One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/10/peak-motifs.2026-01-10.162902_2026-01-10.162902_kwL4BB/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/10/peak-motifs.2026-01-10.162902_2026-01-10.162902_kwL4BB/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGCCCCGCss ; Alignment reference a 725 705 316 171 65 91 59 256 182 120 787 636 c 2632 2541 4705 200 5328 5153 5239 4882 160 5221 2502 2627 g 1518 1738 506 4948 221 324 296 366 5157 321 1574 1675 t 860 751 208 416 121 167 141 231 236 73 872 797

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCCGCss ; cor=; Ncor= a 725 705 316 171 65 91 59 256 182 120 787 636 c 2632 2541 4705 200 5328 5153 5239 4882 160 5221 2502 2627 g 1518 1738 506 4948 221 324 296 366 5157 321 1574 1675 t 860 751 208 416 121 167 141 231 236 73 872 797

oligos_6nt_mkv4_m2_rc_shift1 (oligos_6nt_mkv4_m2_rc)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m2_rc; m=2/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.715422; -ssGCTCCGCss ; cor=; Ncor= a 0 533 648 88 129 116 76 10 52 249 555 518 c 0 1514 1245 119 3301 49 3388 3530 8 2563 1009 1269 g 0 1155 1250 3365 175 560 172 110 3605 690 1691 1263 t 0 473 532 103 70 2950 39 25 10 173 420 625

oligos_6nt_mkv4_m4_rc_shift0 (oligos_6nt_mkv4_m4_rc)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m4_rc; m=3/5; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.707747; sstGCCCTGCcs ; cor=; Ncor= a 374 354 205 30 35 68 38 67 32 85 332 354 c 968 990 412 89 2250 2141 2286 151 77 2078 1339 888 g 630 695 302 2224 48 139 56 116 2241 141 470 703 t 438 371 1491 67 77 62 30 2076 60 106 269 465

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m3; m=4/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.678506; ssCGCCCCCss- ; cor=; Ncor= a 655 621 0 13 97 136 227 153 53 729 516 0 c 2111 1997 4876 0 4520 4085 3488 4094 4460 1236 2129 0 g 1573 1748 0 4868 118 589 1110 590 354 2359 1695 0 t 542 515 5 0 146 71 56 44 14 557 541 0

oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)
; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.617573; --ssCCCCGCCC ; cor=; Ncor= a 0 0 1080 985 151 193 241 128 292 158 154 158 c 0 0 2571 2191 6056 6029 5971 6261 23 6240 6171 6162 g 0 0 2265 2421 393 409 465 396 6474 319 408 373 t 0 0 990 1309 306 275 229 121 117 189 173 213

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGCAGGCGss ; Alignment reference a 459 392 118 64 56 2366 26 48 121 95 406 519 c 907 1014 2576 205 2702 220 98 194 2626 172 1150 1049 g 1143 1156 186 2617 190 273 2773 2683 112 2566 1074 977 t 456 403 85 79 17 106 68 40 106 132 335 420

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCAGGCGss ; cor=; Ncor= a 459 392 118 64 56 2366 26 48 121 95 406 519 c 907 1014 2576 205 2702 220 98 194 2626 172 1150 1049 g 1143 1156 186 2617 190 273 2773 2683 112 2566 1074 977 t 456 403 85 79 17 106 68 40 106 132 335 420

oligos_7nt_mkv5_m5_rc_shift0 (oligos_7nt_mkv5_m5_rc)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m5_rc; m=2/3; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.827581; ssCGCAGCCGss ; cor=; Ncor= a 577 439 165 81 63 2748 25 48 142 134 437 612 c 1248 1794 3418 202 3618 660 77 3685 3521 263 1891 1519 g 1556 1161 215 3540 222 334 3814 162 154 3394 1225 1264 t 554 541 137 112 32 193 19 40 118 144 382 540

oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3_rc; m=3/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.648024; -ssGGGGGCGss ; cor=; Ncor= a 0 541 557 14 44 56 71 146 0 5 515 542 c 0 1695 2359 354 590 1110 589 118 4868 0 1748 1573 g 0 2129 1236 4460 4094 3488 4085 4520 0 4876 1997 2111 t 0 516 729 53 153 227 136 97 13 0 621 655

