One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/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/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; caCAaAGACACam ; Alignment reference a 624 1332 99 2673 1955 2617 162 2531 140 2594 139 1103 762 c 1152 418 2632 51 610 98 445 184 2642 116 2563 629 901 g 534 635 98 100 209 125 2129 116 55 116 124 640 655 t 617 542 98 103 153 87 191 96 90 101 101 555 609

positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; caCAaAGACACam ; cor=; Ncor= a 624 1332 99 2673 1955 2617 162 2531 140 2594 139 1103 762 c 1152 418 2632 51 610 98 445 184 2642 116 2563 629 901 g 534 635 98 100 209 125 2129 116 55 116 124 640 655 t 617 542 98 103 153 87 191 96 90 101 101 555 609

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m4 versus positions_7nt_m1; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.70819; -ACACACACACAc ; cor=; Ncor= a 0 18178 2471 22621 438 23588 401 23613 537 23428 629 18676 2604 c 0 1818 17097 413 22221 229 22540 233 22527 281 21839 1962 16031 g 0 2334 1782 915 539 367 547 301 514 324 740 1382 2134 t 0 2130 3110 511 1262 276 972 313 882 427 1252 2440 3691

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift4 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----syACGTGCTaa ; Alignment reference a 0 0 0 0 1190 868 4086 236 453 115 108 189 234 1779 1550 c 0 0 0 0 1250 2027 218 4003 221 294 788 4446 358 1014 1164 g 0 0 0 0 1317 771 455 253 3996 93 3876 125 562 909 1090 t 0 0 0 0 1170 1261 168 435 257 4425 155 167 3773 1225 1123

positions_6nt_m4_shift4 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----syACGTGCTaa ; cor=; Ncor= a 0 0 0 0 1190 868 4086 236 453 115 108 189 234 1779 1550 c 0 0 0 0 1250 2027 218 4003 221 294 788 4446 358 1014 1164 g 0 0 0 0 1317 771 455 253 3996 93 3876 125 562 909 1090 t 0 0 0 0 1170 1261 168 435 257 4425 155 167 3773 1225 1123

positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)
; positions_6nt_m4 versus positions_7nt_m5_rc; m=2/3; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.591909; rhaaGCACGTGCttd ; cor=; Ncor= a 146 135 354 346 33 24 425 60 53 13 48 27 53 59 148 c 112 133 34 75 26 429 25 389 17 63 22 438 49 78 107 g 149 108 75 49 438 22 59 19 393 25 429 26 75 34 133 t 116 147 60 53 26 48 14 55 60 422 24 32 346 352 135

oligos_7nt_mkv5_m5_shift5 (oligos_7nt_mkv5_m5)
; positions_6nt_m4 versus oligos_7nt_mkv5_m5; m=3/3; ncol2=12; w=0; offset=1; strand=D; shift=5; score=0.585314; -----caCGTCCTAc ; cor=; Ncor= a 0 0 0 0 0 469 1181 200 84 80 86 57 54 1945 479 c 0 0 0 0 0 1103 420 2091 113 107 2276 2341 126 202 1477 g 0 0 0 0 0 325 506 106 2183 88 80 52 110 137 345 t 0 0 0 0 0 630 420 130 147 2252 85 77 2237 243 226

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 2 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=11; shift=0; ncol=11; wwAACACAAwh ; Alignment reference a 2000 2180 5040 5744 131 5872 123 5351 5163 2459 1892 c 979 688 257 135 5513 76 5576 106 245 1100 1683 g 1315 879 100 104 48 87 49 171 172 736 988 t 1859 2406 756 170 461 118 405 525 573 1858 1590

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAACACAAwh ; cor=; Ncor= a 2000 2180 5040 5744 131 5872 123 5351 5163 2459 1892 c 979 688 257 135 5513 76 5576 106 245 1100 1683 g 1315 879 100 104 48 87 49 171 172 736 988 t 1859 2406 756 170 461 118 405 525 573 1858 1590

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wyATTTTCawt ; Alignment reference a 3044 2292 10859 90 536 472 470 445 6607 3433 2463 c 1685 3133 12 34 50 69 66 10225 2621 1826 1842 g 1579 2146 54 32 151 98 49 47 120 2520 1854 t 5156 3893 539 11308 10727 10825 10879 747 2116 3685 5305

