One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.075027_2026-01-05.075027_raWB4h/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/2026/01/05/peak-motifs.2026-01-05.075027_2026-01-05.075027_raWB4h/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

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=10; shift=0; ncol=10; wtATTCCAbr ; Alignment reference a 313 265 1062 12 75 96 10 1029 194 302 c 222 245 9 14 15 962 1002 12 277 239 g 254 242 14 13 10 15 50 44 309 282 t 305 342 9 1055 994 21 32 9 314 271

oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4 versus oligos_6nt_mkv4_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wtATTCCAbr ; cor=; Ncor= a 313 265 1062 12 75 96 10 1029 194 302 c 222 245 9 14 15 962 1002 12 277 239 g 254 242 14 13 10 15 50 44 309 282 t 305 342 9 1055 994 21 32 9 314 271

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift7 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift7 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=17; shift=7; ncol=24; -------yycACTTCCytcttyyy ; Alignment reference a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 418 419 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 582 566 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 420 478 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548 576 533

positions_6nt_m2_shift7 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=7; score= 1; -------yycACTTCCytcttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 418 419 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 582 566 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 420 478 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548 576 533

positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)
; positions_6nt_m2 versus positions_6nt_m1_rc; m=2/8; ncol2=16; w=0; offset=0; strand=R; shift=7; score=0.78224; -------yycACTTCCTCttyyy- ; cor=; Ncor= a 0 0 0 0 0 0 0 355 290 235 1309 26 49 28 41 50 58 57 259 214 290 327 367 0 c 0 0 0 0 0 0 0 479 534 963 122 1429 67 57 1555 1557 110 1436 314 295 580 526 503 0 g 0 0 0 0 0 0 0 327 329 211 101 114 57 70 31 23 29 80 123 229 278 325 307 0 t 0 0 0 0 0 0 0 527 535 279 156 119 1515 1533 61 58 1491 115 992 950 540 510 511 0

positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)
; positions_6nt_m2 versus positions_7nt_m3_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=7; score=0.684424; -------yyygCTTCCTCttyyy- ; cor=; Ncor= a 0 0 0 0 0 0 0 459 387 437 527 48 41 37 36 53 69 55 289 220 341 430 465 0 c 0 0 0 0 0 0 0 652 767 607 428 2057 81 75 2176 2166 105 2041 384 403 603 715 681 0 g 0 0 0 0 0 0 0 502 433 424 854 102 80 110 37 29 52 113 152 277 362 491 470 0 t 0 0 0 0 0 0 0 719 745 864 523 125 2130 2110 83 84 2106 123 1507 1432 1026 696 716 0

positions_7nt_m1_shift4 (positions_7nt_m1)
; positions_6nt_m2 versus positions_7nt_m1; m=4/8; ncol2=19; w=-3; offset=-3; strand=D; shift=4; score=0.665439; ----wyyytcACTTCCTCtttyy- ; cor=; Ncor= a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 369 0 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 466 0 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 274 0 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500 508 0

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_6nt_m2 versus positions_7nt_m2; m=5/8; ncol2=18; w=-3; offset=-3; strand=D; shift=4; score=0.664085; ----wcttTCACTTCCCcttyy-- ; cor=; Ncor= a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 0 0 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 0 0 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 0 0 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301 0 0

positions_7nt_m5_rc_shift4 (positions_7nt_m5_rc)
; positions_6nt_m2 versus positions_7nt_m5_rc; m=6/8; ncol2=18; w=-3; offset=-3; strand=R; shift=4; score=0.638151; ----hcyytcACTTCCTCytyy-- ; cor=; Ncor= a 0 0 0 0 411 354 314 287 197 177 1255 33 42 33 36 41 71 60 289 252 295 296 0 0 c 0 0 0 0 418 532 420 422 401 1036 135 1370 88 57 1514 1503 96 1370 727 341 492 520 0 0 g 0 0 0 0 370 349 324 290 256 176 85 117 65 69 18 17 40 77 130 216 302 340 0 0 t 0 0 0 0 428 392 569 628 773 238 152 107 1432 1468 59 66 1420 120 481 818 538 471 0 0

oligos_7nt_mkv5_m3_rc_shift9 (oligos_7nt_mkv5_m3_rc)
; positions_6nt_m2 versus oligos_7nt_mkv5_m3_rc; m=7/8; ncol2=13; w=0; offset=2; strand=R; shift=9; score=0.548422; ---------ywCTTCCTCTTyy-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 324 469 45 43 17 24 32 44 32 82 49 249 282 0 0 c 0 0 0 0 0 0 0 0 0 541 423 1453 61 48 1582 1583 110 1517 147 128 565 588 0 0 g 0 0 0 0 0 0 0 0 0 295 363 102 67 67 29 24 32 75 51 88 280 295 0 0 t 0 0 0 0 0 0 0 0 0 554 459 114 1543 1582 79 75 1528 90 1434 1449 620 549 0 0

positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_6nt_m2 versus positions_7nt_m4; m=8/8; ncol2=23; w=-7; offset=-7; strand=D; shift=0; score=0.512834; wwaaagaggaACTTCCTCtttyh- ; cor=; Ncor= a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 151 0 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 169 0 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 98 0 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175 157 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift1 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=16; shift=1; ncol=17; -rrraaGAGGAAGTgrr ; Alignment reference a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 527 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 327 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 479 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290 355

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -rrraaGAGGAAGTgrr ; cor=; Ncor= a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 527 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 327 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 479 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290 355

positions_7nt_m3_shift1 (positions_7nt_m3)
; positions_6nt_m1 versus positions_7nt_m3; m=2/9; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.934619; -rrraaGAGGAAGcrrr ; cor=; Ncor= a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 719 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 502 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 652 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387 459

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_6nt_m1 versus positions_6nt_m5; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.873445; -rrraaGAGGAAstrr- ; cor=; Ncor= a 0 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 0 c 0 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 0 g 0 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 0 t 0 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442 0

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_6nt_m1 versus positions_7nt_m1_rc; m=4/9; ncol2=19; w=0; offset=0; strand=R; shift=1; score=0.834212; -rraaaGAGGAAGTgar ; cor=; Ncor= a 0 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 791 654 c 0 274 311 226 199 89 73 28 24 34 68 39 118 73 180 226 268 g 0 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 395 405 t 0 369 300 257 172 238 67 62 49 50 33 47 32 1246 212 205 290

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_6nt_m1 versus positions_6nt_m2_rc; m=5/9; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.78224; rrraagarGGAAGTgrr ; cor=; Ncor= a 533 576 548 974 1109 473 1001 517 100 64 1828 1762 80 74 241 585 610 c 478 420 406 305 244 291 236 144 29 32 70 92 74 84 219 408 401 g 566 582 748 435 372 945 473 1108 1830 1843 62 80 1809 105 1274 588 544 t 419 418 294 282 271 287 286 227 37 57 36 62 33 1733 262 415 441

positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_6nt_m1 versus positions_7nt_m5; m=6/9; ncol2=18; w=0; offset=1; strand=D; shift=2; score=0.771626; --rrarGAGGAAGTgar ; cor=; Ncor= a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 628 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 290 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 422 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197 287

oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)
; positions_6nt_m1 versus oligos_7nt_mkv5_m3; m=7/9; ncol2=13; w=0; offset=1; strand=D; shift=2; score=0.759689; --rrAAGAGGAAGwr-- ; cor=; Ncor= a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 0 0 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 0 0 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 0 0 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324 0 0

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_6nt_m1 versus positions_7nt_m2_rc; m=8/9; ncol2=18; w=0; offset=1; strand=R; shift=2; score=0.675276; --rraagGGGAAGTGAa ; cor=; Ncor= a 0 0 301 323 579 637 173 181 75 67 911 902 67 96 75 700 572 c 0 0 169 168 125 85 46 24 22 30 23 26 55 41 41 90 106 g 0 0 349 323 167 151 671 729 863 864 35 34 851 93 820 135 201 t 0 0 176 181 124 122 105 61 35 34 26 33 22 765 59 70 116

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; positions_6nt_m1 versus positions_7nt_m4_rc; m=9/9; ncol2=23; w=0; offset=0; strand=R; shift=1; score=0.653168; -draaaGAGGAAGTtcc ; cor=; Ncor= a 0 157 175 245 339 357 34 497 30 27 511 508 38 33 80 111 115 c 0 98 112 86 76 30 36 9 22 20 29 17 32 28 79 253 276 g 0 169 145 139 95 96 477 36 498 504 25 26 481 29 105 108 85 t 0 151 143 105 65 92 28 33 25 24 10 24 24 485 311 103 99

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift0 ; 10 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=23; shift=0; ncol=23; wwaaagaggaACTTCCTCtttyh ; Alignment reference a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 151 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 169 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 98 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175 157

positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m4 versus positions_7nt_m4; m=1/9; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; wwaaagaggaACTTCCTCtttyh ; cor=; Ncor= a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 151 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 169 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 98 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175 157

positions_7nt_m1_shift4 (positions_7nt_m1)
; positions_7nt_m4 versus positions_7nt_m1; m=2/9; ncol2=19; w=0; offset=4; strand=D; shift=4; score=0.734649; ----wyyytcACTTCCTCtttyy ; cor=; Ncor= a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 369 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 466 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 274 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500 508

positions_7nt_m5_rc_shift4 (positions_7nt_m5_rc)
; positions_7nt_m4 versus positions_7nt_m5_rc; m=3/9; ncol2=18; w=0; offset=4; strand=R; shift=4; score=0.674236; ----hcyytcACTTCCTCytyy- ; cor=; Ncor= a 0 0 0 0 411 354 314 287 197 177 1255 33 42 33 36 41 71 60 289 252 295 296 0 c 0 0 0 0 418 532 420 422 401 1036 135 1370 88 57 1514 1503 96 1370 727 341 492 520 0 g 0 0 0 0 370 349 324 290 256 176 85 117 65 69 18 17 40 77 130 216 302 340 0 t 0 0 0 0 428 392 569 628 773 238 152 107 1432 1468 59 66 1420 120 481 818 538 471 0

positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)
; positions_7nt_m4 versus positions_6nt_m1_rc; m=4/9; ncol2=16; w=0; offset=7; strand=R; shift=7; score=0.653168; -------yycACTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 355 290 235 1309 26 49 28 41 50 58 57 259 214 290 327 367 c 0 0 0 0 0 0 0 479 534 963 122 1429 67 57 1555 1557 110 1436 314 295 580 526 503 g 0 0 0 0 0 0 0 327 329 211 101 114 57 70 31 23 29 80 123 229 278 325 307 t 0 0 0 0 0 0 0 527 535 279 156 119 1515 1533 61 58 1491 115 992 950 540 510 511

positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)
; positions_7nt_m4 versus positions_7nt_m3_rc; m=5/9; ncol2=16; w=0; offset=7; strand=R; shift=7; score=0.623552; -------yyygCTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 459 387 437 527 48 41 37 36 53 69 55 289 220 341 430 465 c 0 0 0 0 0 0 0 652 767 607 428 2057 81 75 2176 2166 105 2041 384 403 603 715 681 g 0 0 0 0 0 0 0 502 433 424 854 102 80 110 37 29 52 113 152 277 362 491 470 t 0 0 0 0 0 0 0 719 745 864 523 125 2130 2110 83 84 2106 123 1507 1432 1026 696 716

positions_6nt_m5_rc_shift8 (positions_6nt_m5_rc)
; positions_7nt_m4 versus positions_6nt_m5_rc; m=6/9; ncol2=15; w=0; offset=8; strand=R; shift=8; score=0.588102; --------yyasTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 442 514 1095 213 40 31 47 59 40 62 353 261 413 480 526 c 0 0 0 0 0 0 0 0 705 754 406 816 56 42 2266 2296 73 2188 379 441 828 727 723 g 0 0 0 0 0 0 0 0 504 470 404 885 55 35 36 21 35 99 163 353 409 466 444 t 0 0 0 0 0 0 0 0 768 681 514 505 2268 2311 70 43 2271 70 1524 1364 769 746 726