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=13; shift=2; ncol=15; --bsCAGGACCTgss ; Alignment reference a 0 0 748 664 218 3786 75 73 3252 104 72 146 492 739 926 c 0 0 1040 1667 3575 89 74 146 184 3783 3861 519 943 1160 1262 g 0 0 1302 1060 203 165 3948 3863 161 171 84 179 1915 1620 1220 t 0 0 1051 750 145 101 44 59 544 83 124 3297 791 622 733

oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --bsCAGGACCTgss ; cor=; Ncor= a 0 0 748 664 218 3786 75 73 3252 104 72 146 492 739 926 c 0 0 1040 1667 3575 89 74 146 184 3783 3861 519 943 1160 1262 g 0 0 1302 1060 203 165 3948 3863 161 171 84 179 1915 1620 1220 t 0 0 1051 750 145 101 44 59 544 83 124 3297 791 622 733

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1; m=2/2; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.78833; sskcCAGGACCTGgs ; cor=; Ncor= a 502 589 476 330 325 2740 64 45 2460 64 45 87 232 332 709 c 1197 890 657 1843 2108 105 56 104 121 2811 2868 283 334 541 962 g 898 863 826 570 372 185 2925 2879 122 139 103 111 2224 1927 961 t 493 748 1131 347 285 60 45 62 387 76 74 2609 300 290 458

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGGCTGCGss ; Alignment reference a 540 382 144 118 40 19 193 32 112 137 541 554 c 1264 1225 3394 154 162 3814 334 222 3540 215 1161 1556 g 1519 1891 263 3521 3685 77 660 3618 202 3418 1794 1248 t 612 437 134 142 48 25 2748 63 81 165 439 577

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGCTGCGss ; cor=; Ncor= a 540 382 144 118 40 19 193 32 112 137 541 554 c 1264 1225 3394 154 162 3814 334 222 3540 215 1161 1556 g 1519 1891 263 3521 3685 77 660 3618 202 3418 1794 1248 t 612 437 134 142 48 25 2748 63 81 165 439 577

oligos_7nt_mkv5_m2_rc_shift0 (oligos_7nt_mkv5_m2_rc)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m2_rc; m=2/3; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.827581; ssCGCCTGCGss ; cor=; Ncor= a 420 335 132 106 40 68 106 17 79 85 403 456 c 977 1074 2566 112 2683 2773 273 190 2617 186 1156 1143 g 1049 1150 172 2626 194 98 220 2702 205 2576 1014 907 t 519 406 95 121 48 26 2366 56 64 118 392 459

oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m3_rc; m=3/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.685769; -ssGGGGGCGss ; cor=; Ncor= a 0 541 557 14 44 56 71 146 0 5 515 542 c 0 1695 2359 354 590 1110 589 118 4868 0 1748 1573 g 0 2129 1236 4460 4094 3488 4085 4520 0 4876 1997 2111 t 0 516 729 53 153 227 136 97 13 0 621 655

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; sskcCAGGACCTGgss ; Alignment reference a 502 589 476 330 325 2740 64 45 2460 64 45 87 232 332 709 712 c 1197 890 657 1843 2108 105 56 104 121 2811 2868 283 334 541 962 857 g 898 863 826 570 372 185 2925 2879 122 139 103 111 2224 1927 961 931 t 493 748 1131 347 285 60 45 62 387 76 74 2609 300 290 458 590

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/2; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; sskcCAGGACCTGgss ; cor=; Ncor= a 502 589 476 330 325 2740 64 45 2460 64 45 87 232 332 709 712 c 1197 890 657 1843 2108 105 56 104 121 2811 2868 283 334 541 962 857 g 898 863 826 570 372 185 2925 2879 122 139 103 111 2224 1927 961 931 t 493 748 1131 347 285 60 45 62 387 76 74 2609 300 290 458 590

oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1; m=2/2; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.78833; --bsCAGGACCTgss- ; cor=; Ncor= a 0 0 748 664 218 3786 75 73 3252 104 72 146 492 739 926 0 c 0 0 1040 1667 3575 89 74 146 184 3783 3861 519 943 1160 1262 0 g 0 0 1302 1060 203 165 3948 3863 161 171 84 179 1915 1620 1220 0 t 0 0 1051 750 145 101 44 59 544 83 124 3297 791 622 733 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; ssGCGGAGCss ; Alignment reference a 625 420 173 10 25 39 2950 70 103 532 473 c 1263 1691 690 3605 110 172 560 175 3365 1250 1155 g 1269 1009 2563 8 3530 3388 49 3301 119 1245 1514 t 518 555 249 52 10 76 116 129 88 648 533

oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssGCGGAGCss ; cor=; Ncor= a 625 420 173 10 25 39 2950 70 103 532 473 c 1263 1691 690 3605 110 172 560 175 3365 1250 1155 g 1269 1009 2563 8 3530 3388 49 3301 119 1245 1514 t 518 555 249 52 10 76 116 129 88 648 533

oligos_6nt_mkv4_m5_rc_shift0 (oligos_6nt_mkv4_m5_rc)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m5_rc; m=2/2; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.715422; ssGCGGGGCGs ; cor=; Ncor= a 797 872 73 236 231 141 167 121 416 208 751 c 1675 1574 321 5157 366 296 324 221 4948 506 1738 g 2627 2502 5221 160 4882 5239 5153 5328 200 4705 2541 t 636 787 120 182 256 59 91 65 171 316 705

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; byCTTTTCyy ; Alignment reference a 297 398 33 8 45 28 25 26 362 303 c 446 492 1684 0 0 1 0 1697 599 522 g 432 354 9 58 11 3 0 4 214 373 t 552 483 1 1661 1671 1695 1702 0 552 529

oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; byCTTTTCyy ; cor=; Ncor= a 297 398 33 8 45 28 25 26 362 303 c 446 492 1684 0 0 1 0 1697 599 522 g 432 354 9 58 11 3 0 4 214 373 t 552 483 1 1661 1671 1695 1702 0 552 529

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; ssgGCAGGGCass ; Alignment reference a 480 465 269 106 60 2076 30 62 77 67 1491 371 438 c 752 703 470 141 2241 116 56 139 48 2224 302 695 630 g 842 888 1339 2078 77 151 2286 2141 2250 89 412 990 968 t 336 354 332 85 32 67 38 68 35 30 205 354 374

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ssgGCAGGGCass ; cor=; Ncor= a 480 465 269 106 60 2076 30 62 77 67 1491 371 438 c 752 703 470 141 2241 116 56 139 48 2224 302 695 630 g 842 888 1339 2078 77 151 2286 2141 2250 89 412 990 968 t 336 354 332 85 32 67 38 68 35 30 205 354 374

oligos_6nt_mkv4_m5_rc_shift1 (oligos_6nt_mkv4_m5_rc)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m5_rc; m=2/2; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.707747; -ssGCGGGGCGss ; cor=; Ncor= a 0 797 872 73 236 231 141 167 121 416 208 751 860 c 0 1675 1574 321 5157 366 296 324 221 4948 506 1738 1518 g 0 2627 2502 5221 160 4882 5239 5153 5328 200 4705 2541 2632 t 0 636 787 120 182 256 59 91 65 171 316 705 725

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssCGCCCCCss ; Alignment reference a 0 0 0 655 621 0 13 97 136 227 153 53 729 516 c 0 0 0 2111 1997 4876 0 4520 4085 3488 4094 4460 1236 2129 g 0 0 0 1573 1748 0 4868 118 589 1110 590 354 2359 1695 t 0 0 0 542 515 5 0 146 71 56 44 14 557 541

oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCCCss ; cor=; Ncor= a 0 0 0 655 621 0 13 97 136 227 153 53 729 516 c 0 0 0 2111 1997 4876 0 4520 4085 3488 4094 4460 1236 2129 g 0 0 0 1573 1748 0 4868 118 589 1110 590 354 2359 1695 t 0 0 0 542 515 5 0 146 71 56 44 14 557 541

oligos_7nt_mkv5_m5_rc_shift3 (oligos_7nt_mkv5_m5_rc)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m5_rc; m=2/5; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.685769; ---ssCGCAGCCGs ; cor=; Ncor= a 0 0 0 577 439 165 81 63 2748 25 48 142 134 437 c 0 0 0 1248 1794 3418 202 3618 660 77 3685 3521 263 1891 g 0 0 0 1556 1161 215 3540 222 334 3814 162 154 3394 1225 t 0 0 0 554 541 137 112 32 193 19 40 118 144 382

oligos_6nt_mkv4_m5_shift3 (oligos_6nt_mkv4_m5)
; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m5; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.678506; ---ssCGCCCCGCs ; cor=; Ncor= a 0 0 0 725 705 316 171 65 91 59 256 182 120 787 c 0 0 0 2632 2541 4705 200 5328 5153 5239 4882 160 5221 2502 g 0 0 0 1518 1738 506 4948 221 324 296 366 5157 321 1574 t 0 0 0 860 751 208 416 121 167 141 231 236 73 872

