One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/05/18/peak-motifs.2026-05-18.125526_2026-05-18.125526_2J7kWa/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.2026-05-18.125526_2026-05-18.125526_2J7kWa/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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=17; shift=2; ncol=19; --wwTTTTTTGATTGATww ; Alignment reference a 0 0 723 924 323 166 213 466 94 92 179 1795 138 139 198 1856 353 642 721 c 0 0 174 211 96 34 48 50 35 24 35 85 49 34 37 76 68 176 185 g 0 0 399 200 79 47 266 53 43 31 1838 58 55 49 1817 54 98 185 492 t 0 0 953 914 1751 2002 1722 1680 2077 2102 197 311 2007 2027 197 263 1730 1246 851

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=17; w=0; offset=0; strand=D; shift=2; score= 1; --wwTTTTTTGATTGATww ; cor=; Ncor= a 0 0 723 924 323 166 213 466 94 92 179 1795 138 139 198 1856 353 642 721 c 0 0 174 211 96 34 48 50 35 24 35 85 49 34 37 76 68 176 185 g 0 0 399 200 79 47 266 53 43 31 1838 58 55 49 1817 54 98 185 492 t 0 0 953 914 1751 2002 1722 1680 2077 2102 197 311 2007 2027 197 263 1730 1246 851

oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.850023; --wwTTTTTTGcTTGCTww ; cor=; Ncor= a 0 0 554 544 267 155 185 131 79 147 114 198 116 186 169 215 277 584 601 c 0 0 186 253 89 35 48 121 40 27 22 1151 26 30 50 1231 68 155 175 g 0 0 290 190 93 46 198 39 40 26 1517 54 41 49 1346 47 64 151 363 t 0 0 740 783 1321 1534 1339 1479 1611 1570 117 367 1587 1505 205 277 1361 880 631

oligos_6nt_test_vs_ctrl_m4_rc_shift2 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.836656; --wwTTTTTTGAATgAww- ; cor=; Ncor= a 0 0 725 794 258 143 153 181 110 104 101 1642 1488 168 285 1558 865 716 0 c 0 0 179 173 69 35 22 30 33 20 30 66 61 36 61 65 156 162 0 g 0 0 232 190 53 41 65 40 50 41 1705 42 80 55 1281 62 195 204 0 t 0 0 813 792 1569 1730 1709 1698 1756 1784 113 199 320 1690 322 264 733 867 0

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=4/8; ncol2=21; w=-2; offset=-2; strand=R; shift=0; score=0.780553; wwhTTTTTTTGATTGATTt ; cor=; Ncor= a 306 336 282 222 103 105 117 215 54 67 87 840 46 53 115 875 81 83 166 c 90 97 326 55 24 22 30 24 25 12 23 37 21 16 29 47 13 27 42 g 106 109 148 40 27 19 156 19 28 18 876 33 25 14 811 22 24 28 188 t 586 546 332 771 934 942 785 830 981 991 102 178 996 1005 133 144 970 950 692

oligos_6nt_test_vs_ctrl_m1_rc_shift2 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/8; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.774691; --wwTTtTTTGTTTGTww- ; cor=; Ncor= a 0 0 894 807 293 203 364 157 127 118 337 143 141 130 317 309 736 784 0 c 0 0 245 250 121 40 57 58 29 27 50 85 23 24 50 134 160 164 0 g 0 0 543 285 140 67 483 61 59 34 2203 43 77 32 2131 91 273 212 0 t 0 0 1082 1422 2210 2454 1860 2488 2549 2585 174 2493 2523 2578 266 2230 1595 1604 0

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2_rc; m=6/8; ncol2=19; w=-2; offset=-2; strand=R; shift=0; score=0.720818; wwwTTTtTTTGTTTGTTtd ; cor=; Ncor= a 605 710 640 336 208 262 376 158 97 124 219 117 93 146 239 214 175 602 724 c 205 181 573 133 79 53 110 57 31 23 70 56 18 21 81 104 45 146 172 g 215 238 461 120 95 87 537 64 54 36 1903 39 53 26 1827 55 59 193 676 t 1392 1288 743 1828 2035 2015 1394 2138 2235 2234 225 2205 2253 2224 270 2044 2138 1476 845

