One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/05/18/peak-motifs.2026-05-18.120740_2026-05-18.120740_qxsUFj/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.2026-05-18.120740_2026-05-18.120740_qxsUFj/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 2 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=14; shift=0; ncol=14; waGCTAGCTAGCtw ; Alignment reference a 299 674 126 96 120 941 91 49 103 920 131 103 241 605 c 74 66 20 812 16 10 17 909 12 10 27 817 85 88 g 88 85 817 27 10 12 909 17 10 16 812 20 66 74 t 605 241 103 131 920 103 49 91 941 120 96 126 674 299

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=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; waGCTAGCTAGCtw ; cor=; Ncor= a 299 674 126 96 120 941 91 49 103 920 131 103 241 605 c 74 66 20 812 16 10 17 909 12 10 27 817 85 88 g 88 85 817 27 10 12 909 17 10 16 812 20 66 74 t 605 241 103 131 920 103 49 91 941 120 96 126 674 299

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift2 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --wwTCAtTCAww ; Alignment reference a 0 0 1445 1064 256 6 2583 589 186 7 2540 1121 838 c 0 0 300 360 117 2796 67 186 88 2791 56 380 288 g 0 0 240 286 75 0 54 131 32 1 44 231 191 t 0 0 820 1095 2357 3 101 1899 2499 6 165 1073 1488

oligos_6nt_test_vs_ctrl_m5_shift2 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wwTCAtTCAww ; cor=; Ncor= a 0 0 1445 1064 256 6 2583 589 186 7 2540 1121 838 c 0 0 300 360 117 2796 67 186 88 2791 56 380 288 g 0 0 240 286 75 0 54 131 32 1 44 231 191 t 0 0 820 1095 2357 3 101 1899 2499 6 165 1073 1488

oligos_7nt_test_vs_ctrl_m3_rc_shift1 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/3; ncol2=13; w=-1; offset=-1; strand=R; shift=1; score=0.756943; -hwTTCATTCATw ; cor=; Ncor= a 0 632 998 65 96 152 1816 43 100 145 1794 146 552 c 0 498 206 36 36 1527 33 29 16 1561 27 63 201 g 0 141 131 18 21 56 38 15 10 49 44 33 145 t 0 688 624 1840 1806 224 72 1872 1833 204 94 1717 1061

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=3/3; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.45246; wwwATCAATCAAA ; cor=; Ncor= a 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 c 124 269 104 33 26 968 23 34 56 1092 14 29 35 g 120 93 84 26 56 30 19 29 49 19 11 15 15 t 529 457 485 178 1039 157 108 81 1001 103 64 47 245

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=19; shift=2; ncol=21; --wwwAgCAAgCAAAAAamww ; Alignment reference a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/6; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --wwwAgCAAgCAAAAAamww ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=2/6; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.86363; --wwwATCAATCAAAAAahww ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414

oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/6; ncol2=18; w=0; offset=1; strand=D; shift=3; score=0.816844; ---wwmACAAACAAAAAAmww ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485

oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=4/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.748913; --whAAgCAAgCAAAcwa--- ; cor=; Ncor= a 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 0 0 c 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 0 0 g 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 0 0 t 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0 0 0

oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=5/6; ncol2=20; w=0; offset=1; strand=D; shift=3; score=0.701791; ---haAACAAACAAAmAAAcA ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=6/6; ncol2=23; w=-2; offset=-2; strand=D; shift=0; score=0.65819; wwhaAATCAATCAAAaAAwcA ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 8 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=23; shift=0; ncol=23; wwhaAATCAATCAAAaAAwcAaw ; Alignment reference a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 423 317 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 88 78 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 41 63 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86 165 259

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=1/7; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; wwhaAATCAATCAAAaAAwcAaw ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 423 317 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 88 78 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 41 63 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86 165 259

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=2/7; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.765157; --wwwATCAATCAAAAAahww-- ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 0 0 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 0 0 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 0 0 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414 0 0

oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=3/7; ncol2=20; w=0; offset=3; strand=D; shift=3; score=0.752182; ---haAACAAACAAAmAAAcAaw ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 872 762 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 131 146 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 99 123 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211 294 365