oligos_7nt_mkv5_m2_rc_shift3 (oligos_7nt_mkv5_m2_rc)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2_rc; m=4/5; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.648024; ---ssCGCCTGCGs ; cor=; Ncor= a 0 0 0 420 335 132 106 40 68 106 17 79 85 403 c 0 0 0 977 1074 2566 112 2683 2773 273 190 2617 186 1156 g 0 0 0 1049 1150 172 2626 194 98 220 2702 205 2576 1014 t 0 0 0 519 406 95 121 48 26 2366 56 64 118 392

oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.542676; ssCCCCGCCCss-- ; cor=; Ncor= a 1080 985 151 193 241 128 292 158 154 158 922 808 0 0 c 2571 2191 6056 6029 5971 6261 23 6240 6171 6162 2996 2761 0 0 g 2265 2421 393 409 465 396 6474 319 408 373 1904 2427 0 0 t 990 1309 306 275 229 121 117 189 173 213 1084 910 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --ssCCCCGCCCss ; Alignment reference a 0 0 1080 985 151 193 241 128 292 158 154 158 922 808 c 0 0 2571 2191 6056 6029 5971 6261 23 6240 6171 6162 2996 2761 g 0 0 2265 2421 393 409 465 396 6474 319 408 373 1904 2427 t 0 0 990 1309 306 275 229 121 117 189 173 213 1084 910

oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ssCCCCGCCCss ; cor=; Ncor= a 0 0 1080 985 151 193 241 128 292 158 154 158 922 808 c 0 0 2571 2191 6056 6029 5971 6261 23 6240 6171 6162 2996 2761 g 0 0 2265 2421 393 409 465 396 6474 319 408 373 1904 2427 t 0 0 990 1309 306 275 229 121 117 189 173 213 1084 910

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m5; m=2/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.617573; ssCGCCCCGCss-- ; cor=; Ncor= a 725 705 316 171 65 91 59 256 182 120 787 636 0 0 c 2632 2541 4705 200 5328 5153 5239 4882 160 5221 2502 2627 0 0 g 1518 1738 506 4948 221 324 296 366 5157 321 1574 1675 0 0 t 860 751 208 416 121 167 141 231 236 73 872 797 0 0

oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=5; score=0.542676; -----ssCGCCCCC ; cor=; Ncor= a 0 0 0 0 0 655 621 0 13 97 136 227 153 53 c 0 0 0 0 0 2111 1997 4876 0 4520 4085 3488 4094 4460 g 0 0 0 0 0 1573 1748 0 4868 118 589 1110 590 354 t 0 0 0 0 0 542 515 5 0 146 71 56 44 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGCCCCGCss ; Alignment reference a 725 705 316 171 65 91 59 256 182 120 787 636 c 2632 2541 4705 200 5328 5153 5239 4882 160 5221 2502 2627 g 1518 1738 506 4948 221 324 296 366 5157 321 1574 1675 t 860 751 208 416 121 167 141 231 236 73 872 797
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCCGCss ; cor=; Ncor= a 725 705 316 171 65 91 59 256 182 120 787 636 c 2632 2541 4705 200 5328 5153 5239 4882 160 5221 2502 2627 g 1518 1738 506 4948 221 324 296 366 5157 321 1574 1675 t 860 751 208 416 121 167 141 231 236 73 872 797
oligos_6nt_mkv4_m2_rc_shift1 (oligos_6nt_mkv4_m2_rc)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m2_rc; m=2/5; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.715422; -ssGCTCCGCss ; cor=; Ncor= a 0 533 648 88 129 116 76 10 52 249 555 518 c 0 1514 1245 119 3301 49 3388 3530 8 2563 1009 1269 g 0 1155 1250 3365 175 560 172 110 3605 690 1691 1263 t 0 473 532 103 70 2950 39 25 10 173 420 625
oligos_6nt_mkv4_m4_rc_shift0 (oligos_6nt_mkv4_m4_rc)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m4_rc; m=3/5; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.707747; sstGCCCTGCcs ; cor=; Ncor= a 374 354 205 30 35 68 38 67 32 85 332 354 c 968 990 412 89 2250 2141 2286 151 77 2078 1339 888 g 630 695 302 2224 48 139 56 116 2241 141 470 703 t 438 371 1491 67 77 62 30 2076 60 106 269 465
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)				; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m3; m=4/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.678506; ssCGCCCCCss- ; cor=; Ncor= a 655 621 0 13 97 136 227 153 53 729 516 0 c 2111 1997 4876 0 4520 4085 3488 4094 4460 1236 2129 0 g 1573 1748 0 4868 118 589 1110 590 354 2359 1695 0 t 542 515 5 0 146 71 56 44 14 557 541 0
oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)				; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.617573; --ssCCCCGCCC ; cor=; Ncor= a 0 0 1080 985 151 193 241 128 292 158 154 158 c 0 0 2571 2191 6056 6029 5971 6261 23 6240 6171 6162 g 0 0 2265 2421 393 409 465 396 6474 319 408 373 t 0 0 990 1309 306 275 229 121 117 189 173 213