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wyATTTTCawt ; cor=; Ncor= a 3044 2292 10859 90 536 472 470 445 6607 3433 2463 c 1685 3133 12 34 50 69 66 10225 2621 1826 1842 g 1579 2146 54 32 151 98 49 47 120 2520 1854 t 5156 3893 539 11308 10727 10825 10879 747 2116 3685 5305

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.669184; tyATTTTTCAt ; cor=; Ncor= a 2805 2460 9976 297 593 223 248 290 806 10094 2748 c 1446 4401 395 277 208 214 1246 1640 9675 324 2441 g 2329 1446 451 230 179 108 197 173 255 220 1744 t 4727 3000 485 10503 10327 10762 9616 9204 571 669 4374

oligos_6nt_mkv4_m2_rc_shift3 (oligos_6nt_mkv4_m2_rc)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m2_rc; m=3/3; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.444835; ---ttTTCAGT ; cor=; Ncor= a 0 0 0 1131 952 14 55 26 5667 4 44 c 0 0 0 1488 1525 19 12 6160 291 16 69 g 0 0 0 986 1166 65 24 9 223 6187 4 t 0 0 0 2614 2576 6121 6128 24 38 12 6102

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 4 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=12; shift=0; ncol=12; tyATTTTTCAtk ; Alignment reference a 2805 2460 9976 297 593 223 248 290 806 10094 2748 2433 c 1446 4401 395 277 208 214 1246 1640 9675 324 2441 1518 g 2329 1446 451 230 179 108 197 173 255 220 1744 3406 t 4727 3000 485 10503 10327 10762 9616 9204 571 669 4374 3950

oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; tyATTTTTCAtk ; cor=; Ncor= a 2805 2460 9976 297 593 223 248 290 806 10094 2748 2433 c 1446 4401 395 277 208 214 1246 1640 9675 324 2441 1518 g 2329 1446 451 230 179 108 197 173 255 220 1744 3406 t 4727 3000 485 10503 10327 10762 9616 9204 571 669 4374 3950

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.669184; wyATTTTCawt- ; cor=; Ncor= a 3044 2292 10859 90 536 472 470 445 6607 3433 2463 0 c 1685 3133 12 34 50 69 66 10225 2621 1826 1842 0 g 1579 2146 54 32 151 98 49 47 120 2520 1854 0 t 5156 3893 539 11308 10727 10825 10879 747 2116 3685 5305 0

oligos_6nt_mkv4_m3_rc_shift0 (oligos_6nt_mkv4_m3_rc)
; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m3_rc; m=3/3; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.578953; rtrTTTCTCATT ; cor=; Ncor= a 1265 673 1010 99 75 49 139 102 107 2953 111 114 c 354 598 197 128 93 106 2972 68 3083 241 64 101 g 1047 338 1796 133 114 49 91 33 125 47 142 159 t 776 1833 439 3082 3160 3238 240 3239 127 201 3125 3068

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=10; shift=0; ncol=10; amACTGAAaa ; Alignment reference a 3064 2447 6102 12 38 24 6128 6121 2576 2614 c 771 1857 4 6187 223 9 24 65 1166 986 g 1146 1006 69 16 291 6160 12 19 1525 1488 t 1238 909 44 4 5667 26 55 14 952 1131

oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; amACTGAAaa ; cor=; Ncor= a 3064 2447 6102 12 38 24 6128 6121 2576 2614 c 771 1857 4 6187 223 9 24 65 1166 986 g 1146 1006 69 16 291 6160 12 19 1525 1488 t 1238 909 44 4 5667 26 55 14 952 1131

oligos_6nt_mkv4_m1_rc_shift2 (oligos_6nt_mkv4_m1_rc)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m1_rc; m=2/2; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.444835; --awtGAAAA ; cor=; Ncor= a 0 0 5305 3685 2116 747 10879 10825 10727 11308 c 0 0 1854 2520 120 47 49 98 151 32 g 0 0 1842 1826 2621 10225 66 69 50 34 t 0 0 2463 3433 6607 445 470 472 536 90

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; AaAAAAAAAaA ; Alignment reference a 19250 18525 26699 26379 26277 25271 26112 26259 26647 18371 19321 c 2006 1667 22 44 57 77 32 58 365 2091 2333 g 2115 1773 85 61 56 54 32 38 17 1868 2269 t 3902 5308 467 789 883 1871 1097 918 244 4943 3350

positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; AaAAAAAAAaA ; cor=; Ncor= a 19250 18525 26699 26379 26277 25271 26112 26259 26647 18371 19321 c 2006 1667 22 44 57 77 32 58 365 2091 2333 g 2115 1773 85 61 56 54 32 38 17 1868 2269 t 3902 5308 467 789 883 1871 1097 918 244 4943 3350