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=4/7; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.65819; --wwwAgCAAgCAAAAAamww-- ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 0 0 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 0 0 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 0 0 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339 0 0

oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=5/7; ncol2=18; w=0; offset=3; strand=D; shift=3; score=0.634997; ---wwmACAAACAAAAAAmww-- ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 0 0 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 0 0 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 0 0 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485 0 0

oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=6/7; ncol2=16; w=0; offset=2; strand=D; shift=2; score=0.55177; --whAAgCAAgCAAAcwa----- ; cor=; Ncor= a 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 0 0 0 0 c 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 0 0 0 0 g 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 0 0 0 0 t 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=7/7; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.400332; ---wwATGAATGAAwd------- ; cor=; Ncor= a 0 0 0 768 1061 1717 94 204 1833 1872 72 224 1806 1840 624 688 0 0 0 0 0 0 0 c 0 0 0 161 145 33 44 49 10 15 38 56 21 18 131 141 0 0 0 0 0 0 0 g 0 0 0 462 201 63 27 1561 16 29 33 1527 36 36 206 498 0 0 0 0 0 0 0 t 0 0 0 568 552 146 1794 145 100 43 1816 152 96 65 998 632 0 0 0 0 0 0 0

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=13; shift=3; ncol=16; ---wwATGAATGAAwd ; Alignment reference a 0 0 0 768 1061 1717 94 204 1833 1872 72 224 1806 1840 624 688 c 0 0 0 161 145 33 44 49 10 15 38 56 21 18 131 141 g 0 0 0 462 201 63 27 1561 16 29 33 1527 36 36 206 498 t 0 0 0 568 552 146 1794 145 100 43 1816 152 96 65 998 632

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=13; w=0; offset=0; strand=D; shift=3; score= 1; ---wwATGAATGAAwd ; cor=; Ncor= a 0 0 0 768 1061 1717 94 204 1833 1872 72 224 1806 1840 624 688 c 0 0 0 161 145 33 44 49 10 15 38 56 21 18 131 141 g 0 0 0 462 201 63 27 1561 16 29 33 1527 36 36 206 498 t 0 0 0 568 552 146 1794 145 100 43 1816 152 96 65 998 632

oligos_6nt_test_vs_ctrl_m5_rc_shift4 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/4; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.756943; ----wwTGAaTGAww- ; cor=; Ncor= a 0 0 0 0 1488 1073 165 6 2499 1899 101 3 2357 1095 820 0 c 0 0 0 0 191 231 44 1 32 131 54 0 75 286 240 0 g 0 0 0 0 288 380 56 2791 88 186 67 2796 117 360 300 0 t 0 0 0 0 838 1121 2540 7 186 589 2583 6 256 1064 1445 0

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=3/4; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.483871; --wwwATCAATCAAAA ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=4/4; ncol2=23; w=-3; offset=-3; strand=D; shift=0; score=0.400332; wwhaAATCAATCAAAa ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=19; shift=2; ncol=21; --wwwATCAATCAAAAAahww ; Alignment reference a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/8; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --wwwATCAATCAAAAAahww ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/8; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.86363; --wwwAgCAAgCAAAAAamww ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339

oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/8; ncol2=18; w=0; offset=1; strand=D; shift=3; score=0.789271; ---wwmACAAACAAAAAAmww ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=4/8; ncol2=23; w=-2; offset=-2; strand=D; shift=0; score=0.765157; wwhaAATCAATCAAAaAAwcA ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86

