One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204313_2025-11-26.204313_HfPHmA/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/2025/11/26/peak-motifs.2025-11-26.204313_2025-11-26.204313_HfPHmA/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=16; shift=3; ncol=19; ---GAATGGAATGGAATGG ; Alignment reference a 0 0 0 1318 14612 13710 810 810 960 15844 14887 625 592 549 15896 15137 672 881 2449 c 0 0 0 845 992 1019 870 2379 680 161 339 552 664 652 149 436 508 2582 766 g 0 0 0 12959 284 1274 203 12414 14353 121 885 205 14626 14894 110 519 155 12209 12596 t 0 0 0 1252 486 371 14491 771 381 248 263 14992 492 279 219 282 15039 702 563

oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---GAATGGAATGGAATGG ; cor=; Ncor= a 0 0 0 1318 14612 13710 810 810 960 15844 14887 625 592 549 15896 15137 672 881 2449 c 0 0 0 845 992 1019 870 2379 680 161 339 552 664 652 149 436 508 2582 766 g 0 0 0 12959 284 1274 203 12414 14353 121 885 205 14626 14894 110 519 155 12209 12596 t 0 0 0 1252 486 371 14491 771 381 248 263 14992 492 279 219 282 15039 702 563

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2; m=2/3; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.79986; ATGGAATGGAATGGAATGG ; cor=; Ncor= a 12791 1403 1614 1215 15333 13899 849 847 900 16201 15101 700 643 618 16290 15273 813 882 2632 c 1133 1634 1858 730 882 1060 929 2273 713 184 383 601 726 794 147 505 563 2884 755 g 1837 395 12438 13687 209 1414 209 12744 14759 138 997 171 14933 15060 133 691 159 12343 12909 t 1023 13352 874 1152 360 411 14797 920 412 261 303 15312 482 312 214 315 15249 675 488

oligos_6nt_mkv3_m2_rc_shift3 (oligos_6nt_mkv3_m2_rc)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2_rc; m=3/3; ncol2=19; w=0; offset=0; strand=R; shift=3; score=0.757468; ---gAATsGAATGGAmwGs ; cor=; Ncor= a 0 0 0 116 929 965 39 208 77 1047 1169 30 12 14 1270 672 789 11 78 c 0 0 0 211 191 66 143 333 195 169 45 67 19 19 10 578 31 128 624 g 0 0 0 765 80 212 87 699 968 42 60 46 1259 1244 2 31 13 1123 535 t 0 0 0 206 98 55 1029 58 58 40 24 1155 8 21 16 17 465 36 61

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=17; shift=1; ncol=18; -skGGcGCTGTCCrtGGt ; Alignment reference a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663

oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -skGGcGCTGTCCrtGGt ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663

oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.990797; -bgGGmGCTGTCCatGGt ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 76 58 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 102 131 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 649 115 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86 86 609

positions_7nt_m2_shift1 (positions_7nt_m2)
; oligos_7nt_mkv4_m3 versus positions_7nt_m2; m=3/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.854041; -bgggmGCTGTCCatg-- ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 0 0 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 0 0 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 0 0 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153 0 0

positions_7nt_m3_shift3 (positions_7nt_m3)
; oligos_7nt_mkv4_m3 versus positions_7nt_m3; m=4/8; ncol2=13; w=0; offset=2; strand=D; shift=3; score=0.732669; ---rghGCTGTCCAtg-- ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0

positions_6nt_m1_shift0 (positions_6nt_m1)
; oligos_7nt_mkv4_m3 versus positions_6nt_m1; m=5/8; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.656948; ssgGGaGCTGTCCATGGw ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 3 30 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 9 7 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 52 12 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2 3 18

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=6/8; ncol2=24; w=0; offset=1; strand=D; shift=2; score=0.621099; --kGgcgCTGTCCrtGGT ; cor=; Ncor= a 0 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 7 5 c 0 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 2 2 g 0 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 774 2 t 0 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8 2 776

positions_6nt_m5_shift2 (positions_6nt_m5)
; oligos_7nt_mkv4_m3 versus positions_6nt_m5; m=7/8; ncol2=24; w=0; offset=1; strand=D; shift=2; score=0.584847; --ssGmGCTGtCCatGGa ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 2 26 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 9 10 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 46 11 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1 1 11

oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m4_rc; m=8/8; ncol2=23; w=0; offset=2; strand=R; shift=3; score=0.584226; ---GgmgCTGTCCrtGGT ; cor=; Ncor= a 0 0 0 110 58 193 84 17 4 27 18 1 4 334 134 22 7 5 c 0 0 0 33 161 383 74 731 9 104 21 744 738 85 104 7 1 5 g 0 0 0 550 452 23 516 6 11 632 44 8 4 257 72 731 756 2 t 0 0 0 74 96 168 93 13 743 4 684 14 21 91 457 7 3 755

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssGmGCTGtCCatGGaCAGCgcsc ; Alignment reference a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 2 26 4 44 4 4 9 5 9 9 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 9 10 51 8 8 42 4 35 22 24 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 46 11 3 4 40 9 33 13 19 14 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1 1 11 0 2 6 3 12 5 8 11

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssGmGCTGtCCatGGaCAGCgcsc ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 2 26 4 44 4 4 9 5 9 9 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 9 10 51 8 8 42 4 35 22 24 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 46 11 3 4 40 9 33 13 19 14 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1 1 11 0 2 6 3 12 5 8 11

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m5 versus positions_6nt_m1; m=2/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.816928; ssgGGaGCTGTCCATGGwCagcrs-- ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 3 30 7 44 4 5 22 8 0 0 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 9 7 51 14 10 43 8 27 0 0 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 52 12 7 4 39 16 22 22 0 0 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2 3 18 2 5 14 3 15 10 0 0

oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)
; positions_6nt_m5 versus oligos_7nt_mkv4_m5_rc; m=3/6; ncol2=17; w=-1; offset=-1; strand=R; shift=1; score=0.590701; -bgGGmGCTGTCCatGGt-------- ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 76 58 0 0 0 0 0 0 0 0 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 102 131 0 0 0 0 0 0 0 0 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 649 115 0 0 0 0 0 0 0 0 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86 86 609 0 0 0 0 0 0 0 0

oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; positions_6nt_m5 versus oligos_7nt_mkv4_m3; m=4/6; ncol2=17; w=-1; offset=-1; strand=D; shift=1; score=0.584847; -skGGcGCTGTCCrtGGt-------- ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 0 0 0 0 0 0 0 0 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 0 0 0 0 0 0 0 0 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 0 0 0 0 0 0 0 0 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663 0 0 0 0 0 0 0 0

positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_6nt_m5 versus positions_7nt_m2; m=5/6; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.520251; -bgggmGCTGTCCatg---------- ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 0 0 0 0 0 0 0 0 0 0 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 0 0 0 0 0 0 0 0 0 0 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 0 0 0 0 0 0 0 0 0 0 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153 0 0 0 0 0 0 0 0 0 0

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_6nt_m5 versus positions_7nt_m3; m=6/6; ncol2=13; w=0; offset=1; strand=D; shift=3; score=0.496647; ---rghGCTGTCCAtg---------- ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 0 0 0 0 0 0 0 0 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 0 0 0 0 0 0 0 0 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 0 0 0 0 0 0 0 0 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 7 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=24; shift=0; ncol=24; ssgGGaGCTGTCCATGGwCagcrs ; Alignment reference a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 3 30 7 44 4 5 22 8 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 9 7 51 14 10 43 8 27 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 52 12 7 4 39 16 22 22 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2 3 18 2 5 14 3 15 10

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ssgGGaGCTGTCCATGGwCagcrs ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 3 30 7 44 4 5 22 8 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 9 7 51 14 10 43 8 27 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 52 12 7 4 39 16 22 22 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2 3 18 2 5 14 3 15 10

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_6nt_m1 versus positions_6nt_m5; m=2/6; ncol2=24; w=0; offset=2; strand=D; shift=2; score=0.816928; --ssGmGCTGtCCatGGaCAGCgc ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 2 26 4 44 4 4 9 5 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 9 10 51 8 8 42 4 35 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 46 11 3 4 40 9 33 13 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1 1 11 0 2 6 3 12 5

oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)
; positions_6nt_m1 versus oligos_7nt_mkv4_m5_rc; m=3/6; ncol2=17; w=0; offset=1; strand=R; shift=1; score=0.669412; -bgGGmGCTGTCCatGGt------ ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 76 58 0 0 0 0 0 0 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 102 131 0 0 0 0 0 0 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 649 115 0 0 0 0 0 0 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86 86 609 0 0 0 0 0 0

oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; positions_6nt_m1 versus oligos_7nt_mkv4_m3; m=4/6; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.656948; -skGGcGCTGTCCrtGGt------ ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 0 0 0 0 0 0 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 0 0 0 0 0 0 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 0 0 0 0 0 0 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663 0 0 0 0 0 0

positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_6nt_m1 versus positions_7nt_m2; m=5/6; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.586462; -bgggmGCTGTCCatg-------- ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 0 0 0 0 0 0 0 0 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 0 0 0 0 0 0 0 0 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 0 0 0 0 0 0 0 0 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153 0 0 0 0 0 0 0 0

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_6nt_m1 versus positions_7nt_m3; m=6/6; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.504073; ---rghGCTGTCCAtg-------- ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 0 0 0 0 0 0 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 0 0 0 0 0 0 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 0 0 0 0 0 0 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=19; shift=0; ncol=19; atTsCwkTCCATTCsATTc ; Alignment reference a 841 76 132 61 36 465 17 16 21 8 1155 24 40 58 58 1029 55 98 206 c 60 145 202 535 1123 13 31 2 1244 1259 46 60 42 968 699 87 212 80 765 g 256 229 47 624 128 31 578 10 19 19 67 45 169 195 333 143 66 191 211 t 141 848 917 78 11 789 672 1270 14 12 30 1169 1047 77 208 39 965 929 116

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; atTsCwkTCCATTCsATTc ; cor=; Ncor= a 841 76 132 61 36 465 17 16 21 8 1155 24 40 58 58 1029 55 98 206 c 60 145 202 535 1123 13 31 2 1244 1259 46 60 42 968 699 87 212 80 765 g 256 229 47 624 128 31 578 10 19 19 67 45 169 195 333 143 66 191 211 t 141 848 917 78 11 789 672 1270 14 12 30 1169 1047 77 208 39 965 929 116

oligos_6nt_mkv3_m3_rc_shift3 (oligos_6nt_mkv3_m3_rc)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3_rc; m=2/4; ncol2=16; w=0; offset=3; strand=R; shift=3; score=0.757468; ---CCATTCCATTCCATTC ; cor=; Ncor= a 0 0 0 563 702 15039 282 219 279 492 14992 263 248 381 771 14491 371 486 1252 c 0 0 0 12596 12209 155 519 110 14894 14626 205 885 121 14353 12414 203 1274 284 12959 g 0 0 0 766 2582 508 436 149 652 664 552 339 161 680 2379 870 1019 992 845 t 0 0 0 2449 881 672 15137 15896 549 592 625 14887 15844 960 810 810 13710 14612 1318

oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2_rc; m=3/4; ncol2=20; w=0; offset=2; strand=R; shift=2; score=0.697299; --TCCATTCCATTCCATTC ; cor=; Ncor= a 0 0 1262 488 675 15249 315 214 312 482 15312 303 261 412 920 14797 411 360 1152 c 0 0 214 12909 12343 159 691 133 15060 14933 171 997 138 14759 12744 209 1414 209 13687 g 0 0 294 755 2884 563 505 147 794 726 601 383 184 713 2273 929 1060 882 730 t 0 0 15014 2632 882 813 15273 16290 618 643 700 15101 16201 900 847 849 13899 15333 1215

positions_7nt_m3_shift0 (positions_7nt_m3)
; oligos_6nt_mkv3_m2 versus positions_7nt_m3; m=4/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.491887; rghGCTGTCCAtg------ ; cor=; Ncor= a 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 0 0 0 0 c 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 0 0 0 0 g 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 0 0 0 0 t 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; ATGGAATGGAATGGAATGGA ; Alignment reference a 12791 1403 1614 1215 15333 13899 849 847 900 16201 15101 700 643 618 16290 15273 813 882 2632 15014 c 1133 1634 1858 730 882 1060 929 2273 713 184 383 601 726 794 147 505 563 2884 755 294 g 1837 395 12438 13687 209 1414 209 12744 14759 138 997 171 14933 15060 133 691 159 12343 12909 214 t 1023 13352 874 1152 360 411 14797 920 412 261 303 15312 482 312 214 315 15249 675 488 1262