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_7nt_m4 versus positions_7nt_m2; m=7/9; ncol2=18; w=0; offset=4; strand=D; shift=4; score=0.558616; ----wcttTCACTTCCCcttyy- ; cor=; Ncor= a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 0 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 0 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 0 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301 0

oligos_7nt_mkv5_m3_rc_shift9 (oligos_7nt_mkv5_m3_rc)
; positions_7nt_m4 versus oligos_7nt_mkv5_m3_rc; m=8/9; ncol2=13; w=0; offset=9; strand=R; shift=9; score=0.517439; ---------ywCTTCCTCTTyy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 324 469 45 43 17 24 32 44 32 82 49 249 282 0 c 0 0 0 0 0 0 0 0 0 541 423 1453 61 48 1582 1583 110 1517 147 128 565 588 0 g 0 0 0 0 0 0 0 0 0 295 363 102 67 67 29 24 32 75 51 88 280 295 0 t 0 0 0 0 0 0 0 0 0 554 459 114 1543 1582 79 75 1528 90 1434 1449 620 549 0

positions_6nt_m2_shift7 (positions_6nt_m2)
; positions_7nt_m4 versus positions_6nt_m2; m=9/9; ncol2=17; w=0; offset=7; strand=D; shift=7; score=0.512834; -------yycACTTCCytcttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 418 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 582 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 420 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548 576

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=10; shift=0; ncol=10; ssCGGCCGss ; Alignment reference a 393 386 81 96 51 86 63 53 357 459 c 1492 1091 3099 459 447 2875 2847 226 1631 1113 g 1115 1631 226 2837 2875 447 459 3098 1090 1492 t 459 351 53 67 86 51 90 82 381 395

oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGCCGss ; cor=; Ncor= a 393 386 81 96 51 86 63 53 357 459 c 1492 1091 3099 459 447 2875 2847 226 1631 1113 g 1115 1631 226 2837 2875 447 459 3098 1090 1492 t 459 351 53 67 86 51 90 82 381 395

oligos_6nt_mkv4_m1_rc_shift0 (oligos_6nt_mkv4_m1_rc)
; oligos_6nt_mkv4_m3 versus oligos_6nt_mkv4_m1_rc; m=2/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.841409; ssCGGGCGss ; cor=; Ncor= a 366 409 78 141 156 86 98 61 310 366 c 1140 1060 2612 302 346 377 2750 143 1340 982 g 1087 1290 291 2546 2438 2543 116 2794 997 1337 t 464 298 76 68 117 51 93 59 410 372

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift11 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift11 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=11; ncol=22; -----------wwATTTTTAww ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 1088 1053 3436 179 249 174 228 276 3363 1244 1388 c 0 0 0 0 0 0 0 0 0 0 0 547 813 84 142 137 125 192 145 138 638 688 g 0 0 0 0 0 0 0 0 0 0 0 818 588 170 150 158 93 143 109 179 707 498 t 0 0 0 0 0 0 0 0 0 0 0 1496 1495 259 3478 3405 3557 3386 3419 269 1360 1375

oligos_7nt_mkv5_m1_shift11 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=11; score= 1; -----------wwATTTTTAww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1088 1053 3436 179 249 174 228 276 3363 1244 1388 c 0 0 0 0 0 0 0 0 0 0 0 547 813 84 142 137 125 192 145 138 638 688 g 0 0 0 0 0 0 0 0 0 0 0 818 588 170 150 158 93 143 109 179 707 498 t 0 0 0 0 0 0 0 0 0 0 0 1496 1495 259 3478 3405 3557 3386 3419 269 1360 1375

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; oligos_7nt_mkv5_m1 versus positions_6nt_m3_rc; m=2/2; ncol2=24; w=-11; offset=-11; strand=R; shift=0; score=0.402835; wwaaaTwaTTTaTATTTTTAaT ; cor=; Ncor= a 110 115 213 221 225 58 196 221 31 63 43 217 38 234 28 61 31 45 46 228 202 62 c 40 55 30 20 20 22 18 22 14 14 16 13 25 15 11 17 17 10 25 28 15 24 g 80 50 23 26 23 16 18 16 19 22 17 39 12 14 16 22 10 23 22 15 42 18 t 102 112 66 65 64 236 100 73 268 233 256 63 257 69 277 232 274 254 239 61 73 228

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 9 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=15; shift=0; ncol=15; rrraaGAGGAAstrr ; Alignment reference a 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 c 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 g 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 t 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; rrraaGAGGAAstrr ; cor=; Ncor= a 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 c 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 g 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 t 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442

positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_6nt_m5 versus positions_7nt_m3; m=2/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.877332; rrraaGAGGAAGcrr ; cor=; Ncor= a 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 c 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 g 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 t 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m5 versus positions_6nt_m1; m=3/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.873445; rrraaGAGGAAGTgr ; cor=; Ncor= a 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 c 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 g 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 t 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290

oligos_7nt_mkv5_m3_shift1 (oligos_7nt_mkv5_m3)
; positions_6nt_m5 versus oligos_7nt_mkv5_m3; m=4/8; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.812119; -rrAAGAGGAAGwr- ; cor=; Ncor= a 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 0 c 0 295 280 88 51 75 32 24 29 67 67 102 363 295 0 g 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 0 t 0 282 249 49 82 32 44 32 24 17 43 45 469 324 0

positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc)
; positions_6nt_m5 versus positions_7nt_m1_rc; m=5/8; ncol2=19; w=0; offset=0; strand=R; shift=0; score=0.731398; rraaaGAGGAAGTga ; cor=; Ncor= a 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 791 c 274 311 226 199 89 73 28 24 34 68 39 118 73 180 226 g 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 395 t 369 300 257 172 238 67 62 49 50 33 47 32 1246 212 205

positions_7nt_m5_shift1 (positions_7nt_m5)
; positions_6nt_m5 versus positions_7nt_m5; m=6/8; ncol2=18; w=0; offset=1; strand=D; shift=1; score=0.662081; -rrarGAGGAAGTga ; cor=; Ncor= a 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 c 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 g 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 t 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197

positions_7nt_m4_rc_shift0 (positions_7nt_m4_rc)
; positions_6nt_m5 versus positions_7nt_m4_rc; m=7/8; ncol2=23; w=0; offset=0; strand=R; shift=0; score=0.588102; draaaGAGGAAGTtc ; cor=; Ncor= a 157 175 245 339 357 34 497 30 27 511 508 38 33 80 111 c 98 112 86 76 30 36 9 22 20 29 17 32 28 79 253 g 169 145 139 95 96 477 36 498 504 25 26 481 29 105 108 t 151 143 105 65 92 28 33 25 24 10 24 24 485 311 103

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; positions_6nt_m5 versus positions_7nt_m2_rc; m=8/8; ncol2=18; w=0; offset=1; strand=R; shift=1; score=0.553238; -rraagGGGAAGTGA ; cor=; Ncor= a 0 301 323 579 637 173 181 75 67 911 902 67 96 75 700 c 0 169 168 125 85 46 24 22 30 23 26 55 41 41 90 g 0 349 323 167 151 671 729 863 864 35 34 851 93 820 135 t 0 176 181 124 122 105 61 35 34 26 33 22 765 59 70

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 4 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=24; shift=0; ncol=24; wwAtTAAAAATAtAAAtwAtttww ; Alignment reference a 132 132 228 73 61 239 254 274 232 277 69 257 63 256 233 268 73 100 236 64 65 66 112 102 c 60 60 18 42 15 22 23 10 22 16 14 12 39 17 22 19 16 18 16 23 26 23 50 80 g 47 32 24 15 28 25 10 17 17 11 15 25 13 16 14 14 22 18 22 20 20 30 55 40 t 93 108 62 202 228 46 45 31 61 28 234 38 217 43 63 31 221 196 58 225 221 213 115 110

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wwAtTAAAAATAtAAAtwAtttww ; cor=; Ncor= a 132 132 228 73 61 239 254 274 232 277 69 257 63 256 233 268 73 100 236 64 65 66 112 102 c 60 60 18 42 15 22 23 10 22 16 14 12 39 17 22 19 16 18 16 23 26 23 50 80 g 47 32 24 15 28 25 10 17 17 11 15 25 13 16 14 14 22 18 22 20 20 30 55 40 t 93 108 62 202 228 46 45 31 61 28 234 38 217 43 63 31 221 196 58 225 221 213 115 110

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m3 versus positions_6nt_m4; m=2/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.782988; awAwwAAAAAtAAtAAAwwAwtww ; cor=; Ncor= a 114 114 185 69 71 206 203 193 198 216 51 216 195 58 199 200 185 72 75 179 65 53 90 99 c 47 35 21 23 19 12 13 14 12 9 15 14 23 13 16 16 17 9 10 18 16 21 39 44 g 36 21 15 15 16 11 10 14 18 10 17 6 11 15 10 11 11 19 11 19 11 17 40 36 t 60 87 36 150 151 28 31 36 29 22 174 21 28 171 32 30 44 157 161 41 165 166 88 78

oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)
; positions_6nt_m3 versus oligos_7nt_mkv5_m1_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.402835; --wwTAAAAATww----------- ; cor=; Ncor= a 0 0 1375 1360 269 3419 3386 3557 3405 3478 259 1495 1496 0 0 0 0 0 0 0 0 0 0 0 c 0 0 498 707 179 109 143 93 158 150 170 588 818 0 0 0 0 0 0 0 0 0 0 0 g 0 0 688 638 138 145 192 125 137 142 84 813 547 0 0 0 0 0 0 0 0 0 0 0 t 0 0 1388 1244 3363 276 228 174 249 179 3436 1053 1088 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift0 ; 2 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=12; shift=0; ncol=12; sggGCAGGGCss ; Alignment reference a 570 626 258 243 54 2018 38 90 68 60 563 492 c 835 701 436 435 2632 293 113 258 51 2672 843 803 g 972 1068 1883 2040 112 427 2639 2438 2694 72 877 1099 t 473 455 273 132 52 112 60 64 37 46 567 456

oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2 versus oligos_6nt_mkv4_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; sggGCAGGGCss ; cor=; Ncor= a 570 626 258 243 54 2018 38 90 68 60 563 492 c 835 701 436 435 2632 293 113 258 51 2672 843 803 g 972 1068 1883 2040 112 427 2639 2438 2694 72 877 1099 t 473 455 273 132 52 112 60 64 37 46 567 456

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

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCGaGCGss ; Alignment reference a 0 267 279 48 28 996 39 38 36 251 286 c 0 651 629 1647 73 346 51 1667 97 747 581 g 0 678 775 123 1722 412 1762 59 1701 567 772 t 0 274 187 52 47 116 18 106 36 305 231

oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ssCGaGCGss ; cor=; Ncor= a 0 267 279 48 28 996 39 38 36 251 286 c 0 651 629 1647 73 346 51 1667 97 747 581 g 0 678 775 123 1722 412 1762 59 1701 567 772 t 0 274 187 52 47 116 18 106 36 305 231

oligos_6nt_mkv4_m1_rc_shift1 (oligos_6nt_mkv4_m1_rc)
; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m1_rc; m=2/3; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.905046; -ssCGGGCGss ; cor=; Ncor= a 0 366 409 78 141 156 86 98 61 310 366 c 0 1140 1060 2612 302 346 377 2750 143 1340 982 g 0 1087 1290 291 2546 2438 2543 116 2794 997 1337 t 0 464 298 76 68 117 51 93 59 410 372

oligos_7nt_mkv5_m2_rc_shift0 (oligos_7nt_mkv5_m2_rc)
; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m2_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.643415; ssGAGGGCGss ; cor=; Ncor= a 465 471 77 1652 121 89 109 71 44 381 365 c 699 663 175 302 81 197 211 2165 64 823 624 g 889 910 2083 280 2109 2025 1998 67 2229 845 1052 t 318 327 36 137 60 60 53 68 34 322 330

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; waCAAAAACwa ; Alignment reference a 601 795 56 1632 1487 1581 1500 1670 44 779 614 c 292 316 1527 39 110 100 123 42 1554 262 407 g 324 283 39 29 81 34 41 22 18 234 327 t 570 393 165 87 109 72 123 53 171 512 439

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; waCAAAAACwa ; cor=; Ncor= a 601 795 56 1632 1487 1581 1500 1670 44 779 614 c 292 316 1527 39 110 100 123 42 1554 262 407 g 324 283 39 29 81 34 41 22 18 234 327 t 570 393 165 87 109 72 123 53 171 512 439

