One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.161408_2026-02-26.161408_KNDlH3/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/2026/02/26/peak-motifs.2026-02-26.161408_2026-02-26.161408_KNDlH3/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv5_m1_shift1 (oligos_8nt_mkv5_m1)
; oligos_8nt_mkv5_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -maACAAaAACaa ; Alignment reference a 0 198 246 542 3 528 519 375 509 501 10 316 307 c 0 167 103 10 543 11 21 137 19 23 536 79 70 g 0 67 119 9 8 23 12 21 19 10 5 60 69 t 0 140 104 11 18 10 20 39 25 38 21 117 126

oligos_8nt_mkv5_m1_shift1 (oligos_8nt_mkv5_m1)
; oligos_8nt_mkv5_m1 versus oligos_8nt_mkv5_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -maACAAaAACaa ; cor=; Ncor= a 0 198 246 542 3 528 519 375 509 501 10 316 307 c 0 167 103 10 543 11 21 137 19 23 536 79 70 g 0 67 119 9 8 23 12 21 19 10 5 60 69 t 0 140 104 11 18 10 20 39 25 38 21 117 126

oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)
; oligos_8nt_mkv5_m1 versus oligos_7nt_mkv4_m9; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.686379; --wwCAAAATCww ; cor=; Ncor= a 0 0 97 113 0 227 207 215 254 0 1 107 92 c 0 0 49 35 263 7 6 11 6 0 268 43 58 g 0 0 41 40 0 13 22 11 4 0 0 32 35 t 0 0 82 81 6 22 34 32 5 269 0 87 84

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_8nt_mkv5_m1 versus oligos_7nt_mkv4_m3; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.614515; waCACAAAACma- ; cor=; Ncor= a 122 135 53 306 5 297 303 304 297 12 128 154 0 c 51 67 234 8 302 9 15 5 7 266 85 62 0 g 68 49 22 5 7 6 3 4 11 20 38 36 0 t 84 74 16 6 11 13 4 12 10 27 74 73 0

oligos_6nt_mkv3_m10_shift2 (oligos_6nt_mkv3_m10)
; oligos_8nt_mkv5_m1 versus oligos_6nt_mkv3_m10; m=4/4; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.609377; --waCAACAATAa ; cor=; Ncor= a 0 0 213 239 51 517 509 19 510 512 17 460 222 c 0 0 96 96 415 1 12 480 9 3 79 15 70 g 0 0 96 77 19 11 12 8 5 17 9 22 130 t 0 0 135 128 55 11 7 33 16 8 435 43 118

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m6_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m6_shift1 (oligos_7nt_mkv4_m6)
; oligos_7nt_mkv4_m6; m=0 (reference); ncol1=12; shift=1; ncol=13; -whAACAATAGwa ; Alignment reference a 0 178 152 439 453 32 457 464 18 418 81 181 196 c 0 84 134 4 11 405 4 2 26 15 21 85 99 g 0 76 67 21 6 16 6 9 14 21 352 82 86 t 0 141 126 15 9 26 12 4 421 25 25 131 98

oligos_7nt_mkv4_m6_shift1 (oligos_7nt_mkv4_m6)
; oligos_7nt_mkv4_m6 versus oligos_7nt_mkv4_m6; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -whAACAATAGwa ; cor=; Ncor= a 0 178 152 439 453 32 457 464 18 418 81 181 196 c 0 84 134 4 11 405 4 2 26 15 21 85 99 g 0 76 67 21 6 16 6 9 14 21 352 82 86 t 0 141 126 15 9 26 12 4 421 25 25 131 98

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; oligos_7nt_mkv4_m6 versus oligos_6nt_mkv3_m10; m=2/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.780411; waCAACAATAaw- ; cor=; Ncor= a 213 239 51 517 509 19 510 512 17 460 222 169 0 c 96 96 415 1 12 480 9 3 79 15 70 127 0 g 96 77 19 11 12 8 5 17 9 22 130 91 0 t 135 128 55 11 7 33 16 8 435 43 118 153 0

positions_6nt_m5_shift1 (positions_6nt_m5)
; oligos_7nt_mkv4_m6 versus positions_6nt_m5; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.663837; -aaAAAAATwww- ; cor=; Ncor= a 0 386 388 800 800 800 800 800 0 299 241 263 0 c 0 103 105 0 0 0 0 0 0 93 115 149 0 g 0 155 172 0 0 0 0 0 0 118 128 115 0 t 0 156 135 0 0 0 0 0 800 290 316 273 0

positions_6nt_m8_shift2 (positions_6nt_m8)
; oligos_7nt_mkv4_m6 versus positions_6nt_m8; m=4/4; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.618464; --waATAATAaw- ; cor=; Ncor= a 0 0 115 170 314 0 314 314 0 314 159 91 0 c 0 0 56 33 0 0 0 0 0 0 47 39 0 g 0 0 31 48 0 0 0 0 0 0 48 43 0 t 0 0 112 63 0 314 0 0 314 0 60 141 0

One-to-n matrix alignment; reference matrix: positions_6nt_m9_shift1 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m9_shift1 (positions_6nt_m9)
; positions_6nt_m9; m=0 (reference); ncol1=11; shift=1; ncol=12; -tyCTCGTCAww ; Alignment reference a 0 112 113 67 11 18 17 11 19 391 230 172 c 0 73 132 348 15 435 10 8 444 13 70 105 g 0 77 72 50 21 14 443 12 8 10 57 65 t 0 225 170 22 440 20 17 456 16 73 130 145

positions_6nt_m9_shift1 (positions_6nt_m9)
; positions_6nt_m9 versus positions_6nt_m9; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -tyCTCGTCAww ; cor=; Ncor= a 0 112 113 67 11 18 17 11 19 391 230 172 c 0 73 132 348 15 435 10 8 444 13 70 105 g 0 77 72 50 21 14 443 12 8 10 57 65 t 0 225 170 22 440 20 17 456 16 73 130 145

positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)
; positions_6nt_m9 versus positions_6nt_m1_rc; m=2/7; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.769109; -tycTCGTCTAw ; cor=; Ncor= a 0 70 50 56 7 4 5 5 4 33 303 170 c 0 73 89 206 10 330 1 0 300 3 15 38 g 0 43 46 38 7 1 320 16 17 2 16 44 t 0 153 154 39 315 4 13 318 18 301 5 87

positions_7nt_m2_shift2 (positions_7nt_m2)
; positions_6nt_m9 versus positions_7nt_m2; m=3/7; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.766192; --yaTCGTCAAw ; cor=; Ncor= a 0 0 155 246 33 27 40 23 15 478 585 262 c 0 0 204 139 19 617 3 22 608 10 16 125 g 0 0 79 142 18 6 599 32 7 12 18 66 t 0 0 216 127 584 4 12 577 24 154 35 201

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_6nt_m9 versus positions_7nt_m1_rc; m=4/7; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.759307; -tymTCGTCTAw ; cor=; Ncor= a 0 106 104 137 10 11 13 16 21 59 454 216 c 0 105 145 205 25 502 2 4 447 7 26 73 g 0 75 58 85 10 1 482 29 32 11 24 71 t 0 234 213 93 475 6 23 471 20 443 16 160

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; positions_6nt_m9 versus oligos_6nt_mkv3_m1; m=5/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.671232; -tycTCGTCTAA ; cor=; Ncor= a 0 107 94 121 15 11 7 18 14 63 481 373 c 0 115 138 169 28 498 4 5 413 7 20 27 g 0 79 69 113 13 2 495 26 56 3 16 45 t 0 220 220 118 465 10 15 472 38 448 4 76

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_6nt_m9 versus positions_6nt_m4_rc; m=6/7; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.65039; wwtgTCGTCTAw ; cor=; Ncor= a 107 112 44 80 3 5 4 8 13 34 354 187 c 86 69 79 62 15 385 2 4 320 3 21 59 g 80 66 57 216 5 6 401 15 56 10 14 46 t 134 160 227 49 384 11 0 380 18 360 18 115

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; positions_6nt_m9 versus oligos_7nt_mkv4_m1; m=7/7; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.591173; --yyTCGTCTAA ; cor=; Ncor= a 0 0 71 108 2 5 3 11 11 58 419 375 c 0 0 117 111 17 420 3 2 326 7 5 13 g 0 0 51 102 9 2 415 15 58 1 8 19 t 0 0 196 114 407 8 14 407 40 369 3 28

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; acCACCACCAmm ; Alignment reference a 245 98 22 424 22 16 425 9 14 409 115 117 c 56 191 381 10 378 383 6 412 415 21 186 183 g 65 73 10 6 20 21 7 12 1 5 64 41 t 82 86 35 8 28 28 10 15 18 13 83 107

oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; acCACCACCAmm ; cor=; Ncor= a 245 98 22 424 22 16 425 9 14 409 115 117 c 56 191 381 10 378 383 6 412 415 21 186 183 g 65 73 10 6 20 21 7 12 1 5 64 41 t 82 86 35 8 28 28 10 15 18 13 83 107

One-to-n matrix alignment; reference matrix: positions_6nt_m8_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m8_shift2 (positions_6nt_m8)
; positions_6nt_m8; m=0 (reference); ncol1=10; shift=2; ncol=12; --waATAATAaw ; Alignment reference a 0 0 115 170 314 0 314 314 0 314 159 91 c 0 0 56 33 0 0 0 0 0 0 47 39 g 0 0 31 48 0 0 0 0 0 0 48 43 t 0 0 112 63 0 314 0 0 314 0 60 141

positions_6nt_m8_shift2 (positions_6nt_m8)
; positions_6nt_m8 versus positions_6nt_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --waATAATAaw ; cor=; Ncor= a 0 0 115 170 314 0 314 314 0 314 159 91 c 0 0 56 33 0 0 0 0 0 0 47 39 g 0 0 31 48 0 0 0 0 0 0 48 43 t 0 0 112 63 0 314 0 0 314 0 60 141

oligos_7nt_mkv4_m6_shift1 (oligos_7nt_mkv4_m6)
; positions_6nt_m8 versus oligos_7nt_mkv4_m6; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.618464; -whAACAATAGw ; cor=; Ncor= a 0 178 152 439 453 32 457 464 18 418 81 181 c 0 84 134 4 11 405 4 2 26 15 21 85 g 0 76 67 21 6 16 6 9 14 21 352 82 t 0 141 126 15 9 26 12 4 421 25 25 131

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; positions_6nt_m8 versus oligos_6nt_mkv3_m10; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.604189; waCAACAATAaw ; cor=; Ncor= a 213 239 51 517 509 19 510 512 17 460 222 169 c 96 96 415 1 12 480 9 3 79 15 70 127 g 96 77 19 11 12 8 5 17 9 22 130 91 t 135 128 55 11 7 33 16 8 435 43 118 153

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=11; shift=0; ncol=11; yaCACrCACam ; Alignment reference a 95 176 5 378 20 106 13 374 19 190 101 c 127 76 363 5 347 33 352 9 347 61 144 g 53 55 14 2 7 212 4 3 9 57 58 t 115 83 8 5 16 39 21 4 15 82 87

oligos_6nt_mkv3_m7_shift0 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; yaCACrCACam ; cor=; Ncor= a 95 176 5 378 20 106 13 374 19 190 101 c 127 76 363 5 347 33 352 9 347 61 144 g 53 55 14 2 7 212 4 3 9 57 58 t 115 83 8 5 16 39 21 4 15 82 87

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=13; shift=0; ncol=13; wywTACATAcAha ; Alignment reference a 169 99 163 16 384 9 382 11 385 43 284 104 193 c 56 107 44 17 8 328 10 24 2 260 27 103 52 g 63 42 66 4 11 8 3 8 12 24 30 76 63 t 122 162 137 373 7 65 15 367 11 83 69 127 102

oligos_6nt_mkv3_m8_shift0 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wywTACATAcAha ; cor=; Ncor= a 169 99 163 16 384 9 382 11 385 43 284 104 193 c 56 107 44 17 8 328 10 24 2 260 27 103 52 g 63 42 66 4 11 8 3 8 12 24 30 76 63 t 122 162 137 373 7 65 15 367 11 83 69 127 102

oligos_6nt_mkv3_m9_rc_shift1 (oligos_6nt_mkv3_m9_rc)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m9_rc; m=2/2; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.556927; -hhTGCATAtw-- ; cor=; Ncor= a 0 48 48 19 4 0 174 0 179 40 85 0 0 c 0 59 55 4 0 177 0 0 0 29 17 0 0 g 0 19 17 4 175 0 5 3 0 20 20 0 0 t 0 53 59 152 0 2 0 176 0 90 57 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wawAAATATww ; Alignment reference a 0 211 280 190 539 404 542 0 544 0 234 153 c 0 61 81 59 0 12 1 0 0 0 52 80 g 0 98 115 83 1 7 0 0 0 0 77 74 t 0 174 68 212 4 121 1 544 0 544 181 237

positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wawAAATATww ; cor=; Ncor= a 0 211 280 190 539 404 542 0 544 0 234 153 c 0 61 81 59 0 12 1 0 0 0 52 80 g 0 98 115 83 1 7 0 0 0 0 77 74 t 0 174 68 212 4 121 1 544 0 544 181 237

positions_6nt_m7_shift1 (positions_6nt_m7)
; positions_6nt_m3 versus positions_6nt_m7; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.716412; -wwaAACTATwa ; cor=; Ncor= a 0 115 87 184 215 235 0 0 270 3 109 102 c 0 44 42 33 13 5 271 1 3 1 52 45 g 0 43 53 16 8 12 0 9 0 9 35 62 t 0 71 91 40 37 21 2 263 0 260 77 64

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m3 versus positions_6nt_m5; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.635241; aaAAAAATwww- ; cor=; Ncor= a 386 388 800 800 800 800 800 0 299 241 263 0 c 103 105 0 0 0 0 0 0 93 115 149 0 g 155 172 0 0 0 0 0 0 118 128 115 0 t 156 135 0 0 0 0 0 800 290 316 273 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift1 ; 13 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=12; shift=1; ncol=13; -wwTAGACGAgra ; Alignment reference a 0 140 87 5 301 18 318 13 4 315 39 154 153 c 0 55 44 16 2 17 16 320 1 7 38 46 43 g 0 42 38 15 3 300 0 1 330 10 206 89 73 t 0 102 170 303 33 4 5 5 4 7 56 50 70

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/12; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -wwTAGACGAgra ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 153 c 0 55 44 16 2 17 16 320 1 7 38 46 43 g 0 42 38 15 3 300 0 1 330 10 206 89 73 t 0 102 170 303 33 4 5 5 4 7 56 50 70

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=2/12; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.99169; -wwTAGACGAkra ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 234 c 0 88 71 24 11 32 29 482 1 10 85 58 75 g 0 69 73 26 7 447 4 2 502 25 205 145 105 t 0 147 216 454 59 21 16 13 11 10 137 104 106

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m1_rc; m=3/12; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.903262; wwTTAGACGAgra ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 220 c 68 70 45 16 3 56 26 495 2 13 113 69 79 g 93 79 27 20 7 413 5 4 498 28 169 138 115 t 153 176 373 481 63 14 18 7 11 15 121 94 107

positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_6nt_m1 versus positions_6nt_m4; m=4/12; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.878611; -wwTAGACGAcaw ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 160 c 0 52 46 14 10 56 15 401 6 5 216 57 66 g 0 61 59 21 3 320 4 2 385 15 62 79 69 t 0 122 187 354 34 13 8 4 5 3 80 44 112

oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; positions_6nt_m1 versus oligos_7nt_mkv4_m10; m=5/12; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.82233; -wtTAGmCGAwa- ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 0 c 0 65 69 1 6 25 281 431 5 7 78 64 0 g 0 48 67 8 6 371 5 3 424 10 108 110 0 t 0 158 211 429 33 25 18 10 5 7 141 91 0

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; positions_6nt_m1 versus oligos_7nt_mkv4_m1_rc; m=6/12; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.810295; wwTTAGACGArr- ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 0 c 46 62 19 8 1 58 15 415 2 9 102 51 0 g 66 64 13 5 7 326 2 3 420 17 111 117 0 t 138 157 375 419 58 11 11 3 5 2 108 71 0

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; positions_6nt_m1 versus positions_7nt_m2_rc; m=7/12; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.799622; -wwTTGACGAtr- ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 0 c 0 105 66 18 12 7 32 599 6 18 142 79 0 g 0 106 125 16 10 608 22 3 617 19 139 204 0 t 0 219 262 585 478 15 23 40 27 33 246 155 0

positions_6nt_m9_rc_shift2 (positions_6nt_m9_rc)
; positions_6nt_m1 versus positions_6nt_m9_rc; m=8/12; ncol2=11; w=0; offset=1; strand=R; shift=2; score=0.769109; --wwTGACGAGra ; cor=; Ncor= a 0 0 145 130 73 16 456 17 20 440 22 170 225 c 0 0 65 57 10 8 12 443 14 21 50 72 77 g 0 0 105 70 13 444 8 10 435 15 348 132 73 t 0 0 172 230 391 19 11 17 18 11 67 113 112

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; positions_6nt_m1 versus oligos_7nt_mkv4_m4; m=9/12; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.744405; wwTTAaACGAwr- ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 0 c 61 76 33 5 3 66 22 463 5 2 106 64 0 g 95 80 17 16 8 116 11 4 463 13 106 126 0 t 147 166 399 472 18 24 14 27 20 3 148 102 0

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m3_rc; m=10/12; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.684194; waTTArACGAd-- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 0 c 41 68 25 0 2 39 10 369 0 24 69 0 0 g 62 49 18 2 1 110 14 0 368 51 99 0 0 t 102 88 287 364 7 20 21 0 1 42 101 0 0

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; positions_6nt_m1 versus oligos_7nt_mkv4_m2; m=11/12; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.652872; wwtTACACGACcw ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 123 c 54 39 26 17 10 258 4 300 13 11 213 173 65 g 61 37 41 16 10 27 10 2 262 7 31 29 44 t 88 130 189 264 8 13 8 4 22 15 27 38 81

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m2_rc; m=12/12; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.606997; -wwTACACGACAt ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 69 c 0 45 47 27 15 243 8 305 7 8 231 50 52 g 0 43 73 20 10 38 9 7 282 8 26 7 21 t 0 108 117 227 10 17 9 2 14 9 24 29 175

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m7_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m7_shift1 (oligos_7nt_mkv4_m7)
; oligos_7nt_mkv4_m7; m=0 (reference); ncol1=11; shift=1; ncol=12; -aaAAGAAAAaa ; Alignment reference a 0 220 210 457 467 0 468 449 451 467 271 253 c 0 91 94 0 1 0 0 2 0 0 42 48 g 0 93 101 1 0 468 0 4 0 1 59 80 t 0 64 63 10 0 0 0 13 17 0 96 87

oligos_7nt_mkv4_m7_shift1 (oligos_7nt_mkv4_m7)
; oligos_7nt_mkv4_m7 versus oligos_7nt_mkv4_m7; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -aaAAGAAAAaa ; cor=; Ncor= a 0 220 210 457 467 0 468 449 451 467 271 253 c 0 91 94 0 1 0 0 2 0 0 42 48 g 0 93 101 1 0 468 0 4 0 1 59 80 t 0 64 63 10 0 0 0 13 17 0 96 87

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m7 versus oligos_6nt_mkv3_m5; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.807946; aaaAAGAAAaa- ; cor=; Ncor= a 379 339 340 758 757 0 759 751 757 394 405 0 c 80 147 162 0 5 0 1 0 0 79 77 0 g 176 160 180 1 0 763 0 2 0 139 110 0 t 128 117 81 4 1 0 3 10 6 151 171 0

positions_6nt_m5_shift4 (positions_6nt_m5)
; oligos_7nt_mkv4_m7 versus positions_6nt_m5; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.417361; ----aaAAAAAT ; cor=; Ncor= a 0 0 0 0 386 388 800 800 800 800 800 0 c 0 0 0 0 103 105 0 0 0 0 0 0 g 0 0 0 0 155 172 0 0 0 0 0 0 t 0 0 0 0 156 135 0 0 0 0 0 800