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=5/8; ncol2=20; w=0; offset=1; strand=D; shift=3; score=0.677617; ---haAACAAACAAAmAAAcA ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211

oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=6/8; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.63824; --whAAgCAAgCAAAcwa--- ; cor=; Ncor= a 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 0 0 c 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 0 0 g 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 0 0 t 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0 0 0

oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=7/8; ncol2=13; w=0; offset=1; strand=D; shift=3; score=0.483871; ---wwATGAATGAAwd----- ; cor=; Ncor= a 0 0 0 768 1061 1717 94 204 1833 1872 72 224 1806 1840 624 688 0 0 0 0 0 c 0 0 0 161 145 33 44 49 10 15 38 56 21 18 131 141 0 0 0 0 0 g 0 0 0 462 201 63 27 1561 16 29 33 1527 36 36 206 498 0 0 0 0 0 t 0 0 0 568 552 146 1794 145 100 43 1816 152 96 65 998 632 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=8/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.45246; ----wwTCAtTCAww------ ; cor=; Ncor= a 0 0 0 0 1445 1064 256 6 2583 589 186 7 2540 1121 838 0 0 0 0 0 0 c 0 0 0 0 300 360 117 2796 67 186 88 2791 56 380 288 0 0 0 0 0 0 g 0 0 0 0 240 286 75 0 54 131 32 1 44 231 191 0 0 0 0 0 0 t 0 0 0 0 820 1095 2357 3 101 1899 2499 6 165 1073 1488 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 2 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=14; shift=0; ncol=14; wwcTTAGCTAAgww ; Alignment reference a 509 450 177 63 123 1051 83 59 103 1034 1082 189 460 467 c 126 109 777 55 45 34 20 1064 28 21 19 85 196 116 g 118 197 85 19 21 28 1052 20 34 45 55 766 110 122 t 468 465 182 1084 1032 108 66 78 1056 121 65 181 455 516

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=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wwcTTAGCTAAgww ; cor=; Ncor= a 509 450 177 63 123 1051 83 59 103 1034 1082 189 460 467 c 126 109 777 55 45 34 20 1064 28 21 19 85 196 116 g 118 197 85 19 21 28 1052 20 34 45 55 766 110 122 t 468 465 182 1084 1032 108 66 78 1056 121 65 181 455 516

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift3 ; 7 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=18; shift=3; ncol=21; ---wwmACAAACAAAAAAmww ; Alignment reference a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485

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=1/6; ncol2=18; w=0; offset=0; strand=D; shift=3; score= 1; ---wwmACAAACAAAAAAmww ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485

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=2/6; ncol2=20; w=0; offset=0; strand=D; shift=3; score=0.843551; ---haAACAAACAAAmAAAcA ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=3/6; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.816844; --wwwAgCAAgCAAAAAamww ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=4/6; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.789271; --wwwATCAATCAAAAAahww ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=5/6; ncol2=23; w=-3; offset=-3; strand=D; shift=0; score=0.634997; wwhaAATCAATCAAAaAAwcA ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86

oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=6/6; ncol2=16; w=-1; offset=-1; strand=D; shift=2; score=0.607122; --whAAgCAAgCAAAcwa--- ; cor=; Ncor= a 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 0 0 c 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 0 0 g 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 0 0 t 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift3 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift3 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=16; shift=3; ncol=19; ---whAAgCAAgCAAAcwa ; Alignment reference a 0 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 c 0 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 g 0 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 t 0 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252

oligos_7nt_test_vs_ctrl_m5_shift3 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/6; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---whAAgCAAgCAAAcwa ; cor=; Ncor= a 0 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 c 0 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 g 0 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 t 0 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=2/6; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.748913; ---wwwAgCAAgCAAAAAa ; cor=; Ncor= a 0 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 c 0 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 g 0 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 t 0 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209

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=3/6; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.63824; ---wwwATCAATCAAAAAa ; cor=; Ncor= a 0 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 c 0 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 g 0 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 t 0 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=4/6; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.619565; haAACAAACAAAmAAAcAa ; cor=; Ncor= a 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 872 c 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 131 g 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 99 t 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211 294

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=5/6; ncol2=18; w=0; offset=1; strand=D; shift=4; score=0.607122; ----wwmACAAACAAAAAA ; cor=; Ncor= a 0 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 c 0 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 g 0 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 t 0 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=6/6; ncol2=23; w=-2; offset=-2; strand=D; shift=1; score=0.55177; -wwhaAATCAATCAAAaAA ; cor=; Ncor= a 0 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 c 0 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 g 0 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 t 0 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift3 ; 7 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=20; shift=3; ncol=23; ---haAACAAACAAAmAAAcAaw ; Alignment reference a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 872 762 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 131 146 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 99 123 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211 294 365