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; ATGGAATGGAATGGAATGGA ; cor=; Ncor= a 12791 1403 1614 1215 15333 13899 849 847 900 16201 15101 700 643 618 16290 15273 813 882 2632 15014 c 1133 1634 1858 730 882 1060 929 2273 713 184 383 601 726 794 147 505 563 2884 755 294 g 1837 395 12438 13687 209 1414 209 12744 14759 138 997 171 14933 15060 133 691 159 12343 12909 214 t 1023 13352 874 1152 360 411 14797 920 412 261 303 15312 482 312 214 315 15249 675 488 1262

oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3; m=2/3; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.79986; ---GAATGGAATGGAATGG- ; cor=; Ncor= a 0 0 0 1318 14612 13710 810 810 960 15844 14887 625 592 549 15896 15137 672 881 2449 0 c 0 0 0 845 992 1019 870 2379 680 161 339 552 664 652 149 436 508 2582 766 0 g 0 0 0 12959 284 1274 203 12414 14353 121 885 205 14626 14894 110 519 155 12209 12596 0 t 0 0 0 1252 486 371 14491 771 381 248 263 14992 492 279 219 282 15039 702 563 0

oligos_6nt_mkv3_m2_rc_shift3 (oligos_6nt_mkv3_m2_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2_rc; m=3/3; ncol2=19; w=0; offset=3; strand=R; shift=3; score=0.697299; ---gAATsGAATGGAmwGsA ; cor=; Ncor= a 0 0 0 116 929 965 39 208 77 1047 1169 30 12 14 1270 672 789 11 78 917 c 0 0 0 211 191 66 143 333 195 169 45 67 19 19 10 578 31 128 624 47 g 0 0 0 765 80 212 87 699 968 42 60 46 1259 1244 2 31 13 1123 535 202 t 0 0 0 206 98 55 1029 58 58 40 24 1155 8 21 16 17 465 36 61 132

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift8 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift8 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=17; shift=8; ncol=25; --------aCCatGGACAGCkCCcv ; Alignment reference a 0 0 0 0 0 0 0 0 609 86 86 470 83 15 9 835 9 876 8 54 160 67 61 227 238 c 0 0 0 0 0 0 0 0 115 649 671 146 228 6 10 30 820 21 8 770 27 681 714 387 268 g 0 0 0 0 0 0 0 0 131 102 84 166 93 887 881 17 61 10 887 31 320 101 31 122 245 t 0 0 0 0 0 0 0 0 58 76 72 131 509 5 13 31 23 6 10 58 406 64 107 177 162

oligos_7nt_mkv4_m5_shift8 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=8; score= 1; --------aCCatGGACAGCkCCcv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 609 86 86 470 83 15 9 835 9 876 8 54 160 67 61 227 238 c 0 0 0 0 0 0 0 0 115 649 671 146 228 6 10 30 820 21 8 770 27 681 714 387 268 g 0 0 0 0 0 0 0 0 131 102 84 166 93 887 881 17 61 10 887 31 320 101 31 122 245 t 0 0 0 0 0 0 0 0 58 76 72 131 509 5 13 31 23 6 10 58 406 64 107 177 162

oligos_7nt_mkv4_m3_rc_shift8 (oligos_7nt_mkv4_m3_rc)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m3_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=8; score=0.990797; --------aCCayGGACAGCgCCms ; cor=; Ncor= a 0 0 0 0 0 0 0 0 663 80 59 509 91 29 11 884 15 936 9 96 145 90 75 246 235 c 0 0 0 0 0 0 0 0 108 700 773 148 250 12 12 50 880 19 21 778 25 672 754 403 290 g 0 0 0 0 0 0 0 0 142 130 79 186 107 932 951 20 68 18 946 48 573 149 46 146 282 t 0 0 0 0 0 0 0 0 68 71 70 138 533 8 7 27 18 8 5 59 238 70 106 186 174

positions_7nt_m2_rc_shift10 (positions_7nt_m2_rc)
; oligos_7nt_mkv4_m5 versus positions_7nt_m2_rc; m=3/8; ncol2=15; w=0; offset=2; strand=R; shift=10; score=0.864831; ----------catGGACAGCkcccv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 153 415 92 29 11 1114 17 1125 9 57 241 110 101 287 340 c 0 0 0 0 0 0 0 0 0 0 638 247 206 8 25 36 1022 40 14 1035 88 659 721 432 316 g 0 0 0 0 0 0 0 0 0 0 177 264 101 1146 1139 16 75 14 1156 45 368 225 105 278 308 t 0 0 0 0 0 0 0 0 0 0 225 267 794 10 18 27 79 14 14 56 496 199 266 196 229

positions_7nt_m3_rc_shift10 (positions_7nt_m3_rc)
; oligos_7nt_mkv4_m5 versus positions_7nt_m3_rc; m=4/8; ncol2=13; w=0; offset=2; strand=R; shift=10; score=0.739505; ----------caTGGACAGCdcy-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 191 460 95 29 14 1218 44 1255 11 74 339 185 133 0 0 c 0 0 0 0 0 0 0 0 0 0 668 284 174 5 28 42 1112 28 17 1114 129 607 691 0 0 g 0 0 0 0 0 0 0 0 0 0 212 283 98 1272 1251 25 84 11 1276 66 404 281 163 0 0 t 0 0 0 0 0 0 0 0 0 0 246 290 950 11 24 32 77 23 13 63 445 244 330 0 0

positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)
; oligos_7nt_mkv4_m5 versus positions_6nt_m1_rc; m=5/8; ncol2=24; w=-6; offset=-6; strand=R; shift=2; score=0.669412; --sygctGwCCATGGACAGCtCCcs ; cor=; Ncor= a 0 0 10 15 3 14 5 2 18 3 2 48 5 1 1 47 1 58 2 4 10 2 5 10 14 c 0 0 22 22 16 39 4 7 12 52 54 8 8 5 3 3 63 6 5 54 6 48 49 39 20 g 0 0 27 8 43 10 14 51 7 9 5 8 7 60 60 6 2 1 56 5 13 10 10 10 23 t 0 0 8 22 5 4 44 7 30 3 6 3 47 1 3 11 1 2 4 4 38 7 3 8 10

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m1_rc; m=6/8; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.613551; gbtTCAGCACCayGGACAGcgcCm- ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 18 676 8 740 18 95 171 106 86 234 0 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 12 54 633 13 12 515 26 463 554 310 0 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 745 32 112 21 734 88 401 158 30 110 0 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5 10 23 32 11 21 87 187 58 115 131 0

positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)
; oligos_7nt_mkv4_m5 versus positions_6nt_m5_rc; m=7/8; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.590701; gsgcGCTGtCCatGGaCAGCkCss- ; cor=; Ncor= a 11 8 5 12 3 6 2 0 11 1 1 36 7 3 0 33 2 43 1 3 6 2 9 10 0 c 14 19 13 33 9 40 4 3 11 46 49 9 8 4 6 6 55 10 4 47 5 41 31 21 0 g 24 22 35 4 42 8 8 51 10 9 5 9 5 50 50 10 1 3 49 7 18 11 15 15 0 t 9 9 5 9 4 4 44 4 26 2 3 4 38 1 2 9 0 2 4 1 29 4 3 12 0

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m4; m=8/8; ncol2=23; w=-8; offset=-8; strand=D; shift=0; score=0.577914; gbtTCAGCACCayGGACAGckcC-- ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 14 684 4 743 13 93 168 96 74 0 0 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 8 44 632 11 6 516 23 452 550 0 0 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 744 21 104 9 731 74 383 161 33 0 0 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4 1 18 27 4 17 84 193 58 110 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=16; shift=4; ncol=20; ----ssGCGGCGGGGCgGss ; Alignment reference a 0 0 0 0 101 118 20 49 28 30 34 16 31 32 23 56 43 62 103 93 c 0 0 0 0 404 296 70 662 89 101 800 68 119 186 64 686 201 150 249 274 g 0 0 0 0 323 435 806 181 764 750 64 818 736 674 816 144 617 648 462 449 t 0 0 0 0 92 71 24 28 39 39 22 18 34 28 17 34 59 60 106 104

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=4; score= 1; ----ssGCGGCGGGGCgGss ; cor=; Ncor= a 0 0 0 0 101 118 20 49 28 30 34 16 31 32 23 56 43 62 103 93 c 0 0 0 0 404 296 70 662 89 101 800 68 119 186 64 686 201 150 249 274 g 0 0 0 0 323 435 806 181 764 750 64 818 736 674 816 144 617 648 462 449 t 0 0 0 0 92 71 24 28 39 39 22 18 34 28 17 34 59 60 106 104

positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)
; oligos_6nt_mkv3_m5 versus positions_6nt_m3_rc; m=2/3; ncol2=16; w=-1; offset=-1; strand=R; shift=3; score=0.798609; ---sssGGGGCGGGGcsgg- ; cor=; Ncor= a 0 0 0 180 167 144 66 66 25 31 36 25 38 61 47 121 123 182 159 0 c 0 0 0 415 511 407 138 203 108 119 1233 83 117 158 104 815 627 324 322 0 g 0 0 0 593 484 653 1046 1024 1174 1142 21 1197 1128 1075 1141 304 438 639 691 0 t 0 0 0 138 164 122 76 33 19 34 36 21 43 32 34 86 138 181 154 0

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; oligos_6nt_mkv3_m5 versus positions_6nt_m4_rc; m=3/3; ncol2=19; w=-4; offset=-4; strand=R; shift=0; score=0.711732; ssgGsGGCGGCGGGGssgg- ; cor=; Ncor= a 106 114 98 55 55 60 31 54 23 23 32 17 43 39 46 93 83 111 107 0 c 254 363 226 127 237 138 71 688 70 49 768 74 92 194 91 526 424 227 229 0 g 459 347 528 710 581 698 800 144 801 816 84 809 774 660 759 253 307 478 486 0 t 105 100 72 32 51 28 22 38 30 36 40 24 15 31 28 52 110 108 102 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; skTTCAkCACCatGGTGmTGAAms ; Alignment reference a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 5 21 2 47 2 11 91 90 44 29 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 2 13 18 67 5 23 6 17 34 34 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 118 6 101 6 23 89 19 17 27 52 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2 2 87 6 7 97 4 11 3 22 12

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; skTTCAkCACCatGGTGmTGAAms ; cor=; Ncor= a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 5 21 2 47 2 11 91 90 44 29 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 2 13 18 67 5 23 6 17 34 34 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 118 6 101 6 23 89 19 17 27 52 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2 2 87 6 7 97 4 11 3 22 12

positions_6nt_m2_shift0 (positions_6nt_m2)
; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=2/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.574038; sbtTCAGCACCaygg--------- ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 155 0 0 0 0 0 0 0 0 0 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 177 0 0 0 0 0 0 0 0 0 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 726 0 0 0 0 0 0 0 0 0 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92 93 0 0 0 0 0 0 0 0 0