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m8_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m8_shift0 (oligos_7nt_mkv4_m8)
; oligos_7nt_mkv4_m8; m=0 (reference); ncol1=13; shift=0; ncol=13; ywaTATGCAGGwt ; Alignment reference a 29 49 66 2 119 3 10 4 127 7 10 58 33 c 38 15 14 3 0 1 0 123 3 2 0 18 33 g 27 13 24 9 9 0 124 3 2 114 107 17 20 t 41 58 31 121 7 131 1 5 3 12 18 42 49

oligos_7nt_mkv4_m8_shift0 (oligos_7nt_mkv4_m8)
; oligos_7nt_mkv4_m8 versus oligos_7nt_mkv4_m8; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ywaTATGCAGGwt ; cor=; Ncor= a 29 49 66 2 119 3 10 4 127 7 10 58 33 c 38 15 14 3 0 1 0 123 3 2 0 18 33 g 27 13 24 9 9 0 124 3 2 114 107 17 20 t 41 58 31 121 7 131 1 5 3 12 18 42 49

oligos_8nt_mkv5_m2_rc_shift1 (oligos_8nt_mkv5_m2_rc)
; oligos_7nt_mkv4_m8 versus oligos_8nt_mkv5_m2_rc; m=2/3; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.922814; -waTATGCAGGww ; cor=; Ncor= a 0 49 62 2 115 3 8 4 125 7 10 56 33 c 0 15 14 3 0 1 0 121 3 2 0 18 31 g 0 13 24 7 9 0 122 3 2 110 103 15 18 t 0 54 31 119 7 127 1 3 1 12 18 42 49

oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)
; oligos_7nt_mkv4_m8 versus oligos_6nt_mkv3_m9; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.703998; -waTATGCAdd-- ; cor=; Ncor= a 0 57 90 0 176 0 2 0 152 59 53 0 0 c 0 20 20 0 3 5 0 175 4 17 19 0 0 g 0 17 29 0 0 0 177 0 4 55 59 0 0 t 0 85 40 179 0 174 0 4 19 48 48 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift4 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----yyTCGTCTAAww ; Alignment reference a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 138 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 66 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 46 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152 185

oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/12; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----yyTCGTCTAAww ; cor=; Ncor= a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 138 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 66 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 46 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152 185

oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=2/12; ncol2=12; w=0; offset=0; strand=R; shift=4; score=0.939175; ----ywTCGTtTAAww ; cor=; Ncor= a 0 0 0 0 102 148 3 20 27 14 24 18 472 399 166 147 c 0 0 0 0 126 106 13 463 4 11 116 8 16 17 80 95 g 0 0 0 0 64 106 2 5 463 22 66 3 5 33 76 61 t 0 0 0 0 211 143 485 15 9 456 297 474 10 54 181 200

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/12; ncol2=13; w=-1; offset=-1; strand=D; shift=3; score=0.918664; ---tycTCGTCTAAww ; cor=; Ncor= a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 153 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 93 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 68 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196 207

oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m3; m=4/12; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.859026; -----hTCGTyTAAtw ; cor=; Ncor= a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 102 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 62 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 41 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164 164

oligos_7nt_mkv4_m10_rc_shift4 (oligos_7nt_mkv4_m10_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m10_rc; m=5/12; ncol2=11; w=0; offset=0; strand=R; shift=4; score=0.818909; ----twTCGkCTAaw- ; cor=; Ncor= a 0 0 0 0 91 141 7 5 10 18 25 33 429 211 158 0 c 0 0 0 0 110 108 10 424 3 5 371 6 8 67 48 0 g 0 0 0 0 64 78 7 5 431 281 25 6 1 69 65 0 t 0 0 0 0 193 131 434 24 14 154 37 413 20 111 187 0

positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)
; oligos_7nt_mkv4_m1 versus positions_7nt_m1_rc; m=6/12; ncol2=12; w=-1; offset=-1; strand=R; shift=3; score=0.813321; ---tymTCGTCTAww- ; cor=; Ncor= a 0 0 0 106 104 137 10 11 13 16 21 59 454 216 147 0 c 0 0 0 105 145 205 25 502 2 4 447 7 26 73 69 0 g 0 0 0 75 58 85 10 1 482 29 32 11 24 71 88 0 t 0 0 0 234 213 93 475 6 23 471 20 443 16 160 216 0

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; oligos_7nt_mkv4_m1 versus positions_6nt_m1_rc; m=7/12; ncol2=12; w=-1; offset=-1; strand=R; shift=3; score=0.810295; ---tycTCGTCTAww- ; cor=; Ncor= a 0 0 0 70 50 56 7 4 5 5 4 33 303 170 102 0 c 0 0 0 73 89 206 10 330 1 0 300 3 15 38 42 0 g 0 0 0 43 46 38 7 1 320 16 17 2 16 44 55 0 t 0 0 0 153 154 39 315 4 13 318 18 301 5 87 140 0

positions_7nt_m2_shift4 (positions_7nt_m2)
; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=8/12; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.79793; ----yaTCGTCAAww- ; cor=; Ncor= a 0 0 0 0 155 246 33 27 40 23 15 478 585 262 219 0 c 0 0 0 0 204 139 19 617 3 22 608 10 16 125 106 0 g 0 0 0 0 79 142 18 6 599 32 7 12 18 66 105 0 t 0 0 0 0 216 127 584 4 12 577 24 154 35 201 224 0

positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)
; oligos_7nt_mkv4_m1 versus positions_6nt_m4_rc; m=9/12; ncol2=13; w=-2; offset=-2; strand=R; shift=2; score=0.751581; --wwtgTCGTCTAww- ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 34 354 187 122 0 c 0 0 86 69 79 62 15 385 2 4 320 3 21 59 61 0 g 0 0 80 66 57 216 5 6 401 15 56 10 14 46 52 0 t 0 0 134 160 227 49 384 11 0 380 18 360 18 115 172 0

oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2_rc; m=10/12; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.706169; --wwgGTCGTGTAaww ; cor=; Ncor= a 0 0 90 81 38 27 15 22 4 8 13 8 264 189 130 88 c 0 0 60 44 29 31 7 262 2 10 27 10 16 41 37 61 g 0 0 64 65 173 213 11 13 300 4 258 10 17 26 39 54 t 0 0 99 123 73 42 280 16 7 291 15 285 16 57 107 110

positions_6nt_m9_shift3 (positions_6nt_m9)
; oligos_7nt_mkv4_m1 versus positions_6nt_m9; m=11/12; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.591173; ---tyCTCGTCAww-- ; cor=; Ncor= a 0 0 0 112 113 67 11 18 17 11 19 391 230 172 0 0 c 0 0 0 73 132 348 15 435 10 8 444 13 70 105 0 0 g 0 0 0 77 72 50 21 14 443 12 8 10 57 65 0 0 t 0 0 0 225 170 22 440 20 17 456 16 73 130 145 0 0

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m2; m=12/12; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.557701; wwwaTGTCGTGTAww- ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 0 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 0 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 0 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift1 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTAGACGAkra ; Alignment reference a 0 216 160 16 443 20 471 23 6 475 93 213 234 c 0 88 71 24 11 32 29 482 1 10 85 58 75 g 0 69 73 26 7 447 4 2 502 25 205 145 105 t 0 147 216 454 59 21 16 13 11 10 137 104 106

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/12; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -wwTAGACGAkra ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 234 c 0 88 71 24 11 32 29 482 1 10 85 58 75 g 0 69 73 26 7 447 4 2 502 25 205 145 105 t 0 147 216 454 59 21 16 13 11 10 137 104 106

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=2/12; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.99169; -wwTAGACGAgra ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 153 c 0 55 44 16 2 17 16 320 1 7 38 46 43 g 0 42 38 15 3 300 0 1 330 10 206 89 73 t 0 102 170 303 33 4 5 5 4 7 56 50 70

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; positions_7nt_m1 versus oligos_6nt_mkv3_m1_rc; m=3/12; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.906115; wwTTAGACGAgra ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 220 c 68 70 45 16 3 56 26 495 2 13 113 69 79 g 93 79 27 20 7 413 5 4 498 28 169 138 115 t 153 176 373 481 63 14 18 7 11 15 121 94 107

positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_7nt_m1 versus positions_6nt_m4; m=4/12; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.89404; -wwTAGACGAcaw ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 160 c 0 52 46 14 10 56 15 401 6 5 216 57 66 g 0 61 59 21 3 320 4 2 385 15 62 79 69 t 0 122 187 354 34 13 8 4 5 3 80 44 112

oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; positions_7nt_m1 versus oligos_7nt_mkv4_m10; m=5/12; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.836417; -wtTAGmCGAwa- ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 0 c 0 65 69 1 6 25 281 431 5 7 78 64 0 g 0 48 67 8 6 371 5 3 424 10 108 110 0 t 0 158 211 429 33 25 18 10 5 7 141 91 0

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; positions_7nt_m1 versus positions_7nt_m2_rc; m=6/12; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.821006; -wwTTGACGAtr- ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 0 c 0 105 66 18 12 7 32 599 6 18 142 79 0 g 0 106 125 16 10 608 22 3 617 19 139 204 0 t 0 219 262 585 478 15 23 40 27 33 246 155 0

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; positions_7nt_m1 versus oligos_7nt_mkv4_m1_rc; m=7/12; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.813321; wwTTAGACGArr- ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 0 c 46 62 19 8 1 58 15 415 2 9 102 51 0 g 66 64 13 5 7 326 2 3 420 17 111 117 0 t 138 157 375 419 58 11 11 3 5 2 108 71 0

positions_6nt_m9_rc_shift2 (positions_6nt_m9_rc)
; positions_7nt_m1 versus positions_6nt_m9_rc; m=8/12; ncol2=11; w=0; offset=1; strand=R; shift=2; score=0.759307; --wwTGACGAGra ; cor=; Ncor= a 0 0 145 130 73 16 456 17 20 440 22 170 225 c 0 0 65 57 10 8 12 443 14 21 50 72 77 g 0 0 105 70 13 444 8 10 435 15 348 132 73 t 0 0 172 230 391 19 11 17 18 11 67 113 112

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; positions_7nt_m1 versus oligos_7nt_mkv4_m4; m=9/12; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.74836; wwTTAaACGAwr- ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 0 c 61 76 33 5 3 66 22 463 5 2 106 64 0 g 95 80 17 16 8 116 11 4 463 13 106 126 0 t 147 166 399 472 18 24 14 27 20 3 148 102 0

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; positions_7nt_m1 versus oligos_6nt_mkv3_m3_rc; m=10/12; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.685715; waTTArACGAd-- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 0 c 41 68 25 0 2 39 10 369 0 24 69 0 0 g 62 49 18 2 1 110 14 0 368 51 99 0 0 t 102 88 287 364 7 20 21 0 1 42 101 0 0

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; positions_7nt_m1 versus oligos_7nt_mkv4_m2; m=11/12; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.662223; wwtTACACGACcw ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 123 c 54 39 26 17 10 258 4 300 13 11 213 173 65 g 61 37 41 16 10 27 10 2 262 7 31 29 44 t 88 130 189 264 8 13 8 4 22 15 27 38 81

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; positions_7nt_m1 versus oligos_6nt_mkv3_m2_rc; m=12/12; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.619292; -wwTACACGACAt ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 69 c 0 45 47 27 15 243 8 305 7 8 231 50 52 g 0 43 73 20 10 38 9 7 282 8 26 7 21 t 0 108 117 227 10 17 9 2 14 9 24 29 175

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift3 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=13; shift=3; ncol=16; ---tycTCGTCTAAww ; Alignment reference a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 153 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 93 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 68 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196 207

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/12; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---tycTCGTCTAAww ; cor=; Ncor= a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 153 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 93 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 68 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196 207

oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/12; ncol2=12; w=0; offset=1; strand=D; shift=4; score=0.918664; ----yyTCGTCTAAww ; cor=; Ncor= a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 138 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 66 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 46 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152 185

positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)
; oligos_6nt_mkv3_m1 versus positions_7nt_m1_rc; m=3/12; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.906115; ---tymTCGTCTAww- ; cor=; Ncor= a 0 0 0 106 104 137 10 11 13 16 21 59 454 216 147 0 c 0 0 0 105 145 205 25 502 2 4 447 7 26 73 69 0 g 0 0 0 75 58 85 10 1 482 29 32 11 24 71 88 0 t 0 0 0 234 213 93 475 6 23 471 20 443 16 160 216 0

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=4/12; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.903262; ---tycTCGTCTAww- ; cor=; Ncor= a 0 0 0 70 50 56 7 4 5 5 4 33 303 170 102 0 c 0 0 0 73 89 206 10 330 1 0 300 3 15 38 42 0 g 0 0 0 43 46 38 7 1 320 16 17 2 16 44 55 0 t 0 0 0 153 154 39 315 4 13 318 18 301 5 87 140 0

oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4_rc; m=5/12; ncol2=12; w=0; offset=1; strand=R; shift=4; score=0.855959; ----ywTCGTtTAAww ; cor=; Ncor= a 0 0 0 0 102 148 3 20 27 14 24 18 472 399 166 147 c 0 0 0 0 126 106 13 463 4 11 116 8 16 17 80 95 g 0 0 0 0 64 106 2 5 463 22 66 3 5 33 76 61 t 0 0 0 0 211 143 485 15 9 456 297 474 10 54 181 200

positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)
; oligos_6nt_mkv3_m1 versus positions_6nt_m4_rc; m=6/12; ncol2=13; w=-1; offset=-1; strand=R; shift=2; score=0.82907; --wwtgTCGTCTAww- ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 34 354 187 122 0 c 0 0 86 69 79 62 15 385 2 4 320 3 21 59 61 0 g 0 0 80 66 57 216 5 6 401 15 56 10 14 46 52 0 t 0 0 134 160 227 49 384 11 0 380 18 360 18 115 172 0

oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3; m=7/12; ncol2=11; w=0; offset=2; strand=D; shift=5; score=0.787939; -----hTCGTyTAAtw ; cor=; Ncor= a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 102 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 62 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 41 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164 164

oligos_7nt_mkv4_m10_rc_shift4 (oligos_7nt_mkv4_m10_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m10_rc; m=8/12; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.768354; ----twTCGkCTAaw- ; cor=; Ncor= a 0 0 0 0 91 141 7 5 10 18 25 33 429 211 158 0 c 0 0 0 0 110 108 10 424 3 5 371 6 8 67 48 0 g 0 0 0 0 64 78 7 5 431 281 25 6 1 69 65 0 t 0 0 0 0 193 131 434 24 14 154 37 413 20 111 187 0

oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2_rc; m=9/12; ncol2=14; w=-1; offset=-1; strand=R; shift=2; score=0.756876; --wwgGTCGTGTAaww ; cor=; Ncor= a 0 0 90 81 38 27 15 22 4 8 13 8 264 189 130 88 c 0 0 60 44 29 31 7 262 2 10 27 10 16 41 37 61 g 0 0 64 65 173 213 11 13 300 4 258 10 17 26 39 54 t 0 0 99 123 73 42 280 16 7 291 15 285 16 57 107 110

positions_7nt_m2_shift4 (positions_7nt_m2)
; oligos_6nt_mkv3_m1 versus positions_7nt_m2; m=10/12; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.745444; ----yaTCGTCAAww- ; cor=; Ncor= a 0 0 0 0 155 246 33 27 40 23 15 478 585 262 219 0 c 0 0 0 0 204 139 19 617 3 22 608 10 16 125 106 0 g 0 0 0 0 79 142 18 6 599 32 7 12 18 66 105 0 t 0 0 0 0 216 127 584 4 12 577 24 154 35 201 224 0

positions_6nt_m9_shift3 (positions_6nt_m9)
; oligos_6nt_mkv3_m1 versus positions_6nt_m9; m=11/12; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.671232; ---tyCTCGTCAww-- ; cor=; Ncor= a 0 0 0 112 113 67 11 18 17 11 19 391 230 172 0 0 c 0 0 0 73 132 348 15 435 10 8 444 13 70 105 0 0 g 0 0 0 77 72 50 21 14 443 12 8 10 57 65 0 0 t 0 0 0 225 170 22 440 20 17 456 16 73 130 145 0 0

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m2; m=12/12; ncol2=15; w=-3; offset=-3; strand=D; shift=0; score=0.59339; wwwaTGTCGTGTAww- ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 0 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 0 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 0 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift1 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -wwTAGACGAcaww ; Alignment reference a 0 172 115 18 360 18 380 0 11 384 49 227 160 134 c 0 52 46 14 10 56 15 401 6 5 216 57 66 80 g 0 61 59 21 3 320 4 2 385 15 62 79 69 86 t 0 122 187 354 34 13 8 4 5 3 80 44 112 107

positions_6nt_m4_shift1 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/13; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -wwTAGACGAcaww ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 160 134 c 0 52 46 14 10 56 15 401 6 5 216 57 66 80 g 0 61 59 21 3 320 4 2 385 15 62 79 69 86 t 0 122 187 354 34 13 8 4 5 3 80 44 112 107

positions_7nt_m1_shift1 (positions_7nt_m1)
; positions_6nt_m4 versus positions_7nt_m1; m=2/13; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.89404; -wwTAGACGAkra- ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 234 0 c 0 88 71 24 11 32 29 482 1 10 85 58 75 0 g 0 69 73 26 7 447 4 2 502 25 205 145 105 0 t 0 147 216 454 59 21 16 13 11 10 137 104 106 0

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m4 versus positions_6nt_m1; m=3/13; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.878611; -wwTAGACGAgra- ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 153 0 c 0 55 44 16 2 17 16 320 1 7 38 46 43 0 g 0 42 38 15 3 300 0 1 330 10 206 89 73 0 t 0 102 170 303 33 4 5 5 4 7 56 50 70 0

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; positions_6nt_m4 versus oligos_6nt_mkv3_m1_rc; m=4/13; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.82907; wwTTAGACGAgra- ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 220 0 c 68 70 45 16 3 56 26 495 2 13 113 69 79 0 g 93 79 27 20 7 413 5 4 498 28 169 138 115 0 t 153 176 373 481 63 14 18 7 11 15 121 94 107 0

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; positions_6nt_m4 versus oligos_7nt_mkv4_m2; m=5/13; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.786225; wwtTACACGACcww ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 123 99 c 54 39 26 17 10 258 4 300 13 11 213 173 65 64 g 61 37 41 16 10 27 10 2 262 7 31 29 44 60 t 88 130 189 264 8 13 8 4 22 15 27 38 81 90

oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; positions_6nt_m4 versus oligos_7nt_mkv4_m10; m=6/13; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.754282; -wtTAGmCGAwa-- ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 0 0 c 0 65 69 1 6 25 281 431 5 7 78 64 0 0 g 0 48 67 8 6 371 5 3 424 10 108 110 0 0 t 0 158 211 429 33 25 18 10 5 7 141 91 0 0

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; positions_6nt_m4 versus oligos_6nt_mkv3_m2_rc; m=7/13; ncol2=15; w=0; offset=0; strand=R; shift=1; score= 0.7539; -wwTACACGACAtw ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 69 82 c 0 45 47 27 15 243 8 305 7 8 231 50 52 57 g 0 43 73 20 10 38 9 7 282 8 26 7 21 55 t 0 108 117 227 10 17 9 2 14 9 24 29 175 123

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; positions_6nt_m4 versus oligos_7nt_mkv4_m1_rc; m=8/13; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.751581; wwTTAGACGArr-- ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 0 0 c 46 62 19 8 1 58 15 415 2 9 102 51 0 0 g 66 64 13 5 7 326 2 3 420 17 111 117 0 0 t 138 157 375 419 58 11 11 3 5 2 108 71 0 0

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; positions_6nt_m4 versus positions_7nt_m2_rc; m=9/13; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.733261; -wwTTGACGAtr-- ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 0 0 c 0 105 66 18 12 7 32 599 6 18 142 79 0 0 g 0 106 125 16 10 608 22 3 617 19 139 204 0 0 t 0 219 262 585 478 15 23 40 27 33 246 155 0 0

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; positions_6nt_m4 versus oligos_7nt_mkv4_m4; m=10/13; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.699844; wwTTAaACGAwr-- ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 0 0 c 61 76 33 5 3 66 22 463 5 2 106 64 0 0 g 95 80 17 16 8 116 11 4 463 13 106 126 0 0 t 147 166 399 472 18 24 14 27 20 3 148 102 0 0

positions_6nt_m9_rc_shift2 (positions_6nt_m9_rc)
; positions_6nt_m4 versus positions_6nt_m9_rc; m=11/13; ncol2=11; w=0; offset=1; strand=R; shift=2; score=0.65039; --wwTGACGAGra- ; cor=; Ncor= a 0 0 145 130 73 16 456 17 20 440 22 170 225 0 c 0 0 65 57 10 8 12 443 14 21 50 72 77 0 g 0 0 105 70 13 444 8 10 435 15 348 132 73 0 t 0 0 172 230 391 19 11 17 18 11 67 113 112 0