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

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; wwCCCCTTAwh ; Alignment reference a 1279 1282 330 190 247 317 365 181 3656 1030 1099 c 608 697 2744 3508 3434 3235 139 61 61 824 1116 g 729 669 314 35 57 51 118 43 35 754 504 t 1251 1219 479 134 129 264 3245 3582 115 1259 1148

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwCCCCTTAwh ; cor=; Ncor= a 1279 1282 330 190 247 317 365 181 3656 1030 1099 c 608 697 2744 3508 3434 3235 139 61 61 824 1116 g 729 669 314 35 57 51 118 43 35 754 504 t 1251 1219 479 134 129 264 3245 3582 115 1259 1148

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; gwCGAAATCac ; Alignment reference a 552 1095 226 81 2231 2217 2068 103 67 1103 566 c 479 364 1994 31 41 62 199 75 2173 447 858 g 851 268 75 2055 58 60 62 96 97 283 524 t 534 689 121 249 86 77 87 2142 79 583 468

oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4 versus oligos_7nt_mkv5_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; gwCGAAATCac ; cor=; Ncor= a 552 1095 226 81 2231 2217 2068 103 67 1103 566 c 479 364 1994 31 41 62 199 75 2173 447 858 g 851 268 75 2055 58 60 62 96 97 283 524 t 534 689 121 249 86 77 87 2142 79 583 468

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 2 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=11; shift=0; ncol=11; awACAAAACwa ; Alignment reference a 2927 2653 4773 373 6440 6317 6430 6605 75 3122 2659 c 1632 961 652 5642 83 148 64 59 6570 1157 1408 g 906 1242 592 482 106 88 66 60 19 770 1168 t 1345 1954 793 313 181 257 250 86 146 1761 1575

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; awACAAAACwa ; cor=; Ncor= a 2927 2653 4773 373 6440 6317 6430 6605 75 3122 2659 c 1632 961 652 5642 83 148 64 59 6570 1157 1408 g 906 1242 592 482 106 88 66 60 19 770 1168 t 1345 1954 793 313 181 257 250 86 146 1761 1575

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

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; csGtCGCGaCsg ; Alignment reference a 272 221 187 102 79 63 68 35 823 83 250 233 c 481 371 106 217 1034 91 1061 127 132 894 430 295 g 293 430 901 131 128 1052 88 1035 215 111 373 481 t 231 255 83 827 36 71 60 80 107 189 224 268

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; csGtCGCGaCsg ; cor=; Ncor= a 272 221 187 102 79 63 68 35 823 83 250 233 c 481 371 106 217 1034 91 1061 127 132 894 430 295 g 293 430 901 131 128 1052 88 1035 215 111 373 481 t 231 255 83 827 36 71 60 80 107 189 224 268

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=16; shift=0; ncol=16; rhaaGCACGTGCttdy ; Alignment reference a 147 135 352 346 32 24 422 60 55 14 48 26 53 60 147 116 c 111 133 34 75 26 429 25 393 19 59 22 438 49 75 108 149 g 150 107 78 49 438 22 63 17 389 25 429 26 75 34 133 112 t 115 148 59 53 27 48 13 53 60 425 24 33 346 354 135 146

positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/2; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; rhaaGCACGTGCttdy ; cor=; Ncor= a 147 135 352 346 32 24 422 60 55 14 48 26 53 60 147 116 c 111 133 34 75 26 429 25 393 19 59 22 438 49 75 108 149 g 150 107 78 49 438 22 63 17 389 25 429 26 75 34 133 112 t 115 148 59 53 27 48 13 53 60 425 24 33 346 354 135 146

positions_6nt_m4_rc_shift1 (positions_6nt_m4_rc)
; positions_7nt_m5 versus positions_6nt_m4_rc; m=2/2; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.591909; -ttAGCACGTrs---- ; cor=; Ncor= a 0 1123 1225 3773 167 155 4425 257 435 168 1261 1170 0 0 0 0 c 0 1090 909 562 125 3876 93 3996 253 455 771 1317 0 0 0 0 g 0 1164 1014 358 4446 788 294 221 4003 218 2027 1250 0 0 0 0 t 0 1550 1779 234 189 108 115 453 236 4086 868 1190 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -ACACACACACAc ; Alignment reference a 0 18178 2471 22621 438 23588 401 23613 537 23428 629 18676 2604 c 0 1818 17097 413 22221 229 22540 233 22527 281 21839 1962 16031 g 0 2334 1782 915 539 367 547 301 514 324 740 1382 2134 t 0 2130 3110 511 1262 276 972 313 882 427 1252 2440 3691