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=7/8; ncol2=21; w=-2; offset=-2; strand=R; shift=0; score=0.66293; wwyTTTtTTTGcTTGcTTt ; cor=; Ncor= a 242 262 198 111 51 75 105 65 34 64 73 70 41 58 78 97 51 96 116 c 85 72 291 65 26 24 41 70 26 14 18 548 13 13 22 580 16 30 44 g 81 78 126 53 23 15 132 11 16 12 692 33 15 18 636 15 15 29 142 t 454 450 247 633 762 748 584 716 786 772 79 211 793 773 126 170 780 707 560

oligos_7nt_test_vs_ctrl_m1_rc_shift4 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=8/8; ncol2=14; w=0; offset=2; strand=R; shift=4; score=0.600519; ----twGTTTGTTTGTww- ; cor=; Ncor= a 0 0 0 0 810 987 475 290 243 339 192 224 257 371 247 391 882 999 0 c 0 0 0 0 230 186 97 132 77 35 40 99 66 41 62 144 203 224 0 g 0 0 0 0 410 291 2331 98 153 66 2983 51 116 59 2825 87 326 291 0 t 0 0 0 0 1880 1866 427 2810 2857 2890 115 2956 2891 2859 196 2708 1919 1816 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=19; shift=2; ncol=21; --haAACAAACAAAaAAAwww ; Alignment reference a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 1288 1392 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 238 215 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 181 205 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640 710 605

oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/7; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --haAACAAACAAAaAAAwww ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 1288 1392 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 238 215 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 181 205 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640 710 605

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=2/7; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.824629; ---wwACAAACAAAaAAww-- ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 0 0 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 0 0 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 0 0 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894 0 0

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/7; ncol2=21; w=-2; offset=-2; strand=D; shift=0; score=0.785898; wwaAAgCAAgCAAAaAAArww ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=4/7; ncol2=21; w=-2; offset=-2; strand=D; shift=0; score=0.756466; wwaAATCAATCAAAAAAAdww ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306

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=5/7; ncol2=17; w=0; offset=0; strand=D; shift=2; score=0.751065; --wwAGCAAgCAAAAAAww-- ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 0 0 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 0 0 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 0 0 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554 0 0

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/7; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.720818; --wwATCAATCAAAAAAww-- ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 0 0 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 0 0 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 0 0 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723 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=7/7; ncol2=14; w=0; offset=1; strand=D; shift=3; score=0.687449; ---wwACAAACAAACwa---- ; cor=; Ncor= a 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 0 0 0 0 c 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 0 0 0 0 g 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 0 0 0 0 t 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 8 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=21; shift=0; ncol=21; wwaAAgCAAgCAAAaAAArww ; Alignment reference a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242

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=1/7; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; wwaAAgCAAgCAAAaAAArww ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=2/7; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.879103; wwaAATCAATCAAAAAAAdww ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306

oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=3/7; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.785898; --haAACAAACAAAaAAAwww ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 1288 1392 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 238 215 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 181 205 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640 710 605

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=4/7; ncol2=17; w=0; offset=2; strand=D; shift=2; score=0.775264; --wwAGCAAgCAAAAAAww-- ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 0 0 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 0 0 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 0 0 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554 0 0

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/7; ncol2=17; w=0; offset=2; strand=R; shift=2; score=0.66293; --wwATCAATCAAAAAAww-- ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 0 0 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 0 0 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 0 0 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723 0 0

oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=6/7; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.645299; ---wwACAAACAAAaAAww-- ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 0 0 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 0 0 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 0 0 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894 0 0

oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1; m=7/7; ncol2=14; w=0; offset=7; strand=D; shift=7; score=0.511863; -------wwACAAACAAACwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 c 0 0 0 0 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 g 0 0 0 0 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 t 0 0 0 0 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift7 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=7; ncol=21; -------wwACAAACAAACwa ; Alignment reference a 0 0 0 0 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 c 0 0 0 0 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 g 0 0 0 0 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 t 0 0 0 0 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810

oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/7; ncol2=14; w=0; offset=0; strand=D; shift=7; score= 1; -------wwACAAACAAACwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 c 0 0 0 0 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 g 0 0 0 0 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 t 0 0 0 0 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810

oligos_6nt_test_vs_ctrl_m1_shift7 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/7; ncol2=16; w=0; offset=0; strand=D; shift=7; score=0.812215; -------wwACAAACAAAaAA ; cor=; Ncor= a 0 0 0 0 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 c 0 0 0 0 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 g 0 0 0 0 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 t 0 0 0 0 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293