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; positions_6nt_m4 versus oligos_6nt_mkv3_m3_rc; m=12/13; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.636814; waTTArACGAd--- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 0 0 c 41 68 25 0 2 39 10 369 0 24 69 0 0 0 g 62 49 18 2 1 110 14 0 368 51 99 0 0 0 t 102 88 287 364 7 20 21 0 1 42 101 0 0 0

oligos_7nt_mkv4_m5_rc_shift5 (oligos_7nt_mkv4_m5_rc)
; positions_6nt_m4 versus oligos_7nt_mkv4_m5_rc; m=13/13; ncol2=11; w=0; offset=4; strand=R; shift=5; score=0.421897; -----baCGACATT ; cor=; Ncor= a 0 0 0 0 0 98 182 16 14 377 11 403 34 17 c 0 0 0 0 0 111 85 402 10 8 384 15 13 22 g 0 0 0 0 0 113 83 5 378 21 26 4 12 12 t 0 0 0 0 0 116 88 15 36 32 17 16 379 387

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; waCACAAAACma ; Alignment reference a 122 135 53 306 5 297 303 304 297 12 128 154 c 51 67 234 8 302 9 15 5 7 266 85 62 g 68 49 22 5 7 6 3 4 11 20 38 36 t 84 74 16 6 11 13 4 12 10 27 74 73

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; waCACAAAACma ; cor=; Ncor= a 122 135 53 306 5 297 303 304 297 12 128 154 c 51 67 234 8 302 9 15 5 7 266 85 62 g 68 49 22 5 7 6 3 4 11 20 38 36 t 84 74 16 6 11 13 4 12 10 27 74 73

oligos_8nt_mkv5_m1_shift1 (oligos_8nt_mkv5_m1)
; oligos_7nt_mkv4_m3 versus oligos_8nt_mkv5_m1; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.614515; -maACAAaAACa ; cor=; Ncor= a 0 198 246 542 3 528 519 375 509 501 10 316 c 0 167 103 10 543 11 21 137 19 23 536 79 g 0 67 119 9 8 23 12 21 19 10 5 60 t 0 140 104 11 18 10 20 39 25 38 21 117

One-to-n matrix alignment; reference matrix: positions_6nt_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m7_shift0 (positions_6nt_m7)
; positions_6nt_m7; m=0 (reference); ncol1=11; shift=0; ncol=11; wwaAACTATwa ; Alignment reference a 115 87 184 215 235 0 0 270 3 109 102 c 44 42 33 13 5 271 1 3 1 52 45 g 43 53 16 8 12 0 9 0 9 35 62 t 71 91 40 37 21 2 263 0 260 77 64

positions_6nt_m7_shift0 (positions_6nt_m7)
; positions_6nt_m7 versus positions_6nt_m7; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwaAACTATwa ; cor=; Ncor= a 115 87 184 215 235 0 0 270 3 109 102 c 44 42 33 13 5 271 1 3 1 52 45 g 43 53 16 8 12 0 9 0 9 35 62 t 71 91 40 37 21 2 263 0 260 77 64

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m7 versus positions_6nt_m3; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.716412; wawAAATATww ; cor=; Ncor= a 211 280 190 539 404 542 0 544 0 234 153 c 61 81 59 0 12 1 0 0 0 52 80 g 98 115 83 1 7 0 0 0 0 77 74 t 174 68 212 4 121 1 544 0 544 181 237

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; wwtTACACGACcww ; Alignment reference a 110 107 57 16 285 15 291 7 16 280 42 73 123 99 c 54 39 26 17 10 258 4 300 13 11 213 173 65 64 g 61 37 41 16 10 27 10 2 262 7 31 29 44 60 t 88 130 189 264 8 13 8 4 22 15 27 38 81 90

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wwtTACACGACcww ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 123 99 c 54 39 26 17 10 258 4 300 13 11 213 173 65 64 g 61 37 41 16 10 27 10 2 262 7 31 29 44 60 t 88 130 189 264 8 13 8 4 22 15 27 38 81 90

positions_6nt_m4_shift1 (positions_6nt_m4)
; oligos_7nt_mkv4_m2 versus positions_6nt_m4; m=2/10; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.786225; -wwTAGACGAcaww ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 160 134 c 0 52 46 14 10 56 15 401 6 5 216 57 66 80 g 0 61 59 21 3 320 4 2 385 15 62 79 69 86 t 0 122 187 354 34 13 8 4 5 3 80 44 112 107

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1_rc; m=3/10; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.756876; wwTTAGACGAgra- ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 220 0 c 68 70 45 16 3 56 26 495 2 13 113 69 79 0 g 93 79 27 20 7 413 5 4 498 28 169 138 115 0 t 153 176 373 481 63 14 18 7 11 15 121 94 107 0

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2_rc; m=4/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.751862; -wwTACACGACAtw ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 69 82 c 0 45 47 27 15 243 8 305 7 8 231 50 52 57 g 0 43 73 20 10 38 9 7 282 8 26 7 21 55 t 0 108 117 227 10 17 9 2 14 9 24 29 175 123

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m4; m=5/10; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.717489; wwTTAaACGAwr-- ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 0 0 c 61 76 33 5 3 66 22 463 5 2 106 64 0 0 g 95 80 17 16 8 116 11 4 463 13 106 126 0 0 t 147 166 399 472 18 24 14 27 20 3 148 102 0 0

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1_rc; m=6/10; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.706169; wwTTAGACGArr-- ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 0 0 c 46 62 19 8 1 58 15 415 2 9 102 51 0 0 g 66 64 13 5 7 326 2 3 420 17 111 117 0 0 t 138 157 375 419 58 11 11 3 5 2 108 71 0 0

positions_7nt_m1_shift1 (positions_7nt_m1)
; oligos_7nt_mkv4_m2 versus positions_7nt_m1; m=7/10; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.662223; -wwTAGACGAkra- ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 234 0 c 0 88 71 24 11 32 29 482 1 10 85 58 75 0 g 0 69 73 26 7 447 4 2 502 25 205 145 105 0 t 0 147 216 454 59 21 16 13 11 10 137 104 106 0

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3_rc; m=8/10; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.661092; waTTArACGAd--- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 0 0 c 41 68 25 0 2 39 10 369 0 24 69 0 0 0 g 62 49 18 2 1 110 14 0 368 51 99 0 0 0 t 102 88 287 364 7 20 21 0 1 42 101 0 0 0

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_7nt_mkv4_m2 versus positions_6nt_m1; m=9/10; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.652872; -wwTAGACGAgra- ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 153 0 c 0 55 44 16 2 17 16 320 1 7 38 46 43 0 g 0 42 38 15 3 300 0 1 330 10 206 89 73 0 t 0 102 170 303 33 4 5 5 4 7 56 50 70 0

oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m10; m=10/10; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.552691; -wtTAGmCGAwa-- ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 0 0 c 0 65 69 1 6 25 281 431 5 7 78 64 0 0 g 0 48 67 8 6 371 5 3 424 10 108 110 0 0 t 0 158 211 429 33 25 18 10 5 7 141 91 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; wwwaTGTCGTGTAww ; Alignment reference a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/11; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wwwaTGTCGTGTAww ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121

positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)
; oligos_6nt_mkv3_m2 versus positions_6nt_m4_rc; m=2/11; ncol2=13; w=0; offset=2; strand=R; shift=2; score= 0.7539; --wwtgTCGTCTAww ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 34 354 187 122 c 0 0 86 69 79 62 15 385 2 4 320 3 21 59 61 g 0 0 80 66 57 216 5 6 401 15 56 10 14 46 52 t 0 0 134 160 227 49 384 11 0 380 18 360 18 115 172

oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2_rc; m=3/11; ncol2=14; w=0; offset=2; strand=R; shift=2; score=0.751862; --wwgGTCGTGTAaw ; cor=; Ncor= a 0 0 90 81 38 27 15 22 4 8 13 8 264 189 130 c 0 0 60 44 29 31 7 262 2 10 27 10 16 41 37 g 0 0 64 65 173 213 11 13 300 4 258 10 17 26 39 t 0 0 99 123 73 42 280 16 7 291 15 285 16 57 107

positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)
; oligos_6nt_mkv3_m2 versus positions_7nt_m1_rc; m=4/11; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.619292; ---tymTCGTCTAww ; cor=; Ncor= a 0 0 0 106 104 137 10 11 13 16 21 59 454 216 147 c 0 0 0 105 145 205 25 502 2 4 447 7 26 73 69 g 0 0 0 75 58 85 10 1 482 29 32 11 24 71 88 t 0 0 0 234 213 93 475 6 23 471 20 443 16 160 216

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5; m=5/11; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.609236; wwAATGTCGtv---- ; cor=; Ncor= a 124 148 387 379 16 17 32 36 15 88 116 0 0 0 0 c 82 88 12 12 4 26 21 378 5 83 113 0 0 0 0 g 104 64 22 13 15 384 8 10 402 85 111 0 0 0 0 t 128 138 17 34 403 11 377 14 16 182 98 0 0 0 0

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m2 versus positions_6nt_m1_rc; m=6/11; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.606997; ---tycTCGTCTAww ; cor=; Ncor= a 0 0 0 70 50 56 7 4 5 5 4 33 303 170 102 c 0 0 0 73 89 206 10 330 1 0 300 3 15 38 42 g 0 0 0 43 46 38 7 1 320 16 17 2 16 44 55 t 0 0 0 153 154 39 315 4 13 318 18 301 5 87 140

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m1; m=7/11; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.59339; ---tycTCGTCTAAw ; cor=; Ncor= a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196

oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m4_rc; m=8/11; ncol2=12; w=0; offset=4; strand=R; shift=4; score=0.564874; ----ywTCGTtTAAw ; cor=; Ncor= a 0 0 0 0 102 148 3 20 27 14 24 18 472 399 166 c 0 0 0 0 126 106 13 463 4 11 116 8 16 17 80 g 0 0 0 0 64 106 2 5 463 22 66 3 5 33 76 t 0 0 0 0 211 143 485 15 9 456 297 474 10 54 181

oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m1; m=9/11; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.557701; ----yyTCGTCTAAw ; cor=; Ncor= a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152

oligos_7nt_mkv4_m10_rc_shift4 (oligos_7nt_mkv4_m10_rc)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m10_rc; m=10/11; ncol2=11; w=0; offset=4; strand=R; shift=4; score=0.526518; ----twTCGkCTAaw ; cor=; Ncor= a 0 0 0 0 91 141 7 5 10 18 25 33 429 211 158 c 0 0 0 0 110 108 10 424 3 5 371 6 8 67 48 g 0 0 0 0 64 78 7 5 431 281 25 6 1 69 65 t 0 0 0 0 193 131 434 24 14 154 37 413 20 111 187

oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3; m=11/11; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.508496; -----hTCGTyTAAt ; cor=; Ncor= a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift5 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=5; ncol=16; -----hTCGTyTAAtw ; Alignment reference a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 102 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 62 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 41 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164 164

oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/11; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----hTCGTyTAAtw ; cor=; Ncor= a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 102 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 62 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 41 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164 164

oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m4_rc; m=2/11; ncol2=12; w=-1; offset=-1; strand=R; shift=4; score=0.899372; ----ywTCGTtTAAww ; cor=; Ncor= a 0 0 0 0 102 148 3 20 27 14 24 18 472 399 166 147 c 0 0 0 0 126 106 13 463 4 11 116 8 16 17 80 95 g 0 0 0 0 64 106 2 5 463 22 66 3 5 33 76 61 t 0 0 0 0 211 143 485 15 9 456 297 474 10 54 181 200

oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m1; m=3/11; ncol2=12; w=-1; offset=-1; strand=D; shift=4; score=0.859026; ----yyTCGTCTAAww ; cor=; Ncor= a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 138 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 66 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 46 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152 185

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=4/11; ncol2=13; w=-2; offset=-2; strand=D; shift=3; score=0.787939; ---tycTCGTCTAAww ; cor=; Ncor= a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 153 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 93 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 68 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196 207

oligos_7nt_mkv4_m10_rc_shift4 (oligos_7nt_mkv4_m10_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m10_rc; m=5/11; ncol2=11; w=-1; offset=-1; strand=R; shift=4; score=0.692313; ----twTCGkCTAaw- ; cor=; Ncor= a 0 0 0 0 91 141 7 5 10 18 25 33 429 211 158 0 c 0 0 0 0 110 108 10 424 3 5 371 6 8 67 48 0 g 0 0 0 0 64 78 7 5 431 281 25 6 1 69 65 0 t 0 0 0 0 193 131 434 24 14 154 37 413 20 111 187 0

positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)
; oligos_6nt_mkv3_m3 versus positions_7nt_m1_rc; m=6/11; ncol2=12; w=-2; offset=-2; strand=R; shift=3; score=0.685715; ---tymTCGTCTAww- ; cor=; Ncor= a 0 0 0 106 104 137 10 11 13 16 21 59 454 216 147 0 c 0 0 0 105 145 205 25 502 2 4 447 7 26 73 69 0 g 0 0 0 75 58 85 10 1 482 29 32 11 24 71 88 0 t 0 0 0 234 213 93 475 6 23 471 20 443 16 160 216 0

positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m3 versus positions_6nt_m1_rc; m=7/11; ncol2=12; w=-2; offset=-2; strand=R; shift=3; score=0.684194; ---tycTCGTCTAww- ; cor=; Ncor= a 0 0 0 70 50 56 7 4 5 5 4 33 303 170 102 0 c 0 0 0 73 89 206 10 330 1 0 300 3 15 38 42 0 g 0 0 0 43 46 38 7 1 320 16 17 2 16 44 55 0 t 0 0 0 153 154 39 315 4 13 318 18 301 5 87 140 0

oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2_rc; m=8/11; ncol2=14; w=-3; offset=-3; strand=R; shift=2; score=0.661092; --wwgGTCGTGTAaww ; cor=; Ncor= a 0 0 90 81 38 27 15 22 4 8 13 8 264 189 130 88 c 0 0 60 44 29 31 7 262 2 10 27 10 16 41 37 61 g 0 0 64 65 173 213 11 13 300 4 258 10 17 26 39 54 t 0 0 99 123 73 42 280 16 7 291 15 285 16 57 107 110

positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)
; oligos_6nt_mkv3_m3 versus positions_6nt_m4_rc; m=9/11; ncol2=13; w=-3; offset=-3; strand=R; shift=2; score=0.636814; --wwtgTCGTCTAww- ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 34 354 187 122 0 c 0 0 86 69 79 62 15 385 2 4 320 3 21 59 61 0 g 0 0 80 66 57 216 5 6 401 15 56 10 14 46 52 0 t 0 0 134 160 227 49 384 11 0 380 18 360 18 115 172 0

positions_7nt_m2_shift4 (positions_7nt_m2)
; oligos_6nt_mkv3_m3 versus positions_7nt_m2; m=10/11; ncol2=11; w=-1; offset=-1; strand=D; shift=4; score=0.625717; ----yaTCGTCAAww- ; cor=; Ncor= a 0 0 0 0 155 246 33 27 40 23 15 478 585 262 219 0 c 0 0 0 0 204 139 19 617 3 22 608 10 16 125 106 0 g 0 0 0 0 79 142 18 6 599 32 7 12 18 66 105 0 t 0 0 0 0 216 127 584 4 12 577 24 154 35 201 224 0

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2; m=11/11; ncol2=15; w=-5; offset=-5; strand=D; shift=0; score=0.508496; wwwaTGTCGTGTAww- ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 0 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 0 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 0 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAATGTCGtv ; Alignment reference a 124 148 387 379 16 17 32 36 15 88 116 c 82 88 12 12 4 26 21 378 5 83 113 g 104 64 22 13 15 384 8 10 402 85 111 t 128 138 17 34 403 11 377 14 16 182 98

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAATGTCGtv ; cor=; Ncor= a 124 148 387 379 16 17 32 36 15 88 116 c 82 88 12 12 4 26 21 378 5 83 113 g 104 64 22 13 15 384 8 10 402 85 111 t 128 138 17 34 403 11 377 14 16 182 98

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.609236; wwwaTGTCGTG ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 c 48 68 55 21 7 26 8 282 7 9 38 g 74 43 57 52 50 231 8 7 305 8 243 t 100 101 82 69 231 36 292 14 3 291 19

positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)
; oligos_7nt_mkv4_m5 versus positions_6nt_m4_rc; m=3/3; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.421897; --wwtgTCGTC ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 c 0 0 86 69 79 62 15 385 2 4 320 g 0 0 80 66 57 216 5 6 401 15 56 t 0 0 134 160 227 49 384 11 0 380 18

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m10_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=12; shift=1; ncol=13; -waCAACAATAaw ; Alignment reference a 0 213 239 51 517 509 19 510 512 17 460 222 169 c 0 96 96 415 1 12 480 9 3 79 15 70 127 g 0 96 77 19 11 12 8 5 17 9 22 130 91 t 0 135 128 55 11 7 33 16 8 435 43 118 153

oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -waCAACAATAaw ; cor=; Ncor= a 0 213 239 51 517 509 19 510 512 17 460 222 169 c 0 96 96 415 1 12 480 9 3 79 15 70 127 g 0 96 77 19 11 12 8 5 17 9 22 130 91 t 0 135 128 55 11 7 33 16 8 435 43 118 153

oligos_7nt_mkv4_m6_shift2 (oligos_7nt_mkv4_m6)
; oligos_6nt_mkv3_m10 versus oligos_7nt_mkv4_m6; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.780411; --whAACAATAGw ; cor=; Ncor= a 0 0 178 152 439 453 32 457 464 18 418 81 181 c 0 0 84 134 4 11 405 4 2 26 15 21 85 g 0 0 76 67 21 6 16 6 9 14 21 352 82 t 0 0 141 126 15 9 26 12 4 421 25 25 131

positions_6nt_m5_shift2 (positions_6nt_m5)
; oligos_6nt_mkv3_m10 versus positions_6nt_m5; m=3/5; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.642075; --aaAAAAATwww ; cor=; Ncor= a 0 0 386 388 800 800 800 800 800 0 299 241 263 c 0 0 103 105 0 0 0 0 0 0 93 115 149 g 0 0 155 172 0 0 0 0 0 0 118 128 115 t 0 0 156 135 0 0 0 0 0 800 290 316 273

oligos_8nt_mkv5_m1_shift0 (oligos_8nt_mkv5_m1)
; oligos_6nt_mkv3_m10 versus oligos_8nt_mkv5_m1; m=4/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.609377; maACAAaAACaa- ; cor=; Ncor= a 198 246 542 3 528 519 375 509 501 10 316 307 0 c 167 103 10 543 11 21 137 19 23 536 79 70 0 g 67 119 9 8 23 12 21 19 10 5 60 69 0 t 140 104 11 18 10 20 39 25 38 21 117 126 0

positions_6nt_m8_shift3 (positions_6nt_m8)
; oligos_6nt_mkv3_m10 versus positions_6nt_m8; m=5/5; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.604189; ---waATAATAaw ; cor=; Ncor= a 0 0 0 115 170 314 0 314 314 0 314 159 91 c 0 0 0 56 33 0 0 0 0 0 0 47 39 g 0 0 0 31 48 0 0 0 0 0 0 48 43 t 0 0 0 112 63 0 314 0 0 314 0 60 141