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_6nt_mkv3_m1 versus positions_7nt_m1; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.545196; sbtTCAGCACCayg---------- ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 0 0 0 0 0 0 0 0 0 0 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 0 0 0 0 0 0 0 0 0 0 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 0 0 0 0 0 0 0 0 0 0 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107 0 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4; m=4/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.484408; -btTCAGsACCayG---------- ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 0 0 0 0 0 0 0 0 0 0 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 0 0 0 0 0 0 0 0 0 0 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 0 0 0 0 0 0 0 0 0 0 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift1 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=24; shift=1; ncol=25; -kGgcgCTGTCCrtGGTGCTGAavc ; Alignment reference a 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 7 5 47 3 3 19 638 478 221 159 c 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 2 2 124 767 8 6 43 158 231 287 g 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 774 2 568 6 2 753 82 65 210 175 t 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8 2 776 46 9 772 7 22 84 123 164

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -kGgcgCTGTCCrtGGTGCTGAavc ; cor=; Ncor= a 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 7 5 47 3 3 19 638 478 221 159 c 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 2 2 124 767 8 6 43 158 231 287 g 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 774 2 568 6 2 753 82 65 210 175 t 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8 2 776 46 9 772 7 22 84 123 164

oligos_6nt_mkv3_m4_rc_shift2 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=2/9; ncol2=23; w=0; offset=1; strand=R; shift=2; score=0.957984; --GgmgCTGTCCrtGGTGCTGAavc ; cor=; Ncor= a 0 0 110 58 193 84 17 4 27 18 1 4 334 134 22 7 5 50 1 3 21 609 453 211 159 c 0 0 33 161 383 74 731 9 104 21 744 738 85 104 7 1 5 126 750 12 8 48 161 231 276 g 0 0 550 452 23 516 6 11 632 44 8 4 257 72 731 756 2 544 5 3 731 86 70 205 177 t 0 0 74 96 168 93 13 743 4 684 14 21 91 457 7 3 755 47 11 749 7 24 83 120 155

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=3/9; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.621099; skGGcGCTGTCCrtGGt-------- ; cor=; Ncor= a 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 0 0 0 0 0 0 0 0 c 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 0 0 0 0 0 0 0 0 g 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 0 0 0 0 0 0 0 0 t 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663 0 0 0 0 0 0 0 0

oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5_rc; m=4/9; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.613551; bgGGmGCTGTCCatGGt-------- ; cor=; Ncor= a 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 76 58 0 0 0 0 0 0 0 0 c 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 102 131 0 0 0 0 0 0 0 0 g 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 649 115 0 0 0 0 0 0 0 0 t 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86 86 609 0 0 0 0 0 0 0 0

positions_6nt_m2_rc_shift10 (positions_6nt_m2_rc)
; oligos_7nt_mkv4_m1 versus positions_6nt_m2_rc; m=5/9; ncol2=15; w=0; offset=9; strand=R; shift=10; score=0.610442; ----------ccrtGGTGCTGAavs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 93 92 324 139 49 19 16 46 47 21 15 980 708 329 215 c 0 0 0 0 0 0 0 0 0 0 726 756 203 160 13 13 19 94 1008 6 20 45 202 313 382 g 0 0 0 0 0 0 0 0 0 0 177 176 417 98 1067 1108 33 961 78 16 1107 80 90 295 306 t 0 0 0 0 0 0 0 0 0 0 155 127 207 754 22 11 1083 50 18 1108 9 46 151 214 248

positions_7nt_m1_rc_shift11 (positions_7nt_m1_rc)
; oligos_7nt_mkv4_m1 versus positions_7nt_m1_rc; m=6/9; ncol2=14; w=0; offset=10; strand=R; shift=11; score=0.574002; -----------crtGGTGCTGAavs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 107 373 148 48 22 27 47 58 21 21 1009 769 333 221 c 0 0 0 0 0 0 0 0 0 0 0 767 222 144 11 12 16 103 1018 7 18 47 189 309 385 g 0 0 0 0 0 0 0 0 0 0 0 173 362 100 1093 1131 31 975 80 23 1129 82 79 307 322 t 0 0 0 0 0 0 0 0 0 0 0 131 221 786 26 13 1104 53 22 1127 10 40 141 229 250

oligos_7nt_mkv4_m4_rc_shift11 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=7/9; ncol2=13; w=0; offset=10; strand=R; shift=11; score=0.527531; -----------CrtGGTsCTGAav- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 57 219 76 18 8 10 41 4 10 21 766 421 234 0 c 0 0 0 0 0 0 0 0 0 0 0 606 200 136 15 13 10 380 829 13 8 38 187 238 0 g 0 0 0 0 0 0 0 0 0 0 0 99 301 90 805 822 14 388 8 11 810 34 138 237 0 t 0 0 0 0 0 0 0 0 0 0 0 89 131 549 13 8 817 42 10 817 12 13 105 142 0

positions_7nt_m2_shift0 (positions_7nt_m2)
; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=8/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score= 0.5267; bgggmGCTGTCCatg---------- ; cor=; Ncor= a 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 0 0 0 0 0 0 0 0 0 0 c 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 0 0 0 0 0 0 0 0 0 0 g 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 0 0 0 0 0 0 0 0 0 0 t 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153 0 0 0 0 0 0 0 0 0 0

positions_7nt_m3_shift2 (positions_7nt_m3)
; oligos_7nt_mkv4_m1 versus positions_7nt_m3; m=9/9; ncol2=13; w=0; offset=1; strand=D; shift=2; score=0.504392; --rghGCTGTCCAtg---------- ; cor=; Ncor= a 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 0 0 0 0 0 0 0 0 c 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 0 0 0 0 0 0 0 0 g 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 0 0 0 0 0 0 0 0 t 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -bgggmGCTGTCCatg ; Alignment reference a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153

positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -bgggmGCTGTCCatg ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153

oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)
; positions_7nt_m2 versus oligos_7nt_mkv4_m5_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.864831; -bgGGmGCTGTCCatG ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m2 versus positions_7nt_m3; m=3/8; ncol2=13; w=0; offset=2; strand=D; shift=3; score=0.86346; ---rghGCTGTCCAtg ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191

oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; positions_7nt_m2 versus oligos_7nt_mkv4_m3; m=4/8; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.854041; -skGGcGCTGTCCrtG ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m2 versus positions_6nt_m1; m=5/8; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.586462; ssgGGaGCTGTCCATG ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; positions_7nt_m2 versus oligos_7nt_mkv4_m1; m=6/8; ncol2=24; w=0; offset=1; strand=D; shift=2; score= 0.5267; --kGgcgCTGTCCrtG ; cor=; Ncor= a 0 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 c 0 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 g 0 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 t 0 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_7nt_m2 versus positions_6nt_m5; m=7/8; ncol2=24; w=0; offset=1; strand=D; shift=2; score=0.520251; --ssGmGCTGtCCatG ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1

oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)
; positions_7nt_m2 versus oligos_6nt_mkv3_m4_rc; m=8/8; ncol2=23; w=0; offset=2; strand=R; shift=3; score=0.492441; ---GgmgCTGTCCrtG ; cor=; Ncor= a 0 0 0 110 58 193 84 17 4 27 18 1 4 334 134 22 c 0 0 0 33 161 383 74 731 9 104 21 744 738 85 104 7 g 0 0 0 550 452 23 516 6 11 632 44 8 4 257 72 731 t 0 0 0 74 96 168 93 13 743 4 684 14 21 91 457 7

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift3 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=13; shift=3; ncol=16; ---rghGCTGTCCAtg ; Alignment reference a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191

positions_7nt_m3_shift3 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/9; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---rghGCTGTCCAtg ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191

positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_7nt_m3 versus positions_7nt_m2; m=2/9; ncol2=15; w=-2; offset=-2; strand=D; shift=1; score=0.86346; -bgggmGCTGTCCatg ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153

oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)
; positions_7nt_m3 versus oligos_7nt_mkv4_m5_rc; m=3/9; ncol2=17; w=-2; offset=-2; strand=R; shift=1; score=0.739505; -bgGGmGCTGTCCatG ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86

oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; positions_7nt_m3 versus oligos_7nt_mkv4_m3; m=4/9; ncol2=17; w=-2; offset=-2; strand=D; shift=1; score=0.732669; -skGGcGCTGTCCrtG ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59

oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)
; positions_7nt_m3 versus oligos_6nt_mkv3_m4_rc; m=5/9; ncol2=23; w=0; offset=0; strand=R; shift=3; score=0.529684; ---GgmgCTGTCCrtG ; cor=; Ncor= a 0 0 0 110 58 193 84 17 4 27 18 1 4 334 134 22 c 0 0 0 33 161 383 74 731 9 104 21 744 738 85 104 7 g 0 0 0 550 452 23 516 6 11 632 44 8 4 257 72 731 t 0 0 0 74 96 168 93 13 743 4 684 14 21 91 457 7

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; positions_7nt_m3 versus oligos_7nt_mkv4_m1; m=6/9; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.504392; --kGgcgCTGTCCrtG ; cor=; Ncor= a 0 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 c 0 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 g 0 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 t 0 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m3 versus positions_6nt_m1; m=7/9; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.504073; ssgGGaGCTGTCCATG ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2

positions_6nt_m5_shift2 (positions_6nt_m5)
; positions_7nt_m3 versus positions_6nt_m5; m=8/9; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.496647; --ssGmGCTGtCCatG ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1

oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)
; positions_7nt_m3 versus oligos_6nt_mkv3_m2; m=9/9; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.491887; ---atTsCwkTCCATT ; cor=; Ncor= a 0 0 0 841 76 132 61 36 465 17 16 21 8 1155 24 40 c 0 0 0 60 145 202 535 1123 13 31 2 1244 1259 46 60 42 g 0 0 0 256 229 47 624 128 31 578 10 19 19 67 45 169 t 0 0 0 141 848 917 78 11 789 672 1270 14 12 30 1169 1047

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 7 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=14; shift=0; ncol=14; sbtTCAGCACCayg ; Alignment reference a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; sbtTCAGCACCayg ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_7nt_m1 versus positions_6nt_m2; m=2/6; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.932651; sbtTCAGCACCayg ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92

oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; positions_7nt_m1 versus oligos_7nt_mkv4_m4; m=3/6; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.898605; -btTCAGsACCayG ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; positions_7nt_m1 versus oligos_6nt_mkv3_m4; m=4/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.597116; gbtTCAGCACCayG ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; positions_7nt_m1 versus oligos_7nt_mkv4_m1_rc; m=5/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.574002; gbtTCAGCACCayG ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; positions_7nt_m1 versus oligos_6nt_mkv3_m1; m=6/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.545196; skTTCAkCACCatG ; cor=; Ncor= a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=19; shift=1; ncol=20; -ccssCCCCGCCGCCsCcss ; Alignment reference a 0 102 108 110 52 28 31 15 24 40 36 30 38 22 28 51 32 72 100 105 c 0 486 478 307 253 759 660 774 809 84 816 801 144 800 698 581 710 528 347 459 g 0 229 227 424 526 91 194 92 74 768 49 70 688 71 138 237 127 226 363 254 t 0 107 111 83 93 46 39 43 17 32 23 23 54 31 60 55 55 98 114 106

positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -ccssCCCCGCCGCCsCcss ; cor=; Ncor= a 0 102 108 110 52 28 31 15 24 40 36 30 38 22 28 51 32 72 100 105 c 0 486 478 307 253 759 660 774 809 84 816 801 144 800 698 581 710 528 347 459 g 0 229 227 424 526 91 194 92 74 768 49 70 688 71 138 237 127 226 363 254 t 0 107 111 83 93 46 39 43 17 32 23 23 54 31 60 55 55 98 114 106

positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=2/3; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.753167; -ccsgCCCCGCCCCsss--- ; cor=; Ncor= a 0 154 181 138 86 34 32 43 21 36 34 19 33 76 122 164 138 0 0 0 c 0 691 639 438 304 1141 1075 1128 1197 21 1142 1174 1024 1046 653 484 593 0 0 0 g 0 322 324 627 815 104 158 117 83 1233 119 108 203 138 407 511 415 0 0 0 t 0 159 182 123 121 47 61 38 25 36 31 25 66 66 144 167 180 0 0 0

oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)
; positions_6nt_m4 versus oligos_6nt_mkv3_m5_rc; m=3/3; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.711732; ssCcGCCCCGCCGCss---- ; cor=; Ncor= a 104 106 60 59 34 17 28 34 18 22 39 39 28 24 71 92 0 0 0 0 c 449 462 648 617 144 816 674 736 818 64 750 764 181 806 435 323 0 0 0 0 g 274 249 150 201 686 64 186 119 68 800 101 89 662 70 296 404 0 0 0 0 t 93 103 62 43 56 23 32 31 16 34 30 28 49 20 118 101 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=23; shift=0; ncol=23; gbtTCAGCACCayGGACAGckcC ; Alignment reference a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 14 684 4 743 13 93 168 96 74 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 8 44 632 11 6 516 23 452 550 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 744 21 104 9 731 74 383 161 33 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4 1 18 27 4 17 84 193 58 110

