 25 31 14 853 11 33 14 829 22 113 66 0 0 t 0 0 0 0 387 534 654 858 641 887 897 911 44 877 894 898 83 780 572 614 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=4; ncol=20; ----waACAAACAAAaAaww ; Alignment reference a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=4; score= 1; ----waACAAACAAAaAaww ; cor=; Ncor= a 0 0 0 0 614 572 780 83 898 894 877 44 911 897 887 641 858 654 534 387 c 0 0 0 0 66 113 22 829 14 33 11 853 14 31 25 176 26 88 96 206 g 0 0 0 0 51 61 65 14 7 10 31 15 12 13 24 26 19 57 107 85 t 0 0 0 0 256 241 120 61 68 50 68 75 50 46 51 144 84 188 250 309
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=2/5; ncol2=17; w=-1; offset=-1; strand=D; shift=3; score=0.927477; ---haAACAAACAAAaAAaw ; cor=; Ncor= a 0 0 0 405 697 942 923 132 998 1016 999 120 991 1017 961 628 904 903 614 421 c 0 0 0 294 83 43 24 838 8 25 10 849 18 31 19 232 41 55 104 242 g 0 0 0 92 51 25 47 33 9 10 23 30 9 11 36 50 29 29 109 95 t 0 0 0 298 258 79 95 86 74 38 57 90 71 30 73 179 115 102 262 331
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=3/5; ncol2=17; w=-1; offset=-1; strand=D; shift=3; score=0.775527; ---wwATCAATCAAAAAaww ; cor=; Ncor= a 0 0 0 323 494 644 120 89 778 786 107 69 808 791 639 671 752 541 365 350 c 0 0 0 178 77 36 12 646 16 11 17 707 7 15 23 94 17 45 85 161 g 0 0 0 69 58 38 30 19 10 22 33 17 8 14 20 15 16 57 84 69 t 0 0 0 287 228 139 695 103 53 38 700 64 34 37 175 77 72 214 323 277
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=4/5; ncol2=20; w=-4; offset=-4; strand=D; shift=0; score=0.656805; wwAAAATCAATCAAAAAAww ; cor=; Ncor= a 200 220 307 344 391 377 60 48 390 383 68 69 389 400 323 335 365 348 184 177 c 52 46 25 39 4 8 7 324 7 10 17 300 7 5 10 40 9 13 49 75 g 33 44 19 12 4 8 16 11 5 12 17 8 9 5 10 14 7 14 38 32 t 142 117 76 32 28 34 344 44 25 22 325 50 22 17 84 38 46 52 156 143
oligos_6nt_test_vs_ctrl_m5_rc_shift2 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5_rc; m=5/5; ncol2=21; w=-2; offset=-2; strand=R; shift=2; score=0.64212; --ahwAACAAACAArCAArC ; cor=; Ncor= a 0 0 236 103 259 365 301 24 361 384 303 18 355 381 176 30 342 369 162 41 c 0 0 20 163 18 14 2 323 3 4 5 351 7 9 9 341 5 9 5 312 g 0 0 59 29 17 9 55 15 4 5 65 5 4 4 176 8 7 8 194 11 t 0 0 91 111 112 18 48 44 38 13 33 32 40 12 45 27 52 20 45 42

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=22; shift=0; ncol=22; dwTwgyTAGCTAGCTArywAwh ; Alignment reference a 177 137 72 256 112 64 31 428 59 24 37 403 75 25 19 408 248 81 161 342 189 115 c 32 90 14 11 18 125 9 4 4 347 8 5 5 363 2 5 15 240 25 25 38 128 g 130 36 25 25 243 15 5 2 366 5 5 8 350 4 4 9 126 18 11 14 90 31 t 114 190 342 161 80 249 408 19 24 77 403 37 23 61 428 31 64 114 256 72 136 179
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=1/3; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; dwTwgyTAGCTAGCTArywAwh ; cor=; Ncor= a 177 137 72 256 112 64 31 428 59 24 37 403 75 25 19 408 248 81 161 342 189 115 c 32 90 14 11 18 125 9 4 4 347 8 5 5 363 2 5 15 240 25 25 38 128 g 130 36 25 25 243 15 5 2 366 5 5 8 350 4 4 9 126 18 11 14 90 31 t 114 190 342 161 80 249 408 19 24 77 403 37 23 61 428 31 64 114 256 72 136 179
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/3; ncol2=19; w=0; offset=0; strand=R; shift=0; score=0.766021; dwTwgtTWGCTwGcTwght--- ; cor=; Ncor= a 175 154 59 214 88 85 17 427 23 39 23 193 27 72 27 366 135 177 138 0 0 0 c 43 104 24 13 23 113 9 5 8 424 11 9 5 397 10 17 27 151 49 0 0 0 g 207 45 29 22 398 27 14 9 537 6 9 9 539 12 17 18 333 44 43 0 0 0 t 165 287 478 341 81 365 550 149 22 121 547 379 19 109 536 189 95 218 360 0 0 0
oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/3; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.636876; --wwcTTAGCTAGCTwd----- ; cor=; Ncor= a 0 0 145 220 67 48 35 409 15 20 26 406 36 41 30 244 163 0 0 0 0 0 c 0 0 42 38 215 59 12 10 7 376 7 8 21 369 19 46 44 0 0 0 0 0 g 0 0 35 50 94 20 32 3 416 8 3 9 391 8 11 50 121 0 0 0 0 0 t 0 0 238 152 84 333 381 38 22 56 424 37 12 42 400 120 132 0 0 0 0 0