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGCAGGCGss ; Alignment reference a 459 392 118 64 56 2366 26 48 121 95 406 519 c 907 1014 2576 205 2702 220 98 194 2626 172 1150 1049 g 1143 1156 186 2617 190 273 2773 2683 112 2566 1074 977 t 456 403 85 79 17 106 68 40 106 132 335 420
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCAGGCGss ; cor=; Ncor= a 459 392 118 64 56 2366 26 48 121 95 406 519 c 907 1014 2576 205 2702 220 98 194 2626 172 1150 1049 g 1143 1156 186 2617 190 273 2773 2683 112 2566 1074 977 t 456 403 85 79 17 106 68 40 106 132 335 420
oligos_7nt_mkv5_m5_rc_shift0 (oligos_7nt_mkv5_m5_rc)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m5_rc; m=2/3; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.827581; ssCGCAGCCGss ; cor=; Ncor= a 577 439 165 81 63 2748 25 48 142 134 437 612 c 1248 1794 3418 202 3618 660 77 3685 3521 263 1891 1519 g 1556 1161 215 3540 222 334 3814 162 154 3394 1225 1264 t 554 541 137 112 32 193 19 40 118 144 382 540
oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3_rc; m=3/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.648024; -ssGGGGGCGss ; cor=; Ncor= a 0 541 557 14 44 56 71 146 0 5 515 542 c 0 1695 2359 354 590 1110 589 118 4868 0 1748 1573 g 0 2129 1236 4460 4094 3488 4085 4520 0 4876 1997 2111 t 0 516 729 53 153 227 136 97 13 0 621 655

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCGGCTGCGss ; Alignment reference a 540 382 144 118 40 19 193 32 112 137 541 554 c 1264 1225 3394 154 162 3814 334 222 3540 215 1161 1556 g 1519 1891 263 3521 3685 77 660 3618 202 3418 1794 1248 t 612 437 134 142 48 25 2748 63 81 165 439 577
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGCTGCGss ; cor=; Ncor= a 540 382 144 118 40 19 193 32 112 137 541 554 c 1264 1225 3394 154 162 3814 334 222 3540 215 1161 1556 g 1519 1891 263 3521 3685 77 660 3618 202 3418 1794 1248 t 612 437 134 142 48 25 2748 63 81 165 439 577
oligos_7nt_mkv5_m2_rc_shift0 (oligos_7nt_mkv5_m2_rc)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m2_rc; m=2/3; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.827581; ssCGCCTGCGss ; cor=; Ncor= a 420 335 132 106 40 68 106 17 79 85 403 456 c 977 1074 2566 112 2683 2773 273 190 2617 186 1156 1143 g 1049 1150 172 2626 194 98 220 2702 205 2576 1014 907 t 519 406 95 121 48 26 2366 56 64 118 392 459
oligos_7nt_mkv5_m3_rc_shift1 (oligos_7nt_mkv5_m3_rc)				; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m3_rc; m=3/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.685769; -ssGGGGGCGss ; cor=; Ncor= a 0 541 557 14 44 56 71 146 0 5 515 542 c 0 1695 2359 354 590 1110 589 118 4868 0 1748 1573 g 0 2129 1236 4460 4094 3488 4085 4520 0 4876 1997 2111 t 0 516 729 53 153 227 136 97 13 0 621 655