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift2 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift2 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --yaTCGTCAAww ; Alignment reference a 0 0 155 246 33 27 40 23 15 478 585 262 219 c 0 0 204 139 19 617 3 22 608 10 16 125 106 g 0 0 79 142 18 6 599 32 7 12 18 66 105 t 0 0 216 127 584 4 12 577 24 154 35 201 224

positions_7nt_m2_shift2 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/10; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --yaTCGTCAAww ; cor=; Ncor= a 0 0 155 246 33 27 40 23 15 478 585 262 219 c 0 0 204 139 19 617 3 22 608 10 16 125 106 g 0 0 79 142 18 6 599 32 7 12 18 66 105 t 0 0 216 127 584 4 12 577 24 154 35 201 224

positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)
; positions_7nt_m2 versus positions_7nt_m1_rc; m=2/10; ncol2=12; w=-1; offset=-1; strand=R; shift=1; score=0.821006; -tymTCGTCTAww ; cor=; Ncor= a 0 106 104 137 10 11 13 16 21 59 454 216 147 c 0 105 145 205 25 502 2 4 447 7 26 73 69 g 0 75 58 85 10 1 482 29 32 11 24 71 88 t 0 234 213 93 475 6 23 471 20 443 16 160 216

oligos_7nt_mkv4_m10_rc_shift2 (oligos_7nt_mkv4_m10_rc)
; positions_7nt_m2 versus oligos_7nt_mkv4_m10_rc; m=3/10; ncol2=11; w=0; offset=0; strand=R; shift=2; score=0.80024; --twTCGkCTAaw ; cor=; Ncor= a 0 0 91 141 7 5 10 18 25 33 429 211 158 c 0 0 110 108 10 424 3 5 371 6 8 67 48 g 0 0 64 78 7 5 431 281 25 6 1 69 65 t 0 0 193 131 434 24 14 154 37 413 20 111 187

positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)
; positions_7nt_m2 versus positions_6nt_m1_rc; m=4/10; ncol2=12; w=-1; offset=-1; strand=R; shift=1; score=0.799622; -tycTCGTCTAww ; cor=; Ncor= a 0 70 50 56 7 4 5 5 4 33 303 170 102 c 0 73 89 206 10 330 1 0 300 3 15 38 42 g 0 43 46 38 7 1 320 16 17 2 16 44 55 t 0 153 154 39 315 4 13 318 18 301 5 87 140

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; positions_7nt_m2 versus oligos_7nt_mkv4_m1; m=5/10; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.79793; --yyTCGTCTAAw ; cor=; Ncor= a 0 0 71 108 2 5 3 11 11 58 419 375 157 c 0 0 117 111 17 420 3 2 326 7 5 13 64 g 0 0 51 102 9 2 415 15 58 1 8 19 62 t 0 0 196 114 407 8 14 407 40 369 3 28 152

positions_6nt_m9_shift1 (positions_6nt_m9)
; positions_7nt_m2 versus positions_6nt_m9; m=6/10; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.766192; -tyCTCGTCAww- ; cor=; Ncor= a 0 112 113 67 11 18 17 11 19 391 230 172 0 c 0 73 132 348 15 435 10 8 444 13 70 105 0 g 0 77 72 50 21 14 443 12 8 10 57 65 0 t 0 225 170 22 440 20 17 456 16 73 130 145 0

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; positions_7nt_m2 versus oligos_6nt_mkv3_m1; m=7/10; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.745444; -tycTCGTCTAAw ; cor=; Ncor= a 0 107 94 121 15 11 7 18 14 63 481 373 176 c 0 115 138 169 28 498 4 5 413 7 20 27 79 g 0 79 69 113 13 2 495 26 56 3 16 45 70 t 0 220 220 118 465 10 15 472 38 448 4 76 196

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_7nt_m2 versus positions_6nt_m4_rc; m=8/10; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.733261; wwtgTCGTCTAww ; cor=; Ncor= a 107 112 44 80 3 5 4 8 13 34 354 187 122 c 86 69 79 62 15 385 2 4 320 3 21 59 61 g 80 66 57 216 5 6 401 15 56 10 14 46 52 t 134 160 227 49 384 11 0 380 18 360 18 115 172

oligos_7nt_mkv4_m4_rc_shift2 (oligos_7nt_mkv4_m4_rc)
; positions_7nt_m2 versus oligos_7nt_mkv4_m4_rc; m=9/10; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.691856; --ywTCGTtTAAw ; cor=; Ncor= a 0 0 102 148 3 20 27 14 24 18 472 399 166 c 0 0 126 106 13 463 4 11 116 8 16 17 80 g 0 0 64 106 2 5 463 22 66 3 5 33 76 t 0 0 211 143 485 15 9 456 297 474 10 54 181

oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; positions_7nt_m2 versus oligos_6nt_mkv3_m3; m=10/10; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.625717; ---hTCGTyTAAt ; cor=; Ncor= a 0 0 0 101 42 1 0 21 20 7 364 287 88 c 0 0 0 99 51 368 0 14 110 1 2 18 49 g 0 0 0 69 24 0 369 10 39 2 0 25 68 t 0 0 0 100 252 0 0 324 200 359 3 39 164

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m9_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m9_shift1 (oligos_7nt_mkv4_m9)
; oligos_7nt_mkv4_m9; m=0 (reference); ncol1=11; shift=1; ncol=12; -wwCAAAATCww ; Alignment reference a 0 97 113 0 227 207 215 254 0 1 107 92 c 0 49 35 263 7 6 11 6 0 268 43 58 g 0 41 40 0 13 22 11 4 0 0 32 35 t 0 82 81 6 22 34 32 5 269 0 87 84

oligos_7nt_mkv4_m9_shift1 (oligos_7nt_mkv4_m9)
; oligos_7nt_mkv4_m9 versus oligos_7nt_mkv4_m9; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wwCAAAATCww ; cor=; Ncor= a 0 97 113 0 227 207 215 254 0 1 107 92 c 0 49 35 263 7 6 11 6 0 268 43 58 g 0 41 40 0 13 22 11 4 0 0 32 35 t 0 82 81 6 22 34 32 5 269 0 87 84

oligos_8nt_mkv5_m1_shift0 (oligos_8nt_mkv5_m1)
; oligos_7nt_mkv4_m9 versus oligos_8nt_mkv5_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.686379; maACAAaAACaa ; cor=; Ncor= a 198 246 542 3 528 519 375 509 501 10 316 307 c 167 103 10 543 11 21 137 19 23 536 79 70 g 67 119 9 8 23 12 21 19 10 5 60 69 t 140 104 11 18 10 20 39 25 38 21 117 126

positions_6nt_m6_shift4 (positions_6nt_m6)
; oligos_7nt_mkv4_m9 versus positions_6nt_m6; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.469414; ----wwAATCAA ; cor=; Ncor= a 0 0 0 0 107 80 222 245 4 4 214 237 c 0 0 0 0 59 60 13 9 0 269 10 13 g 0 0 0 0 37 42 19 6 13 2 15 17 t 0 0 0 0 72 93 21 15 258 0 36 8

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m10_shift1 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; oligos_7nt_mkv4_m10; m=0 (reference); ncol1=11; shift=1; ncol=12; -wtTAGmCGAwa ; Alignment reference a 0 187 111 20 413 37 154 14 24 434 131 193 c 0 65 69 1 6 25 281 431 5 7 78 64 g 0 48 67 8 6 371 5 3 424 10 108 110 t 0 158 211 429 33 25 18 10 5 7 141 91

oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m10; m=1/11; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wtTAGmCGAwa ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 c 0 65 69 1 6 25 281 431 5 7 78 64 g 0 48 67 8 6 371 5 3 424 10 108 110 t 0 158 211 429 33 25 18 10 5 7 141 91

positions_7nt_m1_shift1 (positions_7nt_m1)
; oligos_7nt_mkv4_m10 versus positions_7nt_m1; m=2/11; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.836417; -wwTAGACGAkr ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 c 0 88 71 24 11 32 29 482 1 10 85 58 g 0 69 73 26 7 447 4 2 502 25 205 145 t 0 147 216 454 59 21 16 13 11 10 137 104

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_7nt_mkv4_m10 versus positions_6nt_m1; m=3/11; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.82233; -wwTAGACGAgr ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 c 0 55 44 16 2 17 16 320 1 7 38 46 g 0 42 38 15 3 300 0 1 330 10 206 89 t 0 102 170 303 33 4 5 5 4 7 56 50

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m1_rc; m=4/11; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.818909; wwTTAGACGArr ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 c 46 62 19 8 1 58 15 415 2 9 102 51 g 66 64 13 5 7 326 2 3 420 17 111 117 t 138 157 375 419 58 11 11 3 5 2 108 71

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; oligos_7nt_mkv4_m10 versus positions_7nt_m2_rc; m=5/11; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.80024; -wwTTGACGAtr ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 c 0 105 66 18 12 7 32 599 6 18 142 79 g 0 106 125 16 10 608 22 3 617 19 139 204 t 0 219 262 585 478 15 23 40 27 33 246 155

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m10 versus oligos_6nt_mkv3_m1_rc; m=6/11; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.768354; wwTTAGACGAgr ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 c 68 70 45 16 3 56 26 495 2 13 113 69 g 93 79 27 20 7 413 5 4 498 28 169 138 t 153 176 373 481 63 14 18 7 11 15 121 94

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m4; m=7/11; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.761833; wwTTAaACGAwr ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 c 61 76 33 5 3 66 22 463 5 2 106 64 g 95 80 17 16 8 116 11 4 463 13 106 126 t 147 166 399 472 18 24 14 27 20 3 148 102

positions_6nt_m4_shift1 (positions_6nt_m4)
; oligos_7nt_mkv4_m10 versus positions_6nt_m4; m=8/11; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.754282; -wwTAGACGAca ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 c 0 52 46 14 10 56 15 401 6 5 216 57 g 0 61 59 21 3 320 4 2 385 15 62 79 t 0 122 187 354 34 13 8 4 5 3 80 44

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m10 versus oligos_6nt_mkv3_m3_rc; m=9/11; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.692313; waTTArACGAd- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 c 41 68 25 0 2 39 10 369 0 24 69 0 g 62 49 18 2 1 110 14 0 368 51 99 0 t 102 88 287 364 7 20 21 0 1 42 101 0

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m2; m=10/11; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.552691; wwtTACACGACc ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 c 54 39 26 17 10 258 4 300 13 11 213 173 g 61 37 41 16 10 27 10 2 262 7 31 29 t 88 130 189 264 8 13 8 4 22 15 27 38

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; oligos_7nt_mkv4_m10 versus oligos_6nt_mkv3_m2_rc; m=11/11; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.526518; -wwTACACGACA ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 c 0 45 47 27 15 243 8 305 7 8 231 50 g 0 43 73 20 10 38 9 7 282 8 26 7 t 0 108 117 227 10 17 9 2 14 9 24 29

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift2 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=2; ncol=12; --waTATGCAdd ; Alignment reference a 0 0 57 90 0 176 0 2 0 152 59 53 c 0 0 20 20 0 3 5 0 175 4 17 19 g 0 0 17 29 0 0 0 177 0 4 55 59 t 0 0 85 40 179 0 174 0 4 19 48 48

oligos_6nt_mkv3_m9_shift2 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --waTATGCAdd ; cor=; Ncor= a 0 0 57 90 0 176 0 2 0 152 59 53 c 0 0 20 20 0 3 5 0 175 4 17 19 g 0 0 17 29 0 0 0 177 0 4 55 59 t 0 0 85 40 179 0 174 0 4 19 48 48

oligos_8nt_mkv5_m2_rc_shift2 (oligos_8nt_mkv5_m2_rc)
; oligos_6nt_mkv3_m9 versus oligos_8nt_mkv5_m2_rc; m=2/4; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.764437; --waTATGCAGG ; cor=; Ncor= a 0 0 49 62 2 115 3 8 4 125 7 10 c 0 0 15 14 3 0 1 0 121 3 2 0 g 0 0 13 24 7 9 0 122 3 2 110 103 t 0 0 54 31 119 7 127 1 3 1 12 18

oligos_7nt_mkv4_m8_shift1 (oligos_7nt_mkv4_m8)
; oligos_6nt_mkv3_m9 versus oligos_7nt_mkv4_m8; m=3/4; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.703998; -ywaTATGCAGG ; cor=; Ncor= a 0 29 49 66 2 119 3 10 4 127 7 10 c 0 38 15 14 3 0 1 0 123 3 2 0 g 0 27 13 24 9 9 0 124 3 2 114 107 t 0 41 58 31 121 7 131 1 5 3 12 18

oligos_6nt_mkv3_m8_rc_shift0 (oligos_6nt_mkv3_m8_rc)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m8_rc; m=4/4; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.556927; tdTgTATGTAwr ; cor=; Ncor= a 102 127 69 83 11 367 15 65 7 373 137 162 c 63 76 30 24 12 8 3 8 11 4 66 42 g 52 103 27 260 2 24 10 328 8 17 44 107 t 193 104 284 43 385 11 382 9 384 16 163 99

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; aaaAAGAAAaa ; Alignment reference a 379 339 340 758 757 0 759 751 757 394 405 c 80 147 162 0 5 0 1 0 0 79 77 g 176 160 180 1 0 763 0 2 0 139 110 t 128 117 81 4 1 0 3 10 6 151 171

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; aaaAAGAAAaa ; cor=; Ncor= a 379 339 340 758 757 0 759 751 757 394 405 c 80 147 162 0 5 0 1 0 0 79 77 g 176 160 180 1 0 763 0 2 0 139 110 t 128 117 81 4 1 0 3 10 6 151 171

oligos_7nt_mkv4_m7_shift1 (oligos_7nt_mkv4_m7)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m7; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.807946; -aaAAGAAAAa ; cor=; Ncor= a 0 220 210 457 467 0 468 449 451 467 271 c 0 91 94 0 1 0 0 2 0 0 42 g 0 93 101 1 0 468 0 4 0 1 59 t 0 64 63 10 0 0 0 13 17 0 96

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv5_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv5_m2_shift0 (oligos_8nt_mkv5_m2)
; oligos_8nt_mkv5_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; wwCCTGCATAtw ; Alignment reference a 49 42 18 12 1 3 1 127 7 119 31 54 c 18 15 103 110 2 3 122 0 9 7 24 13 g 31 18 0 2 3 121 0 1 0 3 14 15 t 33 56 10 7 125 4 8 3 115 2 62 49

oligos_8nt_mkv5_m2_shift0 (oligos_8nt_mkv5_m2)
; oligos_8nt_mkv5_m2 versus oligos_8nt_mkv5_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwCCTGCATAtw ; cor=; Ncor= a 49 42 18 12 1 3 1 127 7 119 31 54 c 18 15 103 110 2 3 122 0 9 7 24 13 g 31 18 0 2 3 121 0 1 0 3 14 15 t 33 56 10 7 125 4 8 3 115 2 62 49

oligos_7nt_mkv4_m8_rc_shift0 (oligos_7nt_mkv4_m8_rc)
; oligos_8nt_mkv5_m2 versus oligos_7nt_mkv4_m8_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.922814; awCCTGCATAtw ; cor=; Ncor= a 49 42 18 12 3 5 1 131 7 121 31 58 c 20 17 107 114 2 3 124 0 9 9 24 13 g 33 18 0 2 3 123 0 1 0 3 14 15 t 33 58 10 7 127 4 10 3 119 2 66 49

oligos_6nt_mkv3_m9_rc_shift2 (oligos_6nt_mkv3_m9_rc)
; oligos_8nt_mkv5_m2 versus oligos_6nt_mkv3_m9_rc; m=3/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.764437; --hhTGCATAtw ; cor=; Ncor= a 0 0 48 48 19 4 0 174 0 179 40 85 c 0 0 59 55 4 0 177 0 0 0 29 17 g 0 0 19 17 4 175 0 5 3 0 20 20 t 0 0 53 59 152 0 2 0 176 0 90 57

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

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; wwTTGAAAaw ; Alignment reference a 116 101 0 0 0 335 335 335 129 141 c 51 52 0 0 0 0 0 0 71 46 g 57 68 0 0 335 0 0 0 54 49 t 111 114 335 335 0 0 0 0 81 99

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wwTTGAAAaw ; cor=; Ncor= a 116 101 0 0 0 335 335 335 129 141 c 51 52 0 0 0 0 0 0 71 46 g 57 68 0 0 335 0 0 0 54 49 t 111 114 335 335 0 0 0 0 81 99

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift3 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---aaAAAAATwww ; Alignment reference a 0 0 0 386 388 800 800 800 800 800 0 299 241 263 c 0 0 0 103 105 0 0 0 0 0 0 93 115 149 g 0 0 0 155 172 0 0 0 0 0 0 118 128 115 t 0 0 0 156 135 0 0 0 0 0 800 290 316 273

positions_6nt_m5_shift3 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---aaAAAAATwww ; cor=; Ncor= a 0 0 0 386 388 800 800 800 800 800 0 299 241 263 c 0 0 0 103 105 0 0 0 0 0 0 93 115 149 g 0 0 0 155 172 0 0 0 0 0 0 118 128 115 t 0 0 0 156 135 0 0 0 0 0 800 290 316 273

oligos_7nt_mkv4_m6_shift3 (oligos_7nt_mkv4_m6)
; positions_6nt_m5 versus oligos_7nt_mkv4_m6; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.663837; ---whAACAATAGw ; cor=; Ncor= a 0 0 0 178 152 439 453 32 457 464 18 418 81 181 c 0 0 0 84 134 4 11 405 4 2 26 15 21 85 g 0 0 0 76 67 21 6 16 6 9 14 21 352 82 t 0 0 0 141 126 15 9 26 12 4 421 25 25 131

oligos_6nt_mkv3_m10_shift2 (oligos_6nt_mkv3_m10)
; positions_6nt_m5 versus oligos_6nt_mkv3_m10; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.642075; --waCAACAATAaw ; cor=; Ncor= a 0 0 213 239 51 517 509 19 510 512 17 460 222 169 c 0 0 96 96 415 1 12 480 9 3 79 15 70 127 g 0 0 96 77 19 11 12 8 5 17 9 22 130 91 t 0 0 135 128 55 11 7 33 16 8 435 43 118 153

positions_6nt_m3_shift4 (positions_6nt_m3)
; positions_6nt_m5 versus positions_6nt_m3; m=4/5; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.635241; ----wawAAATATw ; cor=; Ncor= a 0 0 0 0 211 280 190 539 404 542 0 544 0 234 c 0 0 0 0 61 81 59 0 12 1 0 0 0 52 g 0 0 0 0 98 115 83 1 7 0 0 0 0 77 t 0 0 0 0 174 68 212 4 121 1 544 0 544 181

oligos_7nt_mkv4_m7_shift0 (oligos_7nt_mkv4_m7)
; positions_6nt_m5 versus oligos_7nt_mkv4_m7; m=5/5; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.417361; aaAAGAAAAaa--- ; cor=; Ncor= a 220 210 457 467 0 468 449 451 467 271 253 0 0 0 c 91 94 0 1 0 0 2 0 0 42 48 0 0 0 g 93 101 1 0 468 0 4 0 1 59 80 0 0 0 t 64 63 10 0 0 0 13 17 0 96 87 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; rdrAGGCGGGrdr ; Alignment reference a 99 93 101 270 7 19 22 10 18 38 105 81 101 c 57 64 31 10 4 9 243 2 2 31 62 58 48 g 94 85 147 25 305 288 47 300 288 243 103 104 99 t 74 82 45 19 8 8 12 12 16 12 54 81 76

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rdrAGGCGGGrdr ; cor=; Ncor= a 99 93 101 270 7 19 22 10 18 38 105 81 101 c 57 64 31 10 4 9 243 2 2 31 62 58 48 g 94 85 147 25 305 288 47 300 288 243 103 104 99 t 74 82 45 19 8 8 12 12 16 12 54 81 76

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwTTAaACGAwr ; Alignment reference a 200 181 54 10 474 297 456 9 15 485 143 211 c 61 76 33 5 3 66 22 463 5 2 106 64 g 95 80 17 16 8 116 11 4 463 13 106 126 t 147 166 399 472 18 24 14 27 20 3 148 102

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/11; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAaACGAwr ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 c 61 76 33 5 3 66 22 463 5 2 106 64 g 95 80 17 16 8 116 11 4 463 13 106 126 t 147 166 399 472 18 24 14 27 20 3 148 102

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=2/11; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.939175; wwTTAGACGArr ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 c 46 62 19 8 1 58 15 415 2 9 102 51 g 66 64 13 5 7 326 2 3 420 17 111 117 t 138 157 375 419 58 11 11 3 5 2 108 71

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m3_rc; m=3/11; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.899372; waTTArACGAd- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 c 41 68 25 0 2 39 10 369 0 24 69 0 g 62 49 18 2 1 110 14 0 368 51 99 0 t 102 88 287 364 7 20 21 0 1 42 101 0