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=1/6; ncol2=20; w=0; offset=0; strand=D; shift=3; score= 1; ---haAACAAACAAAmAAAcAaw ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 872 762 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 131 146 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 99 123 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211 294 365

oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/6; ncol2=18; w=0; offset=0; strand=D; shift=3; score=0.843551; ---wwmACAAACAAAAAAmww-- ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 0 0 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 0 0 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 0 0 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485 0 0

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=3/6; ncol2=23; w=-3; offset=-3; strand=D; shift=0; score=0.752182; wwhaAATCAATCAAAaAAwcAaw ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 423 317 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 88 78 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 41 63 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86 165 259

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/6; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.701791; --wwwAgCAAgCAAAAAamww-- ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 0 0 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 0 0 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 0 0 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339 0 0

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=5/6; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.677617; --wwwATCAATCAAAAAahww-- ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 0 0 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 0 0 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 0 0 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414 0 0

oligos_7nt_test_vs_ctrl_m5_shift6 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=6/6; ncol2=16; w=0; offset=3; strand=D; shift=6; score=0.619565; ------whAAgCAAgCAAAcwa- ; cor=; Ncor= a 0 0 0 0 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 c 0 0 0 0 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 g 0 0 0 0 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 t 0 0 0 0 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift2 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --wwTCAtTCAww ; Alignment reference a 0 0 1445 1064 256 6 2583 589 186 7 2540 1121 838 c 0 0 300 360 117 2796 67 186 88 2791 56 380 288 g 0 0 240 286 75 0 54 131 32 1 44 231 191 t 0 0 820 1095 2357 3 101 1899 2499 6 165 1073 1488
oligos_6nt_test_vs_ctrl_m5_shift2 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wwTCAtTCAww ; cor=; Ncor= a 0 0 1445 1064 256 6 2583 589 186 7 2540 1121 838 c 0 0 300 360 117 2796 67 186 88 2791 56 380 288 g 0 0 240 286 75 0 54 131 32 1 44 231 191 t 0 0 820 1095 2357 3 101 1899 2499 6 165 1073 1488
oligos_7nt_test_vs_ctrl_m3_rc_shift1 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/3; ncol2=13; w=-1; offset=-1; strand=R; shift=1; score=0.756943; -hwTTCATTCATw ; cor=; Ncor= a 0 632 998 65 96 152 1816 43 100 145 1794 146 552 c 0 498 206 36 36 1527 33 29 16 1561 27 63 201 g 0 141 131 18 21 56 38 15 10 49 44 33 145 t 0 688 624 1840 1806 224 72 1872 1833 204 94 1717 1061
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=3/3; ncol2=19; w=-2; offset=-2; strand=D; shift=0; score=0.45246; wwwATCAATCAAA ; cor=; Ncor= a 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 c 124 269 104 33 26 968 23 34 56 1092 14 29 35 g 120 93 84 26 56 30 19 29 49 19 11 15 15 t 529 457 485 178 1039 157 108 81 1001 103 64 47 245

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=19; shift=2; ncol=21; --wwwAgCAAgCAAAAAamww ; Alignment reference a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/6; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --wwwAgCAAgCAAAAAamww ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=2/6; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.86363; --wwwATCAATCAAAAAahww ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/6; ncol2=18; w=0; offset=1; strand=D; shift=3; score=0.816844; ---wwmACAAACAAAAAAmww ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485
oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=4/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.748913; --whAAgCAAgCAAAcwa--- ; cor=; Ncor= a 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 0 0 c 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 0 0 g 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 0 0 t 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0 0 0
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=5/6; ncol2=20; w=0; offset=1; strand=D; shift=3; score=0.701791; ---haAACAAACAAAmAAAcA ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=6/6; ncol2=23; w=-2; offset=-2; strand=D; shift=0; score=0.65819; wwhaAATCAATCAAAaAAwcA ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86

