One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/10/peak-motifs.2026-01-10.165328_2026-01-10.165328_VAz8tE/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/10/peak-motifs.2026-01-10.165328_2026-01-10.165328_VAz8tE/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; scCAGGCCys ; Alignment reference a 693 856 41 3004 28 60 97 50 730 589 c 1009 1078 3305 226 404 50 3249 2995 955 934 g 893 777 43 163 2907 3278 42 377 802 1128 t 836 720 42 38 92 43 43 9 944 780

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; scCAGGCCys ; cor=; Ncor= a 693 856 41 3004 28 60 97 50 730 589 c 1009 1078 3305 226 404 50 3249 2995 955 934 g 893 777 43 163 2907 3278 42 377 802 1128 t 836 720 42 38 92 43 43 9 944 780

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wwATTTTTAww ; Alignment reference a 1630 1389 4867 262 414 329 339 359 4862 1632 1860 c 645 1011 107 125 155 162 259 154 102 833 952 g 1144 701 240 152 256 179 272 99 180 875 711 t 1953 2271 158 4833 4547 4702 4502 4760 228 2032 1849

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwATTTTTAww ; cor=; Ncor= a 1630 1389 4867 262 414 329 339 359 4862 1632 1860 c 645 1011 107 125 155 162 259 154 102 833 952 g 1144 701 240 152 256 179 272 99 180 875 711 t 1953 2271 158 4833 4547 4702 4502 4760 228 2032 1849

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ccCTTCCAgg ; Alignment reference a 0 706 583 112 24 30 31 3 2818 549 625 c 0 970 920 2668 9 6 2923 2885 38 626 651 g 0 614 736 48 175 16 6 57 104 1080 984 t 0 675 726 137 2757 2913 5 20 5 710 705

positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ccCTTCCAgg ; cor=; Ncor= a 0 706 583 112 24 30 31 3 2818 549 625 c 0 970 920 2668 9 6 2923 2885 38 626 651 g 0 614 736 48 175 16 6 57 104 1080 984 t 0 675 726 137 2757 2913 5 20 5 710 705

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.640923; ywCCTGCCAss ; cor=; Ncor= a 589 842 113 160 87 135 114 53 2548 524 662 c 833 670 2779 2752 194 80 2748 2762 147 910 834 g 758 661 92 118 155 2788 57 87 177 883 902 t 883 890 79 33 2627 60 144 161 191 746 665

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ctkcCAGGACCTkgv ; Alignment reference a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ctkcCAGGACCTkgv ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_6nt_mkv4_m1 versus positions_7nt_m1; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.986624; cttcCAGGACCTggv ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679

positions_6nt_m1_shift0 (positions_6nt_m1)
; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.976915; cttCCAGGACCTggv ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m2; m=4/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.974155; cttcCAGGACCTggv ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567

oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.547855; -wdCAAGGACmt--- ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 0 0 0 c 0 445 434 1896 158 90 24 45 34 2055 655 530 0 0 0 g 0 439 559 51 104 71 2008 2005 28 23 324 455 0 0 0 t 0 718 586 175 227 127 107 114 80 76 532 766 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; cttcCAGGACCTggv ; Alignment reference a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; cttcCAGGACCTggv ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.997057; cttCCAGGACCTggv ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; positions_7nt_m1 versus oligos_7nt_mkv5_m2; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.996395; cttcCAGGACCTggv ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; positions_7nt_m1 versus oligos_6nt_mkv4_m1; m=4/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.986624; ctkcCAGGACCTkgv ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736

oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; positions_7nt_m1 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.549099; -wdCAAGGACmt--- ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 0 0 0 c 0 445 434 1896 158 90 24 45 34 2055 655 530 0 0 0 g 0 439 559 51 104 71 2008 2005 28 23 324 455 0 0 0 t 0 718 586 175 227 127 107 114 80 76 532 766 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; wtTCTTTTTCwt ; Alignment reference a 1079 857 169 182 181 105 94 88 103 156 977 955 c 706 902 236 3176 173 172 111 205 123 3191 902 900 g 628 671 156 207 57 155 70 116 91 255 223 648 t 1426 1409 3278 274 3428 3407 3564 3430 3522 237 1737 1336