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m1_rc; m=4/11; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.855959; wwTTAGACGAgr ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 c 68 70 45 16 3 56 26 495 2 13 113 69 g 93 79 27 20 7 413 5 4 498 28 169 138 t 153 176 373 481 63 14 18 7 11 15 121 94

oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m10; m=5/11; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.761833; -wtTAGmCGAwa ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 c 0 65 69 1 6 25 281 431 5 7 78 64 g 0 48 67 8 6 371 5 3 424 10 108 110 t 0 158 211 429 33 25 18 10 5 7 141 91

positions_7nt_m1_shift1 (positions_7nt_m1)
; oligos_7nt_mkv4_m4 versus positions_7nt_m1; m=6/11; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.74836; -wwTAGACGAkr ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 c 0 88 71 24 11 32 29 482 1 10 85 58 g 0 69 73 26 7 447 4 2 502 25 205 145 t 0 147 216 454 59 21 16 13 11 10 137 104

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_7nt_mkv4_m4 versus positions_6nt_m1; m=7/11; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.744405; -wwTAGACGAgr ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 c 0 55 44 16 2 17 16 320 1 7 38 46 g 0 42 38 15 3 300 0 1 330 10 206 89 t 0 102 170 303 33 4 5 5 4 7 56 50

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m2; m=8/11; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.717489; wwtTACACGACc ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 c 54 39 26 17 10 258 4 300 13 11 213 173 g 61 37 41 16 10 27 10 2 262 7 31 29 t 88 130 189 264 8 13 8 4 22 15 27 38

positions_6nt_m4_shift1 (positions_6nt_m4)
; oligos_7nt_mkv4_m4 versus positions_6nt_m4; m=9/11; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.699844; -wwTAGACGAca ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 c 0 52 46 14 10 56 15 401 6 5 216 57 g 0 61 59 21 3 320 4 2 385 15 62 79 t 0 122 187 354 34 13 8 4 5 3 80 44

positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)
; oligos_7nt_mkv4_m4 versus positions_7nt_m2_rc; m=10/11; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.691856; -wwTTGACGAtr ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 c 0 105 66 18 12 7 32 599 6 18 142 79 g 0 106 125 16 10 608 22 3 617 19 139 204 t 0 219 262 585 478 15 23 40 27 33 246 155

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m2_rc; m=11/11; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.564874; -wwTACACGACA ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 c 0 45 47 27 15 243 8 305 7 8 231 50 g 0 43 73 20 10 38 9 7 282 8 26 7 t 0 108 117 227 10 17 9 2 14 9 24 29

One-to-n matrix alignment; reference matrix: positions_6nt_m6_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m6_shift3 (positions_6nt_m6)
; positions_6nt_m6; m=0 (reference); ncol1=11; shift=3; ncol=14; ---wwAATCAAGww ; Alignment reference a 0 0 0 107 80 222 245 4 4 214 237 0 87 99 c 0 0 0 59 60 13 9 0 269 10 13 2 48 31 g 0 0 0 37 42 19 6 13 2 15 17 266 31 59 t 0 0 0 72 93 21 15 258 0 36 8 7 109 86

positions_6nt_m6_shift3 (positions_6nt_m6)
; positions_6nt_m6 versus positions_6nt_m6; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---wwAATCAAGww ; cor=; Ncor= a 0 0 0 107 80 222 245 4 4 214 237 0 87 99 c 0 0 0 59 60 13 9 0 269 10 13 2 48 31 g 0 0 0 37 42 19 6 13 2 15 17 266 31 59 t 0 0 0 72 93 21 15 258 0 36 8 7 109 86

oligos_7nt_mkv4_m9_shift0 (oligos_7nt_mkv4_m9)
; positions_6nt_m6 versus oligos_7nt_mkv4_m9; m=2/2; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.469414; wwCAAAATCww--- ; cor=; Ncor= a 97 113 0 227 207 215 254 0 1 107 92 0 0 0 c 49 35 263 7 6 11 6 0 268 43 58 0 0 0 g 41 40 0 13 22 11 4 0 0 32 35 0 0 0 t 82 81 6 22 34 32 5 269 0 87 84 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv5_m1_shift1 (oligos_8nt_mkv5_m1)				; oligos_8nt_mkv5_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -maACAAaAACaa ; Alignment reference a 0 198 246 542 3 528 519 375 509 501 10 316 307 c 0 167 103 10 543 11 21 137 19 23 536 79 70 g 0 67 119 9 8 23 12 21 19 10 5 60 69 t 0 140 104 11 18 10 20 39 25 38 21 117 126
oligos_8nt_mkv5_m1_shift1 (oligos_8nt_mkv5_m1)				; oligos_8nt_mkv5_m1 versus oligos_8nt_mkv5_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -maACAAaAACaa ; cor=; Ncor= a 0 198 246 542 3 528 519 375 509 501 10 316 307 c 0 167 103 10 543 11 21 137 19 23 536 79 70 g 0 67 119 9 8 23 12 21 19 10 5 60 69 t 0 140 104 11 18 10 20 39 25 38 21 117 126
oligos_7nt_mkv4_m9_shift2 (oligos_7nt_mkv4_m9)				; oligos_8nt_mkv5_m1 versus oligos_7nt_mkv4_m9; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.686379; --wwCAAAATCww ; cor=; Ncor= a 0 0 97 113 0 227 207 215 254 0 1 107 92 c 0 0 49 35 263 7 6 11 6 0 268 43 58 g 0 0 41 40 0 13 22 11 4 0 0 32 35 t 0 0 82 81 6 22 34 32 5 269 0 87 84
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; oligos_8nt_mkv5_m1 versus oligos_7nt_mkv4_m3; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.614515; waCACAAAACma- ; cor=; Ncor= a 122 135 53 306 5 297 303 304 297 12 128 154 0 c 51 67 234 8 302 9 15 5 7 266 85 62 0 g 68 49 22 5 7 6 3 4 11 20 38 36 0 t 84 74 16 6 11 13 4 12 10 27 74 73 0
oligos_6nt_mkv3_m10_shift2 (oligos_6nt_mkv3_m10)				; oligos_8nt_mkv5_m1 versus oligos_6nt_mkv3_m10; m=4/4; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.609377; --waCAACAATAa ; cor=; Ncor= a 0 0 213 239 51 517 509 19 510 512 17 460 222 c 0 0 96 96 415 1 12 480 9 3 79 15 70 g 0 0 96 77 19 11 12 8 5 17 9 22 130 t 0 0 135 128 55 11 7 33 16 8 435 43 118

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m6_shift1 (oligos_7nt_mkv4_m6)				; oligos_7nt_mkv4_m6; m=0 (reference); ncol1=12; shift=1; ncol=13; -whAACAATAGwa ; Alignment reference a 0 178 152 439 453 32 457 464 18 418 81 181 196 c 0 84 134 4 11 405 4 2 26 15 21 85 99 g 0 76 67 21 6 16 6 9 14 21 352 82 86 t 0 141 126 15 9 26 12 4 421 25 25 131 98
oligos_7nt_mkv4_m6_shift1 (oligos_7nt_mkv4_m6)				; oligos_7nt_mkv4_m6 versus oligos_7nt_mkv4_m6; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -whAACAATAGwa ; cor=; Ncor= a 0 178 152 439 453 32 457 464 18 418 81 181 196 c 0 84 134 4 11 405 4 2 26 15 21 85 99 g 0 76 67 21 6 16 6 9 14 21 352 82 86 t 0 141 126 15 9 26 12 4 421 25 25 131 98
oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)				; oligos_7nt_mkv4_m6 versus oligos_6nt_mkv3_m10; m=2/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.780411; waCAACAATAaw- ; cor=; Ncor= a 213 239 51 517 509 19 510 512 17 460 222 169 0 c 96 96 415 1 12 480 9 3 79 15 70 127 0 g 96 77 19 11 12 8 5 17 9 22 130 91 0 t 135 128 55 11 7 33 16 8 435 43 118 153 0
positions_6nt_m5_shift1 (positions_6nt_m5)				; oligos_7nt_mkv4_m6 versus positions_6nt_m5; m=3/4; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.663837; -aaAAAAATwww- ; cor=; Ncor= a 0 386 388 800 800 800 800 800 0 299 241 263 0 c 0 103 105 0 0 0 0 0 0 93 115 149 0 g 0 155 172 0 0 0 0 0 0 118 128 115 0 t 0 156 135 0 0 0 0 0 800 290 316 273 0
positions_6nt_m8_shift2 (positions_6nt_m8)				; oligos_7nt_mkv4_m6 versus positions_6nt_m8; m=4/4; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.618464; --waATAATAaw- ; cor=; Ncor= a 0 0 115 170 314 0 314 314 0 314 159 91 0 c 0 0 56 33 0 0 0 0 0 0 47 39 0 g 0 0 31 48 0 0 0 0 0 0 48 43 0 t 0 0 112 63 0 314 0 0 314 0 60 141 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m9_shift1 (positions_6nt_m9)				; positions_6nt_m9; m=0 (reference); ncol1=11; shift=1; ncol=12; -tyCTCGTCAww ; Alignment reference a 0 112 113 67 11 18 17 11 19 391 230 172 c 0 73 132 348 15 435 10 8 444 13 70 105 g 0 77 72 50 21 14 443 12 8 10 57 65 t 0 225 170 22 440 20 17 456 16 73 130 145
positions_6nt_m9_shift1 (positions_6nt_m9)				; positions_6nt_m9 versus positions_6nt_m9; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -tyCTCGTCAww ; cor=; Ncor= a 0 112 113 67 11 18 17 11 19 391 230 172 c 0 73 132 348 15 435 10 8 444 13 70 105 g 0 77 72 50 21 14 443 12 8 10 57 65 t 0 225 170 22 440 20 17 456 16 73 130 145
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)				; positions_6nt_m9 versus positions_6nt_m1_rc; m=2/7; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.769109; -tycTCGTCTAw ; cor=; Ncor= a 0 70 50 56 7 4 5 5 4 33 303 170 c 0 73 89 206 10 330 1 0 300 3 15 38 g 0 43 46 38 7 1 320 16 17 2 16 44 t 0 153 154 39 315 4 13 318 18 301 5 87
positions_7nt_m2_shift2 (positions_7nt_m2)				; positions_6nt_m9 versus positions_7nt_m2; m=3/7; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.766192; --yaTCGTCAAw ; cor=; Ncor= a 0 0 155 246 33 27 40 23 15 478 585 262 c 0 0 204 139 19 617 3 22 608 10 16 125 g 0 0 79 142 18 6 599 32 7 12 18 66 t 0 0 216 127 584 4 12 577 24 154 35 201
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_6nt_m9 versus positions_7nt_m1_rc; m=4/7; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.759307; -tymTCGTCTAw ; cor=; Ncor= a 0 106 104 137 10 11 13 16 21 59 454 216 c 0 105 145 205 25 502 2 4 447 7 26 73 g 0 75 58 85 10 1 482 29 32 11 24 71 t 0 234 213 93 475 6 23 471 20 443 16 160
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; positions_6nt_m9 versus oligos_6nt_mkv3_m1; m=5/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.671232; -tycTCGTCTAA ; cor=; Ncor= a 0 107 94 121 15 11 7 18 14 63 481 373 c 0 115 138 169 28 498 4 5 413 7 20 27 g 0 79 69 113 13 2 495 26 56 3 16 45 t 0 220 220 118 465 10 15 472 38 448 4 76
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_6nt_m9 versus positions_6nt_m4_rc; m=6/7; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.65039; wwtgTCGTCTAw ; cor=; Ncor= a 107 112 44 80 3 5 4 8 13 34 354 187 c 86 69 79 62 15 385 2 4 320 3 21 59 g 80 66 57 216 5 6 401 15 56 10 14 46 t 134 160 227 49 384 11 0 380 18 360 18 115
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; positions_6nt_m9 versus oligos_7nt_mkv4_m1; m=7/7; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.591173; --yyTCGTCTAA ; cor=; Ncor= a 0 0 71 108 2 5 3 11 11 58 419 375 c 0 0 117 111 17 420 3 2 326 7 5 13 g 0 0 51 102 9 2 415 15 58 1 8 19 t 0 0 196 114 407 8 14 407 40 369 3 28

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m8_shift2 (positions_6nt_m8)				; positions_6nt_m8; m=0 (reference); ncol1=10; shift=2; ncol=12; --waATAATAaw ; Alignment reference a 0 0 115 170 314 0 314 314 0 314 159 91 c 0 0 56 33 0 0 0 0 0 0 47 39 g 0 0 31 48 0 0 0 0 0 0 48 43 t 0 0 112 63 0 314 0 0 314 0 60 141
positions_6nt_m8_shift2 (positions_6nt_m8)				; positions_6nt_m8 versus positions_6nt_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --waATAATAaw ; cor=; Ncor= a 0 0 115 170 314 0 314 314 0 314 159 91 c 0 0 56 33 0 0 0 0 0 0 47 39 g 0 0 31 48 0 0 0 0 0 0 48 43 t 0 0 112 63 0 314 0 0 314 0 60 141
oligos_7nt_mkv4_m6_shift1 (oligos_7nt_mkv4_m6)				; positions_6nt_m8 versus oligos_7nt_mkv4_m6; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.618464; -whAACAATAGw ; cor=; Ncor= a 0 178 152 439 453 32 457 464 18 418 81 181 c 0 84 134 4 11 405 4 2 26 15 21 85 g 0 76 67 21 6 16 6 9 14 21 352 82 t 0 141 126 15 9 26 12 4 421 25 25 131
oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)				; positions_6nt_m8 versus oligos_6nt_mkv3_m10; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.604189; waCAACAATAaw ; cor=; Ncor= a 213 239 51 517 509 19 510 512 17 460 222 169 c 96 96 415 1 12 480 9 3 79 15 70 127 g 96 77 19 11 12 8 5 17 9 22 130 91 t 135 128 55 11 7 33 16 8 435 43 118 153

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wawAAATATww ; Alignment reference a 0 211 280 190 539 404 542 0 544 0 234 153 c 0 61 81 59 0 12 1 0 0 0 52 80 g 0 98 115 83 1 7 0 0 0 0 77 74 t 0 174 68 212 4 121 1 544 0 544 181 237
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wawAAATATww ; cor=; Ncor= a 0 211 280 190 539 404 542 0 544 0 234 153 c 0 61 81 59 0 12 1 0 0 0 52 80 g 0 98 115 83 1 7 0 0 0 0 77 74 t 0 174 68 212 4 121 1 544 0 544 181 237
positions_6nt_m7_shift1 (positions_6nt_m7)				; positions_6nt_m3 versus positions_6nt_m7; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.716412; -wwaAACTATwa ; cor=; Ncor= a 0 115 87 184 215 235 0 0 270 3 109 102 c 0 44 42 33 13 5 271 1 3 1 52 45 g 0 43 53 16 8 12 0 9 0 9 35 62 t 0 71 91 40 37 21 2 263 0 260 77 64
positions_6nt_m5_shift0 (positions_6nt_m5)				; positions_6nt_m3 versus positions_6nt_m5; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.635241; aaAAAAATwww- ; cor=; Ncor= a 386 388 800 800 800 800 800 0 299 241 263 0 c 103 105 0 0 0 0 0 0 93 115 149 0 g 155 172 0 0 0 0 0 0 118 128 115 0 t 156 135 0 0 0 0 0 800 290 316 273 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTAGACGAgra ; Alignment reference a 0 140 87 5 301 18 318 13 4 315 39 154 153 c 0 55 44 16 2 17 16 320 1 7 38 46 43 g 0 42 38 15 3 300 0 1 330 10 206 89 73 t 0 102 170 303 33 4 5 5 4 7 56 50 70
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/12; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -wwTAGACGAgra ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 153 c 0 55 44 16 2 17 16 320 1 7 38 46 43 g 0 42 38 15 3 300 0 1 330 10 206 89 73 t 0 102 170 303 33 4 5 5 4 7 56 50 70
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=2/12; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.99169; -wwTAGACGAkra ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 234 c 0 88 71 24 11 32 29 482 1 10 85 58 75 g 0 69 73 26 7 447 4 2 502 25 205 145 105 t 0 147 216 454 59 21 16 13 11 10 137 104 106
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m1_rc; m=3/12; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.903262; wwTTAGACGAgra ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 220 c 68 70 45 16 3 56 26 495 2 13 113 69 79 g 93 79 27 20 7 413 5 4 498 28 169 138 115 t 153 176 373 481 63 14 18 7 11 15 121 94 107
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_6nt_m1 versus positions_6nt_m4; m=4/12; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.878611; -wwTAGACGAcaw ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 160 c 0 52 46 14 10 56 15 401 6 5 216 57 66 g 0 61 59 21 3 320 4 2 385 15 62 79 69 t 0 122 187 354 34 13 8 4 5 3 80 44 112
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; positions_6nt_m1 versus oligos_7nt_mkv4_m10; m=5/12; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.82233; -wtTAGmCGAwa- ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 0 c 0 65 69 1 6 25 281 431 5 7 78 64 0 g 0 48 67 8 6 371 5 3 424 10 108 110 0 t 0 158 211 429 33 25 18 10 5 7 141 91 0
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; positions_6nt_m1 versus oligos_7nt_mkv4_m1_rc; m=6/12; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.810295; wwTTAGACGArr- ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 0 c 46 62 19 8 1 58 15 415 2 9 102 51 0 g 66 64 13 5 7 326 2 3 420 17 111 117 0 t 138 157 375 419 58 11 11 3 5 2 108 71 0
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; positions_6nt_m1 versus positions_7nt_m2_rc; m=7/12; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.799622; -wwTTGACGAtr- ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 0 c 0 105 66 18 12 7 32 599 6 18 142 79 0 g 0 106 125 16 10 608 22 3 617 19 139 204 0 t 0 219 262 585 478 15 23 40 27 33 246 155 0
positions_6nt_m9_rc_shift2 (positions_6nt_m9_rc)				; positions_6nt_m1 versus positions_6nt_m9_rc; m=8/12; ncol2=11; w=0; offset=1; strand=R; shift=2; score=0.769109; --wwTGACGAGra ; cor=; Ncor= a 0 0 145 130 73 16 456 17 20 440 22 170 225 c 0 0 65 57 10 8 12 443 14 21 50 72 77 g 0 0 105 70 13 444 8 10 435 15 348 132 73 t 0 0 172 230 391 19 11 17 18 11 67 113 112
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; positions_6nt_m1 versus oligos_7nt_mkv4_m4; m=9/12; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.744405; wwTTAaACGAwr- ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 0 c 61 76 33 5 3 66 22 463 5 2 106 64 0 g 95 80 17 16 8 116 11 4 463 13 106 126 0 t 147 166 399 472 18 24 14 27 20 3 148 102 0
oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m3_rc; m=10/12; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.684194; waTTArACGAd-- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 0 c 41 68 25 0 2 39 10 369 0 24 69 0 0 g 62 49 18 2 1 110 14 0 368 51 99 0 0 t 102 88 287 364 7 20 21 0 1 42 101 0 0
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; positions_6nt_m1 versus oligos_7nt_mkv4_m2; m=11/12; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.652872; wwtTACACGACcw ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 123 c 54 39 26 17 10 258 4 300 13 11 213 173 65 g 61 37 41 16 10 27 10 2 262 7 31 29 44 t 88 130 189 264 8 13 8 4 22 15 27 38 81
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m2_rc; m=12/12; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.606997; -wwTACACGACAt ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 69 c 0 45 47 27 15 243 8 305 7 8 231 50 52 g 0 43 73 20 10 38 9 7 282 8 26 7 21 t 0 108 117 227 10 17 9 2 14 9 24 29 175

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m7_shift1 (oligos_7nt_mkv4_m7)				; oligos_7nt_mkv4_m7; m=0 (reference); ncol1=11; shift=1; ncol=12; -aaAAGAAAAaa ; Alignment reference a 0 220 210 457 467 0 468 449 451 467 271 253 c 0 91 94 0 1 0 0 2 0 0 42 48 g 0 93 101 1 0 468 0 4 0 1 59 80 t 0 64 63 10 0 0 0 13 17 0 96 87
oligos_7nt_mkv4_m7_shift1 (oligos_7nt_mkv4_m7)				; oligos_7nt_mkv4_m7 versus oligos_7nt_mkv4_m7; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -aaAAGAAAAaa ; cor=; Ncor= a 0 220 210 457 467 0 468 449 451 467 271 253 c 0 91 94 0 1 0 0 2 0 0 42 48 g 0 93 101 1 0 468 0 4 0 1 59 80 t 0 64 63 10 0 0 0 13 17 0 96 87
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m7 versus oligos_6nt_mkv3_m5; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.807946; aaaAAGAAAaa- ; cor=; Ncor= a 379 339 340 758 757 0 759 751 757 394 405 0 c 80 147 162 0 5 0 1 0 0 79 77 0 g 176 160 180 1 0 763 0 2 0 139 110 0 t 128 117 81 4 1 0 3 10 6 151 171 0
positions_6nt_m5_shift4 (positions_6nt_m5)				; oligos_7nt_mkv4_m7 versus positions_6nt_m5; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.417361; ----aaAAAAAT ; cor=; Ncor= a 0 0 0 0 386 388 800 800 800 800 800 0 c 0 0 0 0 103 105 0 0 0 0 0 0 g 0 0 0 0 155 172 0 0 0 0 0 0 t 0 0 0 0 156 135 0 0 0 0 0 800