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift2 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --rrAAGAGGAAGwr ; Alignment reference a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324

oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/9; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --rrAAGAGGAAGwr ; cor=; Ncor= a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324

positions_6nt_m5_shift1 (positions_6nt_m5)
; oligos_7nt_mkv5_m3 versus positions_6nt_m5; m=2/9; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.812119; -rrraaGAGGAAstr ; cor=; Ncor= a 0 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 c 0 444 466 409 353 163 99 35 21 36 35 55 885 404 470 g 0 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 t 0 526 480 413 261 353 62 40 59 47 31 40 213 1095 514

positions_7nt_m3_shift1 (positions_7nt_m3)
; oligos_7nt_mkv5_m3 versus positions_7nt_m3; m=3/9; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.798185; -rrraaGAGGAAGcr ; cor=; Ncor= a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_7nt_mkv5_m3 versus positions_6nt_m1; m=4/9; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.759689; -rrraaGAGGAAGTg ; cor=; Ncor= a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; oligos_7nt_mkv5_m3 versus positions_7nt_m1_rc; m=5/9; ncol2=19; w=-1; offset=-1; strand=R; shift=1; score=0.642276; -rraaaGAGGAAGTg ; cor=; Ncor= a 0 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 c 0 274 311 226 199 89 73 28 24 34 68 39 118 73 180 g 0 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 t 0 369 300 257 172 238 67 62 49 50 33 47 32 1246 212

positions_7nt_m5_shift2 (positions_7nt_m5)
; oligos_7nt_mkv5_m3 versus positions_7nt_m5; m=6/9; ncol2=18; w=0; offset=0; strand=D; shift=2; score=0.640152; --rrarGAGGAAGTg ; cor=; Ncor= a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; oligos_7nt_mkv5_m3 versus positions_7nt_m2_rc; m=7/9; ncol2=18; w=0; offset=0; strand=R; shift=2; score=0.58063; --rraagGGGAAGTG ; cor=; Ncor= a 0 0 301 323 579 637 173 181 75 67 911 902 67 96 75 c 0 0 169 168 125 85 46 24 22 30 23 26 55 41 41 g 0 0 349 323 167 151 671 729 863 864 35 34 851 93 820 t 0 0 176 181 124 122 105 61 35 34 26 33 22 765 59

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; oligos_7nt_mkv5_m3 versus positions_6nt_m2_rc; m=8/9; ncol2=17; w=-2; offset=-2; strand=R; shift=0; score=0.548422; rrraagarGGAAGTg ; cor=; Ncor= a 533 576 548 974 1109 473 1001 517 100 64 1828 1762 80 74 241 c 478 420 406 305 244 291 236 144 29 32 70 92 74 84 219 g 566 582 748 435 372 945 473 1108 1830 1843 62 80 1809 105 1274 t 419 418 294 282 271 287 286 227 37 57 36 62 33 1733 262

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; oligos_7nt_mkv5_m3 versus positions_7nt_m4_rc; m=9/9; ncol2=23; w=-1; offset=-1; strand=R; shift=1; score=0.517439; -draaaGAGGAAGTt ; cor=; Ncor= a 0 157 175 245 339 357 34 497 30 27 511 508 38 33 80 c 0 98 112 86 76 30 36 9 22 20 29 17 32 28 79 g 0 169 145 139 95 96 477 36 498 504 25 26 481 29 105 t 0 151 143 105 65 92 28 33 25 24 10 24 24 485 311

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift1 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m3_shift1 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=16; shift=1; ncol=17; -rrraaGAGGAAGcrrr ; Alignment reference a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 719 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 502 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 652 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387 459

positions_7nt_m3_shift1 (positions_7nt_m3)
; positions_7nt_m3 versus positions_7nt_m3; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -rrraaGAGGAAGcrrr ; cor=; Ncor= a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 719 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 502 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 652 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387 459

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m3 versus positions_6nt_m1; m=2/9; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.934619; -rrraaGAGGAAGTgrr ; cor=; Ncor= a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 527 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 327 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 479 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290 355

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_7nt_m3 versus positions_6nt_m5; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.877332; -rrraaGAGGAAstrr- ; cor=; Ncor= a 0 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 0 c 0 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 0 g 0 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 0 t 0 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442 0

oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)
; positions_7nt_m3 versus oligos_7nt_mkv5_m3; m=4/9; ncol2=13; w=0; offset=1; strand=D; shift=2; score=0.798185; --rrAAGAGGAAGwr-- ; cor=; Ncor= a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 0 0 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 0 0 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 0 0 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324 0 0

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_7nt_m3 versus positions_7nt_m1_rc; m=5/9; ncol2=19; w=0; offset=0; strand=R; shift=1; score=0.783954; -rraaaGAGGAAGTgar ; cor=; Ncor= a 0 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 791 654 c 0 274 311 226 199 89 73 28 24 34 68 39 118 73 180 226 268 g 0 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 395 405 t 0 369 300 257 172 238 67 62 49 50 33 47 32 1246 212 205 290

positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_7nt_m3 versus positions_7nt_m5; m=6/9; ncol2=18; w=0; offset=1; strand=D; shift=2; score=0.710863; --rrarGAGGAAGTgar ; cor=; Ncor= a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 628 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 290 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 422 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197 287

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m3 versus positions_6nt_m2_rc; m=7/9; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.684424; rrraagarGGAAGTgrr ; cor=; Ncor= a 533 576 548 974 1109 473 1001 517 100 64 1828 1762 80 74 241 585 610 c 478 420 406 305 244 291 236 144 29 32 70 92 74 84 219 408 401 g 566 582 748 435 372 945 473 1108 1830 1843 62 80 1809 105 1274 588 544 t 419 418 294 282 271 287 286 227 37 57 36 62 33 1733 262 415 441

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; positions_7nt_m3 versus positions_7nt_m4_rc; m=8/9; ncol2=23; w=0; offset=0; strand=R; shift=1; score=0.623552; -draaaGAGGAAGTtcc ; cor=; Ncor= a 0 157 175 245 339 357 34 497 30 27 511 508 38 33 80 111 115 c 0 98 112 86 76 30 36 9 22 20 29 17 32 28 79 253 276 g 0 169 145 139 95 96 477 36 498 504 25 26 481 29 105 108 85 t 0 151 143 105 65 92 28 33 25 24 10 24 24 485 311 103 99

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_7nt_m3 versus positions_7nt_m2_rc; m=9/9; ncol2=18; w=0; offset=1; strand=R; shift=2; score=0.600625; --rraagGGGAAGTGAa ; cor=; Ncor= a 0 0 301 323 579 637 173 181 75 67 911 902 67 96 75 700 572 c 0 0 169 168 125 85 46 24 22 30 23 26 55 41 41 90 106 g 0 0 349 323 167 151 671 729 863 864 35 34 851 93 820 135 201 t 0 0 176 181 124 122 105 61 35 34 26 33 22 765 59 70 116

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 5 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=10; shift=0; ncol=10; ssCGCCCGss ; Alignment reference a 372 410 59 93 51 117 68 76 298 464 c 1337 997 2794 116 2543 2438 2546 291 1290 1087 g 982 1340 143 2750 377 346 302 2612 1060 1140 t 366 310 61 98 86 156 141 78 409 366

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCGss ; cor=; Ncor= a 372 410 59 93 51 117 68 76 298 464 c 1337 997 2794 116 2543 2438 2546 291 1290 1087 g 982 1340 143 2750 377 346 302 2612 1060 1140 t 366 310 61 98 86 156 141 78 409 366

oligos_6nt_mkv4_m5_rc_shift0 (oligos_6nt_mkv4_m5_rc)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m5_rc; m=2/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.905046; ssCGCtCGss ; cor=; Ncor= a 231 305 36 106 18 116 47 52 187 274 c 772 567 1701 59 1762 412 1722 123 775 678 g 581 747 97 1667 51 346 73 1647 629 651 t 286 251 36 38 39 996 28 48 279 267

oligos_6nt_mkv4_m3_rc_shift0 (oligos_6nt_mkv4_m3_rc)
; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m3_rc; m=3/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.841409; ssCGGCCGss ; cor=; Ncor= a 395 381 82 90 51 86 67 53 351 459 c 1492 1090 3098 459 447 2875 2837 226 1631 1115 g 1113 1631 226 2847 2875 447 459 3099 1091 1492 t 459 357 53 63 86 51 96 81 386 393

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m2; m=4/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.735232; ssCGCCCTCs ; cor=; Ncor= a 330 322 34 68 53 60 60 137 36 327 c 1052 845 2229 67 1998 2025 2109 280 2083 910 g 624 823 64 2165 211 197 81 302 175 663 t 365 381 44 71 109 89 121 1652 77 471

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; awAwwAAAAAtAAtAAAwwAwtww ; Alignment reference a 114 114 185 69 71 206 203 193 198 216 51 216 195 58 199 200 185 72 75 179 65 53 90 99 c 47 35 21 23 19 12 13 14 12 9 15 14 23 13 16 16 17 9 10 18 16 21 39 44 g 36 21 15 15 16 11 10 14 18 10 17 6 11 15 10 11 11 19 11 19 11 17 40 36 t 60 87 36 150 151 28 31 36 29 22 174 21 28 171 32 30 44 157 161 41 165 166 88 78

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/2; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; awAwwAAAAAtAAtAAAwwAwtww ; cor=; Ncor= a 114 114 185 69 71 206 203 193 198 216 51 216 195 58 199 200 185 72 75 179 65 53 90 99 c 47 35 21 23 19 12 13 14 12 9 15 14 23 13 16 16 17 9 10 18 16 21 39 44 g 36 21 15 15 16 11 10 14 18 10 17 6 11 15 10 11 11 19 11 19 11 17 40 36 t 60 87 36 150 151 28 31 36 29 22 174 21 28 171 32 30 44 157 161 41 165 166 88 78

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m4 versus positions_6nt_m3; m=2/2; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.782988; wwAtTAAAAATAtAAAtwAtttww ; cor=; Ncor= a 132 132 228 73 61 239 254 274 232 277 69 257 63 256 233 268 73 100 236 64 65 66 112 102 c 60 60 18 42 15 22 23 10 22 16 14 12 39 17 22 19 16 18 16 23 26 23 50 80 g 47 32 24 15 28 25 10 17 17 11 15 25 13 16 14 14 22 18 22 20 20 30 55 40 t 93 108 62 202 228 46 45 31 61 28 234 38 217 43 63 31 221 196 58 225 221 213 115 110

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift2 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=18; shift=2; ncol=20; --rrarGAGGAAGTgarrgd ; Alignment reference a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 628 569 392 428 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 290 324 349 370 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 422 420 532 418 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197 287 314 354 411

positions_7nt_m5_shift2 (positions_7nt_m5)
; positions_7nt_m5 versus positions_7nt_m5; m=1/9; ncol2=18; w=0; offset=0; strand=D; shift=2; score= 1; --rrarGAGGAAGTgarrgd ; cor=; Ncor= a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 628 569 392 428 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 290 324 349 370 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 422 420 532 418 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197 287 314 354 411

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_7nt_m5 versus positions_7nt_m1_rc; m=2/9; ncol2=19; w=-1; offset=-1; strand=R; shift=1; score=0.923817; -rraaaGAGGAAGTgarrrw ; cor=; Ncor= a 0 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 791 654 593 418 440 c 0 274 311 226 199 89 73 28 24 34 68 39 118 73 180 226 268 289 334 356 g 0 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 395 405 408 499 386 t 0 369 300 257 172 238 67 62 49 50 33 47 32 1246 212 205 290 327 366 435

positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)
; positions_7nt_m5 versus positions_7nt_m2_rc; m=3/9; ncol2=18; w=0; offset=0; strand=R; shift=2; score=0.85403; --rraagGGGAAGTGAaagw ; cor=; Ncor= a 0 0 301 323 579 637 173 181 75 67 911 902 67 96 75 700 572 510 241 281 c 0 0 169 168 125 85 46 24 22 30 23 26 55 41 41 90 106 121 205 207 g 0 0 349 323 167 151 671 729 863 864 35 34 851 93 820 135 201 215 327 236 t 0 0 176 181 124 122 105 61 35 34 26 33 22 765 59 70 116 149 222 271