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ACACACACACAc ; cor=; Ncor= a 0 18178 2471 22621 438 23588 401 23613 537 23428 629 18676 2604 c 0 1818 17097 413 22221 229 22540 233 22527 281 21839 1962 16031 g 0 2334 1782 915 539 367 547 301 514 324 740 1382 2134 t 0 2130 3110 511 1262 276 972 313 882 427 1252 2440 3691

positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m1 versus positions_7nt_m4; m=2/2; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.70819; caCAaAGACACam ; cor=; Ncor= a 624 1332 99 2673 1955 2617 162 2531 140 2594 139 1103 762 c 1152 418 2632 51 610 98 445 184 2642 116 2563 629 901 g 534 635 98 100 209 125 2129 116 55 116 124 640 655 t 617 542 98 103 153 87 191 96 90 101 101 555 609

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 2 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=11; shift=0; ncol=11; ywCCCCCAayc ; Alignment reference a 1278 1381 138 72 156 139 84 4559 2672 1224 1273 c 1545 1091 4886 4954 4843 4824 4695 168 1000 1674 1681 g 989 1147 63 90 109 172 195 184 823 929 1140 t 1364 1557 89 60 68 41 202 265 681 1349 1082

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ywCCCCCAayc ; cor=; Ncor= a 1278 1381 138 72 156 139 84 4559 2672 1224 1273 c 1545 1091 4886 4954 4843 4824 4695 168 1000 1674 1681 g 989 1147 63 90 109 172 195 184 823 929 1140 t 1364 1557 89 60 68 41 202 265 681 1349 1082

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; wyAGGTTAACCTrw ; Alignment reference a 364 296 1030 118 61 81 69 1131 1086 94 209 111 351 385 c 298 396 46 47 64 80 52 42 49 1080 926 110 255 254 g 254 257 109 922 1079 48 43 55 80 63 47 46 395 299 t 381 348 112 210 93 1088 1133 69 82 60 115 1030 296 359

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wyAGGTTAACCTrw ; cor=; Ncor= a 364 296 1030 118 61 81 69 1131 1086 94 209 111 351 385 c 298 396 46 47 64 80 52 42 49 1080 926 110 255 254 g 254 257 109 922 1079 48 43 55 80 63 47 46 395 299 t 381 348 112 210 93 1088 1133 69 82 60 115 1030 296 359

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; tcTCTCTCTCtc ; Alignment reference a 1581 1483 308 226 206 281 174 217 269 331 1718 1781 c 2749 10660 571 15644 646 15324 804 15507 643 15449 3521 10306 g 1441 1890 379 505 150 810 138 731 116 719 632 2073 t 11406 3144 15919 802 16175 762 16061 722 16149 678 11306 3017

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; tcTCTCTCTCtc ; cor=; Ncor= a 1581 1483 308 226 206 281 174 217 269 331 1718 1781 c 2749 10660 571 15644 646 15324 804 15507 643 15449 3521 10306 g 1441 1890 379 505 150 810 138 731 116 719 632 2073 t 11406 3144 15919 802 16175 762 16061 722 16149 678 11306 3017

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -caCGTCCTAcas ; Alignment reference a 0 469 1181 200 84 80 86 57 54 1945 479 1054 389 c 0 1103 420 2091 113 107 2276 2341 126 202 1477 539 666 g 0 325 506 106 2183 88 80 52 110 137 345 485 993 t 0 630 420 130 147 2252 85 77 2237 243 226 449 479

oligos_7nt_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -caCGTCCTAcas ; cor=; Ncor= a 0 469 1181 200 84 80 86 57 54 1945 479 1054 389 c 0 1103 420 2091 113 107 2276 2341 126 202 1477 539 666 g 0 325 506 106 2183 88 80 52 110 137 345 485 993 t 0 630 420 130 147 2252 85 77 2237 243 226 449 479

positions_6nt_m4_shift0 (positions_6nt_m4)
; oligos_7nt_mkv5_m5 versus positions_6nt_m4; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.585314; syACGTGCTaa-- ; cor=; Ncor= a 1190 868 4086 236 453 115 108 189 234 1779 1550 0 0 c 1250 2027 218 4003 221 294 788 4446 358 1014 1164 0 0 g 1317 771 455 253 3996 93 3876 125 562 909 1090 0 0 t 1170 1261 168 435 257 4425 155 167 3773 1225 1123 0 0