oligos_7nt_test_vs_ctrl_m2_shift6 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=3/7; ncol2=19; w=-1; offset=-1; strand=D; shift=6; score=0.687449; ------haAACAAACAAAaAA ; cor=; Ncor= a 0 0 0 0 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 c 0 0 0 0 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 g 0 0 0 0 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 t 0 0 0 0 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208

oligos_6nt_test_vs_ctrl_m3_shift6 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/7; ncol2=17; w=-1; offset=-1; strand=D; shift=6; score=0.621406; ------wwAGCAAgCAAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 c 0 0 0 0 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 g 0 0 0 0 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 t 0 0 0 0 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267

oligos_6nt_test_vs_ctrl_m2_rc_shift6 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/7; ncol2=17; w=-1; offset=-1; strand=R; shift=6; score=0.600519; ------wwATCAATCAAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 c 0 0 0 0 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 g 0 0 0 0 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 t 0 0 0 0 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=6/7; ncol2=21; w=-7; offset=-7; strand=D; shift=0; score=0.511863; wwaAAgCAAgCAAAaAAArww ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=7/7; ncol2=21; w=-7; offset=-7; strand=D; shift=0; score=0.49374; wwaAATCAATCAAAAAAAdww ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; wwaAATCAATCAAAAAAAdww ; Alignment reference a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/8; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; wwaAATCAATCAAAAAAAdww ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=2/8; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.879103; wwaAAgCAAgCAAAaAAArww ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=3/8; ncol2=17; w=0; offset=2; strand=R; shift=2; score=0.780553; --wwATCAATCAAAAAAww-- ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 0 0 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 0 0 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 0 0 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723 0 0

oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=4/8; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.756466; --haAACAAACAAAaAAAwww ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 1288 1392 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 238 215 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 181 205 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640 710 605

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=5/8; ncol2=17; w=0; offset=2; strand=D; shift=2; score=0.671641; --wwAGCAAgCAAAAAAww-- ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 0 0 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 0 0 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 0 0 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554 0 0

oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=6/8; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.641631; ---wwTcATTCAAAAAAww-- ; cor=; Ncor= a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 0 0 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 0 0 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 0 0 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725 0 0

oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=7/8; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.623825; ---wwACAAACAAAaAAww-- ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 0 0 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 0 0 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 0 0 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894 0 0

oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=8/8; ncol2=14; w=0; offset=7; strand=D; shift=7; score=0.49374; -------wwACAAACAAACwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 c 0 0 0 0 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 g 0 0 0 0 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 t 0 0 0 0 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift2 ; 9 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=17; shift=2; ncol=19; --wwAGCAAgCAAAAAAww ; Alignment reference a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554

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=1/8; ncol2=17; w=0; offset=0; strand=D; shift=2; score= 1; --wwAGCAAgCAAAAAAww ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.850023; --wwATCAATCAAAAAAww ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723

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=3/8; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.801832; ---wwACAAACAAAaAAww ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=4/8; ncol2=21; w=-2; offset=-2; strand=D; shift=0; score=0.775264; wwaAAgCAAgCAAAaAAAr ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198

oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=5/8; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.751065; --haAACAAACAAAaAAAw ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640

oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=6/8; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.689974; ---wwTcATTCAAAAAAww ; cor=; Ncor= a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=7/8; ncol2=21; w=-2; offset=-2; strand=D; shift=0; score=0.671641; wwaAATCAATCAAAAAAAd ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282

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=8/8; ncol2=14; w=0; offset=1; strand=D; shift=3; score=0.621406; ---wwACAAACAAACwa-- ; cor=; Ncor= a 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 0 0 c 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 0 0 g 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 0 0 t 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift2 ; 3 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=12; shift=2; ncol=14; --wwAGATAGATww ; Alignment reference a 0 0 2150 1367 4055 477 4053 248 3994 379 4057 253 2122 1507 c 0 0 346 353 37 97 116 71 40 116 103 69 373 463 g 0 0 419 474 67 3507 47 123 51 3538 61 99 461 1025 t 0 0 1450 2171 206 284 149 3923 280 332 144 3944 1409 1370