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/9; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; gbtTCAGCACCayGGACAGckcC ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 14 684 4 743 13 93 168 96 74 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 8 44 632 11 6 516 23 452 550 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 744 21 104 9 731 74 383 161 33 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4 1 18 27 4 17 84 193 58 110

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=2/9; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.957984; gbtTCAGCACCayGGACAGcgcC ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 18 676 8 740 18 95 171 106 86 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 12 54 633 13 12 515 26 463 554 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 745 32 112 21 734 88 401 158 30 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5 10 23 32 11 21 87 187 58 115

positions_6nt_m2_shift0 (positions_6nt_m2)
; oligos_6nt_mkv3_m4 versus positions_6nt_m2; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.634321; sbtTCAGCACCaygg-------- ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 155 0 0 0 0 0 0 0 0 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 177 0 0 0 0 0 0 0 0 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 726 0 0 0 0 0 0 0 0 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92 93 0 0 0 0 0 0 0 0

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_6nt_mkv3_m4 versus positions_7nt_m1; m=4/9; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.597116; sbtTCAGCACCayg--------- ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 0 0 0 0 0 0 0 0 0 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 0 0 0 0 0 0 0 0 0 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 0 0 0 0 0 0 0 0 0 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv4_m3_rc_shift8 (oligos_7nt_mkv4_m3_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m3_rc; m=5/9; ncol2=17; w=0; offset=8; strand=R; shift=8; score=0.584226; --------aCCayGGACAGCgCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 663 80 59 509 91 29 11 884 15 936 9 96 145 90 75 c 0 0 0 0 0 0 0 0 108 700 773 148 250 12 12 50 880 19 21 778 25 672 754 g 0 0 0 0 0 0 0 0 142 130 79 186 107 932 951 20 68 18 946 48 573 149 46 t 0 0 0 0 0 0 0 0 68 71 70 138 533 8 7 27 18 8 5 59 238 70 106

oligos_7nt_mkv4_m5_shift8 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m5; m=6/9; ncol2=17; w=0; offset=8; strand=D; shift=8; score=0.577914; --------aCCatGGACAGCkCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 609 86 86 470 83 15 9 835 9 876 8 54 160 67 61 c 0 0 0 0 0 0 0 0 115 649 671 146 228 6 10 30 820 21 8 770 27 681 714 g 0 0 0 0 0 0 0 0 131 102 84 166 93 887 881 17 61 10 887 31 320 101 31 t 0 0 0 0 0 0 0 0 58 76 72 131 509 5 13 31 23 6 10 58 406 64 107

oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m4; m=7/9; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.54983; -btTCAGsACCayG--------- ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 0 0 0 0 0 0 0 0 0 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 0 0 0 0 0 0 0 0 0 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 0 0 0 0 0 0 0 0 0 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57 0 0 0 0 0 0 0 0 0

positions_7nt_m3_rc_shift10 (positions_7nt_m3_rc)
; oligos_6nt_mkv3_m4 versus positions_7nt_m3_rc; m=8/9; ncol2=13; w=0; offset=10; strand=R; shift=10; score=0.529684; ----------caTGGACAGCdcy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 191 460 95 29 14 1218 44 1255 11 74 339 185 133 c 0 0 0 0 0 0 0 0 0 0 668 284 174 5 28 42 1112 28 17 1114 129 607 691 g 0 0 0 0 0 0 0 0 0 0 212 283 98 1272 1251 25 84 11 1276 66 404 281 163 t 0 0 0 0 0 0 0 0 0 0 246 290 950 11 24 32 77 23 13 63 445 244 330

positions_7nt_m2_rc_shift10 (positions_7nt_m2_rc)
; oligos_6nt_mkv3_m4 versus positions_7nt_m2_rc; m=9/9; ncol2=15; w=0; offset=10; strand=R; shift=10; score=0.492441; ----------catGGACAGCkcc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 153 415 92 29 11 1114 17 1125 9 57 241 110 101 c 0 0 0 0 0 0 0 0 0 0 638 247 206 8 25 36 1022 40 14 1035 88 659 721 g 0 0 0 0 0 0 0 0 0 0 177 264 101 1146 1139 16 75 14 1156 45 368 225 105 t 0 0 0 0 0 0 0 0 0 0 225 267 794 10 18 27 79 14 14 56 496 199 266

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -btTCAGsACCayG ; Alignment reference a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57

oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -btTCAGsACCayG ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_7nt_mkv4_m4 versus positions_7nt_m1; m=2/6; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.898605; sbtTCAGCACCayg ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107

positions_6nt_m2_shift0 (positions_6nt_m2)
; oligos_7nt_mkv4_m4 versus positions_6nt_m2; m=3/6; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.839856; sbtTCAGCACCayg ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m4; m=4/6; ncol2=23; w=-1; offset=-1; strand=D; shift=0; score=0.54983; gbtTCAGCACCayG ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=5/6; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.527531; gbtTCAGCACCayG ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m1; m=6/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.484408; skTTCAkCACCatG ; cor=; Ncor= a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 7 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=15; shift=0; ncol=15; sbtTCAGCACCaygg ; Alignment reference a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 155 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 177 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 726 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92 93

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; sbtTCAGCACCaygg ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 155 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 177 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 726 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92 93

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_6nt_m2 versus positions_7nt_m1; m=2/6; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.932651; sbtTCAGCACCayg- ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 0 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 0 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 0 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107 0

oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; positions_6nt_m2 versus oligos_7nt_mkv4_m4; m=3/6; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.839856; -btTCAGsACCayG- ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 0 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 0 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 0 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57 0

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; positions_6nt_m2 versus oligos_6nt_mkv3_m4; m=4/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.634321; gbtTCAGCACCayGG ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 14 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 8 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 744 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4 1

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; positions_6nt_m2 versus oligos_7nt_mkv4_m1_rc; m=5/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.610442; gbtTCAGCACCayGG ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 18 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 12 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 745 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5 10

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; positions_6nt_m2 versus oligos_6nt_mkv3_m1; m=6/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.574038; skTTCAkCACCatGG ; cor=; Ncor= a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 5 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 2 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 118 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2 2

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift1 ; 4 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=16; shift=1; ncol=17; -ccsgCCCCGCCCCsss ; Alignment reference a 0 154 181 138 86 34 32 43 21 36 34 19 33 76 122 164 138 c 0 691 639 438 304 1141 1075 1128 1197 21 1142 1174 1024 1046 653 484 593 g 0 322 324 627 815 104 158 117 83 1233 119 108 203 138 407 511 415 t 0 159 182 123 121 47 61 38 25 36 31 25 66 66 144 167 180

positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -ccsgCCCCGCCCCsss ; cor=; Ncor= a 0 154 181 138 86 34 32 43 21 36 34 19 33 76 122 164 138 c 0 691 639 438 304 1141 1075 1128 1197 21 1142 1174 1024 1046 653 484 593 g 0 322 324 627 815 104 158 117 83 1233 119 108 203 138 407 511 415 t 0 159 182 123 121 47 61 38 25 36 31 25 66 66 144 167 180

oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)
; positions_6nt_m3 versus oligos_6nt_mkv3_m5_rc; m=2/3; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.798609; ssCcGCCCCGCCGCss- ; cor=; Ncor= a 104 106 60 59 34 17 28 34 18 22 39 39 28 24 71 92 0 c 449 462 648 617 144 816 674 736 818 64 750 764 181 806 435 323 0 g 274 249 150 201 686 64 186 119 68 800 101 89 662 70 296 404 0 t 93 103 62 43 56 23 32 31 16 34 30 28 49 20 118 101 0

positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=3/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score=0.753167; -ccssCCCCGCCGCCsC ; cor=; Ncor= a 0 102 108 110 52 28 31 15 24 40 36 30 38 22 28 51 32 c 0 486 478 307 253 759 660 774 809 84 816 801 144 800 698 581 710 g 0 229 227 424 526 91 194 92 74 768 49 70 688 71 138 237 127 t 0 107 111 83 93 46 39 43 17 32 23 23 54 31 60 55 55

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=16; shift=3; ncol=19; ---GAATGGAATGGAATGG ; Alignment reference a 0 0 0 1318 14612 13710 810 810 960 15844 14887 625 592 549 15896 15137 672 881 2449 c 0 0 0 845 992 1019 870 2379 680 161 339 552 664 652 149 436 508 2582 766 g 0 0 0 12959 284 1274 203 12414 14353 121 885 205 14626 14894 110 519 155 12209 12596 t 0 0 0 1252 486 371 14491 771 381 248 263 14992 492 279 219 282 15039 702 563
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=3; score= 1; ---GAATGGAATGGAATGG ; cor=; Ncor= a 0 0 0 1318 14612 13710 810 810 960 15844 14887 625 592 549 15896 15137 672 881 2449 c 0 0 0 845 992 1019 870 2379 680 161 339 552 664 652 149 436 508 2582 766 g 0 0 0 12959 284 1274 203 12414 14353 121 885 205 14626 14894 110 519 155 12209 12596 t 0 0 0 1252 486 371 14491 771 381 248 263 14992 492 279 219 282 15039 702 563
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2; m=2/3; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score=0.79986; ATGGAATGGAATGGAATGG ; cor=; Ncor= a 12791 1403 1614 1215 15333 13899 849 847 900 16201 15101 700 643 618 16290 15273 813 882 2632 c 1133 1634 1858 730 882 1060 929 2273 713 184 383 601 726 794 147 505 563 2884 755 g 1837 395 12438 13687 209 1414 209 12744 14759 138 997 171 14933 15060 133 691 159 12343 12909 t 1023 13352 874 1152 360 411 14797 920 412 261 303 15312 482 312 214 315 15249 675 488
oligos_6nt_mkv3_m2_rc_shift3 (oligos_6nt_mkv3_m2_rc)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2_rc; m=3/3; ncol2=19; w=0; offset=0; strand=R; shift=3; score=0.757468; ---gAATsGAATGGAmwGs ; cor=; Ncor= a 0 0 0 116 929 965 39 208 77 1047 1169 30 12 14 1270 672 789 11 78 c 0 0 0 211 191 66 143 333 195 169 45 67 19 19 10 578 31 128 624 g 0 0 0 765 80 212 87 699 968 42 60 46 1259 1244 2 31 13 1123 535 t 0 0 0 206 98 55 1029 58 58 40 24 1155 8 21 16 17 465 36 61