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; amCCACACChh ; Alignment reference a 3215 2716 992 343 7936 266 7685 324 776 2740 2512 c 1814 2390 7337 8251 380 8203 358 7862 7545 2399 2759 g 2006 1694 348 130 199 115 366 294 207 1019 1351 t 2000 2235 358 311 520 451 626 555 507 2877 2413

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; amCCACACChh ; cor=; Ncor= a 3215 2716 992 343 7936 266 7685 324 776 2740 2512 c 1814 2390 7337 8251 380 8203 358 7862 7545 2399 2759 g 2006 1694 348 130 199 115 366 294 207 1019 1351 t 2000 2235 358 311 520 451 626 555 507 2877 2413

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift0 ; 3 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=15; shift=0; ncol=15; raAAATGAGAAAyay ; Alignment reference a 1085 2150 3072 3068 3125 201 127 3239 240 3238 3160 3082 439 1833 776 c 259 394 149 159 142 47 125 33 91 49 114 133 1796 338 1047 g 1545 423 112 101 64 241 3083 68 2972 106 93 128 197 598 354 t 553 475 109 114 111 2953 107 102 139 49 75 99 1010 673 1265

oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; raAAATGAGAAAyay ; cor=; Ncor= a 1085 2150 3072 3068 3125 201 127 3239 240 3238 3160 3082 439 1833 776 c 259 394 149 159 142 47 125 33 91 49 114 133 1796 338 1047 g 1545 423 112 101 64 241 3083 68 2972 106 93 128 197 598 354 t 553 475 109 114 111 2953 107 102 139 49 75 99 1010 673 1265

oligos_7nt_mkv5_m1_rc_shift3 (oligos_7nt_mkv5_m1_rc)
; oligos_6nt_mkv4_m3 versus oligos_7nt_mkv5_m1_rc; m=2/2; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.578953; ---maTGAAAAATra ; cor=; Ncor= a 0 0 0 3950 4374 669 571 9204 9616 10762 10327 10503 485 3000 4727 c 0 0 0 3406 1744 220 255 173 197 108 179 230 451 1446 2329 g 0 0 0 1518 2441 324 9675 1640 1246 214 208 277 395 4401 1446 t 0 0 0 2433 2748 10094 806 290 248 223 593 297 9976 2460 2805

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 2 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=10; shift=0; ncol=10; yyCTGTGAkb ; Alignment reference a 1303 1412 86 40 33 69 42 6357 1418 1469 c 1968 1755 6489 683 9 373 50 193 1545 1717 g 1292 1641 151 627 6694 63 6599 60 1972 1779 t 2195 1950 32 5408 22 6253 67 148 1823 1793

oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; yyCTGTGAkb ; cor=; Ncor= a 1303 1412 86 40 33 69 42 6357 1418 1469 c 1968 1755 6489 683 9 373 50 193 1545 1717 g 1292 1641 151 627 6694 63 6599 60 1972 1779 t 2195 1950 32 5408 22 6253 67 148 1823 1793