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m8_shift0 (oligos_7nt_mkv4_m8)				; oligos_7nt_mkv4_m8; m=0 (reference); ncol1=13; shift=0; ncol=13; ywaTATGCAGGwt ; Alignment reference a 29 49 66 2 119 3 10 4 127 7 10 58 33 c 38 15 14 3 0 1 0 123 3 2 0 18 33 g 27 13 24 9 9 0 124 3 2 114 107 17 20 t 41 58 31 121 7 131 1 5 3 12 18 42 49
oligos_7nt_mkv4_m8_shift0 (oligos_7nt_mkv4_m8)				; oligos_7nt_mkv4_m8 versus oligos_7nt_mkv4_m8; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ywaTATGCAGGwt ; cor=; Ncor= a 29 49 66 2 119 3 10 4 127 7 10 58 33 c 38 15 14 3 0 1 0 123 3 2 0 18 33 g 27 13 24 9 9 0 124 3 2 114 107 17 20 t 41 58 31 121 7 131 1 5 3 12 18 42 49
oligos_8nt_mkv5_m2_rc_shift1 (oligos_8nt_mkv5_m2_rc)				; oligos_7nt_mkv4_m8 versus oligos_8nt_mkv5_m2_rc; m=2/3; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.922814; -waTATGCAGGww ; cor=; Ncor= a 0 49 62 2 115 3 8 4 125 7 10 56 33 c 0 15 14 3 0 1 0 121 3 2 0 18 31 g 0 13 24 7 9 0 122 3 2 110 103 15 18 t 0 54 31 119 7 127 1 3 1 12 18 42 49
oligos_6nt_mkv3_m9_shift1 (oligos_6nt_mkv3_m9)				; oligos_7nt_mkv4_m8 versus oligos_6nt_mkv3_m9; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.703998; -waTATGCAdd-- ; cor=; Ncor= a 0 57 90 0 176 0 2 0 152 59 53 0 0 c 0 20 20 0 3 5 0 175 4 17 19 0 0 g 0 17 29 0 0 0 177 0 4 55 59 0 0 t 0 85 40 179 0 174 0 4 19 48 48 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----yyTCGTCTAAww ; Alignment reference a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 138 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 66 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 46 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152 185
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/12; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----yyTCGTCTAAww ; cor=; Ncor= a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 138 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 66 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 46 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152 185
oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=2/12; ncol2=12; w=0; offset=0; strand=R; shift=4; score=0.939175; ----ywTCGTtTAAww ; cor=; Ncor= a 0 0 0 0 102 148 3 20 27 14 24 18 472 399 166 147 c 0 0 0 0 126 106 13 463 4 11 116 8 16 17 80 95 g 0 0 0 0 64 106 2 5 463 22 66 3 5 33 76 61 t 0 0 0 0 211 143 485 15 9 456 297 474 10 54 181 200
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/12; ncol2=13; w=-1; offset=-1; strand=D; shift=3; score=0.918664; ---tycTCGTCTAAww ; cor=; Ncor= a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 153 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 93 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 68 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196 207
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m3; m=4/12; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.859026; -----hTCGTyTAAtw ; cor=; Ncor= a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 102 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 62 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 41 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164 164
oligos_7nt_mkv4_m10_rc_shift4 (oligos_7nt_mkv4_m10_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m10_rc; m=5/12; ncol2=11; w=0; offset=0; strand=R; shift=4; score=0.818909; ----twTCGkCTAaw- ; cor=; Ncor= a 0 0 0 0 91 141 7 5 10 18 25 33 429 211 158 0 c 0 0 0 0 110 108 10 424 3 5 371 6 8 67 48 0 g 0 0 0 0 64 78 7 5 431 281 25 6 1 69 65 0 t 0 0 0 0 193 131 434 24 14 154 37 413 20 111 187 0
positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)				; oligos_7nt_mkv4_m1 versus positions_7nt_m1_rc; m=6/12; ncol2=12; w=-1; offset=-1; strand=R; shift=3; score=0.813321; ---tymTCGTCTAww- ; cor=; Ncor= a 0 0 0 106 104 137 10 11 13 16 21 59 454 216 147 0 c 0 0 0 105 145 205 25 502 2 4 447 7 26 73 69 0 g 0 0 0 75 58 85 10 1 482 29 32 11 24 71 88 0 t 0 0 0 234 213 93 475 6 23 471 20 443 16 160 216 0
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; oligos_7nt_mkv4_m1 versus positions_6nt_m1_rc; m=7/12; ncol2=12; w=-1; offset=-1; strand=R; shift=3; score=0.810295; ---tycTCGTCTAww- ; cor=; Ncor= a 0 0 0 70 50 56 7 4 5 5 4 33 303 170 102 0 c 0 0 0 73 89 206 10 330 1 0 300 3 15 38 42 0 g 0 0 0 43 46 38 7 1 320 16 17 2 16 44 55 0 t 0 0 0 153 154 39 315 4 13 318 18 301 5 87 140 0
positions_7nt_m2_shift4 (positions_7nt_m2)				; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=8/12; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.79793; ----yaTCGTCAAww- ; cor=; Ncor= a 0 0 0 0 155 246 33 27 40 23 15 478 585 262 219 0 c 0 0 0 0 204 139 19 617 3 22 608 10 16 125 106 0 g 0 0 0 0 79 142 18 6 599 32 7 12 18 66 105 0 t 0 0 0 0 216 127 584 4 12 577 24 154 35 201 224 0
positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)				; oligos_7nt_mkv4_m1 versus positions_6nt_m4_rc; m=9/12; ncol2=13; w=-2; offset=-2; strand=R; shift=2; score=0.751581; --wwtgTCGTCTAww- ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 34 354 187 122 0 c 0 0 86 69 79 62 15 385 2 4 320 3 21 59 61 0 g 0 0 80 66 57 216 5 6 401 15 56 10 14 46 52 0 t 0 0 134 160 227 49 384 11 0 380 18 360 18 115 172 0
oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2_rc; m=10/12; ncol2=14; w=-2; offset=-2; strand=R; shift=2; score=0.706169; --wwgGTCGTGTAaww ; cor=; Ncor= a 0 0 90 81 38 27 15 22 4 8 13 8 264 189 130 88 c 0 0 60 44 29 31 7 262 2 10 27 10 16 41 37 61 g 0 0 64 65 173 213 11 13 300 4 258 10 17 26 39 54 t 0 0 99 123 73 42 280 16 7 291 15 285 16 57 107 110
positions_6nt_m9_shift3 (positions_6nt_m9)				; oligos_7nt_mkv4_m1 versus positions_6nt_m9; m=11/12; ncol2=11; w=-1; offset=-1; strand=D; shift=3; score=0.591173; ---tyCTCGTCAww-- ; cor=; Ncor= a 0 0 0 112 113 67 11 18 17 11 19 391 230 172 0 0 c 0 0 0 73 132 348 15 435 10 8 444 13 70 105 0 0 g 0 0 0 77 72 50 21 14 443 12 8 10 57 65 0 0 t 0 0 0 225 170 22 440 20 17 456 16 73 130 145 0 0
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m2; m=12/12; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.557701; wwwaTGTCGTGTAww- ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 0 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 0 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 0 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTAGACGAkra ; Alignment reference a 0 216 160 16 443 20 471 23 6 475 93 213 234 c 0 88 71 24 11 32 29 482 1 10 85 58 75 g 0 69 73 26 7 447 4 2 502 25 205 145 105 t 0 147 216 454 59 21 16 13 11 10 137 104 106
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/12; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -wwTAGACGAkra ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 234 c 0 88 71 24 11 32 29 482 1 10 85 58 75 g 0 69 73 26 7 447 4 2 502 25 205 145 105 t 0 147 216 454 59 21 16 13 11 10 137 104 106
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=2/12; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.99169; -wwTAGACGAgra ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 153 c 0 55 44 16 2 17 16 320 1 7 38 46 43 g 0 42 38 15 3 300 0 1 330 10 206 89 73 t 0 102 170 303 33 4 5 5 4 7 56 50 70
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; positions_7nt_m1 versus oligos_6nt_mkv3_m1_rc; m=3/12; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.906115; wwTTAGACGAgra ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 220 c 68 70 45 16 3 56 26 495 2 13 113 69 79 g 93 79 27 20 7 413 5 4 498 28 169 138 115 t 153 176 373 481 63 14 18 7 11 15 121 94 107
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_7nt_m1 versus positions_6nt_m4; m=4/12; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.89404; -wwTAGACGAcaw ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 160 c 0 52 46 14 10 56 15 401 6 5 216 57 66 g 0 61 59 21 3 320 4 2 385 15 62 79 69 t 0 122 187 354 34 13 8 4 5 3 80 44 112
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; positions_7nt_m1 versus oligos_7nt_mkv4_m10; m=5/12; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.836417; -wtTAGmCGAwa- ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 0 c 0 65 69 1 6 25 281 431 5 7 78 64 0 g 0 48 67 8 6 371 5 3 424 10 108 110 0 t 0 158 211 429 33 25 18 10 5 7 141 91 0
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; positions_7nt_m1 versus positions_7nt_m2_rc; m=6/12; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.821006; -wwTTGACGAtr- ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 0 c 0 105 66 18 12 7 32 599 6 18 142 79 0 g 0 106 125 16 10 608 22 3 617 19 139 204 0 t 0 219 262 585 478 15 23 40 27 33 246 155 0
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; positions_7nt_m1 versus oligos_7nt_mkv4_m1_rc; m=7/12; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.813321; wwTTAGACGArr- ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 0 c 46 62 19 8 1 58 15 415 2 9 102 51 0 g 66 64 13 5 7 326 2 3 420 17 111 117 0 t 138 157 375 419 58 11 11 3 5 2 108 71 0
positions_6nt_m9_rc_shift2 (positions_6nt_m9_rc)				; positions_7nt_m1 versus positions_6nt_m9_rc; m=8/12; ncol2=11; w=0; offset=1; strand=R; shift=2; score=0.759307; --wwTGACGAGra ; cor=; Ncor= a 0 0 145 130 73 16 456 17 20 440 22 170 225 c 0 0 65 57 10 8 12 443 14 21 50 72 77 g 0 0 105 70 13 444 8 10 435 15 348 132 73 t 0 0 172 230 391 19 11 17 18 11 67 113 112
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; positions_7nt_m1 versus oligos_7nt_mkv4_m4; m=9/12; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.74836; wwTTAaACGAwr- ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 0 c 61 76 33 5 3 66 22 463 5 2 106 64 0 g 95 80 17 16 8 116 11 4 463 13 106 126 0 t 147 166 399 472 18 24 14 27 20 3 148 102 0
oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)				; positions_7nt_m1 versus oligos_6nt_mkv3_m3_rc; m=10/12; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.685715; waTTArACGAd-- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 0 c 41 68 25 0 2 39 10 369 0 24 69 0 0 g 62 49 18 2 1 110 14 0 368 51 99 0 0 t 102 88 287 364 7 20 21 0 1 42 101 0 0
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; positions_7nt_m1 versus oligos_7nt_mkv4_m2; m=11/12; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.662223; wwtTACACGACcw ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 123 c 54 39 26 17 10 258 4 300 13 11 213 173 65 g 61 37 41 16 10 27 10 2 262 7 31 29 44 t 88 130 189 264 8 13 8 4 22 15 27 38 81
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; positions_7nt_m1 versus oligos_6nt_mkv3_m2_rc; m=12/12; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.619292; -wwTACACGACAt ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 69 c 0 45 47 27 15 243 8 305 7 8 231 50 52 g 0 43 73 20 10 38 9 7 282 8 26 7 21 t 0 108 117 227 10 17 9 2 14 9 24 29 175

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=13; shift=3; ncol=16; ---tycTCGTCTAAww ; Alignment reference a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 153 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 93 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 68 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196 207
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/12; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---tycTCGTCTAAww ; cor=; Ncor= a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 153 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 93 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 68 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196 207
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/12; ncol2=12; w=0; offset=1; strand=D; shift=4; score=0.918664; ----yyTCGTCTAAww ; cor=; Ncor= a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 138 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 66 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 46 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152 185
positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)				; oligos_6nt_mkv3_m1 versus positions_7nt_m1_rc; m=3/12; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.906115; ---tymTCGTCTAww- ; cor=; Ncor= a 0 0 0 106 104 137 10 11 13 16 21 59 454 216 147 0 c 0 0 0 105 145 205 25 502 2 4 447 7 26 73 69 0 g 0 0 0 75 58 85 10 1 482 29 32 11 24 71 88 0 t 0 0 0 234 213 93 475 6 23 471 20 443 16 160 216 0
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=4/12; ncol2=12; w=0; offset=0; strand=R; shift=3; score=0.903262; ---tycTCGTCTAww- ; cor=; Ncor= a 0 0 0 70 50 56 7 4 5 5 4 33 303 170 102 0 c 0 0 0 73 89 206 10 330 1 0 300 3 15 38 42 0 g 0 0 0 43 46 38 7 1 320 16 17 2 16 44 55 0 t 0 0 0 153 154 39 315 4 13 318 18 301 5 87 140 0
oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4_rc; m=5/12; ncol2=12; w=0; offset=1; strand=R; shift=4; score=0.855959; ----ywTCGTtTAAww ; cor=; Ncor= a 0 0 0 0 102 148 3 20 27 14 24 18 472 399 166 147 c 0 0 0 0 126 106 13 463 4 11 116 8 16 17 80 95 g 0 0 0 0 64 106 2 5 463 22 66 3 5 33 76 61 t 0 0 0 0 211 143 485 15 9 456 297 474 10 54 181 200
positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)				; oligos_6nt_mkv3_m1 versus positions_6nt_m4_rc; m=6/12; ncol2=13; w=-1; offset=-1; strand=R; shift=2; score=0.82907; --wwtgTCGTCTAww- ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 34 354 187 122 0 c 0 0 86 69 79 62 15 385 2 4 320 3 21 59 61 0 g 0 0 80 66 57 216 5 6 401 15 56 10 14 46 52 0 t 0 0 134 160 227 49 384 11 0 380 18 360 18 115 172 0
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3; m=7/12; ncol2=11; w=0; offset=2; strand=D; shift=5; score=0.787939; -----hTCGTyTAAtw ; cor=; Ncor= a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 102 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 62 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 41 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164 164
oligos_7nt_mkv4_m10_rc_shift4 (oligos_7nt_mkv4_m10_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m10_rc; m=8/12; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.768354; ----twTCGkCTAaw- ; cor=; Ncor= a 0 0 0 0 91 141 7 5 10 18 25 33 429 211 158 0 c 0 0 0 0 110 108 10 424 3 5 371 6 8 67 48 0 g 0 0 0 0 64 78 7 5 431 281 25 6 1 69 65 0 t 0 0 0 0 193 131 434 24 14 154 37 413 20 111 187 0
oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2_rc; m=9/12; ncol2=14; w=-1; offset=-1; strand=R; shift=2; score=0.756876; --wwgGTCGTGTAaww ; cor=; Ncor= a 0 0 90 81 38 27 15 22 4 8 13 8 264 189 130 88 c 0 0 60 44 29 31 7 262 2 10 27 10 16 41 37 61 g 0 0 64 65 173 213 11 13 300 4 258 10 17 26 39 54 t 0 0 99 123 73 42 280 16 7 291 15 285 16 57 107 110
positions_7nt_m2_shift4 (positions_7nt_m2)				; oligos_6nt_mkv3_m1 versus positions_7nt_m2; m=10/12; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.745444; ----yaTCGTCAAww- ; cor=; Ncor= a 0 0 0 0 155 246 33 27 40 23 15 478 585 262 219 0 c 0 0 0 0 204 139 19 617 3 22 608 10 16 125 106 0 g 0 0 0 0 79 142 18 6 599 32 7 12 18 66 105 0 t 0 0 0 0 216 127 584 4 12 577 24 154 35 201 224 0
positions_6nt_m9_shift3 (positions_6nt_m9)				; oligos_6nt_mkv3_m1 versus positions_6nt_m9; m=11/12; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.671232; ---tyCTCGTCAww-- ; cor=; Ncor= a 0 0 0 112 113 67 11 18 17 11 19 391 230 172 0 0 c 0 0 0 73 132 348 15 435 10 8 444 13 70 105 0 0 g 0 0 0 77 72 50 21 14 443 12 8 10 57 65 0 0 t 0 0 0 225 170 22 440 20 17 456 16 73 130 145 0 0
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m2; m=12/12; ncol2=15; w=-3; offset=-3; strand=D; shift=0; score=0.59339; wwwaTGTCGTGTAww- ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 0 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 0 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 0 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -wwTAGACGAcaww ; Alignment reference a 0 172 115 18 360 18 380 0 11 384 49 227 160 134 c 0 52 46 14 10 56 15 401 6 5 216 57 66 80 g 0 61 59 21 3 320 4 2 385 15 62 79 69 86 t 0 122 187 354 34 13 8 4 5 3 80 44 112 107
positions_6nt_m4_shift1 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/13; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -wwTAGACGAcaww ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 160 134 c 0 52 46 14 10 56 15 401 6 5 216 57 66 80 g 0 61 59 21 3 320 4 2 385 15 62 79 69 86 t 0 122 187 354 34 13 8 4 5 3 80 44 112 107
positions_7nt_m1_shift1 (positions_7nt_m1)				; positions_6nt_m4 versus positions_7nt_m1; m=2/13; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.89404; -wwTAGACGAkra- ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 234 0 c 0 88 71 24 11 32 29 482 1 10 85 58 75 0 g 0 69 73 26 7 447 4 2 502 25 205 145 105 0 t 0 147 216 454 59 21 16 13 11 10 137 104 106 0
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m4 versus positions_6nt_m1; m=3/13; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.878611; -wwTAGACGAgra- ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 153 0 c 0 55 44 16 2 17 16 320 1 7 38 46 43 0 g 0 42 38 15 3 300 0 1 330 10 206 89 73 0 t 0 102 170 303 33 4 5 5 4 7 56 50 70 0
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; positions_6nt_m4 versus oligos_6nt_mkv3_m1_rc; m=4/13; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.82907; wwTTAGACGAgra- ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 220 0 c 68 70 45 16 3 56 26 495 2 13 113 69 79 0 g 93 79 27 20 7 413 5 4 498 28 169 138 115 0 t 153 176 373 481 63 14 18 7 11 15 121 94 107 0
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; positions_6nt_m4 versus oligos_7nt_mkv4_m2; m=5/13; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.786225; wwtTACACGACcww ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 123 99 c 54 39 26 17 10 258 4 300 13 11 213 173 65 64 g 61 37 41 16 10 27 10 2 262 7 31 29 44 60 t 88 130 189 264 8 13 8 4 22 15 27 38 81 90
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; positions_6nt_m4 versus oligos_7nt_mkv4_m10; m=6/13; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.754282; -wtTAGmCGAwa-- ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 0 0 c 0 65 69 1 6 25 281 431 5 7 78 64 0 0 g 0 48 67 8 6 371 5 3 424 10 108 110 0 0 t 0 158 211 429 33 25 18 10 5 7 141 91 0 0
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; positions_6nt_m4 versus oligos_6nt_mkv3_m2_rc; m=7/13; ncol2=15; w=0; offset=0; strand=R; shift=1; score= 0.7539; -wwTACACGACAtw ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 69 82 c 0 45 47 27 15 243 8 305 7 8 231 50 52 57 g 0 43 73 20 10 38 9 7 282 8 26 7 21 55 t 0 108 117 227 10 17 9 2 14 9 24 29 175 123
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; positions_6nt_m4 versus oligos_7nt_mkv4_m1_rc; m=8/13; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.751581; wwTTAGACGArr-- ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 0 0 c 46 62 19 8 1 58 15 415 2 9 102 51 0 0 g 66 64 13 5 7 326 2 3 420 17 111 117 0 0 t 138 157 375 419 58 11 11 3 5 2 108 71 0 0
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; positions_6nt_m4 versus positions_7nt_m2_rc; m=9/13; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.733261; -wwTTGACGAtr-- ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 0 0 c 0 105 66 18 12 7 32 599 6 18 142 79 0 0 g 0 106 125 16 10 608 22 3 617 19 139 204 0 0 t 0 219 262 585 478 15 23 40 27 33 246 155 0 0
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; positions_6nt_m4 versus oligos_7nt_mkv4_m4; m=10/13; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.699844; wwTTAaACGAwr-- ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 0 0 c 61 76 33 5 3 66 22 463 5 2 106 64 0 0 g 95 80 17 16 8 116 11 4 463 13 106 126 0 0 t 147 166 399 472 18 24 14 27 20 3 148 102 0 0
positions_6nt_m9_rc_shift2 (positions_6nt_m9_rc)				; positions_6nt_m4 versus positions_6nt_m9_rc; m=11/13; ncol2=11; w=0; offset=1; strand=R; shift=2; score=0.65039; --wwTGACGAGra- ; cor=; Ncor= a 0 0 145 130 73 16 456 17 20 440 22 170 225 0 c 0 0 65 57 10 8 12 443 14 21 50 72 77 0 g 0 0 105 70 13 444 8 10 435 15 348 132 73 0 t 0 0 172 230 391 19 11 17 18 11 67 113 112 0
oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)				; positions_6nt_m4 versus oligos_6nt_mkv3_m3_rc; m=12/13; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.636814; waTTArACGAd--- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 0 0 c 41 68 25 0 2 39 10 369 0 24 69 0 0 0 g 62 49 18 2 1 110 14 0 368 51 99 0 0 0 t 102 88 287 364 7 20 21 0 1 42 101 0 0 0
oligos_7nt_mkv4_m5_rc_shift5 (oligos_7nt_mkv4_m5_rc)				; positions_6nt_m4 versus oligos_7nt_mkv4_m5_rc; m=13/13; ncol2=11; w=0; offset=4; strand=R; shift=5; score=0.421897; -----baCGACATT ; cor=; Ncor= a 0 0 0 0 0 98 182 16 14 377 11 403 34 17 c 0 0 0 0 0 111 85 402 10 8 384 15 13 22 g 0 0 0 0 0 113 83 5 378 21 26 4 12 12 t 0 0 0 0 0 116 88 15 36 32 17 16 379 387