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=1/2; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --wwAGATAGATww ; cor=; Ncor= a 0 0 2150 1367 4055 477 4053 248 3994 379 4057 253 2122 1507 c 0 0 346 353 37 97 116 71 40 116 103 69 373 463 g 0 0 419 474 67 3507 47 123 51 3538 61 99 461 1025 t 0 0 1450 2171 206 284 149 3923 280 332 144 3944 1409 1370

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=2/2; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.82213; wdATAGATAGATwd ; cor=; Ncor= a 1157 731 1771 133 1812 172 1943 64 1827 142 1926 126 1132 628 c 186 177 50 51 83 29 19 45 70 33 28 60 187 236 g 195 684 97 62 51 1879 59 34 38 1889 59 65 214 641 t 614 560 234 1906 206 72 131 2009 217 88 139 1901 619 647

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=16; shift=3; ncol=19; ---wwTcATTCAAAAAAww ; Alignment reference a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725

oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---wwTcATTCAAAAAAww ; cor=; Ncor= a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/5; ncol2=17; w=-1; offset=-1; strand=R; shift=2; score=0.836656; --wwATCAATCAAAAAAww ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723

oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/5; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.721528; ---wwACAAACAAAaAAww ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=4/5; ncol2=17; w=-1; offset=-1; strand=D; shift=2; score=0.689974; --wwAGCAAgCAAAAAAww ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=5/5; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.641631; wwaAATCAATCAAAAAAAd ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 3 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=14; shift=0; ncol=14; wdATAGATAGATwd ; Alignment reference a 1157 731 1771 133 1812 172 1943 64 1827 142 1926 126 1132 628 c 186 177 50 51 83 29 19 45 70 33 28 60 187 236 g 195 684 97 62 51 1879 59 34 38 1889 59 65 214 641 t 614 560 234 1906 206 72 131 2009 217 88 139 1901 619 647

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=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wdATAGATAGATwd ; cor=; Ncor= a 1157 731 1771 133 1812 172 1943 64 1827 142 1926 126 1132 628 c 186 177 50 51 83 29 19 45 70 33 28 60 187 236 g 195 684 97 62 51 1879 59 34 38 1889 59 65 214 641 t 614 560 234 1906 206 72 131 2009 217 88 139 1901 619 647

oligos_6nt_test_vs_ctrl_m5_shift2 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=2/2; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.82213; --wwAGATAGATww ; cor=; Ncor= a 0 0 2150 1367 4055 477 4053 248 3994 379 4057 253 2122 1507 c 0 0 346 353 37 97 116 71 40 116 103 69 373 463 g 0 0 419 474 67 3507 47 123 51 3538 61 99 461 1025 t 0 0 1450 2171 206 284 149 3923 280 332 144 3944 1409 1370

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift3 ; 9 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=16; shift=3; ncol=19; ---wwACAAACAAAaAAww ; Alignment reference a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894

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=1/8; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---wwACAAACAAAaAAww ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894

oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=2/8; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.824629; --haAACAAACAAAaAAAw ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640

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=3/8; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.812215; ---wwACAAACAAACwa-- ; cor=; Ncor= a 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 0 0 c 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 0 0 g 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 0 0 t 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810 0 0

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=4/8; ncol2=17; w=-1; offset=-1; strand=D; shift=2; score=0.801832; --wwAGCAAgCAAAAAAww ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=17; w=-1; offset=-1; strand=R; shift=2; score=0.774691; --wwATCAATCAAAAAAww ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723

oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=6/8; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.721528; ---wwTcATTCAAAAAAww ; cor=; Ncor= a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=7/8; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.645299; wwaAAgCAAgCAAAaAAAr ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=8/8; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.623825; wwaAATCAATCAAAAAAAd ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282