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=23; shift=0; ncol=23; wwhaAATCAATCAAAaAAwcAaw ; Alignment reference a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 423 317 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 88 78 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 41 63 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86 165 259
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=1/7; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; wwhaAATCAATCAAAaAAwcAaw ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 423 317 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 88 78 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 41 63 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86 165 259
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=2/7; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.765157; --wwwATCAATCAAAAAahww-- ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 0 0 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 0 0 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 0 0 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414 0 0
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=3/7; ncol2=20; w=0; offset=3; strand=D; shift=3; score=0.752182; ---haAACAAACAAAmAAAcAaw ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 872 762 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 131 146 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 99 123 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211 294 365
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=4/7; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.65819; --wwwAgCAAgCAAAAAamww-- ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 0 0 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 0 0 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 0 0 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339 0 0
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=5/7; ncol2=18; w=0; offset=3; strand=D; shift=3; score=0.634997; ---wwmACAAACAAAAAAmww-- ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 0 0 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 0 0 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 0 0 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485 0 0
oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=6/7; ncol2=16; w=0; offset=2; strand=D; shift=2; score=0.55177; --whAAgCAAgCAAAcwa----- ; cor=; Ncor= a 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 0 0 0 0 c 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 0 0 0 0 g 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 0 0 0 0 t 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=7/7; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.400332; ---wwATGAATGAAwd------- ; cor=; Ncor= a 0 0 0 768 1061 1717 94 204 1833 1872 72 224 1806 1840 624 688 0 0 0 0 0 0 0 c 0 0 0 161 145 33 44 49 10 15 38 56 21 18 131 141 0 0 0 0 0 0 0 g 0 0 0 462 201 63 27 1561 16 29 33 1527 36 36 206 498 0 0 0 0 0 0 0 t 0 0 0 568 552 146 1794 145 100 43 1816 152 96 65 998 632 0 0 0 0 0 0 0