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift4 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----syACGTGCTaa ; Alignment reference a 0 0 0 0 1190 868 4086 236 453 115 108 189 234 1779 1550 c 0 0 0 0 1250 2027 218 4003 221 294 788 4446 358 1014 1164 g 0 0 0 0 1317 771 455 253 3996 93 3876 125 562 909 1090 t 0 0 0 0 1170 1261 168 435 257 4425 155 167 3773 1225 1123
positions_6nt_m4_shift4 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----syACGTGCTaa ; cor=; Ncor= a 0 0 0 0 1190 868 4086 236 453 115 108 189 234 1779 1550 c 0 0 0 0 1250 2027 218 4003 221 294 788 4446 358 1014 1164 g 0 0 0 0 1317 771 455 253 3996 93 3876 125 562 909 1090 t 0 0 0 0 1170 1261 168 435 257 4425 155 167 3773 1225 1123
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc)				; positions_6nt_m4 versus positions_7nt_m5_rc; m=2/3; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.591909; rhaaGCACGTGCttd ; cor=; Ncor= a 146 135 354 346 33 24 425 60 53 13 48 27 53 59 148 c 112 133 34 75 26 429 25 389 17 63 22 438 49 78 107 g 149 108 75 49 438 22 59 19 393 25 429 26 75 34 133 t 116 147 60 53 26 48 14 55 60 422 24 32 346 352 135
oligos_7nt_mkv5_m5_shift5 (oligos_7nt_mkv5_m5)				; positions_6nt_m4 versus oligos_7nt_mkv5_m5; m=3/3; ncol2=12; w=0; offset=1; strand=D; shift=5; score=0.585314; -----caCGTCCTAc ; cor=; Ncor= a 0 0 0 0 0 469 1181 200 84 80 86 57 54 1945 479 c 0 0 0 0 0 1103 420 2091 113 107 2276 2341 126 202 1477 g 0 0 0 0 0 325 506 106 2183 88 80 52 110 137 345 t 0 0 0 0 0 630 420 130 147 2252 85 77 2237 243 226

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wyATTTTCawt ; Alignment reference a 3044 2292 10859 90 536 472 470 445 6607 3433 2463 c 1685 3133 12 34 50 69 66 10225 2621 1826 1842 g 1579 2146 54 32 151 98 49 47 120 2520 1854 t 5156 3893 539 11308 10727 10825 10879 747 2116 3685 5305
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wyATTTTCawt ; cor=; Ncor= a 3044 2292 10859 90 536 472 470 445 6607 3433 2463 c 1685 3133 12 34 50 69 66 10225 2621 1826 1842 g 1579 2146 54 32 151 98 49 47 120 2520 1854 t 5156 3893 539 11308 10727 10825 10879 747 2116 3685 5305
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.669184; tyATTTTTCAt ; cor=; Ncor= a 2805 2460 9976 297 593 223 248 290 806 10094 2748 c 1446 4401 395 277 208 214 1246 1640 9675 324 2441 g 2329 1446 451 230 179 108 197 173 255 220 1744 t 4727 3000 485 10503 10327 10762 9616 9204 571 669 4374
oligos_6nt_mkv4_m2_rc_shift3 (oligos_6nt_mkv4_m2_rc)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m2_rc; m=3/3; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.444835; ---ttTTCAGT ; cor=; Ncor= a 0 0 0 1131 952 14 55 26 5667 4 44 c 0 0 0 1488 1525 19 12 6160 291 16 69 g 0 0 0 986 1166 65 24 9 223 6187 4 t 0 0 0 2614 2576 6121 6128 24 38 12 6102

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=12; shift=0; ncol=12; tyATTTTTCAtk ; Alignment reference a 2805 2460 9976 297 593 223 248 290 806 10094 2748 2433 c 1446 4401 395 277 208 214 1246 1640 9675 324 2441 1518 g 2329 1446 451 230 179 108 197 173 255 220 1744 3406 t 4727 3000 485 10503 10327 10762 9616 9204 571 669 4374 3950
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; tyATTTTTCAtk ; cor=; Ncor= a 2805 2460 9976 297 593 223 248 290 806 10094 2748 2433 c 1446 4401 395 277 208 214 1246 1640 9675 324 2441 1518 g 2329 1446 451 230 179 108 197 173 255 220 1744 3406 t 4727 3000 485 10503 10327 10762 9616 9204 571 669 4374 3950
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m1; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.669184; wyATTTTCawt- ; cor=; Ncor= a 3044 2292 10859 90 536 472 470 445 6607 3433 2463 0 c 1685 3133 12 34 50 69 66 10225 2621 1826 1842 0 g 1579 2146 54 32 151 98 49 47 120 2520 1854 0 t 5156 3893 539 11308 10727 10825 10879 747 2116 3685 5305 0
oligos_6nt_mkv4_m3_rc_shift0 (oligos_6nt_mkv4_m3_rc)				; oligos_7nt_mkv5_m1 versus oligos_6nt_mkv4_m3_rc; m=3/3; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.578953; rtrTTTCTCATT ; cor=; Ncor= a 1265 673 1010 99 75 49 139 102 107 2953 111 114 c 354 598 197 128 93 106 2972 68 3083 241 64 101 g 1047 338 1796 133 114 49 91 33 125 47 142 159 t 776 1833 439 3082 3160 3238 240 3239 127 201 3125 3068