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wtTCTTTTTCwt ; cor=; Ncor= a 1079 857 169 182 181 105 94 88 103 156 977 955 c 706 902 236 3176 173 172 111 205 123 3191 902 900 g 628 671 156 207 57 155 70 116 91 255 223 648 t 1426 1409 3278 274 3428 3407 3564 3430 3522 237 1737 1336

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_7nt_mkv5_m5 versus oligos_6nt_mkv4_m2; m=2/2; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.475943; --ttCTTTTCtt ; cor=; Ncor= a 0 0 823 832 171 140 95 115 105 161 462 430 c 0 0 656 836 2973 54 56 67 47 3083 447 387 g 0 0 571 591 96 118 66 67 37 46 181 348 t 0 0 1300 1091 110 3038 3133 3101 3161 60 2260 2185

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; sstgCCCAGCCys ; Alignment reference a 670 921 819 303 143 116 56 3014 41 97 245 952 736 c 1369 1116 916 487 3491 3434 3624 300 126 3348 2800 1174 1190 g 971 1051 791 2554 136 194 124 364 3637 346 340 688 1251 t 851 773 1335 517 91 117 57 183 57 70 476 1047 684

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; sstgCCCAGCCys ; cor=; Ncor= a 670 921 819 303 143 116 56 3014 41 97 245 952 736 c 1369 1116 916 487 3491 3434 3624 300 126 3348 2800 1174 1190 g 971 1051 791 2554 136 194 124 364 3637 346 340 688 1251 t 851 773 1335 517 91 117 57 183 57 70 476 1047 684

oligos_6nt_mkv4_m5_rc_shift1 (oligos_6nt_mkv4_m5_rc)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m5_rc; m=2/2; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.787802; -cgGCCCTGCCys ; cor=; Ncor= a 0 902 831 155 178 130 84 245 49 96 139 881 702 c 0 1260 856 230 3244 3237 3452 290 212 3283 3259 1243 1108 g 0 933 1241 3198 150 196 156 359 3361 248 205 647 1191 t 0 703 870 215 226 235 106 2904 176 171 195 1027 797

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; cyCTCCTCyy ; Alignment reference a 745 543 46 53 128 33 110 18 554 553 c 901 1084 2967 26 2928 2966 40 3100 985 956 g 704 678 74 186 35 106 174 4 768 757 t 775 820 38 2860 34 20 2801 3 818 859

oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; cyCTCCTCyy ; cor=; Ncor= a 745 543 46 53 128 33 110 18 554 553 c 901 1084 2967 26 2928 2966 40 3100 985 956 g 704 678 74 186 35 106 174 4 768 757 t 775 820 38 2860 34 20 2801 3 818 859

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; arTGGACCAyw ; Alignment reference a 557 575 71 93 132 1629 104 103 1588 317 485 c 384 384 29 23 118 26 1450 1495 50 585 340 g 383 469 63 1555 1325 26 36 34 51 359 403 t 417 313 1578 70 166 60 151 109 52 480 513

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; arTGGACCAyw ; cor=; Ncor= a 557 575 71 93 132 1629 104 103 1588 317 485 c 384 384 29 23 118 26 1450 1495 50 585 340 g 383 469 63 1555 1325 26 36 34 51 359 403 t 417 313 1578 70 166 60 151 109 52 480 513

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=1; ncol=12; -wdCAAGGACmt ; Alignment reference a 0 602 625 82 1715 1916 65 40 2062 50 693 453 c 0 445 434 1896 158 90 24 45 34 2055 655 530 g 0 439 559 51 104 71 2008 2005 28 23 324 455 t 0 718 586 175 227 127 107 114 80 76 532 766

oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wdCAAGGACmt ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 c 0 445 434 1896 158 90 24 45 34 2055 655 530 g 0 439 559 51 104 71 2008 2005 28 23 324 455 t 0 718 586 175 227 127 107 114 80 76 532 766

positions_6nt_m1_shift0 (positions_6nt_m1)
; oligos_7nt_mkv5_m4 versus positions_6nt_m1; m=2/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.554605; cttCCAGGACCT ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 g 653 537 688 347 105 170 2945 2893 136 90 76 82 t 520 1266 1603 363 197 92 63 68 448 88 83 2697

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m2; m=3/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.55131; cttcCAGGACCT ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 g 621 502 650 361 131 129 2863 2810 131 95 73 70 t 505 1232 1641 406 220 89 61 58 415 86 84 2692