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=17; shift=1; ncol=18; -skGGcGCTGTCCrtGGt ; Alignment reference a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=1; score= 1; -skGGcGCTGTCCrtGGt ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663
oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.990797; -bgGGmGCTGTCCatGGt ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 76 58 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 102 131 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 649 115 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86 86 609
positions_7nt_m2_shift1 (positions_7nt_m2)				; oligos_7nt_mkv4_m3 versus positions_7nt_m2; m=3/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.854041; -bgggmGCTGTCCatg-- ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 0 0 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 0 0 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 0 0 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)				; oligos_7nt_mkv4_m3 versus positions_7nt_m3; m=4/8; ncol2=13; w=0; offset=2; strand=D; shift=3; score=0.732669; ---rghGCTGTCCAtg-- ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0
positions_6nt_m1_shift0 (positions_6nt_m1)				; oligos_7nt_mkv4_m3 versus positions_6nt_m1; m=5/8; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.656948; ssgGGaGCTGTCCATGGw ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 3 30 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 9 7 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 52 12 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2 3 18
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=6/8; ncol2=24; w=0; offset=1; strand=D; shift=2; score=0.621099; --kGgcgCTGTCCrtGGT ; cor=; Ncor= a 0 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 7 5 c 0 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 2 2 g 0 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 774 2 t 0 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8 2 776
positions_6nt_m5_shift2 (positions_6nt_m5)				; oligos_7nt_mkv4_m3 versus positions_6nt_m5; m=7/8; ncol2=24; w=0; offset=1; strand=D; shift=2; score=0.584847; --ssGmGCTGtCCatGGa ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 2 26 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 9 10 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 46 11 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1 1 11
oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m4_rc; m=8/8; ncol2=23; w=0; offset=2; strand=R; shift=3; score=0.584226; ---GgmgCTGTCCrtGGT ; cor=; Ncor= a 0 0 0 110 58 193 84 17 4 27 18 1 4 334 134 22 7 5 c 0 0 0 33 161 383 74 731 9 104 21 744 738 85 104 7 1 5 g 0 0 0 550 452 23 516 6 11 632 44 8 4 257 72 731 756 2 t 0 0 0 74 96 168 93 13 743 4 684 14 21 91 457 7 3 755

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssGmGCTGtCCatGGaCAGCgcsc ; Alignment reference a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 2 26 4 44 4 4 9 5 9 9 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 9 10 51 8 8 42 4 35 22 24 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 46 11 3 4 40 9 33 13 19 14 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1 1 11 0 2 6 3 12 5 8 11
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssGmGCTGtCCatGGaCAGCgcsc ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 2 26 4 44 4 4 9 5 9 9 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 9 10 51 8 8 42 4 35 22 24 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 46 11 3 4 40 9 33 13 19 14 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1 1 11 0 2 6 3 12 5 8 11
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m5 versus positions_6nt_m1; m=2/6; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.816928; ssgGGaGCTGTCCATGGwCagcrs-- ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 3 30 7 44 4 5 22 8 0 0 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 9 7 51 14 10 43 8 27 0 0 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 52 12 7 4 39 16 22 22 0 0 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2 3 18 2 5 14 3 15 10 0 0
oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)				; positions_6nt_m5 versus oligos_7nt_mkv4_m5_rc; m=3/6; ncol2=17; w=-1; offset=-1; strand=R; shift=1; score=0.590701; -bgGGmGCTGTCCatGGt-------- ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 76 58 0 0 0 0 0 0 0 0 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 102 131 0 0 0 0 0 0 0 0 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 649 115 0 0 0 0 0 0 0 0 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86 86 609 0 0 0 0 0 0 0 0
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)				; positions_6nt_m5 versus oligos_7nt_mkv4_m3; m=4/6; ncol2=17; w=-1; offset=-1; strand=D; shift=1; score=0.584847; -skGGcGCTGTCCrtGGt-------- ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 0 0 0 0 0 0 0 0 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 0 0 0 0 0 0 0 0 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 0 0 0 0 0 0 0 0 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663 0 0 0 0 0 0 0 0
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_6nt_m5 versus positions_7nt_m2; m=5/6; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.520251; -bgggmGCTGTCCatg---------- ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 0 0 0 0 0 0 0 0 0 0 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 0 0 0 0 0 0 0 0 0 0 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 0 0 0 0 0 0 0 0 0 0 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153 0 0 0 0 0 0 0 0 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_6nt_m5 versus positions_7nt_m3; m=6/6; ncol2=13; w=0; offset=1; strand=D; shift=3; score=0.496647; ---rghGCTGTCCAtg---------- ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 0 0 0 0 0 0 0 0 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 0 0 0 0 0 0 0 0 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 0 0 0 0 0 0 0 0 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; ssgGGaGCTGTCCATGGwCagcrs ; Alignment reference a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 3 30 7 44 4 5 22 8 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 9 7 51 14 10 43 8 27 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 52 12 7 4 39 16 22 22 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2 3 18 2 5 14 3 15 10
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ssgGGaGCTGTCCATGGwCagcrs ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 3 30 7 44 4 5 22 8 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 9 7 51 14 10 43 8 27 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 52 12 7 4 39 16 22 22 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2 3 18 2 5 14 3 15 10
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_6nt_m1 versus positions_6nt_m5; m=2/6; ncol2=24; w=0; offset=2; strand=D; shift=2; score=0.816928; --ssGmGCTGtCCatGGaCAGCgc ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 2 26 4 44 4 4 9 5 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 9 10 51 8 8 42 4 35 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 46 11 3 4 40 9 33 13 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1 1 11 0 2 6 3 12 5
oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)				; positions_6nt_m1 versus oligos_7nt_mkv4_m5_rc; m=3/6; ncol2=17; w=0; offset=1; strand=R; shift=1; score=0.669412; -bgGGmGCTGTCCatGGt------ ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 76 58 0 0 0 0 0 0 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 102 131 0 0 0 0 0 0 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 649 115 0 0 0 0 0 0 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86 86 609 0 0 0 0 0 0
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)				; positions_6nt_m1 versus oligos_7nt_mkv4_m3; m=4/6; ncol2=17; w=0; offset=1; strand=D; shift=1; score=0.656948; -skGGcGCTGTCCrtGGt------ ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 0 0 0 0 0 0 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 0 0 0 0 0 0 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 0 0 0 0 0 0 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663 0 0 0 0 0 0
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_6nt_m1 versus positions_7nt_m2; m=5/6; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.586462; -bgggmGCTGTCCatg-------- ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 0 0 0 0 0 0 0 0 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 0 0 0 0 0 0 0 0 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 0 0 0 0 0 0 0 0 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153 0 0 0 0 0 0 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_6nt_m1 versus positions_7nt_m3; m=6/6; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.504073; ---rghGCTGTCCAtg-------- ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 0 0 0 0 0 0 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 0 0 0 0 0 0 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 0 0 0 0 0 0 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=19; shift=0; ncol=19; atTsCwkTCCATTCsATTc ; Alignment reference a 841 76 132 61 36 465 17 16 21 8 1155 24 40 58 58 1029 55 98 206 c 60 145 202 535 1123 13 31 2 1244 1259 46 60 42 968 699 87 212 80 765 g 256 229 47 624 128 31 578 10 19 19 67 45 169 195 333 143 66 191 211 t 141 848 917 78 11 789 672 1270 14 12 30 1169 1047 77 208 39 965 929 116
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=0; score= 1; atTsCwkTCCATTCsATTc ; cor=; Ncor= a 841 76 132 61 36 465 17 16 21 8 1155 24 40 58 58 1029 55 98 206 c 60 145 202 535 1123 13 31 2 1244 1259 46 60 42 968 699 87 212 80 765 g 256 229 47 624 128 31 578 10 19 19 67 45 169 195 333 143 66 191 211 t 141 848 917 78 11 789 672 1270 14 12 30 1169 1047 77 208 39 965 929 116
oligos_6nt_mkv3_m3_rc_shift3 (oligos_6nt_mkv3_m3_rc)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3_rc; m=2/4; ncol2=16; w=0; offset=3; strand=R; shift=3; score=0.757468; ---CCATTCCATTCCATTC ; cor=; Ncor= a 0 0 0 563 702 15039 282 219 279 492 14992 263 248 381 771 14491 371 486 1252 c 0 0 0 12596 12209 155 519 110 14894 14626 205 885 121 14353 12414 203 1274 284 12959 g 0 0 0 766 2582 508 436 149 652 664 552 339 161 680 2379 870 1019 992 845 t 0 0 0 2449 881 672 15137 15896 549 592 625 14887 15844 960 810 810 13710 14612 1318
oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2_rc; m=3/4; ncol2=20; w=0; offset=2; strand=R; shift=2; score=0.697299; --TCCATTCCATTCCATTC ; cor=; Ncor= a 0 0 1262 488 675 15249 315 214 312 482 15312 303 261 412 920 14797 411 360 1152 c 0 0 214 12909 12343 159 691 133 15060 14933 171 997 138 14759 12744 209 1414 209 13687 g 0 0 294 755 2884 563 505 147 794 726 601 383 184 713 2273 929 1060 882 730 t 0 0 15014 2632 882 813 15273 16290 618 643 700 15101 16201 900 847 849 13899 15333 1215
positions_7nt_m3_shift0 (positions_7nt_m3)				; oligos_6nt_mkv3_m2 versus positions_7nt_m3; m=4/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.491887; rghGCTGTCCAtg------ ; cor=; Ncor= a 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 0 0 0 0 c 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 0 0 0 0 g 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 0 0 0 0 t 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; ATGGAATGGAATGGAATGGA ; Alignment reference a 12791 1403 1614 1215 15333 13899 849 847 900 16201 15101 700 643 618 16290 15273 813 882 2632 15014 c 1133 1634 1858 730 882 1060 929 2273 713 184 383 601 726 794 147 505 563 2884 755 294 g 1837 395 12438 13687 209 1414 209 12744 14759 138 997 171 14933 15060 133 691 159 12343 12909 214 t 1023 13352 874 1152 360 411 14797 920 412 261 303 15312 482 312 214 315 15249 675 488 1262
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; ATGGAATGGAATGGAATGGA ; cor=; Ncor= a 12791 1403 1614 1215 15333 13899 849 847 900 16201 15101 700 643 618 16290 15273 813 882 2632 15014 c 1133 1634 1858 730 882 1060 929 2273 713 184 383 601 726 794 147 505 563 2884 755 294 g 1837 395 12438 13687 209 1414 209 12744 14759 138 997 171 14933 15060 133 691 159 12343 12909 214 t 1023 13352 874 1152 360 411 14797 920 412 261 303 15312 482 312 214 315 15249 675 488 1262
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3; m=2/3; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.79986; ---GAATGGAATGGAATGG- ; cor=; Ncor= a 0 0 0 1318 14612 13710 810 810 960 15844 14887 625 592 549 15896 15137 672 881 2449 0 c 0 0 0 845 992 1019 870 2379 680 161 339 552 664 652 149 436 508 2582 766 0 g 0 0 0 12959 284 1274 203 12414 14353 121 885 205 14626 14894 110 519 155 12209 12596 0 t 0 0 0 1252 486 371 14491 771 381 248 263 14992 492 279 219 282 15039 702 563 0
oligos_6nt_mkv3_m2_rc_shift3 (oligos_6nt_mkv3_m2_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2_rc; m=3/3; ncol2=19; w=0; offset=3; strand=R; shift=3; score=0.697299; ---gAATsGAATGGAmwGsA ; cor=; Ncor= a 0 0 0 116 929 965 39 208 77 1047 1169 30 12 14 1270 672 789 11 78 917 c 0 0 0 211 191 66 143 333 195 169 45 67 19 19 10 578 31 128 624 47 g 0 0 0 765 80 212 87 699 968 42 60 46 1259 1244 2 31 13 1123 535 202 t 0 0 0 206 98 55 1029 58 58 40 24 1155 8 21 16 17 465 36 61 132