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=13; shift=3; ncol=16; ---wwATGAATGAAwd ; Alignment reference a 0 0 0 768 1061 1717 94 204 1833 1872 72 224 1806 1840 624 688 c 0 0 0 161 145 33 44 49 10 15 38 56 21 18 131 141 g 0 0 0 462 201 63 27 1561 16 29 33 1527 36 36 206 498 t 0 0 0 568 552 146 1794 145 100 43 1816 152 96 65 998 632
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=13; w=0; offset=0; strand=D; shift=3; score= 1; ---wwATGAATGAAwd ; cor=; Ncor= a 0 0 0 768 1061 1717 94 204 1833 1872 72 224 1806 1840 624 688 c 0 0 0 161 145 33 44 49 10 15 38 56 21 18 131 141 g 0 0 0 462 201 63 27 1561 16 29 33 1527 36 36 206 498 t 0 0 0 568 552 146 1794 145 100 43 1816 152 96 65 998 632
oligos_6nt_test_vs_ctrl_m5_rc_shift4 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/4; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.756943; ----wwTGAaTGAww- ; cor=; Ncor= a 0 0 0 0 1488 1073 165 6 2499 1899 101 3 2357 1095 820 0 c 0 0 0 0 191 231 44 1 32 131 54 0 75 286 240 0 g 0 0 0 0 288 380 56 2791 88 186 67 2796 117 360 300 0 t 0 0 0 0 838 1121 2540 7 186 589 2583 6 256 1064 1445 0
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=3/4; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.483871; --wwwATCAATCAAAA ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=4/4; ncol2=23; w=-3; offset=-3; strand=D; shift=0; score=0.400332; wwhaAATCAATCAAAa ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=19; shift=2; ncol=21; --wwwATCAATCAAAAAahww ; Alignment reference a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/8; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --wwwATCAATCAAAAAahww ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/8; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.86363; --wwwAgCAAgCAAAAAamww ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/8; ncol2=18; w=0; offset=1; strand=D; shift=3; score=0.789271; ---wwmACAAACAAAAAAmww ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=4/8; ncol2=23; w=-2; offset=-2; strand=D; shift=0; score=0.765157; wwhaAATCAATCAAAaAAwcA ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86
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=5/8; ncol2=20; w=0; offset=1; strand=D; shift=3; score=0.677617; ---haAACAAACAAAmAAAcA ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211
oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=6/8; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.63824; --whAAgCAAgCAAAcwa--- ; cor=; Ncor= a 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 0 0 c 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 0 0 g 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 0 0 t 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0 0 0
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=7/8; ncol2=13; w=0; offset=1; strand=D; shift=3; score=0.483871; ---wwATGAATGAAwd----- ; cor=; Ncor= a 0 0 0 768 1061 1717 94 204 1833 1872 72 224 1806 1840 624 688 0 0 0 0 0 c 0 0 0 161 145 33 44 49 10 15 38 56 21 18 131 141 0 0 0 0 0 g 0 0 0 462 201 63 27 1561 16 29 33 1527 36 36 206 498 0 0 0 0 0 t 0 0 0 568 552 146 1794 145 100 43 1816 152 96 65 998 632 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=8/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.45246; ----wwTCAtTCAww------ ; cor=; Ncor= a 0 0 0 0 1445 1064 256 6 2583 589 186 7 2540 1121 838 0 0 0 0 0 0 c 0 0 0 0 300 360 117 2796 67 186 88 2791 56 380 288 0 0 0 0 0 0 g 0 0 0 0 240 286 75 0 54 131 32 1 44 231 191 0 0 0 0 0 0 t 0 0 0 0 820 1095 2357 3 101 1899 2499 6 165 1073 1488 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=18; shift=3; ncol=21; ---wwmACAAACAAAAAAmww ; Alignment reference a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485
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=1/6; ncol2=18; w=0; offset=0; strand=D; shift=3; score= 1; ---wwmACAAACAAAAAAmww ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485
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=2/6; ncol2=20; w=0; offset=0; strand=D; shift=3; score=0.843551; ---haAACAAACAAAmAAAcA ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=3/6; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.816844; --wwwAgCAAgCAAAAAamww ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=4/6; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.789271; --wwwATCAATCAAAAAahww ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=5/6; ncol2=23; w=-3; offset=-3; strand=D; shift=0; score=0.634997; wwhaAATCAATCAAAaAAwcA ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86
oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=6/6; ncol2=16; w=-1; offset=-1; strand=D; shift=2; score=0.607122; --whAAgCAAgCAAAcwa--- ; cor=; Ncor= a 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 0 0 c 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 0 0 g 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 0 0 t 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift3 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=16; shift=3; ncol=19; ---whAAgCAAgCAAAcwa ; Alignment reference a 0 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 c 0 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 g 0 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 t 0 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252
oligos_7nt_test_vs_ctrl_m5_shift3 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/6; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---whAAgCAAgCAAAcwa ; cor=; Ncor= a 0 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 c 0 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 g 0 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 t 0 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=2/6; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.748913; ---wwwAgCAAgCAAAAAa ; cor=; Ncor= a 0 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 c 0 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 g 0 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 t 0 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209
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=3/6; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.63824; ---wwwATCAATCAAAAAa ; cor=; Ncor= a 0 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 c 0 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 g 0 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 t 0 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=4/6; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.619565; haAACAAACAAAmAAAcAa ; cor=; Ncor= a 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 872 c 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 131 g 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 99 t 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211 294
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=5/6; ncol2=18; w=0; offset=1; strand=D; shift=4; score=0.607122; ----wwmACAAACAAAAAA ; cor=; Ncor= a 0 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 c 0 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 g 0 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 t 0 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=6/6; ncol2=23; w=-2; offset=-2; strand=D; shift=1; score=0.55177; -wwhaAATCAATCAAAaAA ; cor=; Ncor= a 0 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 c 0 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 g 0 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 t 0 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54