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_7nt_mkv5_m4 versus positions_7nt_m1; m=4/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.549099; cttcCAGGACCT ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 g 715 576 861 446 120 167 3316 3272 136 82 70 66 t 601 1416 1571 490 215 84 73 65 526 106 97 3092

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m1; m=5/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.547855; ctkcCAGGACCT ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 t 599 1514 989 491 212 97 71 66 495 131 122 3104

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -srGGCAGGGCcg ; Alignment reference a 0 797 1027 195 171 176 2904 106 235 226 215 870 703 c 0 1191 647 205 248 3361 359 156 196 150 3198 1241 933 g 0 1108 1243 3259 3283 212 290 3452 3237 3244 230 856 1260 t 0 702 881 139 96 49 245 84 130 178 155 831 902

oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -srGGCAGGGCcg ; cor=; Ncor= a 0 797 1027 195 171 176 2904 106 235 226 215 870 703 c 0 1191 647 205 248 3361 359 156 196 150 3198 1241 933 g 0 1108 1243 3259 3283 212 290 3452 3237 3244 230 856 1260 t 0 702 881 139 96 49 245 84 130 178 155 831 902

oligos_6nt_mkv4_m4_rc_shift1 (oligos_6nt_mkv4_m4_rc)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m4_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=1; score=0.787802; -srGGCTGGGcas ; cor=; Ncor= a 0 684 1047 476 70 57 183 57 117 91 517 1335 773 c 0 1251 688 340 346 3637 364 124 194 136 2554 791 1051 g 0 1190 1174 2800 3348 126 300 3624 3434 3491 487 916 1116 t 0 736 952 245 97 41 3014 56 116 143 303 819 921

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; oligos_6nt_mkv4_m5 versus positions_6nt_m4_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.616417; ssTGGCAGGwr-- ; cor=; Ncor= a 665 746 191 161 144 60 2627 33 79 890 883 0 0 c 902 883 177 87 57 2788 155 118 92 661 758 0 0 g 834 910 147 2762 2748 80 194 2752 2779 670 833 0 0 t 662 524 2548 53 114 135 87 160 113 842 589 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; rsAGGATCdy ; Alignment reference a 469 394 1573 33 83 1729 62 32 458 346 c 442 574 136 139 26 19 49 1719 406 544 g 539 487 41 1579 1646 22 20 14 455 395 t 348 343 48 47 43 28 1667 33 479 513

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; rsAGGATCdy ; cor=; Ncor= a 469 394 1573 33 83 1729 62 32 458 346 c 442 574 136 139 26 19 49 1719 406 544 g 539 487 41 1579 1646 22 20 14 455 395 t 348 343 48 47 43 28 1667 33 479 513

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --ywCCTGCCAss ; Alignment reference a 0 0 589 842 113 160 87 135 114 53 2548 524 662 c 0 0 833 670 2779 2752 194 80 2748 2762 147 910 834 g 0 0 758 661 92 118 155 2788 57 87 177 883 902 t 0 0 883 890 79 33 2627 60 144 161 191 746 665

positions_6nt_m4_shift2 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --ywCCTGCCAss ; cor=; Ncor= a 0 0 589 842 113 160 87 135 114 53 2548 524 662 c 0 0 833 670 2779 2752 194 80 2748 2762 147 910 834 g 0 0 758 661 92 118 155 2788 57 87 177 883 902 t 0 0 883 890 79 33 2627 60 144 161 191 746 665

positions_6nt_m3_shift3 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.640923; ---ccCTTCCAgg ; cor=; Ncor= a 0 0 0 706 583 112 24 30 31 3 2818 549 625 c 0 0 0 970 920 2668 9 6 2923 2885 38 626 651 g 0 0 0 614 736 48 175 16 6 57 104 1080 984 t 0 0 0 675 726 137 2757 2913 5 20 5 710 705