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssCGCCCCCss ; Alignment reference a 0 0 0 655 621 0 13 97 136 227 153 53 729 516 c 0 0 0 2111 1997 4876 0 4520 4085 3488 4094 4460 1236 2129 g 0 0 0 1573 1748 0 4868 118 589 1110 590 354 2359 1695 t 0 0 0 542 515 5 0 146 71 56 44 14 557 541
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCGCCCCCss ; cor=; Ncor= a 0 0 0 655 621 0 13 97 136 227 153 53 729 516 c 0 0 0 2111 1997 4876 0 4520 4085 3488 4094 4460 1236 2129 g 0 0 0 1573 1748 0 4868 118 589 1110 590 354 2359 1695 t 0 0 0 542 515 5 0 146 71 56 44 14 557 541
oligos_7nt_mkv5_m5_rc_shift3 (oligos_7nt_mkv5_m5_rc)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m5_rc; m=2/5; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.685769; ---ssCGCAGCCGs ; cor=; Ncor= a 0 0 0 577 439 165 81 63 2748 25 48 142 134 437 c 0 0 0 1248 1794 3418 202 3618 660 77 3685 3521 263 1891 g 0 0 0 1556 1161 215 3540 222 334 3814 162 154 3394 1225 t 0 0 0 554 541 137 112 32 193 19 40 118 144 382
oligos_6nt_mkv4_m5_shift3 (oligos_6nt_mkv4_m5)				; oligos_7nt_mkv5_m3 versus oligos_6nt_mkv4_m5; m=3/5; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.678506; ---ssCGCCCCGCs ; cor=; Ncor= a 0 0 0 725 705 316 171 65 91 59 256 182 120 787 c 0 0 0 2632 2541 4705 200 5328 5153 5239 4882 160 5221 2502 g 0 0 0 1518 1738 506 4948 221 324 296 366 5157 321 1574 t 0 0 0 860 751 208 416 121 167 141 231 236 73 872
oligos_7nt_mkv5_m2_rc_shift3 (oligos_7nt_mkv5_m2_rc)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m2_rc; m=4/5; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.648024; ---ssCGCCTGCGs ; cor=; Ncor= a 0 0 0 420 335 132 106 40 68 106 17 79 85 403 c 0 0 0 977 1074 2566 112 2683 2773 273 190 2617 186 1156 g 0 0 0 1049 1150 172 2626 194 98 220 2702 205 2576 1014 t 0 0 0 519 406 95 121 48 26 2366 56 64 118 392
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m4; m=5/5; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.542676; ssCCCCGCCCss-- ; cor=; Ncor= a 1080 985 151 193 241 128 292 158 154 158 922 808 0 0 c 2571 2191 6056 6029 5971 6261 23 6240 6171 6162 2996 2761 0 0 g 2265 2421 393 409 465 396 6474 319 408 373 1904 2427 0 0 t 990 1309 306 275 229 121 117 189 173 213 1084 910 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --ssCCCCGCCCss ; Alignment reference a 0 0 1080 985 151 193 241 128 292 158 154 158 922 808 c 0 0 2571 2191 6056 6029 5971 6261 23 6240 6171 6162 2996 2761 g 0 0 2265 2421 393 409 465 396 6474 319 408 373 1904 2427 t 0 0 990 1309 306 275 229 121 117 189 173 213 1084 910
oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ssCCCCGCCCss ; cor=; Ncor= a 0 0 1080 985 151 193 241 128 292 158 154 158 922 808 c 0 0 2571 2191 6056 6029 5971 6261 23 6240 6171 6162 2996 2761 g 0 0 2265 2421 393 409 465 396 6474 319 408 373 1904 2427 t 0 0 990 1309 306 275 229 121 117 189 173 213 1084 910
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_7nt_mkv5_m4 versus oligos_6nt_mkv4_m5; m=2/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.617573; ssCGCCCCGCss-- ; cor=; Ncor= a 725 705 316 171 65 91 59 256 182 120 787 636 0 0 c 2632 2541 4705 200 5328 5153 5239 4882 160 5221 2502 2627 0 0 g 1518 1738 506 4948 221 324 296 366 5157 321 1574 1675 0 0 t 860 751 208 416 121 167 141 231 236 73 872 797 0 0
oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m3; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=5; score=0.542676; -----ssCGCCCCC ; cor=; Ncor= a 0 0 0 0 0 655 621 0 13 97 136 227 153 53 c 0 0 0 0 0 2111 1997 4876 0 4520 4085 3488 4094 4460 g 0 0 0 0 0 1573 1748 0 4868 118 589 1110 590 354 t 0 0 0 0 0 542 515 5 0 146 71 56 44 14