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m5 versus positions_6nt_m1; m=4/9; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.771626; -rrraaGAGGAAGTgrr--- ; cor=; Ncor= a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 527 0 0 0 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 327 0 0 0 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 479 0 0 0 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290 355 0 0 0

positions_7nt_m3_shift1 (positions_7nt_m3)
; positions_7nt_m5 versus positions_7nt_m3; m=5/9; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.710863; -rrraaGAGGAAGcrrr--- ; cor=; Ncor= a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 719 0 0 0 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 502 0 0 0 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 652 0 0 0 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387 459 0 0 0

positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)
; positions_7nt_m5 versus positions_7nt_m4_rc; m=6/9; ncol2=23; w=-1; offset=-1; strand=R; shift=1; score=0.674236; -draaaGAGGAAGTtcctct ; cor=; Ncor= a 0 157 175 245 339 357 34 497 30 27 511 508 38 33 80 111 115 101 77 86 c 0 98 112 86 76 30 36 9 22 20 29 17 32 28 79 253 276 80 278 101 g 0 169 145 139 95 96 477 36 498 504 25 26 481 29 105 108 85 77 114 75 t 0 151 143 105 65 92 28 33 25 24 10 24 24 485 311 103 99 317 106 313

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_7nt_m5 versus positions_6nt_m5; m=7/9; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.662081; -rrraaGAGGAAstrr---- ; cor=; Ncor= a 0 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 0 0 0 0 c 0 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 0 0 0 0 g 0 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 0 0 0 0 t 0 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442 0 0 0 0

oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)
; positions_7nt_m5 versus oligos_7nt_mkv5_m3; m=8/9; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.640152; --rrAAGAGGAAGwr----- ; cor=; Ncor= a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 0 0 0 0 0 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 0 0 0 0 0 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 0 0 0 0 0 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324 0 0 0 0 0

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_7nt_m5 versus positions_6nt_m2_rc; m=9/9; ncol2=17; w=-2; offset=-2; strand=R; shift=0; score=0.638151; rrraagarGGAAGTgrr--- ; cor=; Ncor= a 533 576 548 974 1109 473 1001 517 100 64 1828 1762 80 74 241 585 610 0 0 0 c 478 420 406 305 244 291 236 144 29 32 70 92 74 84 219 408 401 0 0 0 g 566 582 748 435 372 945 473 1108 1830 1843 62 80 1809 105 1274 588 544 0 0 0 t 419 418 294 282 271 287 286 227 37 57 36 62 33 1733 262 415 441 0 0 0

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=11; shift=0; ncol=11; ssCGCCCTCss ; Alignment reference a 330 322 34 68 53 60 60 137 36 327 318 c 1052 845 2229 67 1998 2025 2109 280 2083 910 889 g 624 823 64 2165 211 197 81 302 175 663 699 t 365 381 44 71 109 89 121 1652 77 471 465

oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCTCss ; cor=; Ncor= a 330 322 34 68 53 60 60 137 36 327 318 c 1052 845 2229 67 1998 2025 2109 280 2083 910 889 g 624 823 64 2165 211 197 81 302 175 663 699 t 365 381 44 71 109 89 121 1652 77 471 465

oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.735232; ssCGCCCGss- ; cor=; Ncor= a 372 410 59 93 51 117 68 76 298 464 0 c 1337 997 2794 116 2543 2438 2546 291 1290 1087 0 g 982 1340 143 2750 377 346 302 2612 1060 1140 0 t 366 310 61 98 86 156 141 78 409 366 0

oligos_6nt_mkv4_m5_rc_shift0 (oligos_6nt_mkv4_m5_rc)
; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m5_rc; m=3/3; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.643415; ssCGCtCGss- ; cor=; Ncor= a 231 305 36 106 18 116 47 52 187 274 0 c 772 567 1701 59 1762 412 1722 123 775 678 0 g 581 747 97 1667 51 346 73 1647 629 651 0 t 286 251 36 38 39 996 28 48 279 267 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift4 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=18; shift=4; ncol=22; ----wcttTCACTTCCCcttyy ; Alignment reference a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/9; ncol2=18; w=0; offset=0; strand=D; shift=4; score= 1; ----wcttTCACTTCCCcttyy ; cor=; Ncor= a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301

positions_7nt_m5_rc_shift4 (positions_7nt_m5_rc)
; positions_7nt_m2 versus positions_7nt_m5_rc; m=2/9; ncol2=18; w=0; offset=0; strand=R; shift=4; score=0.85403; ----hcyytcACTTCCTCytyy ; cor=; Ncor= a 0 0 0 0 411 354 314 287 197 177 1255 33 42 33 36 41 71 60 289 252 295 296 c 0 0 0 0 418 532 420 422 401 1036 135 1370 88 57 1514 1503 96 1370 727 341 492 520 g 0 0 0 0 370 349 324 290 256 176 85 117 65 69 18 17 40 77 130 216 302 340 t 0 0 0 0 428 392 569 628 773 238 152 107 1432 1468 59 66 1420 120 481 818 538 471

positions_7nt_m1_shift4 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=3/9; ncol2=19; w=0; offset=0; strand=D; shift=4; score=0.831332; ----wyyytcACTTCCTCttty ; cor=; Ncor= a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500

positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)
; positions_7nt_m2 versus positions_6nt_m1_rc; m=4/9; ncol2=16; w=0; offset=3; strand=R; shift=7; score=0.675276; -------yycACTTCCTCttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 355 290 235 1309 26 49 28 41 50 58 57 259 214 290 327 c 0 0 0 0 0 0 0 479 534 963 122 1429 67 57 1555 1557 110 1436 314 295 580 526 g 0 0 0 0 0 0 0 327 329 211 101 114 57 70 31 23 29 80 123 229 278 325 t 0 0 0 0 0 0 0 527 535 279 156 119 1515 1533 61 58 1491 115 992 950 540 510

positions_6nt_m2_shift7 (positions_6nt_m2)
; positions_7nt_m2 versus positions_6nt_m2; m=5/9; ncol2=17; w=0; offset=3; strand=D; shift=7; score=0.664085; -------yycACTTCCytctty ; cor=; Ncor= a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548

positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)
; positions_7nt_m2 versus positions_7nt_m3_rc; m=6/9; ncol2=16; w=0; offset=3; strand=R; shift=7; score=0.600625; -------yyygCTTCCTCttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 459 387 437 527 48 41 37 36 53 69 55 289 220 341 430 c 0 0 0 0 0 0 0 652 767 607 428 2057 81 75 2176 2166 105 2041 384 403 603 715 g 0 0 0 0 0 0 0 502 433 424 854 102 80 110 37 29 52 113 152 277 362 491 t 0 0 0 0 0 0 0 719 745 864 523 125 2130 2110 83 84 2106 123 1507 1432 1026 696

oligos_7nt_mkv5_m3_rc_shift9 (oligos_7nt_mkv5_m3_rc)
; positions_7nt_m2 versus oligos_7nt_mkv5_m3_rc; m=7/9; ncol2=13; w=0; offset=5; strand=R; shift=9; score=0.58063; ---------ywCTTCCTCTTyy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 324 469 45 43 17 24 32 44 32 82 49 249 282 c 0 0 0 0 0 0 0 0 0 541 423 1453 61 48 1582 1583 110 1517 147 128 565 588 g 0 0 0 0 0 0 0 0 0 295 363 102 67 67 29 24 32 75 51 88 280 295 t 0 0 0 0 0 0 0 0 0 554 459 114 1543 1582 79 75 1528 90 1434 1449 620 549

positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m2 versus positions_7nt_m4; m=8/9; ncol2=23; w=-4; offset=-4; strand=D; shift=0; score=0.558616; wwaaagaggaACTTCCTCttty ; cor=; Ncor= a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175

positions_6nt_m5_rc_shift8 (positions_6nt_m5_rc)
; positions_7nt_m2 versus positions_6nt_m5_rc; m=9/9; ncol2=15; w=0; offset=4; strand=R; shift=8; score=0.553238; --------yyasTTCCTCttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 442 514 1095 213 40 31 47 59 40 62 353 261 413 480 c 0 0 0 0 0 0 0 0 705 754 406 816 56 42 2266 2296 73 2188 379 441 828 727 g 0 0 0 0 0 0 0 0 504 470 404 885 55 35 36 21 35 99 163 353 409 466 t 0 0 0 0 0 0 0 0 768 681 514 505 2268 2311 70 43 2271 70 1524 1364 769 746

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift0 ; 2 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=11; shift=0; ncol=11; twCTTTTTCwh ; Alignment reference a 339 479 139 106 163 104 111 73 86 472 454 c 313 342 1448 25 41 35 38 31 1507 366 434 g 353 307 41 44 51 33 39 18 29 167 293 t 680 557 57 1510 1430 1513 1497 1563 63 680 504

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5 versus oligos_7nt_mkv5_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; twCTTTTTCwh ; cor=; Ncor= a 339 479 139 106 163 104 111 73 86 472 454 c 313 342 1448 25 41 35 38 31 1507 366 434 g 353 307 41 44 51 33 39 18 29 167 293 t 680 557 57 1510 1430 1513 1497 1563 63 680 504

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift4 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift4 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=19; shift=4; ncol=23; ----wyyytcACTTCCTCtttyy ; Alignment reference a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 369 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 466 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 274 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500 508

positions_7nt_m1_shift4 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/9; ncol2=19; w=0; offset=0; strand=D; shift=4; score= 1; ----wyyytcACTTCCTCtttyy ; cor=; Ncor= a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 369 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 466 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 274 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500 508

positions_7nt_m5_rc_shift4 (positions_7nt_m5_rc)
; positions_7nt_m1 versus positions_7nt_m5_rc; m=2/9; ncol2=18; w=0; offset=0; strand=R; shift=4; score=0.923817; ----hcyytcACTTCCTCytyy- ; cor=; Ncor= a 0 0 0 0 411 354 314 287 197 177 1255 33 42 33 36 41 71 60 289 252 295 296 0 c 0 0 0 0 418 532 420 422 401 1036 135 1370 88 57 1514 1503 96 1370 727 341 492 520 0 g 0 0 0 0 370 349 324 290 256 176 85 117 65 69 18 17 40 77 130 216 302 340 0 t 0 0 0 0 428 392 569 628 773 238 152 107 1432 1468 59 66 1420 120 481 818 538 471 0

positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)
; positions_7nt_m1 versus positions_6nt_m1_rc; m=3/9; ncol2=16; w=0; offset=3; strand=R; shift=7; score=0.834212; -------yycACTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 355 290 235 1309 26 49 28 41 50 58 57 259 214 290 327 367 c 0 0 0 0 0 0 0 479 534 963 122 1429 67 57 1555 1557 110 1436 314 295 580 526 503 g 0 0 0 0 0 0 0 327 329 211 101 114 57 70 31 23 29 80 123 229 278 325 307 t 0 0 0 0 0 0 0 527 535 279 156 119 1515 1533 61 58 1491 115 992 950 540 510 511

positions_7nt_m2_shift4 (positions_7nt_m2)
; positions_7nt_m1 versus positions_7nt_m2; m=4/9; ncol2=18; w=0; offset=0; strand=D; shift=4; score=0.831332; ----wcttTCACTTCCCcttyy- ; cor=; Ncor= a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 0 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 0 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 0 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301 0

positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)
; positions_7nt_m1 versus positions_7nt_m3_rc; m=5/9; ncol2=16; w=0; offset=3; strand=R; shift=7; score=0.783954; -------yyygCTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 459 387 437 527 48 41 37 36 53 69 55 289 220 341 430 465 c 0 0 0 0 0 0 0 652 767 607 428 2057 81 75 2176 2166 105 2041 384 403 603 715 681 g 0 0 0 0 0 0 0 502 433 424 854 102 80 110 37 29 52 113 152 277 362 491 470 t 0 0 0 0 0 0 0 719 745 864 523 125 2130 2110 83 84 2106 123 1507 1432 1026 696 716

positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m1 versus positions_7nt_m4; m=6/9; ncol2=23; w=-4; offset=-4; strand=D; shift=0; score=0.734649; wwaaagaggaACTTCCTCtttyh ; cor=; Ncor= a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 151 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 169 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 98 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175 157