oligos_6nt_mkv4_m5_rc_shift0 (oligos_6nt_mkv4_m5_rc)
; positions_6nt_m4 versus oligos_6nt_mkv4_m5_rc; m=3/3; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.616417; cgGCCCTGCCys- ; cor=; Ncor= a 902 831 155 178 130 84 245 49 96 139 881 702 0 c 1260 856 230 3244 3237 3452 290 212 3283 3259 1243 1108 0 g 933 1241 3198 150 196 156 359 3361 248 205 647 1191 0 t 703 870 215 226 235 106 2904 176 171 195 1027 797 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; cttCCAGGACCTggv ; Alignment reference a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; cttCCAGGACCTggv ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; positions_6nt_m1 versus oligos_7nt_mkv5_m2; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.999265; cttcCAGGACCTggv ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.997057; cttcCAGGACCTggv ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; positions_6nt_m1 versus oligos_6nt_mkv4_m1; m=4/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.976915; ctkcCAGGACCTkgv ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736

oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; positions_6nt_m1 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.554605; -wdCAAGGACmt--- ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 0 0 0 c 0 445 434 1896 158 90 24 45 34 2055 655 530 0 0 0 g 0 439 559 51 104 71 2008 2005 28 23 324 455 0 0 0 t 0 718 586 175 227 127 107 114 80 76 532 766 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --ttCTTTTCttttw ; Alignment reference a 0 0 823 832 171 140 95 115 105 161 462 430 833 800 902 c 0 0 656 836 2973 54 56 67 47 3083 447 387 644 780 827 g 0 0 571 591 96 118 66 67 37 46 181 348 464 593 503 t 0 0 1300 1091 110 3038 3133 3101 3161 60 2260 2185 1409 1177 1118

oligos_6nt_mkv4_m2_shift2 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --ttCTTTTCttttw ; cor=; Ncor= a 0 0 823 832 171 140 95 115 105 161 462 430 833 800 902 c 0 0 656 836 2973 54 56 67 47 3083 447 387 644 780 827 g 0 0 571 591 96 118 66 67 37 46 181 348 464 593 503 t 0 0 1300 1091 110 3038 3133 3101 3161 60 2260 2185 1409 1177 1118

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_6nt_mkv4_m2 versus oligos_7nt_mkv5_m5; m=2/2; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.475943; wtTCTTTTTCwt--- ; cor=; Ncor= a 1079 857 169 182 181 105 94 88 103 156 977 955 0 0 0 c 706 902 236 3176 173 172 111 205 123 3191 902 900 0 0 0 g 628 671 156 207 57 155 70 116 91 255 223 648 0 0 0 t 1426 1409 3278 274 3428 3407 3564 3430 3522 237 1737 1336 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; cttcCAGGACCTggv ; Alignment reference a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; cttcCAGGACCTggv ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567

positions_6nt_m1_shift0 (positions_6nt_m1)
; oligos_7nt_mkv5_m2 versus positions_6nt_m1; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.999265; cttCCAGGACCTggv ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_7nt_mkv5_m2 versus positions_7nt_m1; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.996395; cttcCAGGACCTggv ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=4/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.974155; ctkcCAGGACCTkgv ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736

oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.55131; -wdCAAGGACmt--- ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 0 0 0 c 0 445 434 1896 158 90 24 45 34 2055 655 530 0 0 0 g 0 439 559 51 104 71 2008 2005 28 23 324 455 0 0 0 t 0 718 586 175 227 127 107 114 80 76 532 766 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ctkcCAGGACCTkgv ; Alignment reference a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ctkcCAGGACCTkgv ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_6nt_mkv4_m1 versus positions_7nt_m1; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.986624; cttcCAGGACCTggv ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679
positions_6nt_m1_shift0 (positions_6nt_m1)				; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.976915; cttCCAGGACCTggv ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m2; m=4/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.974155; cttcCAGGACCTggv ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.547855; -wdCAAGGACmt--- ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 0 0 0 c 0 445 434 1896 158 90 24 45 34 2055 655 530 0 0 0 g 0 439 559 51 104 71 2008 2005 28 23 324 455 0 0 0 t 0 718 586 175 227 127 107 114 80 76 532 766 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; cttcCAGGACCTggv ; Alignment reference a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; cttcCAGGACCTggv ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.997057; cttCCAGGACCTggv ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; positions_7nt_m1 versus oligos_7nt_mkv5_m2; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.996395; cttcCAGGACCTggv ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; positions_7nt_m1 versus oligos_6nt_mkv4_m1; m=4/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.986624; ctkcCAGGACCTkgv ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; positions_7nt_m1 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.549099; -wdCAAGGACmt--- ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 0 0 0 c 0 445 434 1896 158 90 24 45 34 2055 655 530 0 0 0 g 0 439 559 51 104 71 2008 2005 28 23 324 455 0 0 0 t 0 718 586 175 227 127 107 114 80 76 532 766 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=1; ncol=12; -wdCAAGGACmt ; Alignment reference a 0 602 625 82 1715 1916 65 40 2062 50 693 453 c 0 445 434 1896 158 90 24 45 34 2055 655 530 g 0 439 559 51 104 71 2008 2005 28 23 324 455 t 0 718 586 175 227 127 107 114 80 76 532 766
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wdCAAGGACmt ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 c 0 445 434 1896 158 90 24 45 34 2055 655 530 g 0 439 559 51 104 71 2008 2005 28 23 324 455 t 0 718 586 175 227 127 107 114 80 76 532 766
positions_6nt_m1_shift0 (positions_6nt_m1)				; oligos_7nt_mkv5_m4 versus positions_6nt_m1; m=2/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.554605; cttCCAGGACCT ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 g 653 537 688 347 105 170 2945 2893 136 90 76 82 t 520 1266 1603 363 197 92 63 68 448 88 83 2697
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m2; m=3/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.55131; cttcCAGGACCT ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 g 621 502 650 361 131 129 2863 2810 131 95 73 70 t 505 1232 1641 406 220 89 61 58 415 86 84 2692
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_7nt_mkv5_m4 versus positions_7nt_m1; m=4/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.549099; cttcCAGGACCT ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 g 715 576 861 446 120 167 3316 3272 136 82 70 66 t 601 1416 1571 490 215 84 73 65 526 106 97 3092
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m1; m=5/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.547855; ctkcCAGGACCT ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 t 599 1514 989 491 212 97 71 66 495 131 122 3104