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift8 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=17; shift=8; ncol=25; --------aCCatGGACAGCkCCcv ; Alignment reference a 0 0 0 0 0 0 0 0 609 86 86 470 83 15 9 835 9 876 8 54 160 67 61 227 238 c 0 0 0 0 0 0 0 0 115 649 671 146 228 6 10 30 820 21 8 770 27 681 714 387 268 g 0 0 0 0 0 0 0 0 131 102 84 166 93 887 881 17 61 10 887 31 320 101 31 122 245 t 0 0 0 0 0 0 0 0 58 76 72 131 509 5 13 31 23 6 10 58 406 64 107 177 162
oligos_7nt_mkv4_m5_shift8 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=8; score= 1; --------aCCatGGACAGCkCCcv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 609 86 86 470 83 15 9 835 9 876 8 54 160 67 61 227 238 c 0 0 0 0 0 0 0 0 115 649 671 146 228 6 10 30 820 21 8 770 27 681 714 387 268 g 0 0 0 0 0 0 0 0 131 102 84 166 93 887 881 17 61 10 887 31 320 101 31 122 245 t 0 0 0 0 0 0 0 0 58 76 72 131 509 5 13 31 23 6 10 58 406 64 107 177 162
oligos_7nt_mkv4_m3_rc_shift8 (oligos_7nt_mkv4_m3_rc)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m3_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=8; score=0.990797; --------aCCayGGACAGCgCCms ; cor=; Ncor= a 0 0 0 0 0 0 0 0 663 80 59 509 91 29 11 884 15 936 9 96 145 90 75 246 235 c 0 0 0 0 0 0 0 0 108 700 773 148 250 12 12 50 880 19 21 778 25 672 754 403 290 g 0 0 0 0 0 0 0 0 142 130 79 186 107 932 951 20 68 18 946 48 573 149 46 146 282 t 0 0 0 0 0 0 0 0 68 71 70 138 533 8 7 27 18 8 5 59 238 70 106 186 174
positions_7nt_m2_rc_shift10 (positions_7nt_m2_rc)				; oligos_7nt_mkv4_m5 versus positions_7nt_m2_rc; m=3/8; ncol2=15; w=0; offset=2; strand=R; shift=10; score=0.864831; ----------catGGACAGCkcccv ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 153 415 92 29 11 1114 17 1125 9 57 241 110 101 287 340 c 0 0 0 0 0 0 0 0 0 0 638 247 206 8 25 36 1022 40 14 1035 88 659 721 432 316 g 0 0 0 0 0 0 0 0 0 0 177 264 101 1146 1139 16 75 14 1156 45 368 225 105 278 308 t 0 0 0 0 0 0 0 0 0 0 225 267 794 10 18 27 79 14 14 56 496 199 266 196 229
positions_7nt_m3_rc_shift10 (positions_7nt_m3_rc)				; oligos_7nt_mkv4_m5 versus positions_7nt_m3_rc; m=4/8; ncol2=13; w=0; offset=2; strand=R; shift=10; score=0.739505; ----------caTGGACAGCdcy-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 191 460 95 29 14 1218 44 1255 11 74 339 185 133 0 0 c 0 0 0 0 0 0 0 0 0 0 668 284 174 5 28 42 1112 28 17 1114 129 607 691 0 0 g 0 0 0 0 0 0 0 0 0 0 212 283 98 1272 1251 25 84 11 1276 66 404 281 163 0 0 t 0 0 0 0 0 0 0 0 0 0 246 290 950 11 24 32 77 23 13 63 445 244 330 0 0
positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)				; oligos_7nt_mkv4_m5 versus positions_6nt_m1_rc; m=5/8; ncol2=24; w=-6; offset=-6; strand=R; shift=2; score=0.669412; --sygctGwCCATGGACAGCtCCcs ; cor=; Ncor= a 0 0 10 15 3 14 5 2 18 3 2 48 5 1 1 47 1 58 2 4 10 2 5 10 14 c 0 0 22 22 16 39 4 7 12 52 54 8 8 5 3 3 63 6 5 54 6 48 49 39 20 g 0 0 27 8 43 10 14 51 7 9 5 8 7 60 60 6 2 1 56 5 13 10 10 10 23 t 0 0 8 22 5 4 44 7 30 3 6 3 47 1 3 11 1 2 4 4 38 7 3 8 10
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m1_rc; m=6/8; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.613551; gbtTCAGCACCayGGACAGcgcCm- ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 18 676 8 740 18 95 171 106 86 234 0 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 12 54 633 13 12 515 26 463 554 310 0 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 745 32 112 21 734 88 401 158 30 110 0 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5 10 23 32 11 21 87 187 58 115 131 0
positions_6nt_m5_rc_shift0 (positions_6nt_m5_rc)				; oligos_7nt_mkv4_m5 versus positions_6nt_m5_rc; m=7/8; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.590701; gsgcGCTGtCCatGGaCAGCkCss- ; cor=; Ncor= a 11 8 5 12 3 6 2 0 11 1 1 36 7 3 0 33 2 43 1 3 6 2 9 10 0 c 14 19 13 33 9 40 4 3 11 46 49 9 8 4 6 6 55 10 4 47 5 41 31 21 0 g 24 22 35 4 42 8 8 51 10 9 5 9 5 50 50 10 1 3 49 7 18 11 15 15 0 t 9 9 5 9 4 4 44 4 26 2 3 4 38 1 2 9 0 2 4 1 29 4 3 12 0
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m4; m=8/8; ncol2=23; w=-8; offset=-8; strand=D; shift=0; score=0.577914; gbtTCAGCACCayGGACAGckcC-- ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 14 684 4 743 13 93 168 96 74 0 0 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 8 44 632 11 6 516 23 452 550 0 0 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 744 21 104 9 731 74 383 161 33 0 0 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4 1 18 27 4 17 84 193 58 110 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=16; shift=4; ncol=20; ----ssGCGGCGGGGCgGss ; Alignment reference a 0 0 0 0 101 118 20 49 28 30 34 16 31 32 23 56 43 62 103 93 c 0 0 0 0 404 296 70 662 89 101 800 68 119 186 64 686 201 150 249 274 g 0 0 0 0 323 435 806 181 764 750 64 818 736 674 816 144 617 648 462 449 t 0 0 0 0 92 71 24 28 39 39 22 18 34 28 17 34 59 60 106 104
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=4; score= 1; ----ssGCGGCGGGGCgGss ; cor=; Ncor= a 0 0 0 0 101 118 20 49 28 30 34 16 31 32 23 56 43 62 103 93 c 0 0 0 0 404 296 70 662 89 101 800 68 119 186 64 686 201 150 249 274 g 0 0 0 0 323 435 806 181 764 750 64 818 736 674 816 144 617 648 462 449 t 0 0 0 0 92 71 24 28 39 39 22 18 34 28 17 34 59 60 106 104
positions_6nt_m3_rc_shift3 (positions_6nt_m3_rc)				; oligos_6nt_mkv3_m5 versus positions_6nt_m3_rc; m=2/3; ncol2=16; w=-1; offset=-1; strand=R; shift=3; score=0.798609; ---sssGGGGCGGGGcsgg- ; cor=; Ncor= a 0 0 0 180 167 144 66 66 25 31 36 25 38 61 47 121 123 182 159 0 c 0 0 0 415 511 407 138 203 108 119 1233 83 117 158 104 815 627 324 322 0 g 0 0 0 593 484 653 1046 1024 1174 1142 21 1197 1128 1075 1141 304 438 639 691 0 t 0 0 0 138 164 122 76 33 19 34 36 21 43 32 34 86 138 181 154 0
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; oligos_6nt_mkv3_m5 versus positions_6nt_m4_rc; m=3/3; ncol2=19; w=-4; offset=-4; strand=R; shift=0; score=0.711732; ssgGsGGCGGCGGGGssgg- ; cor=; Ncor= a 106 114 98 55 55 60 31 54 23 23 32 17 43 39 46 93 83 111 107 0 c 254 363 226 127 237 138 71 688 70 49 768 74 92 194 91 526 424 227 229 0 g 459 347 528 710 581 698 800 144 801 816 84 809 774 660 759 253 307 478 486 0 t 105 100 72 32 51 28 22 38 30 36 40 24 15 31 28 52 110 108 102 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; skTTCAkCACCatGGTGmTGAAms ; Alignment reference a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 5 21 2 47 2 11 91 90 44 29 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 2 13 18 67 5 23 6 17 34 34 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 118 6 101 6 23 89 19 17 27 52 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2 2 87 6 7 97 4 11 3 22 12
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; skTTCAkCACCatGGTGmTGAAms ; cor=; Ncor= a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 5 21 2 47 2 11 91 90 44 29 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 2 13 18 67 5 23 6 17 34 34 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 118 6 101 6 23 89 19 17 27 52 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2 2 87 6 7 97 4 11 3 22 12
positions_6nt_m2_shift0 (positions_6nt_m2)				; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=2/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.574038; sbtTCAGCACCaygg--------- ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 155 0 0 0 0 0 0 0 0 0 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 177 0 0 0 0 0 0 0 0 0 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 726 0 0 0 0 0 0 0 0 0 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92 93 0 0 0 0 0 0 0 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_6nt_mkv3_m1 versus positions_7nt_m1; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.545196; sbtTCAGCACCayg---------- ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 0 0 0 0 0 0 0 0 0 0 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 0 0 0 0 0 0 0 0 0 0 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 0 0 0 0 0 0 0 0 0 0 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107 0 0 0 0 0 0 0 0 0 0
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4; m=4/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.484408; -btTCAGsACCayG---------- ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 0 0 0 0 0 0 0 0 0 0 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 0 0 0 0 0 0 0 0 0 0 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 0 0 0 0 0 0 0 0 0 0 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=24; shift=1; ncol=25; -kGgcgCTGTCCrtGGTGCTGAavc ; Alignment reference a 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 7 5 47 3 3 19 638 478 221 159 c 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 2 2 124 767 8 6 43 158 231 287 g 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 774 2 568 6 2 753 82 65 210 175 t 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8 2 776 46 9 772 7 22 84 123 164
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -kGgcgCTGTCCrtGGTGCTGAavc ; cor=; Ncor= a 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 7 5 47 3 3 19 638 478 221 159 c 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 2 2 124 767 8 6 43 158 231 287 g 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 774 2 568 6 2 753 82 65 210 175 t 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8 2 776 46 9 772 7 22 84 123 164
oligos_6nt_mkv3_m4_rc_shift2 (oligos_6nt_mkv3_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=2/9; ncol2=23; w=0; offset=1; strand=R; shift=2; score=0.957984; --GgmgCTGTCCrtGGTGCTGAavc ; cor=; Ncor= a 0 0 110 58 193 84 17 4 27 18 1 4 334 134 22 7 5 50 1 3 21 609 453 211 159 c 0 0 33 161 383 74 731 9 104 21 744 738 85 104 7 1 5 126 750 12 8 48 161 231 276 g 0 0 550 452 23 516 6 11 632 44 8 4 257 72 731 756 2 544 5 3 731 86 70 205 177 t 0 0 74 96 168 93 13 743 4 684 14 21 91 457 7 3 755 47 11 749 7 24 83 120 155
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=3/9; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.621099; skGGcGCTGTCCrtGGt-------- ; cor=; Ncor= a 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 71 68 0 0 0 0 0 0 0 0 c 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 130 142 0 0 0 0 0 0 0 0 g 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 700 108 0 0 0 0 0 0 0 0 t 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59 80 663 0 0 0 0 0 0 0 0
oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5_rc; m=4/9; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.613551; bgGGmGCTGTCCatGGt-------- ; cor=; Ncor= a 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 76 58 0 0 0 0 0 0 0 0 c 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 102 131 0 0 0 0 0 0 0 0 g 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 649 115 0 0 0 0 0 0 0 0 t 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86 86 609 0 0 0 0 0 0 0 0
positions_6nt_m2_rc_shift10 (positions_6nt_m2_rc)				; oligos_7nt_mkv4_m1 versus positions_6nt_m2_rc; m=5/9; ncol2=15; w=0; offset=9; strand=R; shift=10; score=0.610442; ----------ccrtGGTGCTGAavs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 93 92 324 139 49 19 16 46 47 21 15 980 708 329 215 c 0 0 0 0 0 0 0 0 0 0 726 756 203 160 13 13 19 94 1008 6 20 45 202 313 382 g 0 0 0 0 0 0 0 0 0 0 177 176 417 98 1067 1108 33 961 78 16 1107 80 90 295 306 t 0 0 0 0 0 0 0 0 0 0 155 127 207 754 22 11 1083 50 18 1108 9 46 151 214 248
positions_7nt_m1_rc_shift11 (positions_7nt_m1_rc)				; oligos_7nt_mkv4_m1 versus positions_7nt_m1_rc; m=6/9; ncol2=14; w=0; offset=10; strand=R; shift=11; score=0.574002; -----------crtGGTGCTGAavs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 107 373 148 48 22 27 47 58 21 21 1009 769 333 221 c 0 0 0 0 0 0 0 0 0 0 0 767 222 144 11 12 16 103 1018 7 18 47 189 309 385 g 0 0 0 0 0 0 0 0 0 0 0 173 362 100 1093 1131 31 975 80 23 1129 82 79 307 322 t 0 0 0 0 0 0 0 0 0 0 0 131 221 786 26 13 1104 53 22 1127 10 40 141 229 250
oligos_7nt_mkv4_m4_rc_shift11 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=7/9; ncol2=13; w=0; offset=10; strand=R; shift=11; score=0.527531; -----------CrtGGTsCTGAav- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 57 219 76 18 8 10 41 4 10 21 766 421 234 0 c 0 0 0 0 0 0 0 0 0 0 0 606 200 136 15 13 10 380 829 13 8 38 187 238 0 g 0 0 0 0 0 0 0 0 0 0 0 99 301 90 805 822 14 388 8 11 810 34 138 237 0 t 0 0 0 0 0 0 0 0 0 0 0 89 131 549 13 8 817 42 10 817 12 13 105 142 0
positions_7nt_m2_shift0 (positions_7nt_m2)				; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=8/9; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score= 0.5267; bgggmGCTGTCCatg---------- ; cor=; Ncor= a 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 0 0 0 0 0 0 0 0 0 0 c 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 0 0 0 0 0 0 0 0 0 0 g 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 0 0 0 0 0 0 0 0 0 0 t 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153 0 0 0 0 0 0 0 0 0 0
positions_7nt_m3_shift2 (positions_7nt_m3)				; oligos_7nt_mkv4_m1 versus positions_7nt_m3; m=9/9; ncol2=13; w=0; offset=1; strand=D; shift=2; score=0.504392; --rghGCTGTCCAtg---------- ; cor=; Ncor= a 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 0 0 0 0 0 0 0 0 0 0 c 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 0 0 0 0 0 0 0 0 0 0 g 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 0 0 0 0 0 0 0 0 0 0 t 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -bgggmGCTGTCCatg ; Alignment reference a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -bgggmGCTGTCCatg ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153
oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)				; positions_7nt_m2 versus oligos_7nt_mkv4_m5_rc; m=2/8; ncol2=17; w=0; offset=0; strand=R; shift=1; score=0.864831; -bgGGmGCTGTCCatG ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m2 versus positions_7nt_m3; m=3/8; ncol2=13; w=0; offset=2; strand=D; shift=3; score=0.86346; ---rghGCTGTCCAtg ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)				; positions_7nt_m2 versus oligos_7nt_mkv4_m3; m=4/8; ncol2=17; w=0; offset=0; strand=D; shift=1; score=0.854041; -skGGcGCTGTCCrtG ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_7nt_m2 versus positions_6nt_m1; m=5/8; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.586462; ssgGGaGCTGTCCATG ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; positions_7nt_m2 versus oligos_7nt_mkv4_m1; m=6/8; ncol2=24; w=0; offset=1; strand=D; shift=2; score= 0.5267; --kGgcgCTGTCCrtG ; cor=; Ncor= a 0 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 c 0 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 g 0 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 t 0 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_7nt_m2 versus positions_6nt_m5; m=7/8; ncol2=24; w=0; offset=1; strand=D; shift=2; score=0.520251; --ssGmGCTGtCCatG ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1
oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)				; positions_7nt_m2 versus oligos_6nt_mkv3_m4_rc; m=8/8; ncol2=23; w=0; offset=2; strand=R; shift=3; score=0.492441; ---GgmgCTGTCCrtG ; cor=; Ncor= a 0 0 0 110 58 193 84 17 4 27 18 1 4 334 134 22 c 0 0 0 33 161 383 74 731 9 104 21 744 738 85 104 7 g 0 0 0 550 452 23 516 6 11 632 44 8 4 257 72 731 t 0 0 0 74 96 168 93 13 743 4 684 14 21 91 457 7