positions_6nt_m5_rc_shift8 (positions_6nt_m5_rc)
; positions_7nt_m1 versus positions_6nt_m5_rc; m=7/9; ncol2=15; w=0; offset=4; strand=R; shift=8; score=0.731398; --------yyasTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 442 514 1095 213 40 31 47 59 40 62 353 261 413 480 526 c 0 0 0 0 0 0 0 0 705 754 406 816 56 42 2266 2296 73 2188 379 441 828 727 723 g 0 0 0 0 0 0 0 0 504 470 404 885 55 35 36 21 35 99 163 353 409 466 444 t 0 0 0 0 0 0 0 0 768 681 514 505 2268 2311 70 43 2271 70 1524 1364 769 746 726

positions_6nt_m2_shift7 (positions_6nt_m2)
; positions_7nt_m1 versus positions_6nt_m2; m=8/9; ncol2=17; w=0; offset=3; strand=D; shift=7; score=0.665439; -------yycACTTCCytcttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 418 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 582 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 420 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548 576

oligos_7nt_mkv5_m3_rc_shift9 (oligos_7nt_mkv5_m3_rc)
; positions_7nt_m1 versus oligos_7nt_mkv5_m3_rc; m=9/9; ncol2=13; w=0; offset=5; strand=R; shift=9; score=0.642276; ---------ywCTTCCTCTTyy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 324 469 45 43 17 24 32 44 32 82 49 249 282 0 c 0 0 0 0 0 0 0 0 0 541 423 1453 61 48 1582 1583 110 1517 147 128 565 588 0 g 0 0 0 0 0 0 0 0 0 295 363 102 67 67 29 24 32 75 51 88 280 295 0 t 0 0 0 0 0 0 0 0 0 554 459 114 1543 1582 79 75 1528 90 1434 1449 620 549 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift7 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=17; shift=7; ncol=24; -------yycACTTCCytcttyyy ; Alignment reference a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 418 419 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 582 566 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 420 478 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548 576 533
positions_6nt_m2_shift7 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/8; ncol2=17; w=0; offset=0; strand=D; shift=7; score= 1; -------yycACTTCCytcttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 418 419 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 582 566 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 420 478 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548 576 533
positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)				; positions_6nt_m2 versus positions_6nt_m1_rc; m=2/8; ncol2=16; w=0; offset=0; strand=R; shift=7; score=0.78224; -------yycACTTCCTCttyyy- ; cor=; Ncor= a 0 0 0 0 0 0 0 355 290 235 1309 26 49 28 41 50 58 57 259 214 290 327 367 0 c 0 0 0 0 0 0 0 479 534 963 122 1429 67 57 1555 1557 110 1436 314 295 580 526 503 0 g 0 0 0 0 0 0 0 327 329 211 101 114 57 70 31 23 29 80 123 229 278 325 307 0 t 0 0 0 0 0 0 0 527 535 279 156 119 1515 1533 61 58 1491 115 992 950 540 510 511 0
positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)				; positions_6nt_m2 versus positions_7nt_m3_rc; m=3/8; ncol2=16; w=0; offset=0; strand=R; shift=7; score=0.684424; -------yyygCTTCCTCttyyy- ; cor=; Ncor= a 0 0 0 0 0 0 0 459 387 437 527 48 41 37 36 53 69 55 289 220 341 430 465 0 c 0 0 0 0 0 0 0 652 767 607 428 2057 81 75 2176 2166 105 2041 384 403 603 715 681 0 g 0 0 0 0 0 0 0 502 433 424 854 102 80 110 37 29 52 113 152 277 362 491 470 0 t 0 0 0 0 0 0 0 719 745 864 523 125 2130 2110 83 84 2106 123 1507 1432 1026 696 716 0
positions_7nt_m1_shift4 (positions_7nt_m1)				; positions_6nt_m2 versus positions_7nt_m1; m=4/8; ncol2=19; w=-3; offset=-3; strand=D; shift=4; score=0.665439; ----wyyytcACTTCCTCtttyy- ; cor=; Ncor= a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 369 0 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 466 0 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 274 0 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500 508 0
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_6nt_m2 versus positions_7nt_m2; m=5/8; ncol2=18; w=-3; offset=-3; strand=D; shift=4; score=0.664085; ----wcttTCACTTCCCcttyy-- ; cor=; Ncor= a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 0 0 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 0 0 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 0 0 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301 0 0
positions_7nt_m5_rc_shift4 (positions_7nt_m5_rc)				; positions_6nt_m2 versus positions_7nt_m5_rc; m=6/8; ncol2=18; w=-3; offset=-3; strand=R; shift=4; score=0.638151; ----hcyytcACTTCCTCytyy-- ; cor=; Ncor= a 0 0 0 0 411 354 314 287 197 177 1255 33 42 33 36 41 71 60 289 252 295 296 0 0 c 0 0 0 0 418 532 420 422 401 1036 135 1370 88 57 1514 1503 96 1370 727 341 492 520 0 0 g 0 0 0 0 370 349 324 290 256 176 85 117 65 69 18 17 40 77 130 216 302 340 0 0 t 0 0 0 0 428 392 569 628 773 238 152 107 1432 1468 59 66 1420 120 481 818 538 471 0 0
oligos_7nt_mkv5_m3_rc_shift9 (oligos_7nt_mkv5_m3_rc)				; positions_6nt_m2 versus oligos_7nt_mkv5_m3_rc; m=7/8; ncol2=13; w=0; offset=2; strand=R; shift=9; score=0.548422; ---------ywCTTCCTCTTyy-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 324 469 45 43 17 24 32 44 32 82 49 249 282 0 0 c 0 0 0 0 0 0 0 0 0 541 423 1453 61 48 1582 1583 110 1517 147 128 565 588 0 0 g 0 0 0 0 0 0 0 0 0 295 363 102 67 67 29 24 32 75 51 88 280 295 0 0 t 0 0 0 0 0 0 0 0 0 554 459 114 1543 1582 79 75 1528 90 1434 1449 620 549 0 0
positions_7nt_m4_shift0 (positions_7nt_m4)				; positions_6nt_m2 versus positions_7nt_m4; m=8/8; ncol2=23; w=-7; offset=-7; strand=D; shift=0; score=0.512834; wwaaagaggaACTTCCTCtttyh- ; cor=; Ncor= a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 151 0 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 169 0 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 98 0 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175 157 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=16; shift=1; ncol=17; -rrraaGAGGAAGTgrr ; Alignment reference a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 527 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 327 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 479 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290 355
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -rrraaGAGGAAGTgrr ; cor=; Ncor= a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 527 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 327 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 479 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290 355
positions_7nt_m3_shift1 (positions_7nt_m3)				; positions_6nt_m1 versus positions_7nt_m3; m=2/9; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.934619; -rrraaGAGGAAGcrrr ; cor=; Ncor= a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 719 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 502 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 652 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387 459
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_6nt_m1 versus positions_6nt_m5; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.873445; -rrraaGAGGAAstrr- ; cor=; Ncor= a 0 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 0 c 0 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 0 g 0 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 0 t 0 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442 0
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_6nt_m1 versus positions_7nt_m1_rc; m=4/9; ncol2=19; w=0; offset=0; strand=R; shift=1; score=0.834212; -rraaaGAGGAAGTgar ; cor=; Ncor= a 0 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 791 654 c 0 274 311 226 199 89 73 28 24 34 68 39 118 73 180 226 268 g 0 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 395 405 t 0 369 300 257 172 238 67 62 49 50 33 47 32 1246 212 205 290
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_6nt_m1 versus positions_6nt_m2_rc; m=5/9; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.78224; rrraagarGGAAGTgrr ; cor=; Ncor= a 533 576 548 974 1109 473 1001 517 100 64 1828 1762 80 74 241 585 610 c 478 420 406 305 244 291 236 144 29 32 70 92 74 84 219 408 401 g 566 582 748 435 372 945 473 1108 1830 1843 62 80 1809 105 1274 588 544 t 419 418 294 282 271 287 286 227 37 57 36 62 33 1733 262 415 441
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_6nt_m1 versus positions_7nt_m5; m=6/9; ncol2=18; w=0; offset=1; strand=D; shift=2; score=0.771626; --rrarGAGGAAGTgar ; cor=; Ncor= a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 628 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 290 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 422 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197 287
oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)				; positions_6nt_m1 versus oligos_7nt_mkv5_m3; m=7/9; ncol2=13; w=0; offset=1; strand=D; shift=2; score=0.759689; --rrAAGAGGAAGwr-- ; cor=; Ncor= a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 0 0 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 0 0 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 0 0 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324 0 0
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_6nt_m1 versus positions_7nt_m2_rc; m=8/9; ncol2=18; w=0; offset=1; strand=R; shift=2; score=0.675276; --rraagGGGAAGTGAa ; cor=; Ncor= a 0 0 301 323 579 637 173 181 75 67 911 902 67 96 75 700 572 c 0 0 169 168 125 85 46 24 22 30 23 26 55 41 41 90 106 g 0 0 349 323 167 151 671 729 863 864 35 34 851 93 820 135 201 t 0 0 176 181 124 122 105 61 35 34 26 33 22 765 59 70 116
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; positions_6nt_m1 versus positions_7nt_m4_rc; m=9/9; ncol2=23; w=0; offset=0; strand=R; shift=1; score=0.653168; -draaaGAGGAAGTtcc ; cor=; Ncor= a 0 157 175 245 339 357 34 497 30 27 511 508 38 33 80 111 115 c 0 98 112 86 76 30 36 9 22 20 29 17 32 28 79 253 276 g 0 169 145 139 95 96 477 36 498 504 25 26 481 29 105 108 85 t 0 151 143 105 65 92 28 33 25 24 10 24 24 485 311 103 99

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=23; shift=0; ncol=23; wwaaagaggaACTTCCTCtttyh ; Alignment reference a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 151 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 169 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 98 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175 157
positions_7nt_m4_shift0 (positions_7nt_m4)				; positions_7nt_m4 versus positions_7nt_m4; m=1/9; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; wwaaagaggaACTTCCTCtttyh ; cor=; Ncor= a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 151 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 169 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 98 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175 157
positions_7nt_m1_shift4 (positions_7nt_m1)				; positions_7nt_m4 versus positions_7nt_m1; m=2/9; ncol2=19; w=0; offset=4; strand=D; shift=4; score=0.734649; ----wyyytcACTTCCTCtttyy ; cor=; Ncor= a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 369 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 466 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 274 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500 508
positions_7nt_m5_rc_shift4 (positions_7nt_m5_rc)				; positions_7nt_m4 versus positions_7nt_m5_rc; m=3/9; ncol2=18; w=0; offset=4; strand=R; shift=4; score=0.674236; ----hcyytcACTTCCTCytyy- ; cor=; Ncor= a 0 0 0 0 411 354 314 287 197 177 1255 33 42 33 36 41 71 60 289 252 295 296 0 c 0 0 0 0 418 532 420 422 401 1036 135 1370 88 57 1514 1503 96 1370 727 341 492 520 0 g 0 0 0 0 370 349 324 290 256 176 85 117 65 69 18 17 40 77 130 216 302 340 0 t 0 0 0 0 428 392 569 628 773 238 152 107 1432 1468 59 66 1420 120 481 818 538 471 0
positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)				; positions_7nt_m4 versus positions_6nt_m1_rc; m=4/9; ncol2=16; w=0; offset=7; strand=R; shift=7; score=0.653168; -------yycACTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 355 290 235 1309 26 49 28 41 50 58 57 259 214 290 327 367 c 0 0 0 0 0 0 0 479 534 963 122 1429 67 57 1555 1557 110 1436 314 295 580 526 503 g 0 0 0 0 0 0 0 327 329 211 101 114 57 70 31 23 29 80 123 229 278 325 307 t 0 0 0 0 0 0 0 527 535 279 156 119 1515 1533 61 58 1491 115 992 950 540 510 511
positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)				; positions_7nt_m4 versus positions_7nt_m3_rc; m=5/9; ncol2=16; w=0; offset=7; strand=R; shift=7; score=0.623552; -------yyygCTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 459 387 437 527 48 41 37 36 53 69 55 289 220 341 430 465 c 0 0 0 0 0 0 0 652 767 607 428 2057 81 75 2176 2166 105 2041 384 403 603 715 681 g 0 0 0 0 0 0 0 502 433 424 854 102 80 110 37 29 52 113 152 277 362 491 470 t 0 0 0 0 0 0 0 719 745 864 523 125 2130 2110 83 84 2106 123 1507 1432 1026 696 716
positions_6nt_m5_rc_shift8 (positions_6nt_m5_rc)				; positions_7nt_m4 versus positions_6nt_m5_rc; m=6/9; ncol2=15; w=0; offset=8; strand=R; shift=8; score=0.588102; --------yyasTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 442 514 1095 213 40 31 47 59 40 62 353 261 413 480 526 c 0 0 0 0 0 0 0 0 705 754 406 816 56 42 2266 2296 73 2188 379 441 828 727 723 g 0 0 0 0 0 0 0 0 504 470 404 885 55 35 36 21 35 99 163 353 409 466 444 t 0 0 0 0 0 0 0 0 768 681 514 505 2268 2311 70 43 2271 70 1524 1364 769 746 726
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_7nt_m4 versus positions_7nt_m2; m=7/9; ncol2=18; w=0; offset=4; strand=D; shift=4; score=0.558616; ----wcttTCACTTCCCcttyy- ; cor=; Ncor= a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 0 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 0 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 0 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301 0
oligos_7nt_mkv5_m3_rc_shift9 (oligos_7nt_mkv5_m3_rc)				; positions_7nt_m4 versus oligos_7nt_mkv5_m3_rc; m=8/9; ncol2=13; w=0; offset=9; strand=R; shift=9; score=0.517439; ---------ywCTTCCTCTTyy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 324 469 45 43 17 24 32 44 32 82 49 249 282 0 c 0 0 0 0 0 0 0 0 0 541 423 1453 61 48 1582 1583 110 1517 147 128 565 588 0 g 0 0 0 0 0 0 0 0 0 295 363 102 67 67 29 24 32 75 51 88 280 295 0 t 0 0 0 0 0 0 0 0 0 554 459 114 1543 1582 79 75 1528 90 1434 1449 620 549 0
positions_6nt_m2_shift7 (positions_6nt_m2)				; positions_7nt_m4 versus positions_6nt_m2; m=9/9; ncol2=17; w=0; offset=7; strand=D; shift=7; score=0.512834; -------yycACTTCCytcttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 418 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 582 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 420 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548 576