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=17; shift=2; ncol=19; --wwTTTTTTGATTGATww ; Alignment reference a 0 0 723 924 323 166 213 466 94 92 179 1795 138 139 198 1856 353 642 721 c 0 0 174 211 96 34 48 50 35 24 35 85 49 34 37 76 68 176 185 g 0 0 399 200 79 47 266 53 43 31 1838 58 55 49 1817 54 98 185 492 t 0 0 953 914 1751 2002 1722 1680 2077 2102 197 311 2007 2027 197 263 1730 1246 851
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=17; w=0; offset=0; strand=D; shift=2; score= 1; --wwTTTTTTGATTGATww ; cor=; Ncor= a 0 0 723 924 323 166 213 466 94 92 179 1795 138 139 198 1856 353 642 721 c 0 0 174 211 96 34 48 50 35 24 35 85 49 34 37 76 68 176 185 g 0 0 399 200 79 47 266 53 43 31 1838 58 55 49 1817 54 98 185 492 t 0 0 953 914 1751 2002 1722 1680 2077 2102 197 311 2007 2027 197 263 1730 1246 851
oligos_6nt_test_vs_ctrl_m3_rc_shift2 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.850023; --wwTTTTTTGcTTGCTww ; cor=; Ncor= a 0 0 554 544 267 155 185 131 79 147 114 198 116 186 169 215 277 584 601 c 0 0 186 253 89 35 48 121 40 27 22 1151 26 30 50 1231 68 155 175 g 0 0 290 190 93 46 198 39 40 26 1517 54 41 49 1346 47 64 151 363 t 0 0 740 783 1321 1534 1339 1479 1611 1570 117 367 1587 1505 205 277 1361 880 631
oligos_6nt_test_vs_ctrl_m4_rc_shift2 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.836656; --wwTTTTTTGAATgAww- ; cor=; Ncor= a 0 0 725 794 258 143 153 181 110 104 101 1642 1488 168 285 1558 865 716 0 c 0 0 179 173 69 35 22 30 33 20 30 66 61 36 61 65 156 162 0 g 0 0 232 190 53 41 65 40 50 41 1705 42 80 55 1281 62 195 204 0 t 0 0 813 792 1569 1730 1709 1698 1756 1784 113 199 320 1690 322 264 733 867 0
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=4/8; ncol2=21; w=-2; offset=-2; strand=R; shift=0; score=0.780553; wwhTTTTTTTGATTGATTt ; cor=; Ncor= a 306 336 282 222 103 105 117 215 54 67 87 840 46 53 115 875 81 83 166 c 90 97 326 55 24 22 30 24 25 12 23 37 21 16 29 47 13 27 42 g 106 109 148 40 27 19 156 19 28 18 876 33 25 14 811 22 24 28 188 t 586 546 332 771 934 942 785 830 981 991 102 178 996 1005 133 144 970 950 692
oligos_6nt_test_vs_ctrl_m1_rc_shift2 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/8; ncol2=16; w=0; offset=0; strand=R; shift=2; score=0.774691; --wwTTtTTTGTTTGTww- ; cor=; Ncor= a 0 0 894 807 293 203 364 157 127 118 337 143 141 130 317 309 736 784 0 c 0 0 245 250 121 40 57 58 29 27 50 85 23 24 50 134 160 164 0 g 0 0 543 285 140 67 483 61 59 34 2203 43 77 32 2131 91 273 212 0 t 0 0 1082 1422 2210 2454 1860 2488 2549 2585 174 2493 2523 2578 266 2230 1595 1604 0
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2_rc; m=6/8; ncol2=19; w=-2; offset=-2; strand=R; shift=0; score=0.720818; wwwTTTtTTTGTTTGTTtd ; cor=; Ncor= a 605 710 640 336 208 262 376 158 97 124 219 117 93 146 239 214 175 602 724 c 205 181 573 133 79 53 110 57 31 23 70 56 18 21 81 104 45 146 172 g 215 238 461 120 95 87 537 64 54 36 1903 39 53 26 1827 55 59 193 676 t 1392 1288 743 1828 2035 2015 1394 2138 2235 2234 225 2205 2253 2224 270 2044 2138 1476 845
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=7/8; ncol2=21; w=-2; offset=-2; strand=R; shift=0; score=0.66293; wwyTTTtTTTGcTTGcTTt ; cor=; Ncor= a 242 262 198 111 51 75 105 65 34 64 73 70 41 58 78 97 51 96 116 c 85 72 291 65 26 24 41 70 26 14 18 548 13 13 22 580 16 30 44 g 81 78 126 53 23 15 132 11 16 12 692 33 15 18 636 15 15 29 142 t 454 450 247 633 762 748 584 716 786 772 79 211 793 773 126 170 780 707 560
oligos_7nt_test_vs_ctrl_m1_rc_shift4 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=8/8; ncol2=14; w=0; offset=2; strand=R; shift=4; score=0.600519; ----twGTTTGTTTGTww- ; cor=; Ncor= a 0 0 0 0 810 987 475 290 243 339 192 224 257 371 247 391 882 999 0 c 0 0 0 0 230 186 97 132 77 35 40 99 66 41 62 144 203 224 0 g 0 0 0 0 410 291 2331 98 153 66 2983 51 116 59 2825 87 326 291 0 t 0 0 0 0 1880 1866 427 2810 2857 2890 115 2956 2891 2859 196 2708 1919 1816 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=19; shift=2; ncol=21; --haAACAAACAAAaAAAwww ; Alignment reference a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 1288 1392 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 238 215 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 181 205 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640 710 605
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/7; ncol2=19; w=0; offset=0; strand=D; shift=2; score= 1; --haAACAAACAAAaAAAwww ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 1288 1392 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 238 215 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 181 205 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640 710 605
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=2/7; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.824629; ---wwACAAACAAAaAAww-- ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 0 0 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 0 0 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 0 0 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894 0 0
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/7; ncol2=21; w=-2; offset=-2; strand=D; shift=0; score=0.785898; wwaAAgCAAgCAAAaAAArww ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=4/7; ncol2=21; w=-2; offset=-2; strand=D; shift=0; score=0.756466; wwaAATCAATCAAAAAAAdww ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306
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=5/7; ncol2=17; w=0; offset=0; strand=D; shift=2; score=0.751065; --wwAGCAAgCAAAAAAww-- ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 0 0 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 0 0 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 0 0 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554 0 0
oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/7; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.720818; --wwATCAATCAAAAAAww-- ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 0 0 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 0 0 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 0 0 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723 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=7/7; ncol2=14; w=0; offset=1; strand=D; shift=3; score=0.687449; ---wwACAAACAAACwa---- ; cor=; Ncor= a 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 0 0 0 0 c 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 0 0 0 0 g 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 0 0 0 0 t 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810 0 0 0 0