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; wwtTACACGACcww ; Alignment reference a 110 107 57 16 285 15 291 7 16 280 42 73 123 99 c 54 39 26 17 10 258 4 300 13 11 213 173 65 64 g 61 37 41 16 10 27 10 2 262 7 31 29 44 60 t 88 130 189 264 8 13 8 4 22 15 27 38 81 90
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; wwtTACACGACcww ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 123 99 c 54 39 26 17 10 258 4 300 13 11 213 173 65 64 g 61 37 41 16 10 27 10 2 262 7 31 29 44 60 t 88 130 189 264 8 13 8 4 22 15 27 38 81 90
positions_6nt_m4_shift1 (positions_6nt_m4)				; oligos_7nt_mkv4_m2 versus positions_6nt_m4; m=2/10; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.786225; -wwTAGACGAcaww ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 160 134 c 0 52 46 14 10 56 15 401 6 5 216 57 66 80 g 0 61 59 21 3 320 4 2 385 15 62 79 69 86 t 0 122 187 354 34 13 8 4 5 3 80 44 112 107
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1_rc; m=3/10; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.756876; wwTTAGACGAgra- ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 220 0 c 68 70 45 16 3 56 26 495 2 13 113 69 79 0 g 93 79 27 20 7 413 5 4 498 28 169 138 115 0 t 153 176 373 481 63 14 18 7 11 15 121 94 107 0
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2_rc; m=4/10; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.751862; -wwTACACGACAtw ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 69 82 c 0 45 47 27 15 243 8 305 7 8 231 50 52 57 g 0 43 73 20 10 38 9 7 282 8 26 7 21 55 t 0 108 117 227 10 17 9 2 14 9 24 29 175 123
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m4; m=5/10; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.717489; wwTTAaACGAwr-- ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 0 0 c 61 76 33 5 3 66 22 463 5 2 106 64 0 0 g 95 80 17 16 8 116 11 4 463 13 106 126 0 0 t 147 166 399 472 18 24 14 27 20 3 148 102 0 0
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1_rc; m=6/10; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.706169; wwTTAGACGArr-- ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 0 0 c 46 62 19 8 1 58 15 415 2 9 102 51 0 0 g 66 64 13 5 7 326 2 3 420 17 111 117 0 0 t 138 157 375 419 58 11 11 3 5 2 108 71 0 0
positions_7nt_m1_shift1 (positions_7nt_m1)				; oligos_7nt_mkv4_m2 versus positions_7nt_m1; m=7/10; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.662223; -wwTAGACGAkra- ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 234 0 c 0 88 71 24 11 32 29 482 1 10 85 58 75 0 g 0 69 73 26 7 447 4 2 502 25 205 145 105 0 t 0 147 216 454 59 21 16 13 11 10 137 104 106 0
oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3_rc; m=8/10; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.661092; waTTArACGAd--- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 0 0 c 41 68 25 0 2 39 10 369 0 24 69 0 0 0 g 62 49 18 2 1 110 14 0 368 51 99 0 0 0 t 102 88 287 364 7 20 21 0 1 42 101 0 0 0
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_7nt_mkv4_m2 versus positions_6nt_m1; m=9/10; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.652872; -wwTAGACGAgra- ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 153 0 c 0 55 44 16 2 17 16 320 1 7 38 46 43 0 g 0 42 38 15 3 300 0 1 330 10 206 89 73 0 t 0 102 170 303 33 4 5 5 4 7 56 50 70 0
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m10; m=10/10; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.552691; -wtTAGmCGAwa-- ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 0 0 c 0 65 69 1 6 25 281 431 5 7 78 64 0 0 g 0 48 67 8 6 371 5 3 424 10 108 110 0 0 t 0 158 211 429 33 25 18 10 5 7 141 91 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; wwwaTGTCGTGTAww ; Alignment reference a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/11; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wwwaTGTCGTGTAww ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121
positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)				; oligos_6nt_mkv3_m2 versus positions_6nt_m4_rc; m=2/11; ncol2=13; w=0; offset=2; strand=R; shift=2; score= 0.7539; --wwtgTCGTCTAww ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 34 354 187 122 c 0 0 86 69 79 62 15 385 2 4 320 3 21 59 61 g 0 0 80 66 57 216 5 6 401 15 56 10 14 46 52 t 0 0 134 160 227 49 384 11 0 380 18 360 18 115 172
oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2_rc; m=3/11; ncol2=14; w=0; offset=2; strand=R; shift=2; score=0.751862; --wwgGTCGTGTAaw ; cor=; Ncor= a 0 0 90 81 38 27 15 22 4 8 13 8 264 189 130 c 0 0 60 44 29 31 7 262 2 10 27 10 16 41 37 g 0 0 64 65 173 213 11 13 300 4 258 10 17 26 39 t 0 0 99 123 73 42 280 16 7 291 15 285 16 57 107
positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)				; oligos_6nt_mkv3_m2 versus positions_7nt_m1_rc; m=4/11; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.619292; ---tymTCGTCTAww ; cor=; Ncor= a 0 0 0 106 104 137 10 11 13 16 21 59 454 216 147 c 0 0 0 105 145 205 25 502 2 4 447 7 26 73 69 g 0 0 0 75 58 85 10 1 482 29 32 11 24 71 88 t 0 0 0 234 213 93 475 6 23 471 20 443 16 160 216
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5; m=5/11; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.609236; wwAATGTCGtv---- ; cor=; Ncor= a 124 148 387 379 16 17 32 36 15 88 116 0 0 0 0 c 82 88 12 12 4 26 21 378 5 83 113 0 0 0 0 g 104 64 22 13 15 384 8 10 402 85 111 0 0 0 0 t 128 138 17 34 403 11 377 14 16 182 98 0 0 0 0
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m2 versus positions_6nt_m1_rc; m=6/11; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.606997; ---tycTCGTCTAww ; cor=; Ncor= a 0 0 0 70 50 56 7 4 5 5 4 33 303 170 102 c 0 0 0 73 89 206 10 330 1 0 300 3 15 38 42 g 0 0 0 43 46 38 7 1 320 16 17 2 16 44 55 t 0 0 0 153 154 39 315 4 13 318 18 301 5 87 140
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m1; m=7/11; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.59339; ---tycTCGTCTAAw ; cor=; Ncor= a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196
oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m4_rc; m=8/11; ncol2=12; w=0; offset=4; strand=R; shift=4; score=0.564874; ----ywTCGTtTAAw ; cor=; Ncor= a 0 0 0 0 102 148 3 20 27 14 24 18 472 399 166 c 0 0 0 0 126 106 13 463 4 11 116 8 16 17 80 g 0 0 0 0 64 106 2 5 463 22 66 3 5 33 76 t 0 0 0 0 211 143 485 15 9 456 297 474 10 54 181
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m1; m=9/11; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.557701; ----yyTCGTCTAAw ; cor=; Ncor= a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152
oligos_7nt_mkv4_m10_rc_shift4 (oligos_7nt_mkv4_m10_rc)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m10_rc; m=10/11; ncol2=11; w=0; offset=4; strand=R; shift=4; score=0.526518; ----twTCGkCTAaw ; cor=; Ncor= a 0 0 0 0 91 141 7 5 10 18 25 33 429 211 158 c 0 0 0 0 110 108 10 424 3 5 371 6 8 67 48 g 0 0 0 0 64 78 7 5 431 281 25 6 1 69 65 t 0 0 0 0 193 131 434 24 14 154 37 413 20 111 187
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3; m=11/11; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.508496; -----hTCGTyTAAt ; cor=; Ncor= a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=5; ncol=16; -----hTCGTyTAAtw ; Alignment reference a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 102 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 62 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 41 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164 164
oligos_6nt_mkv3_m3_shift5 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/11; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----hTCGTyTAAtw ; cor=; Ncor= a 0 0 0 0 0 101 42 1 0 21 20 7 364 287 88 102 c 0 0 0 0 0 99 51 368 0 14 110 1 2 18 49 62 g 0 0 0 0 0 69 24 0 369 10 39 2 0 25 68 41 t 0 0 0 0 0 100 252 0 0 324 200 359 3 39 164 164
oligos_7nt_mkv4_m4_rc_shift4 (oligos_7nt_mkv4_m4_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m4_rc; m=2/11; ncol2=12; w=-1; offset=-1; strand=R; shift=4; score=0.899372; ----ywTCGTtTAAww ; cor=; Ncor= a 0 0 0 0 102 148 3 20 27 14 24 18 472 399 166 147 c 0 0 0 0 126 106 13 463 4 11 116 8 16 17 80 95 g 0 0 0 0 64 106 2 5 463 22 66 3 5 33 76 61 t 0 0 0 0 211 143 485 15 9 456 297 474 10 54 181 200
oligos_7nt_mkv4_m1_shift4 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m1; m=3/11; ncol2=12; w=-1; offset=-1; strand=D; shift=4; score=0.859026; ----yyTCGTCTAAww ; cor=; Ncor= a 0 0 0 0 71 108 2 5 3 11 11 58 419 375 157 138 c 0 0 0 0 117 111 17 420 3 2 326 7 5 13 64 66 g 0 0 0 0 51 102 9 2 415 15 58 1 8 19 62 46 t 0 0 0 0 196 114 407 8 14 407 40 369 3 28 152 185
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=4/11; ncol2=13; w=-2; offset=-2; strand=D; shift=3; score=0.787939; ---tycTCGTCTAAww ; cor=; Ncor= a 0 0 0 107 94 121 15 11 7 18 14 63 481 373 176 153 c 0 0 0 115 138 169 28 498 4 5 413 7 20 27 79 93 g 0 0 0 79 69 113 13 2 495 26 56 3 16 45 70 68 t 0 0 0 220 220 118 465 10 15 472 38 448 4 76 196 207
oligos_7nt_mkv4_m10_rc_shift4 (oligos_7nt_mkv4_m10_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m10_rc; m=5/11; ncol2=11; w=-1; offset=-1; strand=R; shift=4; score=0.692313; ----twTCGkCTAaw- ; cor=; Ncor= a 0 0 0 0 91 141 7 5 10 18 25 33 429 211 158 0 c 0 0 0 0 110 108 10 424 3 5 371 6 8 67 48 0 g 0 0 0 0 64 78 7 5 431 281 25 6 1 69 65 0 t 0 0 0 0 193 131 434 24 14 154 37 413 20 111 187 0
positions_7nt_m1_rc_shift3 (positions_7nt_m1_rc)				; oligos_6nt_mkv3_m3 versus positions_7nt_m1_rc; m=6/11; ncol2=12; w=-2; offset=-2; strand=R; shift=3; score=0.685715; ---tymTCGTCTAww- ; cor=; Ncor= a 0 0 0 106 104 137 10 11 13 16 21 59 454 216 147 0 c 0 0 0 105 145 205 25 502 2 4 447 7 26 73 69 0 g 0 0 0 75 58 85 10 1 482 29 32 11 24 71 88 0 t 0 0 0 234 213 93 475 6 23 471 20 443 16 160 216 0
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m3 versus positions_6nt_m1_rc; m=7/11; ncol2=12; w=-2; offset=-2; strand=R; shift=3; score=0.684194; ---tycTCGTCTAww- ; cor=; Ncor= a 0 0 0 70 50 56 7 4 5 5 4 33 303 170 102 0 c 0 0 0 73 89 206 10 330 1 0 300 3 15 38 42 0 g 0 0 0 43 46 38 7 1 320 16 17 2 16 44 55 0 t 0 0 0 153 154 39 315 4 13 318 18 301 5 87 140 0
oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2_rc; m=8/11; ncol2=14; w=-3; offset=-3; strand=R; shift=2; score=0.661092; --wwgGTCGTGTAaww ; cor=; Ncor= a 0 0 90 81 38 27 15 22 4 8 13 8 264 189 130 88 c 0 0 60 44 29 31 7 262 2 10 27 10 16 41 37 61 g 0 0 64 65 173 213 11 13 300 4 258 10 17 26 39 54 t 0 0 99 123 73 42 280 16 7 291 15 285 16 57 107 110
positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)				; oligos_6nt_mkv3_m3 versus positions_6nt_m4_rc; m=9/11; ncol2=13; w=-3; offset=-3; strand=R; shift=2; score=0.636814; --wwtgTCGTCTAww- ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 34 354 187 122 0 c 0 0 86 69 79 62 15 385 2 4 320 3 21 59 61 0 g 0 0 80 66 57 216 5 6 401 15 56 10 14 46 52 0 t 0 0 134 160 227 49 384 11 0 380 18 360 18 115 172 0
positions_7nt_m2_shift4 (positions_7nt_m2)				; oligos_6nt_mkv3_m3 versus positions_7nt_m2; m=10/11; ncol2=11; w=-1; offset=-1; strand=D; shift=4; score=0.625717; ----yaTCGTCAAww- ; cor=; Ncor= a 0 0 0 0 155 246 33 27 40 23 15 478 585 262 219 0 c 0 0 0 0 204 139 19 617 3 22 608 10 16 125 106 0 g 0 0 0 0 79 142 18 6 599 32 7 12 18 66 105 0 t 0 0 0 0 216 127 584 4 12 577 24 154 35 201 224 0
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2; m=11/11; ncol2=15; w=-5; offset=-5; strand=D; shift=0; score=0.508496; wwwaTGTCGTGTAww- ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 10 227 117 108 0 c 48 68 55 21 7 26 8 282 7 9 38 10 20 73 43 0 g 74 43 57 52 50 231 8 7 305 8 243 15 27 47 45 0 t 100 101 82 69 231 36 292 14 3 291 19 282 43 80 121 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAATGTCGtv ; Alignment reference a 124 148 387 379 16 17 32 36 15 88 116 c 82 88 12 12 4 26 21 378 5 83 113 g 104 64 22 13 15 384 8 10 402 85 111 t 128 138 17 34 403 11 377 14 16 182 98
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAATGTCGtv ; cor=; Ncor= a 124 148 387 379 16 17 32 36 15 88 116 c 82 88 12 12 4 26 21 378 5 83 113 g 104 64 22 13 15 384 8 10 402 85 111 t 128 138 17 34 403 11 377 14 16 182 98
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.609236; wwwaTGTCGTG ; cor=; Ncor= a 95 105 123 175 29 24 9 14 2 9 17 c 48 68 55 21 7 26 8 282 7 9 38 g 74 43 57 52 50 231 8 7 305 8 243 t 100 101 82 69 231 36 292 14 3 291 19
positions_6nt_m4_rc_shift2 (positions_6nt_m4_rc)				; oligos_7nt_mkv4_m5 versus positions_6nt_m4_rc; m=3/3; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.421897; --wwtgTCGTC ; cor=; Ncor= a 0 0 107 112 44 80 3 5 4 8 13 c 0 0 86 69 79 62 15 385 2 4 320 g 0 0 80 66 57 216 5 6 401 15 56 t 0 0 134 160 227 49 384 11 0 380 18

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=12; shift=1; ncol=13; -waCAACAATAaw ; Alignment reference a 0 213 239 51 517 509 19 510 512 17 460 222 169 c 0 96 96 415 1 12 480 9 3 79 15 70 127 g 0 96 77 19 11 12 8 5 17 9 22 130 91 t 0 135 128 55 11 7 33 16 8 435 43 118 153
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -waCAACAATAaw ; cor=; Ncor= a 0 213 239 51 517 509 19 510 512 17 460 222 169 c 0 96 96 415 1 12 480 9 3 79 15 70 127 g 0 96 77 19 11 12 8 5 17 9 22 130 91 t 0 135 128 55 11 7 33 16 8 435 43 118 153
oligos_7nt_mkv4_m6_shift2 (oligos_7nt_mkv4_m6)				; oligos_6nt_mkv3_m10 versus oligos_7nt_mkv4_m6; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.780411; --whAACAATAGw ; cor=; Ncor= a 0 0 178 152 439 453 32 457 464 18 418 81 181 c 0 0 84 134 4 11 405 4 2 26 15 21 85 g 0 0 76 67 21 6 16 6 9 14 21 352 82 t 0 0 141 126 15 9 26 12 4 421 25 25 131
positions_6nt_m5_shift2 (positions_6nt_m5)				; oligos_6nt_mkv3_m10 versus positions_6nt_m5; m=3/5; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.642075; --aaAAAAATwww ; cor=; Ncor= a 0 0 386 388 800 800 800 800 800 0 299 241 263 c 0 0 103 105 0 0 0 0 0 0 93 115 149 g 0 0 155 172 0 0 0 0 0 0 118 128 115 t 0 0 156 135 0 0 0 0 0 800 290 316 273
oligos_8nt_mkv5_m1_shift0 (oligos_8nt_mkv5_m1)				; oligos_6nt_mkv3_m10 versus oligos_8nt_mkv5_m1; m=4/5; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.609377; maACAAaAACaa- ; cor=; Ncor= a 198 246 542 3 528 519 375 509 501 10 316 307 0 c 167 103 10 543 11 21 137 19 23 536 79 70 0 g 67 119 9 8 23 12 21 19 10 5 60 69 0 t 140 104 11 18 10 20 39 25 38 21 117 126 0
positions_6nt_m8_shift3 (positions_6nt_m8)				; oligos_6nt_mkv3_m10 versus positions_6nt_m8; m=5/5; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.604189; ---waATAATAaw ; cor=; Ncor= a 0 0 0 115 170 314 0 314 314 0 314 159 91 c 0 0 0 56 33 0 0 0 0 0 0 47 39 g 0 0 0 31 48 0 0 0 0 0 0 48 43 t 0 0 0 112 63 0 314 0 0 314 0 60 141