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=20; shift=3; ncol=23; ---haAACAAACAAAmAAAcAaw ; Alignment reference a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 872 762 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 131 146 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 99 123 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211 294 365
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=1/6; ncol2=20; w=0; offset=0; strand=D; shift=3; score= 1; ---haAACAAACAAAmAAAcAaw ; cor=; Ncor= a 0 0 0 453 901 1177 1144 178 1265 1290 1241 124 1284 1296 1258 722 1238 1244 1084 348 1073 872 762 c 0 0 0 406 98 50 39 1042 17 33 26 1095 29 36 27 421 44 46 64 665 68 131 146 g 0 0 0 108 76 34 65 30 12 17 43 32 12 16 33 53 21 37 82 85 44 99 123 t 0 0 0 429 321 135 148 146 102 56 86 145 71 48 78 200 93 69 166 298 211 294 365
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/6; ncol2=18; w=0; offset=0; strand=D; shift=3; score=0.843551; ---wwmACAAACAAAAAAmww-- ; cor=; Ncor= a 0 0 0 634 877 711 1216 237 1384 1409 1360 104 1491 1492 1470 1212 1421 1105 654 687 814 0 0 c 0 0 0 349 136 501 58 1206 45 63 42 1369 24 38 37 199 48 126 485 247 165 0 0 g 0 0 0 132 125 76 77 44 22 26 57 32 13 16 20 44 31 95 109 140 146 0 0 t 0 0 0 495 472 322 259 123 159 112 151 105 82 64 83 155 110 284 362 536 485 0 0
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=3/6; ncol2=23; w=-3; offset=-3; strand=D; shift=0; score=0.752182; wwhaAATCAATCAAAaAAwcAaw ; cor=; Ncor= a 371 375 249 440 634 631 133 93 648 659 147 80 667 661 519 466 638 617 451 167 579 423 317 c 59 57 207 136 21 14 9 551 13 16 26 560 9 18 24 165 12 28 32 379 24 88 78 g 50 75 56 17 18 10 35 6 10 13 28 9 8 10 11 18 13 18 43 39 28 41 63 t 237 210 205 124 44 62 540 67 46 29 516 68 33 28 163 68 54 54 191 132 86 165 259
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/6; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.701791; --wwwAgCAAgCAAAAAamww-- ; cor=; Ncor= a 0 0 512 362 376 760 230 122 924 964 219 70 943 993 938 848 948 727 403 470 515 0 0 c 0 0 107 200 57 57 37 834 24 18 39 918 10 21 26 107 23 71 325 153 116 0 0 g 0 0 161 99 78 66 651 22 13 22 695 18 18 30 40 22 23 77 117 120 114 0 0 t 0 0 304 423 573 201 166 106 123 80 131 78 113 40 80 107 90 209 239 341 339 0 0
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=5/6; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.677617; --wwwATCAATCAAAAAahww-- ; cor=; Ncor= a 0 0 514 468 614 1050 166 132 1137 1143 181 73 1198 1196 992 1011 1154 831 400 569 644 0 0 c 0 0 124 269 104 33 26 968 23 34 56 1092 14 29 35 137 23 77 381 223 131 0 0 g 0 0 120 93 84 26 56 30 19 29 49 19 11 15 15 22 19 83 86 90 98 0 0 t 0 0 529 457 485 178 1039 157 108 81 1001 103 64 47 245 117 91 296 420 405 414 0 0
oligos_7nt_test_vs_ctrl_m5_shift6 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=6/6; ncol2=16; w=0; offset=3; strand=D; shift=6; score=0.619565; ------whAAgCAAgCAAAcwa- ; cor=; Ncor= a 0 0 0 0 0 0 562 368 867 1029 278 78 1089 1147 290 61 1063 1111 843 185 692 773 0 c 0 0 0 0 0 0 111 359 43 32 32 1048 15 12 28 1052 19 24 37 814 104 117 0 g 0 0 0 0 0 0 222 101 66 44 800 18 15 18 799 18 10 21 177 47 75 71 0 t 0 0 0 0 0 0 318 385 237 108 103 69 94 36 96 82 121 57 156 167 342 252 0