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=21; shift=0; ncol=21; wwaAAgCAAgCAAAaAAArww ; Alignment reference a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242
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=1/7; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; wwaAAgCAAgCAAAaAAArww ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=2/7; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.879103; wwaAATCAATCAAAAAAAdww ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=3/7; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.785898; --haAACAAACAAAaAAAwww ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 1288 1392 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 238 215 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 181 205 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640 710 605
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=4/7; ncol2=17; w=0; offset=2; strand=D; shift=2; score=0.775264; --wwAGCAAgCAAAAAAww-- ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 0 0 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 0 0 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 0 0 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554 0 0
oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/7; ncol2=17; w=0; offset=2; strand=R; shift=2; score=0.66293; --wwATCAATCAAAAAAww-- ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 0 0 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 0 0 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 0 0 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723 0 0
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=6/7; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.645299; ---wwACAAACAAAaAAww-- ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 0 0 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 0 0 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 0 0 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894 0 0
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1; m=7/7; ncol2=14; w=0; offset=7; strand=D; shift=7; score=0.511863; -------wwACAAACAAACwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 c 0 0 0 0 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 g 0 0 0 0 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 t 0 0 0 0 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=7; ncol=21; -------wwACAAACAAACwa ; Alignment reference a 0 0 0 0 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 c 0 0 0 0 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 g 0 0 0 0 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 t 0 0 0 0 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/7; ncol2=14; w=0; offset=0; strand=D; shift=7; score= 1; -------wwACAAACAAACwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 c 0 0 0 0 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 g 0 0 0 0 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 t 0 0 0 0 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810
oligos_6nt_test_vs_ctrl_m1_shift7 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/7; ncol2=16; w=0; offset=0; strand=D; shift=7; score=0.812215; -------wwACAAACAAAaAA ; cor=; Ncor= a 0 0 0 0 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 c 0 0 0 0 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 g 0 0 0 0 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 t 0 0 0 0 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293
oligos_7nt_test_vs_ctrl_m2_shift6 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=3/7; ncol2=19; w=-1; offset=-1; strand=D; shift=6; score=0.687449; ------haAACAAACAAAaAA ; cor=; Ncor= a 0 0 0 0 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 c 0 0 0 0 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 g 0 0 0 0 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 t 0 0 0 0 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208
oligos_6nt_test_vs_ctrl_m3_shift6 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/7; ncol2=17; w=-1; offset=-1; strand=D; shift=6; score=0.621406; ------wwAGCAAgCAAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 c 0 0 0 0 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 g 0 0 0 0 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 t 0 0 0 0 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267
oligos_6nt_test_vs_ctrl_m2_rc_shift6 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/7; ncol2=17; w=-1; offset=-1; strand=R; shift=6; score=0.600519; ------wwATCAATCAAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 c 0 0 0 0 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 g 0 0 0 0 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 t 0 0 0 0 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=6/7; ncol2=21; w=-7; offset=-7; strand=D; shift=0; score=0.511863; wwaAAgCAAgCAAAaAAArww ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=7/7; ncol2=21; w=-7; offset=-7; strand=D; shift=0; score=0.49374; wwaAATCAATCAAAAAAAdww ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; wwaAATCAATCAAAAAAAdww ; Alignment reference a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/8; ncol2=21; w=0; offset=0; strand=D; shift=0; score= 1; wwaAATCAATCAAAAAAAdww ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 546 586 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 109 106 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 97 90 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282 336 306
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=2/8; ncol2=21; w=0; offset=0; strand=D; shift=0; score=0.879103; wwaAAgCAAgCAAAaAAArww ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 450 454 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 78 81 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 72 85 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198 262 242
oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=3/8; ncol2=17; w=0; offset=2; strand=R; shift=2; score=0.780553; --wwATCAATCAAAAAAww-- ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 0 0 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 0 0 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 0 0 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723 0 0
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=4/8; ncol2=19; w=0; offset=2; strand=D; shift=2; score=0.756466; --haAACAAACAAAaAAAwww ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 1288 1392 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 238 215 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 181 205 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640 710 605
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=5/8; ncol2=17; w=0; offset=2; strand=D; shift=2; score=0.671641; --wwAGCAAgCAAAAAAww-- ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 0 0 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 0 0 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 0 0 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554 0 0
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=6/8; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.641631; ---wwTcATTCAAAAAAww-- ; cor=; Ncor= a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 0 0 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 0 0 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 0 0 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725 0 0
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=7/8; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.623825; ---wwACAAACAAAaAAww-- ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 0 0 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 0 0 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 0 0 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894 0 0
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=8/8; ncol2=14; w=0; offset=7; strand=D; shift=7; score=0.49374; -------wwACAAACAAACwa ; cor=; Ncor= a 0 0 0 0 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 c 0 0 0 0 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 g 0 0 0 0 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 t 0 0 0 0 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810