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; rrraaGAGGAAstrr ; Alignment reference a 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 c 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 g 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 t 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; rrraaGAGGAAstrr ; cor=; Ncor= a 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 c 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 g 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 t 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442
positions_7nt_m3_shift0 (positions_7nt_m3)				; positions_6nt_m5 versus positions_7nt_m3; m=2/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.877332; rrraaGAGGAAGcrr ; cor=; Ncor= a 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 c 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 g 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 t 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m5 versus positions_6nt_m1; m=3/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.873445; rrraaGAGGAAGTgr ; cor=; Ncor= a 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 c 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 g 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 t 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290
oligos_7nt_mkv5_m3_shift1 (oligos_7nt_mkv5_m3)				; positions_6nt_m5 versus oligos_7nt_mkv5_m3; m=4/8; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.812119; -rrAAGAGGAAGwr- ; cor=; Ncor= a 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 0 c 0 295 280 88 51 75 32 24 29 67 67 102 363 295 0 g 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 0 t 0 282 249 49 82 32 44 32 24 17 43 45 469 324 0
positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc)				; positions_6nt_m5 versus positions_7nt_m1_rc; m=5/8; ncol2=19; w=0; offset=0; strand=R; shift=0; score=0.731398; rraaaGAGGAAGTga ; cor=; Ncor= a 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 791 c 274 311 226 199 89 73 28 24 34 68 39 118 73 180 226 g 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 395 t 369 300 257 172 238 67 62 49 50 33 47 32 1246 212 205
positions_7nt_m5_shift1 (positions_7nt_m5)				; positions_6nt_m5 versus positions_7nt_m5; m=6/8; ncol2=18; w=0; offset=1; strand=D; shift=1; score=0.662081; -rrarGAGGAAGTga ; cor=; Ncor= a 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 c 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 g 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 t 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197
positions_7nt_m4_rc_shift0 (positions_7nt_m4_rc)				; positions_6nt_m5 versus positions_7nt_m4_rc; m=7/8; ncol2=23; w=0; offset=0; strand=R; shift=0; score=0.588102; draaaGAGGAAGTtc ; cor=; Ncor= a 157 175 245 339 357 34 497 30 27 511 508 38 33 80 111 c 98 112 86 76 30 36 9 22 20 29 17 32 28 79 253 g 169 145 139 95 96 477 36 498 504 25 26 481 29 105 108 t 151 143 105 65 92 28 33 25 24 10 24 24 485 311 103
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; positions_6nt_m5 versus positions_7nt_m2_rc; m=8/8; ncol2=18; w=0; offset=1; strand=R; shift=1; score=0.553238; -rraagGGGAAGTGA ; cor=; Ncor= a 0 301 323 579 637 173 181 75 67 911 902 67 96 75 700 c 0 169 168 125 85 46 24 22 30 23 26 55 41 41 90 g 0 349 323 167 151 671 729 863 864 35 34 851 93 820 135 t 0 176 181 124 122 105 61 35 34 26 33 22 765 59 70

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; wwAtTAAAAATAtAAAtwAtttww ; Alignment reference a 132 132 228 73 61 239 254 274 232 277 69 257 63 256 233 268 73 100 236 64 65 66 112 102 c 60 60 18 42 15 22 23 10 22 16 14 12 39 17 22 19 16 18 16 23 26 23 50 80 g 47 32 24 15 28 25 10 17 17 11 15 25 13 16 14 14 22 18 22 20 20 30 55 40 t 93 108 62 202 228 46 45 31 61 28 234 38 217 43 63 31 221 196 58 225 221 213 115 110
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wwAtTAAAAATAtAAAtwAtttww ; cor=; Ncor= a 132 132 228 73 61 239 254 274 232 277 69 257 63 256 233 268 73 100 236 64 65 66 112 102 c 60 60 18 42 15 22 23 10 22 16 14 12 39 17 22 19 16 18 16 23 26 23 50 80 g 47 32 24 15 28 25 10 17 17 11 15 25 13 16 14 14 22 18 22 20 20 30 55 40 t 93 108 62 202 228 46 45 31 61 28 234 38 217 43 63 31 221 196 58 225 221 213 115 110
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m3 versus positions_6nt_m4; m=2/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.782988; awAwwAAAAAtAAtAAAwwAwtww ; cor=; Ncor= a 114 114 185 69 71 206 203 193 198 216 51 216 195 58 199 200 185 72 75 179 65 53 90 99 c 47 35 21 23 19 12 13 14 12 9 15 14 23 13 16 16 17 9 10 18 16 21 39 44 g 36 21 15 15 16 11 10 14 18 10 17 6 11 15 10 11 11 19 11 19 11 17 40 36 t 60 87 36 150 151 28 31 36 29 22 174 21 28 171 32 30 44 157 161 41 165 166 88 78
oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)				; positions_6nt_m3 versus oligos_7nt_mkv5_m1_rc; m=3/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.402835; --wwTAAAAATww----------- ; cor=; Ncor= a 0 0 1375 1360 269 3419 3386 3557 3405 3478 259 1495 1496 0 0 0 0 0 0 0 0 0 0 0 c 0 0 498 707 179 109 143 93 158 150 170 588 818 0 0 0 0 0 0 0 0 0 0 0 g 0 0 688 638 138 145 192 125 137 142 84 813 547 0 0 0 0 0 0 0 0 0 0 0 t 0 0 1388 1244 3363 276 228 174 249 179 3436 1053 1088 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCGaGCGss ; Alignment reference a 0 267 279 48 28 996 39 38 36 251 286 c 0 651 629 1647 73 346 51 1667 97 747 581 g 0 678 775 123 1722 412 1762 59 1701 567 772 t 0 274 187 52 47 116 18 106 36 305 231
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ssCGaGCGss ; cor=; Ncor= a 0 267 279 48 28 996 39 38 36 251 286 c 0 651 629 1647 73 346 51 1667 97 747 581 g 0 678 775 123 1722 412 1762 59 1701 567 772 t 0 274 187 52 47 116 18 106 36 305 231
oligos_6nt_mkv4_m1_rc_shift1 (oligos_6nt_mkv4_m1_rc)				; oligos_6nt_mkv4_m5 versus oligos_6nt_mkv4_m1_rc; m=2/3; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.905046; -ssCGGGCGss ; cor=; Ncor= a 0 366 409 78 141 156 86 98 61 310 366 c 0 1140 1060 2612 302 346 377 2750 143 1340 982 g 0 1087 1290 291 2546 2438 2543 116 2794 997 1337 t 0 464 298 76 68 117 51 93 59 410 372
oligos_7nt_mkv5_m2_rc_shift0 (oligos_7nt_mkv5_m2_rc)				; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m2_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.643415; ssGAGGGCGss ; cor=; Ncor= a 465 471 77 1652 121 89 109 71 44 381 365 c 699 663 175 302 81 197 211 2165 64 823 624 g 889 910 2083 280 2109 2025 1998 67 2229 845 1052 t 318 327 36 137 60 60 53 68 34 322 330

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --rrAAGAGGAAGwr ; Alignment reference a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324
oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m3; m=1/9; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --rrAAGAGGAAGwr ; cor=; Ncor= a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324
positions_6nt_m5_shift1 (positions_6nt_m5)				; oligos_7nt_mkv5_m3 versus positions_6nt_m5; m=2/9; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.812119; -rrraaGAGGAAstr ; cor=; Ncor= a 0 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 c 0 444 466 409 353 163 99 35 21 36 35 55 885 404 470 g 0 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 t 0 526 480 413 261 353 62 40 59 47 31 40 213 1095 514
positions_7nt_m3_shift1 (positions_7nt_m3)				; oligos_7nt_mkv5_m3 versus positions_7nt_m3; m=3/9; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.798185; -rrraaGAGGAAGcr ; cor=; Ncor= a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_7nt_mkv5_m3 versus positions_6nt_m1; m=4/9; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.759689; -rrraaGAGGAAGTg ; cor=; Ncor= a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; oligos_7nt_mkv5_m3 versus positions_7nt_m1_rc; m=5/9; ncol2=19; w=-1; offset=-1; strand=R; shift=1; score=0.642276; -rraaaGAGGAAGTg ; cor=; Ncor= a 0 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 c 0 274 311 226 199 89 73 28 24 34 68 39 118 73 180 g 0 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 t 0 369 300 257 172 238 67 62 49 50 33 47 32 1246 212
positions_7nt_m5_shift2 (positions_7nt_m5)				; oligos_7nt_mkv5_m3 versus positions_7nt_m5; m=6/9; ncol2=18; w=0; offset=0; strand=D; shift=2; score=0.640152; --rrarGAGGAAGTg ; cor=; Ncor= a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; oligos_7nt_mkv5_m3 versus positions_7nt_m2_rc; m=7/9; ncol2=18; w=0; offset=0; strand=R; shift=2; score=0.58063; --rraagGGGAAGTG ; cor=; Ncor= a 0 0 301 323 579 637 173 181 75 67 911 902 67 96 75 c 0 0 169 168 125 85 46 24 22 30 23 26 55 41 41 g 0 0 349 323 167 151 671 729 863 864 35 34 851 93 820 t 0 0 176 181 124 122 105 61 35 34 26 33 22 765 59
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; oligos_7nt_mkv5_m3 versus positions_6nt_m2_rc; m=8/9; ncol2=17; w=-2; offset=-2; strand=R; shift=0; score=0.548422; rrraagarGGAAGTg ; cor=; Ncor= a 533 576 548 974 1109 473 1001 517 100 64 1828 1762 80 74 241 c 478 420 406 305 244 291 236 144 29 32 70 92 74 84 219 g 566 582 748 435 372 945 473 1108 1830 1843 62 80 1809 105 1274 t 419 418 294 282 271 287 286 227 37 57 36 62 33 1733 262
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; oligos_7nt_mkv5_m3 versus positions_7nt_m4_rc; m=9/9; ncol2=23; w=-1; offset=-1; strand=R; shift=1; score=0.517439; -draaaGAGGAAGTt ; cor=; Ncor= a 0 157 175 245 339 357 34 497 30 27 511 508 38 33 80 c 0 98 112 86 76 30 36 9 22 20 29 17 32 28 79 g 0 169 145 139 95 96 477 36 498 504 25 26 481 29 105 t 0 151 143 105 65 92 28 33 25 24 10 24 24 485 311