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=13; shift=3; ncol=16; ---rghGCTGTCCAtg ; Alignment reference a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191
positions_7nt_m3_shift3 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/9; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---rghGCTGTCCAtg ; cor=; Ncor= a 0 0 0 330 244 445 63 13 23 77 32 24 11 950 290 246 c 0 0 0 163 281 404 66 1276 11 84 25 1251 1272 98 283 212 g 0 0 0 691 607 129 1114 17 28 1112 42 28 5 174 284 668 t 0 0 0 133 185 339 74 11 1255 44 1218 14 29 95 460 191
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_7nt_m3 versus positions_7nt_m2; m=2/9; ncol2=15; w=-2; offset=-2; strand=D; shift=1; score=0.86346; -bgggmGCTGTCCatg ; cor=; Ncor= a 0 229 196 266 199 496 56 14 14 79 27 18 10 794 267 225 c 0 308 278 105 225 368 45 1156 14 75 16 1139 1146 101 264 177 g 0 316 432 721 659 88 1035 14 40 1022 36 25 8 206 247 638 t 0 340 287 101 110 241 57 9 1125 17 1114 11 29 92 415 153
oligos_7nt_mkv4_m5_rc_shift1 (oligos_7nt_mkv4_m5_rc)				; positions_7nt_m3 versus oligos_7nt_mkv4_m5_rc; m=3/9; ncol2=17; w=-2; offset=-2; strand=R; shift=1; score=0.739505; -bgGGmGCTGTCCatG ; cor=; Ncor= a 0 162 177 107 64 406 58 10 6 23 31 13 5 509 131 72 c 0 245 122 31 101 320 31 887 10 61 17 881 887 93 166 84 g 0 268 387 714 681 27 770 8 21 820 30 10 6 228 146 671 t 0 238 227 61 67 160 54 8 876 9 835 9 15 83 470 86
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)				; positions_7nt_m3 versus oligos_7nt_mkv4_m3; m=4/9; ncol2=17; w=-2; offset=-2; strand=D; shift=1; score=0.732669; -skGGcGCTGTCCrtG ; cor=; Ncor= a 0 174 186 106 70 238 59 5 8 18 27 7 8 533 138 70 c 0 282 146 46 149 573 48 946 18 68 20 951 932 107 186 79 g 0 290 403 754 672 25 778 21 19 880 50 12 12 250 148 773 t 0 235 246 75 90 145 96 9 936 15 884 11 29 91 509 59
oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)				; positions_7nt_m3 versus oligos_6nt_mkv3_m4_rc; m=5/9; ncol2=23; w=0; offset=0; strand=R; shift=3; score=0.529684; ---GgmgCTGTCCrtG ; cor=; Ncor= a 0 0 0 110 58 193 84 17 4 27 18 1 4 334 134 22 c 0 0 0 33 161 383 74 731 9 104 21 744 738 85 104 7 g 0 0 0 550 452 23 516 6 11 632 44 8 4 257 72 731 t 0 0 0 74 96 168 93 13 743 4 684 14 21 91 457 7
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; positions_7nt_m3 versus oligos_7nt_mkv4_m1; m=6/9; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.504392; --kGgcgCTGTCCrtG ; cor=; Ncor= a 0 0 131 115 58 187 87 21 11 32 23 10 5 328 134 27 c 0 0 110 30 158 401 88 734 21 112 32 745 743 93 108 6 g 0 0 310 554 463 26 515 12 13 633 54 12 11 266 67 744 t 0 0 234 86 106 171 95 18 740 8 676 18 26 98 476 8
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_7nt_m3 versus positions_6nt_m1; m=7/9; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.504073; ssgGGaGCTGTCCATG ; cor=; Ncor= a 10 10 8 3 7 38 4 4 2 1 11 3 1 47 3 6 c 20 23 10 10 10 13 5 56 1 2 6 60 60 7 8 5 g 25 20 39 49 48 6 54 5 6 63 3 3 5 8 8 54 t 12 14 10 5 2 10 4 2 58 1 47 1 1 5 48 2
positions_6nt_m5_shift2 (positions_6nt_m5)				; positions_7nt_m3 versus positions_6nt_m5; m=8/9; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.496647; --ssGmGCTGtCCatG ; cor=; Ncor= a 0 0 12 3 4 29 1 4 2 0 9 2 1 38 4 3 c 0 0 15 15 11 18 7 49 3 1 10 50 50 5 9 5 g 0 0 21 31 41 5 47 4 10 55 6 6 4 8 9 49 t 0 0 10 9 2 6 3 1 43 2 33 0 3 7 36 1
oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)				; positions_7nt_m3 versus oligos_6nt_mkv3_m2; m=9/9; ncol2=19; w=0; offset=0; strand=D; shift=3; score=0.491887; ---atTsCwkTCCATT ; cor=; Ncor= a 0 0 0 841 76 132 61 36 465 17 16 21 8 1155 24 40 c 0 0 0 60 145 202 535 1123 13 31 2 1244 1259 46 60 42 g 0 0 0 256 229 47 624 128 31 578 10 19 19 67 45 169 t 0 0 0 141 848 917 78 11 789 672 1270 14 12 30 1169 1047