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=17; shift=2; ncol=19; --wwAGCAAgCAAAAAAww ; Alignment reference a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554
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=1/8; ncol2=17; w=0; offset=0; strand=D; shift=2; score= 1; --wwAGCAAgCAAAAAAww ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554
oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=2; score=0.850023; --wwATCAATCAAAAAAww ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723
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=3/8; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.801832; ---wwACAAACAAAaAAww ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=4/8; ncol2=21; w=-2; offset=-2; strand=D; shift=0; score=0.775264; wwaAAgCAAgCAAAaAAAr ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=5/8; ncol2=19; w=0; offset=0; strand=D; shift=2; score=0.751065; --haAACAAACAAAaAAAw ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=6/8; ncol2=16; w=0; offset=1; strand=D; shift=3; score=0.689974; ---wwTcATTCAAAAAAww ; cor=; Ncor= a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=7/8; ncol2=21; w=-2; offset=-2; strand=D; shift=0; score=0.671641; wwaAATCAATCAAAAAAAd ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282
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=8/8; ncol2=14; w=0; offset=1; strand=D; shift=3; score=0.621406; ---wwACAAACAAACwa-- ; cor=; Ncor= a 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 0 0 c 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 0 0 g 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 0 0 t 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=16; shift=3; ncol=19; ---wwTcATTCAAAAAAww ; Alignment reference a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/5; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---wwTcATTCAAAAAAww ; cor=; Ncor= a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725
oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/5; ncol2=17; w=-1; offset=-1; strand=R; shift=2; score=0.836656; --wwATCAATCAAAAAAww ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/5; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.721528; ---wwACAAACAAAaAAww ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=4/5; ncol2=17; w=-1; offset=-1; strand=D; shift=2; score=0.689974; --wwAGCAAgCAAAAAAww ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=5/5; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.641631; wwaAATCAATCAAAAAAAd ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282