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -srGGCAGGGCcg ; Alignment reference a 0 797 1027 195 171 176 2904 106 235 226 215 870 703 c 0 1191 647 205 248 3361 359 156 196 150 3198 1241 933 g 0 1108 1243 3259 3283 212 290 3452 3237 3244 230 856 1260 t 0 702 881 139 96 49 245 84 130 178 155 831 902
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -srGGCAGGGCcg ; cor=; Ncor= a 0 797 1027 195 171 176 2904 106 235 226 215 870 703 c 0 1191 647 205 248 3361 359 156 196 150 3198 1241 933 g 0 1108 1243 3259 3283 212 290 3452 3237 3244 230 856 1260 t 0 702 881 139 96 49 245 84 130 178 155 831 902
oligos_6nt_mkv4_m4_rc_shift1 (oligos_6nt_mkv4_m4_rc)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m4_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=1; score=0.787802; -srGGCTGGGcas ; cor=; Ncor= a 0 684 1047 476 70 57 183 57 117 91 517 1335 773 c 0 1251 688 340 346 3637 364 124 194 136 2554 791 1051 g 0 1190 1174 2800 3348 126 300 3624 3434 3491 487 916 1116 t 0 736 952 245 97 41 3014 56 116 143 303 819 921
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; oligos_6nt_mkv4_m5 versus positions_6nt_m4_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.616417; ssTGGCAGGwr-- ; cor=; Ncor= a 665 746 191 161 144 60 2627 33 79 890 883 0 0 c 902 883 177 87 57 2788 155 118 92 661 758 0 0 g 834 910 147 2762 2748 80 194 2752 2779 670 833 0 0 t 662 524 2548 53 114 135 87 160 113 842 589 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --ywCCTGCCAss ; Alignment reference a 0 0 589 842 113 160 87 135 114 53 2548 524 662 c 0 0 833 670 2779 2752 194 80 2748 2762 147 910 834 g 0 0 758 661 92 118 155 2788 57 87 177 883 902 t 0 0 883 890 79 33 2627 60 144 161 191 746 665
positions_6nt_m4_shift2 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --ywCCTGCCAss ; cor=; Ncor= a 0 0 589 842 113 160 87 135 114 53 2548 524 662 c 0 0 833 670 2779 2752 194 80 2748 2762 147 910 834 g 0 0 758 661 92 118 155 2788 57 87 177 883 902 t 0 0 883 890 79 33 2627 60 144 161 191 746 665
positions_6nt_m3_shift3 (positions_6nt_m3)				; positions_6nt_m4 versus positions_6nt_m3; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.640923; ---ccCTTCCAgg ; cor=; Ncor= a 0 0 0 706 583 112 24 30 31 3 2818 549 625 c 0 0 0 970 920 2668 9 6 2923 2885 38 626 651 g 0 0 0 614 736 48 175 16 6 57 104 1080 984 t 0 0 0 675 726 137 2757 2913 5 20 5 710 705
oligos_6nt_mkv4_m5_rc_shift0 (oligos_6nt_mkv4_m5_rc)				; positions_6nt_m4 versus oligos_6nt_mkv4_m5_rc; m=3/3; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.616417; cgGCCCTGCCys- ; cor=; Ncor= a 902 831 155 178 130 84 245 49 96 139 881 702 0 c 1260 856 230 3244 3237 3452 290 212 3283 3259 1243 1108 0 g 933 1241 3198 150 196 156 359 3361 248 205 647 1191 0 t 703 870 215 226 235 106 2904 176 171 195 1027 797 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; cttCCAGGACCTggv ; Alignment reference a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; cttCCAGGACCTggv ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; positions_6nt_m1 versus oligos_7nt_mkv5_m2; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.999265; cttcCAGGACCTggv ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.997057; cttcCAGGACCTggv ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; positions_6nt_m1 versus oligos_6nt_mkv4_m1; m=4/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.976915; ctkcCAGGACCTkgv ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; positions_6nt_m1 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.554605; -wdCAAGGACmt--- ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 0 0 0 c 0 445 434 1896 158 90 24 45 34 2055 655 530 0 0 0 g 0 439 559 51 104 71 2008 2005 28 23 324 455 0 0 0 t 0 718 586 175 227 127 107 114 80 76 532 766 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; cttcCAGGACCTggv ; Alignment reference a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; cttcCAGGACCTggv ; cor=; Ncor= a 491 620 366 312 268 2749 65 81 2367 97 88 84 235 617 775 c 1418 681 378 1956 2416 68 46 86 122 2757 2790 189 253 676 882 g 621 502 650 361 131 129 2863 2810 131 95 73 70 1996 1021 811 t 505 1232 1641 406 220 89 61 58 415 86 84 2692 551 721 567
positions_6nt_m1_shift0 (positions_6nt_m1)				; oligos_7nt_mkv5_m2 versus positions_6nt_m1; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.999265; cttCCAGGACCTggv ; cor=; Ncor= a 507 628 395 255 270 2799 75 86 2422 100 98 122 273 650 814 c 1455 704 449 2170 2563 74 52 88 129 2857 2878 234 288 727 902 g 653 537 688 347 105 170 2945 2893 136 90 76 82 1997 1039 828 t 520 1266 1603 363 197 92 63 68 448 88 83 2697 577 719 591
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_7nt_mkv5_m2 versus positions_7nt_m1; m=3/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.996395; cttcCAGGACCTggv ; cor=; Ncor= a 600 754 488 390 268 3199 77 85 2721 100 108 97 375 722 910 c 1601 771 597 2191 2914 67 51 95 134 3229 3242 262 437 788 1026 g 715 576 861 446 120 167 3316 3272 136 82 70 66 1876 1161 902 t 601 1416 1571 490 215 84 73 65 526 106 97 3092 829 846 679
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=4/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.974155; ctkcCAGGACCTkgv ; cor=; Ncor= a 645 943 444 486 261 3532 79 87 3039 100 88 191 515 771 1000 c 1820 729 585 2311 3287 84 78 117 179 3569 3609 449 706 882 1111 g 840 718 1886 616 144 191 3676 3634 191 104 85 160 1647 1331 1057 t 599 1514 989 491 212 97 71 66 495 131 122 3104 1036 920 736
oligos_7nt_mkv5_m4_shift1 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.55131; -wdCAAGGACmt--- ; cor=; Ncor= a 0 602 625 82 1715 1916 65 40 2062 50 693 453 0 0 0 c 0 445 434 1896 158 90 24 45 34 2055 655 530 0 0 0 g 0 439 559 51 104 71 2008 2005 28 23 324 455 0 0 0 t 0 718 586 175 227 127 107 114 80 76 532 766 0 0 0