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; sbtTCAGCACCayg ; Alignment reference a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; sbtTCAGCACCayg ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_7nt_m1 versus positions_6nt_m2; m=2/6; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.932651; sbtTCAGCACCayg ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; positions_7nt_m1 versus oligos_7nt_mkv4_m4; m=3/6; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.898605; -btTCAGsACCayG ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; positions_7nt_m1 versus oligos_6nt_mkv3_m4; m=4/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.597116; gbtTCAGCACCayG ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; positions_7nt_m1 versus oligos_7nt_mkv4_m1_rc; m=5/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.574002; gbtTCAGCACCayG ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; positions_7nt_m1 versus oligos_6nt_mkv3_m1; m=6/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.545196; skTTCAkCACCatG ; cor=; Ncor= a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=19; shift=1; ncol=20; -ccssCCCCGCCGCCsCcss ; Alignment reference a 0 102 108 110 52 28 31 15 24 40 36 30 38 22 28 51 32 72 100 105 c 0 486 478 307 253 759 660 774 809 84 816 801 144 800 698 581 710 528 347 459 g 0 229 227 424 526 91 194 92 74 768 49 70 688 71 138 237 127 226 363 254 t 0 107 111 83 93 46 39 43 17 32 23 23 54 31 60 55 55 98 114 106
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -ccssCCCCGCCGCCsCcss ; cor=; Ncor= a 0 102 108 110 52 28 31 15 24 40 36 30 38 22 28 51 32 72 100 105 c 0 486 478 307 253 759 660 774 809 84 816 801 144 800 698 581 710 528 347 459 g 0 229 227 424 526 91 194 92 74 768 49 70 688 71 138 237 127 226 363 254 t 0 107 111 83 93 46 39 43 17 32 23 23 54 31 60 55 55 98 114 106
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m4 versus positions_6nt_m3; m=2/3; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.753167; -ccsgCCCCGCCCCsss--- ; cor=; Ncor= a 0 154 181 138 86 34 32 43 21 36 34 19 33 76 122 164 138 0 0 0 c 0 691 639 438 304 1141 1075 1128 1197 21 1142 1174 1024 1046 653 484 593 0 0 0 g 0 322 324 627 815 104 158 117 83 1233 119 108 203 138 407 511 415 0 0 0 t 0 159 182 123 121 47 61 38 25 36 31 25 66 66 144 167 180 0 0 0
oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)				; positions_6nt_m4 versus oligos_6nt_mkv3_m5_rc; m=3/3; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.711732; ssCcGCCCCGCCGCss---- ; cor=; Ncor= a 104 106 60 59 34 17 28 34 18 22 39 39 28 24 71 92 0 0 0 0 c 449 462 648 617 144 816 674 736 818 64 750 764 181 806 435 323 0 0 0 0 g 274 249 150 201 686 64 186 119 68 800 101 89 662 70 296 404 0 0 0 0 t 93 103 62 43 56 23 32 31 16 34 30 28 49 20 118 101 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=23; shift=0; ncol=23; gbtTCAGCACCayGGACAGckcC ; Alignment reference a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 14 684 4 743 13 93 168 96 74 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 8 44 632 11 6 516 23 452 550 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 744 21 104 9 731 74 383 161 33 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4 1 18 27 4 17 84 193 58 110
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/9; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; gbtTCAGCACCayGGACAGckcC ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 14 684 4 743 13 93 168 96 74 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 8 44 632 11 6 516 23 452 550 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 744 21 104 9 731 74 383 161 33 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4 1 18 27 4 17 84 193 58 110
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=2/9; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.957984; gbtTCAGCACCayGGACAGcgcC ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 18 676 8 740 18 95 171 106 86 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 12 54 633 13 12 515 26 463 554 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 745 32 112 21 734 88 401 158 30 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5 10 23 32 11 21 87 187 58 115
positions_6nt_m2_shift0 (positions_6nt_m2)				; oligos_6nt_mkv3_m4 versus positions_6nt_m2; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.634321; sbtTCAGCACCaygg-------- ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 155 0 0 0 0 0 0 0 0 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 177 0 0 0 0 0 0 0 0 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 726 0 0 0 0 0 0 0 0 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92 93 0 0 0 0 0 0 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_6nt_mkv3_m4 versus positions_7nt_m1; m=4/9; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.597116; sbtTCAGCACCayg--------- ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 0 0 0 0 0 0 0 0 0 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 0 0 0 0 0 0 0 0 0 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 0 0 0 0 0 0 0 0 0 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107 0 0 0 0 0 0 0 0 0
oligos_7nt_mkv4_m3_rc_shift8 (oligos_7nt_mkv4_m3_rc)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m3_rc; m=5/9; ncol2=17; w=0; offset=8; strand=R; shift=8; score=0.584226; --------aCCayGGACAGCgCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 663 80 59 509 91 29 11 884 15 936 9 96 145 90 75 c 0 0 0 0 0 0 0 0 108 700 773 148 250 12 12 50 880 19 21 778 25 672 754 g 0 0 0 0 0 0 0 0 142 130 79 186 107 932 951 20 68 18 946 48 573 149 46 t 0 0 0 0 0 0 0 0 68 71 70 138 533 8 7 27 18 8 5 59 238 70 106
oligos_7nt_mkv4_m5_shift8 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m5; m=6/9; ncol2=17; w=0; offset=8; strand=D; shift=8; score=0.577914; --------aCCatGGACAGCkCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 609 86 86 470 83 15 9 835 9 876 8 54 160 67 61 c 0 0 0 0 0 0 0 0 115 649 671 146 228 6 10 30 820 21 8 770 27 681 714 g 0 0 0 0 0 0 0 0 131 102 84 166 93 887 881 17 61 10 887 31 320 101 31 t 0 0 0 0 0 0 0 0 58 76 72 131 509 5 13 31 23 6 10 58 406 64 107
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m4; m=7/9; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.54983; -btTCAGsACCayG--------- ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 0 0 0 0 0 0 0 0 0 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 0 0 0 0 0 0 0 0 0 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 0 0 0 0 0 0 0 0 0 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57 0 0 0 0 0 0 0 0 0
positions_7nt_m3_rc_shift10 (positions_7nt_m3_rc)				; oligos_6nt_mkv3_m4 versus positions_7nt_m3_rc; m=8/9; ncol2=13; w=0; offset=10; strand=R; shift=10; score=0.529684; ----------caTGGACAGCdcy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 191 460 95 29 14 1218 44 1255 11 74 339 185 133 c 0 0 0 0 0 0 0 0 0 0 668 284 174 5 28 42 1112 28 17 1114 129 607 691 g 0 0 0 0 0 0 0 0 0 0 212 283 98 1272 1251 25 84 11 1276 66 404 281 163 t 0 0 0 0 0 0 0 0 0 0 246 290 950 11 24 32 77 23 13 63 445 244 330
positions_7nt_m2_rc_shift10 (positions_7nt_m2_rc)				; oligos_6nt_mkv3_m4 versus positions_7nt_m2_rc; m=9/9; ncol2=15; w=0; offset=10; strand=R; shift=10; score=0.492441; ----------catGGACAGCkcc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 153 415 92 29 11 1114 17 1125 9 57 241 110 101 c 0 0 0 0 0 0 0 0 0 0 638 247 206 8 25 36 1022 40 14 1035 88 659 721 g 0 0 0 0 0 0 0 0 0 0 177 264 101 1146 1139 16 75 14 1156 45 368 225 105 t 0 0 0 0 0 0 0 0 0 0 225 267 794 10 18 27 79 14 14 56 496 199 266

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -btTCAGsACCayG ; Alignment reference a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -btTCAGsACCayG ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_7nt_mkv4_m4 versus positions_7nt_m1; m=2/6; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.898605; sbtTCAGCACCayg ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107
positions_6nt_m2_shift0 (positions_6nt_m2)				; oligos_7nt_mkv4_m4 versus positions_6nt_m2; m=3/6; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.839856; sbtTCAGCACCayg ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m4; m=4/6; ncol2=23; w=-1; offset=-1; strand=D; shift=0; score=0.54983; gbtTCAGCACCayG ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=5/6; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.527531; gbtTCAGCACCayG ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m1; m=6/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.484408; skTTCAkCACCatG ; cor=; Ncor= a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; sbtTCAGCACCaygg ; Alignment reference a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 155 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 177 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 726 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92 93
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; sbtTCAGCACCaygg ; cor=; Ncor= a 248 214 151 46 9 1108 18 50 1083 11 22 754 207 127 155 c 306 295 90 80 1107 16 78 961 33 1108 1067 98 417 176 177 g 382 313 202 45 20 6 1008 94 19 13 13 160 203 756 726 t 215 329 708 980 15 21 47 46 16 19 49 139 324 92 93
positions_7nt_m1_shift0 (positions_7nt_m1)				; positions_6nt_m2 versus positions_7nt_m1; m=2/6; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.932651; sbtTCAGCACCayg- ; cor=; Ncor= a 250 229 141 40 10 1127 22 53 1104 13 26 786 221 131 0 c 322 307 79 82 1129 23 80 975 31 1131 1093 100 362 173 0 g 385 309 189 47 18 7 1018 103 16 12 11 144 222 767 0 t 221 333 769 1009 21 21 58 47 27 22 48 148 373 107 0
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; positions_6nt_m2 versus oligos_7nt_mkv4_m4; m=3/6; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.839856; -btTCAGsACCayG- ; cor=; Ncor= a 0 142 105 13 12 817 10 42 817 8 13 549 131 89 0 c 0 237 138 34 810 11 8 388 14 822 805 90 301 99 0 g 0 238 187 38 8 13 829 380 10 13 15 136 200 606 0 t 0 234 421 766 21 10 4 41 10 8 18 76 219 57 0
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; positions_6nt_m2 versus oligos_6nt_mkv3_m4; m=4/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.634321; gbtTCAGCACCayGG ; cor=; Ncor= a 155 120 83 24 7 749 11 47 755 3 7 457 91 21 14 c 177 205 70 86 731 3 5 544 2 756 731 72 257 4 8 g 276 231 161 48 8 12 750 126 5 1 7 104 85 738 744 t 159 211 453 609 21 3 1 50 5 7 22 134 334 4 1
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; positions_6nt_m2 versus oligos_7nt_mkv4_m1_rc; m=5/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.610442; gbtTCAGCACCayGG ; cor=; Ncor= a 164 123 84 22 7 772 9 46 776 2 8 476 98 26 18 c 175 210 65 82 753 2 6 568 2 774 744 67 266 11 12 g 287 231 158 43 6 8 767 124 2 2 6 108 93 743 745 t 159 221 478 638 19 3 3 47 5 7 27 134 328 5 10
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; positions_6nt_m2 versus oligos_6nt_mkv3_m1; m=6/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.574038; skTTCAkCACCatGG ; cor=; Ncor= a 12 22 4 11 4 98 7 6 88 2 2 65 18 8 5 c 52 27 16 19 90 22 6 101 6 118 113 17 27 4 2 g 35 34 17 6 22 5 68 18 13 2 4 27 17 113 118 t 28 44 90 91 11 2 46 2 20 5 8 18 65 2 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=16; shift=1; ncol=17; -ccsgCCCCGCCCCsss ; Alignment reference a 0 154 181 138 86 34 32 43 21 36 34 19 33 76 122 164 138 c 0 691 639 438 304 1141 1075 1128 1197 21 1142 1174 1024 1046 653 484 593 g 0 322 324 627 815 104 158 117 83 1233 119 108 203 138 407 511 415 t 0 159 182 123 121 47 61 38 25 36 31 25 66 66 144 167 180
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -ccsgCCCCGCCCCsss ; cor=; Ncor= a 0 154 181 138 86 34 32 43 21 36 34 19 33 76 122 164 138 c 0 691 639 438 304 1141 1075 1128 1197 21 1142 1174 1024 1046 653 484 593 g 0 322 324 627 815 104 158 117 83 1233 119 108 203 138 407 511 415 t 0 159 182 123 121 47 61 38 25 36 31 25 66 66 144 167 180
oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)				; positions_6nt_m3 versus oligos_6nt_mkv3_m5_rc; m=2/3; ncol2=16; w=-1; offset=-1; strand=R; shift=0; score=0.798609; ssCcGCCCCGCCGCss- ; cor=; Ncor= a 104 106 60 59 34 17 28 34 18 22 39 39 28 24 71 92 0 c 449 462 648 617 144 816 674 736 818 64 750 764 181 806 435 323 0 g 274 249 150 201 686 64 186 119 68 800 101 89 662 70 296 404 0 t 93 103 62 43 56 23 32 31 16 34 30 28 49 20 118 101 0
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_6nt_m3 versus positions_6nt_m4; m=3/3; ncol2=19; w=0; offset=0; strand=D; shift=1; score=0.753167; -ccssCCCCGCCGCCsC ; cor=; Ncor= a 0 102 108 110 52 28 31 15 24 40 36 30 38 22 28 51 32 c 0 486 478 307 253 759 660 774 809 84 816 801 144 800 698 581 710 g 0 229 227 424 526 91 194 92 74 768 49 70 688 71 138 237 127 t 0 107 111 83 93 46 39 43 17 32 23 23 54 31 60 55 55