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=16; shift=3; ncol=19; ---wwACAAACAAAaAAww ; Alignment reference a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894
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=1/8; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---wwACAAACAAAaAAww ; cor=; Ncor= a 0 0 0 1604 1595 2230 266 2578 2523 2493 174 2585 2549 2488 1860 2454 2210 1422 1082 c 0 0 0 212 273 91 2131 32 77 43 2203 34 59 61 483 67 140 285 543 g 0 0 0 164 160 134 50 24 23 85 50 27 29 58 57 40 121 250 245 t 0 0 0 784 736 309 317 130 141 143 337 118 127 157 364 203 293 807 894
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=2/8; ncol2=19; w=-1; offset=-1; strand=D; shift=2; score=0.824629; --haAACAAACAAAaAAAw ; cor=; Ncor= a 0 0 845 1476 2138 2044 270 2224 2253 2205 225 2234 2235 2138 1394 2015 2035 1828 743 c 0 0 676 193 59 55 1827 26 53 39 1903 36 54 64 537 87 95 120 461 g 0 0 172 146 45 104 81 21 18 56 70 23 31 57 110 53 79 133 573 t 0 0 724 602 175 214 239 146 93 117 219 124 97 158 376 262 208 336 640
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=3/8; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.812215; ---wwACAAACAAACwa-- ; cor=; Ncor= a 0 0 0 1816 1919 2708 196 2859 2891 2956 115 2890 2857 2810 427 1866 1880 0 0 c 0 0 0 291 326 87 2825 59 116 51 2983 66 153 98 2331 291 410 0 0 g 0 0 0 224 203 144 62 41 66 99 40 35 77 132 97 186 230 0 0 t 0 0 0 999 882 391 247 371 257 224 192 339 243 290 475 987 810 0 0
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=4/8; ncol2=17; w=-1; offset=-1; strand=D; shift=2; score=0.801832; --wwAGCAAgCAAAAAAww ; cor=; Ncor= a 0 0 631 880 1361 277 205 1505 1587 367 117 1570 1611 1479 1339 1534 1321 783 740 c 0 0 363 151 64 47 1346 49 41 54 1517 26 40 39 198 46 93 190 290 g 0 0 175 155 68 1231 50 30 26 1151 22 27 40 121 48 35 89 253 186 t 0 0 601 584 277 215 169 186 116 198 114 147 79 131 185 155 267 544 554
oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=17; w=-1; offset=-1; strand=R; shift=2; score=0.774691; --wwATCAATCAAAAAAww ; cor=; Ncor= a 0 0 851 1246 1730 263 197 2027 2007 311 197 2102 2077 1680 1722 2002 1751 914 953 c 0 0 492 185 98 54 1817 49 55 58 1838 31 43 53 266 47 79 200 399 g 0 0 185 176 68 76 37 34 49 85 35 24 35 50 48 34 96 211 174 t 0 0 721 642 353 1856 198 139 138 1795 179 92 94 466 213 166 323 924 723
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=6/8; ncol2=16; w=0; offset=0; strand=D; shift=3; score=0.721528; ---wwTcATTCAAAAAAww ; cor=; Ncor= a 0 0 0 867 733 264 322 1690 320 199 113 1784 1756 1698 1709 1730 1569 792 813 c 0 0 0 204 195 62 1281 55 80 42 1705 41 50 40 65 41 53 190 232 g 0 0 0 162 156 65 61 36 61 66 30 20 33 30 22 35 69 173 179 t 0 0 0 716 865 1558 285 168 1488 1642 101 104 110 181 153 143 258 794 725
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=7/8; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.645299; wwaAAgCAAgCAAAaAAAr ; cor=; Ncor= a 427 400 560 707 780 170 126 773 793 211 79 772 786 716 584 748 762 633 247 c 77 91 142 29 15 15 636 18 15 33 692 12 16 11 132 15 23 53 126 g 85 150 44 30 16 580 22 13 13 548 18 14 26 70 41 24 26 65 291 t 273 221 116 96 51 97 78 58 41 70 73 64 34 65 105 75 51 111 198
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=8/8; ncol2=21; w=-3; offset=-3; strand=D; shift=0; score=0.623825; wwaAATCAATCAAAAAAAd ; cor=; Ncor= a 555 447 692 950 970 144 133 1005 996 178 102 991 981 830 785 942 934 771 332 c 121 109 188 28 24 22 811 14 25 33 876 18 28 19 156 19 27 40 148 g 88 96 42 27 13 47 29 16 21 37 23 12 25 24 30 22 24 55 326 t 324 436 166 83 81 875 115 53 46 840 87 67 54 215 117 105 103 222 282