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m3_shift1 (positions_7nt_m3)				; positions_7nt_m3; m=0 (reference); ncol1=16; shift=1; ncol=17; -rrraaGAGGAAGcrrr ; Alignment reference a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 719 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 502 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 652 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387 459
positions_7nt_m3_shift1 (positions_7nt_m3)				; positions_7nt_m3 versus positions_7nt_m3; m=1/9; ncol2=16; w=0; offset=0; strand=D; shift=1; score= 1; -rrraaGAGGAAGcrrr ; cor=; Ncor= a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 719 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 502 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 652 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387 459
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_7nt_m3 versus positions_6nt_m1; m=2/9; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.934619; -rrraaGAGGAAGTgrr ; cor=; Ncor= a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 527 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 327 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 479 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290 355
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_7nt_m3 versus positions_6nt_m5; m=3/9; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.877332; -rrraaGAGGAAstrr- ; cor=; Ncor= a 0 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 0 c 0 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 0 g 0 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 0 t 0 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442 0
oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)				; positions_7nt_m3 versus oligos_7nt_mkv5_m3; m=4/9; ncol2=13; w=0; offset=1; strand=D; shift=2; score=0.798185; --rrAAGAGGAAGwr-- ; cor=; Ncor= a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 0 0 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 0 0 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 0 0 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324 0 0
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_7nt_m3 versus positions_7nt_m1_rc; m=5/9; ncol2=19; w=0; offset=0; strand=R; shift=1; score=0.783954; -rraaaGAGGAAGTgar ; cor=; Ncor= a 0 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 791 654 c 0 274 311 226 199 89 73 28 24 34 68 39 118 73 180 226 268 g 0 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 395 405 t 0 369 300 257 172 238 67 62 49 50 33 47 32 1246 212 205 290
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_7nt_m3 versus positions_7nt_m5; m=6/9; ncol2=18; w=0; offset=1; strand=D; shift=2; score=0.710863; --rrarGAGGAAGTgar ; cor=; Ncor= a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 628 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 290 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 422 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197 287
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m3 versus positions_6nt_m2_rc; m=7/9; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.684424; rrraagarGGAAGTgrr ; cor=; Ncor= a 533 576 548 974 1109 473 1001 517 100 64 1828 1762 80 74 241 585 610 c 478 420 406 305 244 291 236 144 29 32 70 92 74 84 219 408 401 g 566 582 748 435 372 945 473 1108 1830 1843 62 80 1809 105 1274 588 544 t 419 418 294 282 271 287 286 227 37 57 36 62 33 1733 262 415 441
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; positions_7nt_m3 versus positions_7nt_m4_rc; m=8/9; ncol2=23; w=0; offset=0; strand=R; shift=1; score=0.623552; -draaaGAGGAAGTtcc ; cor=; Ncor= a 0 157 175 245 339 357 34 497 30 27 511 508 38 33 80 111 115 c 0 98 112 86 76 30 36 9 22 20 29 17 32 28 79 253 276 g 0 169 145 139 95 96 477 36 498 504 25 26 481 29 105 108 85 t 0 151 143 105 65 92 28 33 25 24 10 24 24 485 311 103 99
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_7nt_m3 versus positions_7nt_m2_rc; m=9/9; ncol2=18; w=0; offset=1; strand=R; shift=2; score=0.600625; --rraagGGGAAGTGAa ; cor=; Ncor= a 0 0 301 323 579 637 173 181 75 67 911 902 67 96 75 700 572 c 0 0 169 168 125 85 46 24 22 30 23 26 55 41 41 90 106 g 0 0 349 323 167 151 671 729 863 864 35 34 851 93 820 135 201 t 0 0 176 181 124 122 105 61 35 34 26 33 22 765 59 70 116

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=10; shift=0; ncol=10; ssCGCCCGss ; Alignment reference a 372 410 59 93 51 117 68 76 298 464 c 1337 997 2794 116 2543 2438 2546 291 1290 1087 g 982 1340 143 2750 377 346 302 2612 1060 1140 t 366 310 61 98 86 156 141 78 409 366
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m1; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCGss ; cor=; Ncor= a 372 410 59 93 51 117 68 76 298 464 c 1337 997 2794 116 2543 2438 2546 291 1290 1087 g 982 1340 143 2750 377 346 302 2612 1060 1140 t 366 310 61 98 86 156 141 78 409 366
oligos_6nt_mkv4_m5_rc_shift0 (oligos_6nt_mkv4_m5_rc)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m5_rc; m=2/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.905046; ssCGCtCGss ; cor=; Ncor= a 231 305 36 106 18 116 47 52 187 274 c 772 567 1701 59 1762 412 1722 123 775 678 g 581 747 97 1667 51 346 73 1647 629 651 t 286 251 36 38 39 996 28 48 279 267
oligos_6nt_mkv4_m3_rc_shift0 (oligos_6nt_mkv4_m3_rc)				; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m3_rc; m=3/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.841409; ssCGGCCGss ; cor=; Ncor= a 395 381 82 90 51 86 67 53 351 459 c 1492 1090 3098 459 447 2875 2837 226 1631 1115 g 1113 1631 226 2847 2875 447 459 3099 1091 1492 t 459 357 53 63 86 51 96 81 386 393
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m2; m=4/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.735232; ssCGCCCTCs ; cor=; Ncor= a 330 322 34 68 53 60 60 137 36 327 c 1052 845 2229 67 1998 2025 2109 280 2083 910 g 624 823 64 2165 211 197 81 302 175 663 t 365 381 44 71 109 89 121 1652 77 471

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_7nt_m5; m=0 (reference); ncol1=18; shift=2; ncol=20; --rrarGAGGAAGTgarrgd ; Alignment reference a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 628 569 392 428 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 290 324 349 370 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 422 420 532 418 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197 287 314 354 411
positions_7nt_m5_shift2 (positions_7nt_m5)				; positions_7nt_m5 versus positions_7nt_m5; m=1/9; ncol2=18; w=0; offset=0; strand=D; shift=2; score= 1; --rrarGAGGAAGTgarrgd ; cor=; Ncor= a 0 0 471 538 818 481 120 1420 66 59 1468 1432 107 152 238 773 628 569 392 428 c 0 0 340 302 216 130 77 40 17 18 69 65 117 85 176 256 290 324 349 370 g 0 0 520 492 341 727 1370 96 1503 1514 57 88 1370 135 1036 401 422 420 532 418 t 0 0 296 295 252 289 60 71 41 36 33 42 33 1255 177 197 287 314 354 411
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_7nt_m5 versus positions_7nt_m1_rc; m=2/9; ncol2=19; w=-1; offset=-1; strand=R; shift=1; score=0.923817; -rraaaGAGGAAGTgarrrw ; cor=; Ncor= a 0 508 500 736 994 1013 136 1417 59 82 1457 1475 133 173 271 791 654 593 418 440 c 0 274 311 226 199 89 73 28 24 34 68 39 118 73 180 226 268 289 334 356 g 0 466 506 398 252 277 1341 110 1485 1451 59 56 1334 125 954 395 405 408 499 386 t 0 369 300 257 172 238 67 62 49 50 33 47 32 1246 212 205 290 327 366 435
positions_7nt_m2_rc_shift2 (positions_7nt_m2_rc)				; positions_7nt_m5 versus positions_7nt_m2_rc; m=3/9; ncol2=18; w=0; offset=0; strand=R; shift=2; score=0.85403; --rraagGGGAAGTGAaagw ; cor=; Ncor= a 0 0 301 323 579 637 173 181 75 67 911 902 67 96 75 700 572 510 241 281 c 0 0 169 168 125 85 46 24 22 30 23 26 55 41 41 90 106 121 205 207 g 0 0 349 323 167 151 671 729 863 864 35 34 851 93 820 135 201 215 327 236 t 0 0 176 181 124 122 105 61 35 34 26 33 22 765 59 70 116 149 222 271
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_7nt_m5 versus positions_6nt_m1; m=4/9; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.771626; -rrraaGAGGAAGTgrr--- ; cor=; Ncor= a 0 511 510 540 950 992 115 1491 58 61 1533 1515 119 156 279 535 527 0 0 0 c 0 307 325 278 229 123 80 29 23 31 70 57 114 101 211 329 327 0 0 0 g 0 503 526 580 295 314 1436 110 1557 1555 57 67 1429 122 963 534 479 0 0 0 t 0 367 327 290 214 259 57 58 50 41 28 49 26 1309 235 290 355 0 0 0
positions_7nt_m3_shift1 (positions_7nt_m3)				; positions_7nt_m5 versus positions_7nt_m3; m=5/9; ncol2=16; w=-1; offset=-1; strand=D; shift=1; score=0.710863; -rrraaGAGGAAGcrrr--- ; cor=; Ncor= a 0 716 696 1026 1432 1507 123 2106 84 83 2110 2130 125 523 864 745 719 0 0 0 c 0 470 491 362 277 152 113 52 29 37 110 80 102 854 424 433 502 0 0 0 g 0 681 715 603 403 384 2041 105 2166 2176 75 81 2057 428 607 767 652 0 0 0 t 0 465 430 341 220 289 55 69 53 36 37 41 48 527 437 387 459 0 0 0
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc)				; positions_7nt_m5 versus positions_7nt_m4_rc; m=6/9; ncol2=23; w=-1; offset=-1; strand=R; shift=1; score=0.674236; -draaaGAGGAAGTtcctct ; cor=; Ncor= a 0 157 175 245 339 357 34 497 30 27 511 508 38 33 80 111 115 101 77 86 c 0 98 112 86 76 30 36 9 22 20 29 17 32 28 79 253 276 80 278 101 g 0 169 145 139 95 96 477 36 498 504 25 26 481 29 105 108 85 77 114 75 t 0 151 143 105 65 92 28 33 25 24 10 24 24 485 311 103 99 317 106 313
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_7nt_m5 versus positions_6nt_m5; m=7/9; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.662081; -rrraaGAGGAAstrr---- ; cor=; Ncor= a 0 726 746 769 1364 1524 70 2271 43 70 2311 2268 505 514 681 768 0 0 0 0 c 0 444 466 409 353 163 99 35 21 36 35 55 885 404 470 504 0 0 0 0 g 0 723 727 828 441 379 2188 73 2296 2266 42 56 816 406 754 705 0 0 0 0 t 0 526 480 413 261 353 62 40 59 47 31 40 213 1095 514 442 0 0 0 0
oligos_7nt_mkv5_m3_shift2 (oligos_7nt_mkv5_m3)				; positions_7nt_m5 versus oligos_7nt_mkv5_m3; m=8/9; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.640152; --rrAAGAGGAAGwr----- ; cor=; Ncor= a 0 0 549 620 1449 1434 90 1528 75 79 1582 1543 114 459 554 0 0 0 0 0 c 0 0 295 280 88 51 75 32 24 29 67 67 102 363 295 0 0 0 0 0 g 0 0 588 565 128 147 1517 110 1583 1582 48 61 1453 423 541 0 0 0 0 0 t 0 0 282 249 49 82 32 44 32 24 17 43 45 469 324 0 0 0 0 0
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)				; positions_7nt_m5 versus positions_6nt_m2_rc; m=9/9; ncol2=17; w=-2; offset=-2; strand=R; shift=0; score=0.638151; rrraagarGGAAGTgrr--- ; cor=; Ncor= a 533 576 548 974 1109 473 1001 517 100 64 1828 1762 80 74 241 585 610 0 0 0 c 478 420 406 305 244 291 236 144 29 32 70 92 74 84 219 408 401 0 0 0 g 566 582 748 435 372 945 473 1108 1830 1843 62 80 1809 105 1274 588 544 0 0 0 t 419 418 294 282 271 287 286 227 37 57 36 62 33 1733 262 415 441 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; ssCGCCCTCss ; Alignment reference a 330 322 34 68 53 60 60 137 36 327 318 c 1052 845 2229 67 1998 2025 2109 280 2083 910 889 g 624 823 64 2165 211 197 81 302 175 663 699 t 365 381 44 71 109 89 121 1652 77 471 465
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCGCCCTCss ; cor=; Ncor= a 330 322 34 68 53 60 60 137 36 327 318 c 1052 845 2229 67 1998 2025 2109 280 2083 910 889 g 624 823 64 2165 211 197 81 302 175 663 699 t 365 381 44 71 109 89 121 1652 77 471 465
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m1; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.735232; ssCGCCCGss- ; cor=; Ncor= a 372 410 59 93 51 117 68 76 298 464 0 c 1337 997 2794 116 2543 2438 2546 291 1290 1087 0 g 982 1340 143 2750 377 346 302 2612 1060 1140 0 t 366 310 61 98 86 156 141 78 409 366 0
oligos_6nt_mkv4_m5_rc_shift0 (oligos_6nt_mkv4_m5_rc)				; oligos_7nt_mkv5_m2 versus oligos_6nt_mkv4_m5_rc; m=3/3; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.643415; ssCGCtCGss- ; cor=; Ncor= a 231 305 36 106 18 116 47 52 187 274 0 c 772 567 1701 59 1762 412 1722 123 775 678 0 g 581 747 97 1667 51 346 73 1647 629 651 0 t 286 251 36 38 39 996 28 48 279 267 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=18; shift=4; ncol=22; ----wcttTCACTTCCCcttyy ; Alignment reference a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/9; ncol2=18; w=0; offset=0; strand=D; shift=4; score= 1; ----wcttTCACTTCCCcttyy ; cor=; Ncor= a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301
positions_7nt_m5_rc_shift4 (positions_7nt_m5_rc)				; positions_7nt_m2 versus positions_7nt_m5_rc; m=2/9; ncol2=18; w=0; offset=0; strand=R; shift=4; score=0.85403; ----hcyytcACTTCCTCytyy ; cor=; Ncor= a 0 0 0 0 411 354 314 287 197 177 1255 33 42 33 36 41 71 60 289 252 295 296 c 0 0 0 0 418 532 420 422 401 1036 135 1370 88 57 1514 1503 96 1370 727 341 492 520 g 0 0 0 0 370 349 324 290 256 176 85 117 65 69 18 17 40 77 130 216 302 340 t 0 0 0 0 428 392 569 628 773 238 152 107 1432 1468 59 66 1420 120 481 818 538 471
positions_7nt_m1_shift4 (positions_7nt_m1)				; positions_7nt_m2 versus positions_7nt_m1; m=3/9; ncol2=19; w=0; offset=0; strand=D; shift=4; score=0.831332; ----wyyytcACTTCCTCttty ; cor=; Ncor= a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500
positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)				; positions_7nt_m2 versus positions_6nt_m1_rc; m=4/9; ncol2=16; w=0; offset=3; strand=R; shift=7; score=0.675276; -------yycACTTCCTCttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 355 290 235 1309 26 49 28 41 50 58 57 259 214 290 327 c 0 0 0 0 0 0 0 479 534 963 122 1429 67 57 1555 1557 110 1436 314 295 580 526 g 0 0 0 0 0 0 0 327 329 211 101 114 57 70 31 23 29 80 123 229 278 325 t 0 0 0 0 0 0 0 527 535 279 156 119 1515 1533 61 58 1491 115 992 950 540 510
positions_6nt_m2_shift7 (positions_6nt_m2)				; positions_7nt_m2 versus positions_6nt_m2; m=5/9; ncol2=17; w=0; offset=3; strand=D; shift=7; score=0.664085; -------yycACTTCCytctty ; cor=; Ncor= a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548
positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)				; positions_7nt_m2 versus positions_7nt_m3_rc; m=6/9; ncol2=16; w=0; offset=3; strand=R; shift=7; score=0.600625; -------yyygCTTCCTCttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 459 387 437 527 48 41 37 36 53 69 55 289 220 341 430 c 0 0 0 0 0 0 0 652 767 607 428 2057 81 75 2176 2166 105 2041 384 403 603 715 g 0 0 0 0 0 0 0 502 433 424 854 102 80 110 37 29 52 113 152 277 362 491 t 0 0 0 0 0 0 0 719 745 864 523 125 2130 2110 83 84 2106 123 1507 1432 1026 696
oligos_7nt_mkv5_m3_rc_shift9 (oligos_7nt_mkv5_m3_rc)				; positions_7nt_m2 versus oligos_7nt_mkv5_m3_rc; m=7/9; ncol2=13; w=0; offset=5; strand=R; shift=9; score=0.58063; ---------ywCTTCCTCTTyy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 324 469 45 43 17 24 32 44 32 82 49 249 282 c 0 0 0 0 0 0 0 0 0 541 423 1453 61 48 1582 1583 110 1517 147 128 565 588 g 0 0 0 0 0 0 0 0 0 295 363 102 67 67 29 24 32 75 51 88 280 295 t 0 0 0 0 0 0 0 0 0 554 459 114 1543 1582 79 75 1528 90 1434 1449 620 549
positions_7nt_m4_shift0 (positions_7nt_m4)				; positions_7nt_m2 versus positions_7nt_m4; m=8/9; ncol2=23; w=-4; offset=-4; strand=D; shift=0; score=0.558616; wwaaagaggaACTTCCTCttty ; cor=; Ncor= a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175
positions_6nt_m5_rc_shift8 (positions_6nt_m5_rc)				; positions_7nt_m2 versus positions_6nt_m5_rc; m=9/9; ncol2=15; w=0; offset=4; strand=R; shift=8; score=0.553238; --------yyasTTCCTCttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 442 514 1095 213 40 31 47 59 40 62 353 261 413 480 c 0 0 0 0 0 0 0 0 705 754 406 816 56 42 2266 2296 73 2188 379 441 828 727 g 0 0 0 0 0 0 0 0 504 470 404 885 55 35 36 21 35 99 163 353 409 466 t 0 0 0 0 0 0 0 0 768 681 514 505 2268 2311 70 43 2271 70 1524 1364 769 746

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift4 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=19; shift=4; ncol=23; ----wyyytcACTTCCTCtttyy ; Alignment reference a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 369 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 466 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 274 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500 508
positions_7nt_m1_shift4 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/9; ncol2=19; w=0; offset=0; strand=D; shift=4; score= 1; ----wyyytcACTTCCTCtttyy ; cor=; Ncor= a 0 0 0 0 435 366 327 290 205 212 1246 32 47 33 50 49 62 67 238 172 257 300 369 c 0 0 0 0 386 499 408 405 395 954 125 1334 56 59 1451 1485 110 1341 277 252 398 506 466 g 0 0 0 0 356 334 289 268 226 180 73 118 39 68 34 24 28 73 89 199 226 311 274 t 0 0 0 0 440 418 593 654 791 271 173 133 1475 1457 82 59 1417 136 1013 994 736 500 508
positions_7nt_m5_rc_shift4 (positions_7nt_m5_rc)				; positions_7nt_m1 versus positions_7nt_m5_rc; m=2/9; ncol2=18; w=0; offset=0; strand=R; shift=4; score=0.923817; ----hcyytcACTTCCTCytyy- ; cor=; Ncor= a 0 0 0 0 411 354 314 287 197 177 1255 33 42 33 36 41 71 60 289 252 295 296 0 c 0 0 0 0 418 532 420 422 401 1036 135 1370 88 57 1514 1503 96 1370 727 341 492 520 0 g 0 0 0 0 370 349 324 290 256 176 85 117 65 69 18 17 40 77 130 216 302 340 0 t 0 0 0 0 428 392 569 628 773 238 152 107 1432 1468 59 66 1420 120 481 818 538 471 0
positions_6nt_m1_rc_shift7 (positions_6nt_m1_rc)				; positions_7nt_m1 versus positions_6nt_m1_rc; m=3/9; ncol2=16; w=0; offset=3; strand=R; shift=7; score=0.834212; -------yycACTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 355 290 235 1309 26 49 28 41 50 58 57 259 214 290 327 367 c 0 0 0 0 0 0 0 479 534 963 122 1429 67 57 1555 1557 110 1436 314 295 580 526 503 g 0 0 0 0 0 0 0 327 329 211 101 114 57 70 31 23 29 80 123 229 278 325 307 t 0 0 0 0 0 0 0 527 535 279 156 119 1515 1533 61 58 1491 115 992 950 540 510 511
positions_7nt_m2_shift4 (positions_7nt_m2)				; positions_7nt_m1 versus positions_7nt_m2; m=4/9; ncol2=18; w=0; offset=0; strand=D; shift=4; score=0.831332; ----wcttTCACTTCCCcttyy- ; cor=; Ncor= a 0 0 0 0 271 222 149 116 70 59 765 22 33 26 34 35 61 105 122 124 181 176 0 c 0 0 0 0 236 327 215 201 135 820 93 851 34 35 864 863 729 671 151 167 323 349 0 g 0 0 0 0 207 205 121 106 90 41 41 55 26 23 30 22 24 46 85 125 168 169 0 t 0 0 0 0 281 241 510 572 700 75 96 67 902 911 67 75 181 173 637 579 323 301 0
positions_7nt_m3_rc_shift7 (positions_7nt_m3_rc)				; positions_7nt_m1 versus positions_7nt_m3_rc; m=5/9; ncol2=16; w=0; offset=3; strand=R; shift=7; score=0.783954; -------yyygCTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 459 387 437 527 48 41 37 36 53 69 55 289 220 341 430 465 c 0 0 0 0 0 0 0 652 767 607 428 2057 81 75 2176 2166 105 2041 384 403 603 715 681 g 0 0 0 0 0 0 0 502 433 424 854 102 80 110 37 29 52 113 152 277 362 491 470 t 0 0 0 0 0 0 0 719 745 864 523 125 2130 2110 83 84 2106 123 1507 1432 1026 696 716
positions_7nt_m4_shift0 (positions_7nt_m4)				; positions_7nt_m1 versus positions_7nt_m4; m=6/9; ncol2=23; w=-4; offset=-4; strand=D; shift=0; score=0.734649; wwaaagaggaACTTCCTCtttyh ; cor=; Ncor= a 163 153 234 313 313 106 317 99 103 311 485 24 24 10 24 25 33 28 92 65 105 143 151 c 136 127 122 83 75 114 77 85 108 105 29 481 26 25 504 498 36 477 96 95 139 145 169 g 131 139 111 83 101 278 80 276 253 79 28 32 17 29 20 22 9 36 30 76 86 112 98 t 145 156 108 96 86 77 101 115 111 80 33 38 508 511 27 30 497 34 357 339 245 175 157
positions_6nt_m5_rc_shift8 (positions_6nt_m5_rc)				; positions_7nt_m1 versus positions_6nt_m5_rc; m=7/9; ncol2=15; w=0; offset=4; strand=R; shift=8; score=0.731398; --------yyasTTCCTCttyyy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 442 514 1095 213 40 31 47 59 40 62 353 261 413 480 526 c 0 0 0 0 0 0 0 0 705 754 406 816 56 42 2266 2296 73 2188 379 441 828 727 723 g 0 0 0 0 0 0 0 0 504 470 404 885 55 35 36 21 35 99 163 353 409 466 444 t 0 0 0 0 0 0 0 0 768 681 514 505 2268 2311 70 43 2271 70 1524 1364 769 746 726
positions_6nt_m2_shift7 (positions_6nt_m2)				; positions_7nt_m1 versus positions_6nt_m2; m=8/9; ncol2=17; w=0; offset=3; strand=D; shift=7; score=0.665439; -------yycACTTCCytcttyy ; cor=; Ncor= a 0 0 0 0 0 0 0 441 415 262 1733 33 62 36 57 37 227 286 287 271 282 294 418 c 0 0 0 0 0 0 0 544 588 1274 105 1809 80 62 1843 1830 1108 473 945 372 435 748 582 g 0 0 0 0 0 0 0 401 408 219 84 74 92 70 32 29 144 236 291 244 305 406 420 t 0 0 0 0 0 0 0 610 585 241 74 80 1762 1828 64 100 517 1001 473 1109 974 548 576
oligos_7nt_mkv5_m3_rc_shift9 (oligos_7nt_mkv5_m3_rc)				; positions_7nt_m1 versus oligos_7nt_mkv5_m3_rc; m=9/9; ncol2=13; w=0; offset=5; strand=R; shift=9; score=0.642276; ---------ywCTTCCTCTTyy- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 324 469 45 43 17 24 32 44 32 82 49 249 282 0 c 0 0 0 0 0 0 0 0 0 541 423 1453 61 48 1582 1583 110 1517 147 128 565 588 0 g 0 0 0 0 0 0 0 0 0 295 363 102 67 67 29 24 32 75 51 88 280 295 0 t 0 0 0 0 0 0 0 0 0 554 459 114 1543 1582 79 75 1528 90 1434 1449 620 549 0