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift2 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --yaTCGTCAAww ; Alignment reference a 0 0 155 246 33 27 40 23 15 478 585 262 219 c 0 0 204 139 19 617 3 22 608 10 16 125 106 g 0 0 79 142 18 6 599 32 7 12 18 66 105 t 0 0 216 127 584 4 12 577 24 154 35 201 224
positions_7nt_m2_shift2 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/10; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --yaTCGTCAAww ; cor=; Ncor= a 0 0 155 246 33 27 40 23 15 478 585 262 219 c 0 0 204 139 19 617 3 22 608 10 16 125 106 g 0 0 79 142 18 6 599 32 7 12 18 66 105 t 0 0 216 127 584 4 12 577 24 154 35 201 224
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)				; positions_7nt_m2 versus positions_7nt_m1_rc; m=2/10; ncol2=12; w=-1; offset=-1; strand=R; shift=1; score=0.821006; -tymTCGTCTAww ; cor=; Ncor= a 0 106 104 137 10 11 13 16 21 59 454 216 147 c 0 105 145 205 25 502 2 4 447 7 26 73 69 g 0 75 58 85 10 1 482 29 32 11 24 71 88 t 0 234 213 93 475 6 23 471 20 443 16 160 216
oligos_7nt_mkv4_m10_rc_shift2 (oligos_7nt_mkv4_m10_rc)				; positions_7nt_m2 versus oligos_7nt_mkv4_m10_rc; m=3/10; ncol2=11; w=0; offset=0; strand=R; shift=2; score=0.80024; --twTCGkCTAaw ; cor=; Ncor= a 0 0 91 141 7 5 10 18 25 33 429 211 158 c 0 0 110 108 10 424 3 5 371 6 8 67 48 g 0 0 64 78 7 5 431 281 25 6 1 69 65 t 0 0 193 131 434 24 14 154 37 413 20 111 187
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)				; positions_7nt_m2 versus positions_6nt_m1_rc; m=4/10; ncol2=12; w=-1; offset=-1; strand=R; shift=1; score=0.799622; -tycTCGTCTAww ; cor=; Ncor= a 0 70 50 56 7 4 5 5 4 33 303 170 102 c 0 73 89 206 10 330 1 0 300 3 15 38 42 g 0 43 46 38 7 1 320 16 17 2 16 44 55 t 0 153 154 39 315 4 13 318 18 301 5 87 140
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; positions_7nt_m2 versus oligos_7nt_mkv4_m1; m=5/10; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.79793; --yyTCGTCTAAw ; cor=; Ncor= a 0 0 71 108 2 5 3 11 11 58 419 375 157 c 0 0 117 111 17 420 3 2 326 7 5 13 64 g 0 0 51 102 9 2 415 15 58 1 8 19 62 t 0 0 196 114 407 8 14 407 40 369 3 28 152
positions_6nt_m9_shift1 (positions_6nt_m9)				; positions_7nt_m2 versus positions_6nt_m9; m=6/10; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.766192; -tyCTCGTCAww- ; cor=; Ncor= a 0 112 113 67 11 18 17 11 19 391 230 172 0 c 0 73 132 348 15 435 10 8 444 13 70 105 0 g 0 77 72 50 21 14 443 12 8 10 57 65 0 t 0 225 170 22 440 20 17 456 16 73 130 145 0
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; positions_7nt_m2 versus oligos_6nt_mkv3_m1; m=7/10; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.745444; -tycTCGTCTAAw ; cor=; Ncor= a 0 107 94 121 15 11 7 18 14 63 481 373 176 c 0 115 138 169 28 498 4 5 413 7 20 27 79 g 0 79 69 113 13 2 495 26 56 3 16 45 70 t 0 220 220 118 465 10 15 472 38 448 4 76 196
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_7nt_m2 versus positions_6nt_m4_rc; m=8/10; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.733261; wwtgTCGTCTAww ; cor=; Ncor= a 107 112 44 80 3 5 4 8 13 34 354 187 122 c 86 69 79 62 15 385 2 4 320 3 21 59 61 g 80 66 57 216 5 6 401 15 56 10 14 46 52 t 134 160 227 49 384 11 0 380 18 360 18 115 172
oligos_7nt_mkv4_m4_rc_shift2 (oligos_7nt_mkv4_m4_rc)				; positions_7nt_m2 versus oligos_7nt_mkv4_m4_rc; m=9/10; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.691856; --ywTCGTtTAAw ; cor=; Ncor= a 0 0 102 148 3 20 27 14 24 18 472 399 166 c 0 0 126 106 13 463 4 11 116 8 16 17 80 g 0 0 64 106 2 5 463 22 66 3 5 33 76 t 0 0 211 143 485 15 9 456 297 474 10 54 181
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; positions_7nt_m2 versus oligos_6nt_mkv3_m3; m=10/10; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.625717; ---hTCGTyTAAt ; cor=; Ncor= a 0 0 0 101 42 1 0 21 20 7 364 287 88 c 0 0 0 99 51 368 0 14 110 1 2 18 49 g 0 0 0 69 24 0 369 10 39 2 0 25 68 t 0 0 0 100 252 0 0 324 200 359 3 39 164

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m9_shift1 (oligos_7nt_mkv4_m9)				; oligos_7nt_mkv4_m9; m=0 (reference); ncol1=11; shift=1; ncol=12; -wwCAAAATCww ; Alignment reference a 0 97 113 0 227 207 215 254 0 1 107 92 c 0 49 35 263 7 6 11 6 0 268 43 58 g 0 41 40 0 13 22 11 4 0 0 32 35 t 0 82 81 6 22 34 32 5 269 0 87 84
oligos_7nt_mkv4_m9_shift1 (oligos_7nt_mkv4_m9)				; oligos_7nt_mkv4_m9 versus oligos_7nt_mkv4_m9; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wwCAAAATCww ; cor=; Ncor= a 0 97 113 0 227 207 215 254 0 1 107 92 c 0 49 35 263 7 6 11 6 0 268 43 58 g 0 41 40 0 13 22 11 4 0 0 32 35 t 0 82 81 6 22 34 32 5 269 0 87 84
oligos_8nt_mkv5_m1_shift0 (oligos_8nt_mkv5_m1)				; oligos_7nt_mkv4_m9 versus oligos_8nt_mkv5_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.686379; maACAAaAACaa ; cor=; Ncor= a 198 246 542 3 528 519 375 509 501 10 316 307 c 167 103 10 543 11 21 137 19 23 536 79 70 g 67 119 9 8 23 12 21 19 10 5 60 69 t 140 104 11 18 10 20 39 25 38 21 117 126
positions_6nt_m6_shift4 (positions_6nt_m6)				; oligos_7nt_mkv4_m9 versus positions_6nt_m6; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.469414; ----wwAATCAA ; cor=; Ncor= a 0 0 0 0 107 80 222 245 4 4 214 237 c 0 0 0 0 59 60 13 9 0 269 10 13 g 0 0 0 0 37 42 19 6 13 2 15 17 t 0 0 0 0 72 93 21 15 258 0 36 8

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; oligos_7nt_mkv4_m10; m=0 (reference); ncol1=11; shift=1; ncol=12; -wtTAGmCGAwa ; Alignment reference a 0 187 111 20 413 37 154 14 24 434 131 193 c 0 65 69 1 6 25 281 431 5 7 78 64 g 0 48 67 8 6 371 5 3 424 10 108 110 t 0 158 211 429 33 25 18 10 5 7 141 91
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m10; m=1/11; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wtTAGmCGAwa ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 c 0 65 69 1 6 25 281 431 5 7 78 64 g 0 48 67 8 6 371 5 3 424 10 108 110 t 0 158 211 429 33 25 18 10 5 7 141 91
positions_7nt_m1_shift1 (positions_7nt_m1)				; oligos_7nt_mkv4_m10 versus positions_7nt_m1; m=2/11; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.836417; -wwTAGACGAkr ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 c 0 88 71 24 11 32 29 482 1 10 85 58 g 0 69 73 26 7 447 4 2 502 25 205 145 t 0 147 216 454 59 21 16 13 11 10 137 104
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_7nt_mkv4_m10 versus positions_6nt_m1; m=3/11; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.82233; -wwTAGACGAgr ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 c 0 55 44 16 2 17 16 320 1 7 38 46 g 0 42 38 15 3 300 0 1 330 10 206 89 t 0 102 170 303 33 4 5 5 4 7 56 50
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m1_rc; m=4/11; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.818909; wwTTAGACGArr ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 c 46 62 19 8 1 58 15 415 2 9 102 51 g 66 64 13 5 7 326 2 3 420 17 111 117 t 138 157 375 419 58 11 11 3 5 2 108 71
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; oligos_7nt_mkv4_m10 versus positions_7nt_m2_rc; m=5/11; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.80024; -wwTTGACGAtr ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 c 0 105 66 18 12 7 32 599 6 18 142 79 g 0 106 125 16 10 608 22 3 617 19 139 204 t 0 219 262 585 478 15 23 40 27 33 246 155
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m10 versus oligos_6nt_mkv3_m1_rc; m=6/11; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.768354; wwTTAGACGAgr ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 c 68 70 45 16 3 56 26 495 2 13 113 69 g 93 79 27 20 7 413 5 4 498 28 169 138 t 153 176 373 481 63 14 18 7 11 15 121 94
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m4; m=7/11; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.761833; wwTTAaACGAwr ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 c 61 76 33 5 3 66 22 463 5 2 106 64 g 95 80 17 16 8 116 11 4 463 13 106 126 t 147 166 399 472 18 24 14 27 20 3 148 102
positions_6nt_m4_shift1 (positions_6nt_m4)				; oligos_7nt_mkv4_m10 versus positions_6nt_m4; m=8/11; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.754282; -wwTAGACGAca ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 c 0 52 46 14 10 56 15 401 6 5 216 57 g 0 61 59 21 3 320 4 2 385 15 62 79 t 0 122 187 354 34 13 8 4 5 3 80 44
oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m10 versus oligos_6nt_mkv3_m3_rc; m=9/11; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.692313; waTTArACGAd- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 c 41 68 25 0 2 39 10 369 0 24 69 0 g 62 49 18 2 1 110 14 0 368 51 99 0 t 102 88 287 364 7 20 21 0 1 42 101 0
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m10 versus oligos_7nt_mkv4_m2; m=10/11; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.552691; wwtTACACGACc ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 c 54 39 26 17 10 258 4 300 13 11 213 173 g 61 37 41 16 10 27 10 2 262 7 31 29 t 88 130 189 264 8 13 8 4 22 15 27 38
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; oligos_7nt_mkv4_m10 versus oligos_6nt_mkv3_m2_rc; m=11/11; ncol2=15; w=0; offset=0; strand=R; shift=1; score=0.526518; -wwTACACGACA ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 c 0 45 47 27 15 243 8 305 7 8 231 50 g 0 43 73 20 10 38 9 7 282 8 26 7 t 0 108 117 227 10 17 9 2 14 9 24 29

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m9_shift2 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=2; ncol=12; --waTATGCAdd ; Alignment reference a 0 0 57 90 0 176 0 2 0 152 59 53 c 0 0 20 20 0 3 5 0 175 4 17 19 g 0 0 17 29 0 0 0 177 0 4 55 59 t 0 0 85 40 179 0 174 0 4 19 48 48
oligos_6nt_mkv3_m9_shift2 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --waTATGCAdd ; cor=; Ncor= a 0 0 57 90 0 176 0 2 0 152 59 53 c 0 0 20 20 0 3 5 0 175 4 17 19 g 0 0 17 29 0 0 0 177 0 4 55 59 t 0 0 85 40 179 0 174 0 4 19 48 48
oligos_8nt_mkv5_m2_rc_shift2 (oligos_8nt_mkv5_m2_rc)				; oligos_6nt_mkv3_m9 versus oligos_8nt_mkv5_m2_rc; m=2/4; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.764437; --waTATGCAGG ; cor=; Ncor= a 0 0 49 62 2 115 3 8 4 125 7 10 c 0 0 15 14 3 0 1 0 121 3 2 0 g 0 0 13 24 7 9 0 122 3 2 110 103 t 0 0 54 31 119 7 127 1 3 1 12 18
oligos_7nt_mkv4_m8_shift1 (oligos_7nt_mkv4_m8)				; oligos_6nt_mkv3_m9 versus oligos_7nt_mkv4_m8; m=3/4; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.703998; -ywaTATGCAGG ; cor=; Ncor= a 0 29 49 66 2 119 3 10 4 127 7 10 c 0 38 15 14 3 0 1 0 123 3 2 0 g 0 27 13 24 9 9 0 124 3 2 114 107 t 0 41 58 31 121 7 131 1 5 3 12 18
oligos_6nt_mkv3_m8_rc_shift0 (oligos_6nt_mkv3_m8_rc)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m8_rc; m=4/4; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.556927; tdTgTATGTAwr ; cor=; Ncor= a 102 127 69 83 11 367 15 65 7 373 137 162 c 63 76 30 24 12 8 3 8 11 4 66 42 g 52 103 27 260 2 24 10 328 8 17 44 107 t 193 104 284 43 385 11 382 9 384 16 163 99

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv5_m2_shift0 (oligos_8nt_mkv5_m2)				; oligos_8nt_mkv5_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; wwCCTGCATAtw ; Alignment reference a 49 42 18 12 1 3 1 127 7 119 31 54 c 18 15 103 110 2 3 122 0 9 7 24 13 g 31 18 0 2 3 121 0 1 0 3 14 15 t 33 56 10 7 125 4 8 3 115 2 62 49
oligos_8nt_mkv5_m2_shift0 (oligos_8nt_mkv5_m2)				; oligos_8nt_mkv5_m2 versus oligos_8nt_mkv5_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwCCTGCATAtw ; cor=; Ncor= a 49 42 18 12 1 3 1 127 7 119 31 54 c 18 15 103 110 2 3 122 0 9 7 24 13 g 31 18 0 2 3 121 0 1 0 3 14 15 t 33 56 10 7 125 4 8 3 115 2 62 49
oligos_7nt_mkv4_m8_rc_shift0 (oligos_7nt_mkv4_m8_rc)				; oligos_8nt_mkv5_m2 versus oligos_7nt_mkv4_m8_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.922814; awCCTGCATAtw ; cor=; Ncor= a 49 42 18 12 3 5 1 131 7 121 31 58 c 20 17 107 114 2 3 124 0 9 9 24 13 g 33 18 0 2 3 123 0 1 0 3 14 15 t 33 58 10 7 127 4 10 3 119 2 66 49
oligos_6nt_mkv3_m9_rc_shift2 (oligos_6nt_mkv3_m9_rc)				; oligos_8nt_mkv5_m2 versus oligos_6nt_mkv3_m9_rc; m=3/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.764437; --hhTGCATAtw ; cor=; Ncor= a 0 0 48 48 19 4 0 174 0 179 40 85 c 0 0 59 55 4 0 177 0 0 0 29 17 g 0 0 19 17 4 175 0 5 3 0 20 20 t 0 0 53 59 152 0 2 0 176 0 90 57

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift3 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---aaAAAAATwww ; Alignment reference a 0 0 0 386 388 800 800 800 800 800 0 299 241 263 c 0 0 0 103 105 0 0 0 0 0 0 93 115 149 g 0 0 0 155 172 0 0 0 0 0 0 118 128 115 t 0 0 0 156 135 0 0 0 0 0 800 290 316 273
positions_6nt_m5_shift3 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---aaAAAAATwww ; cor=; Ncor= a 0 0 0 386 388 800 800 800 800 800 0 299 241 263 c 0 0 0 103 105 0 0 0 0 0 0 93 115 149 g 0 0 0 155 172 0 0 0 0 0 0 118 128 115 t 0 0 0 156 135 0 0 0 0 0 800 290 316 273
oligos_7nt_mkv4_m6_shift3 (oligos_7nt_mkv4_m6)				; positions_6nt_m5 versus oligos_7nt_mkv4_m6; m=2/5; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.663837; ---whAACAATAGw ; cor=; Ncor= a 0 0 0 178 152 439 453 32 457 464 18 418 81 181 c 0 0 0 84 134 4 11 405 4 2 26 15 21 85 g 0 0 0 76 67 21 6 16 6 9 14 21 352 82 t 0 0 0 141 126 15 9 26 12 4 421 25 25 131
oligos_6nt_mkv3_m10_shift2 (oligos_6nt_mkv3_m10)				; positions_6nt_m5 versus oligos_6nt_mkv3_m10; m=3/5; ncol2=12; w=-1; offset=-1; strand=D; shift=2; score=0.642075; --waCAACAATAaw ; cor=; Ncor= a 0 0 213 239 51 517 509 19 510 512 17 460 222 169 c 0 0 96 96 415 1 12 480 9 3 79 15 70 127 g 0 0 96 77 19 11 12 8 5 17 9 22 130 91 t 0 0 135 128 55 11 7 33 16 8 435 43 118 153
positions_6nt_m3_shift4 (positions_6nt_m3)				; positions_6nt_m5 versus positions_6nt_m3; m=4/5; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.635241; ----wawAAATATw ; cor=; Ncor= a 0 0 0 0 211 280 190 539 404 542 0 544 0 234 c 0 0 0 0 61 81 59 0 12 1 0 0 0 52 g 0 0 0 0 98 115 83 1 7 0 0 0 0 77 t 0 0 0 0 174 68 212 4 121 1 544 0 544 181
oligos_7nt_mkv4_m7_shift0 (oligos_7nt_mkv4_m7)				; positions_6nt_m5 versus oligos_7nt_mkv4_m7; m=5/5; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.417361; aaAAGAAAAaa--- ; cor=; Ncor= a 220 210 457 467 0 468 449 451 467 271 253 0 0 0 c 91 94 0 1 0 0 2 0 0 42 48 0 0 0 g 93 101 1 0 468 0 4 0 1 59 80 0 0 0 t 64 63 10 0 0 0 13 17 0 96 87 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwTTAaACGAwr ; Alignment reference a 200 181 54 10 474 297 456 9 15 485 143 211 c 61 76 33 5 3 66 22 463 5 2 106 64 g 95 80 17 16 8 116 11 4 463 13 106 126 t 147 166 399 472 18 24 14 27 20 3 148 102
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/11; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAaACGAwr ; cor=; Ncor= a 200 181 54 10 474 297 456 9 15 485 143 211 c 61 76 33 5 3 66 22 463 5 2 106 64 g 95 80 17 16 8 116 11 4 463 13 106 126 t 147 166 399 472 18 24 14 27 20 3 148 102
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=2/11; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.939175; wwTTAGACGArr ; cor=; Ncor= a 185 152 28 3 369 40 407 14 8 407 114 196 c 46 62 19 8 1 58 15 415 2 9 102 51 g 66 64 13 5 7 326 2 3 420 17 111 117 t 138 157 375 419 58 11 11 3 5 2 108 71
oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m3_rc; m=3/11; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.899372; waTTArACGAd- ; cor=; Ncor= a 164 164 39 3 359 200 324 0 0 252 100 0 c 41 68 25 0 2 39 10 369 0 24 69 0 g 62 49 18 2 1 110 14 0 368 51 99 0 t 102 88 287 364 7 20 21 0 1 42 101 0
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m1_rc; m=4/11; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.855959; wwTTAGACGAgr ; cor=; Ncor= a 207 196 76 4 448 38 472 15 10 465 118 220 c 68 70 45 16 3 56 26 495 2 13 113 69 g 93 79 27 20 7 413 5 4 498 28 169 138 t 153 176 373 481 63 14 18 7 11 15 121 94
oligos_7nt_mkv4_m10_shift1 (oligos_7nt_mkv4_m10)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m10; m=5/11; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.761833; -wtTAGmCGAwa ; cor=; Ncor= a 0 187 111 20 413 37 154 14 24 434 131 193 c 0 65 69 1 6 25 281 431 5 7 78 64 g 0 48 67 8 6 371 5 3 424 10 108 110 t 0 158 211 429 33 25 18 10 5 7 141 91
positions_7nt_m1_shift1 (positions_7nt_m1)				; oligos_7nt_mkv4_m4 versus positions_7nt_m1; m=6/11; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.74836; -wwTAGACGAkr ; cor=; Ncor= a 0 216 160 16 443 20 471 23 6 475 93 213 c 0 88 71 24 11 32 29 482 1 10 85 58 g 0 69 73 26 7 447 4 2 502 25 205 145 t 0 147 216 454 59 21 16 13 11 10 137 104
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_7nt_mkv4_m4 versus positions_6nt_m1; m=7/11; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.744405; -wwTAGACGAgr ; cor=; Ncor= a 0 140 87 5 301 18 318 13 4 315 39 154 c 0 55 44 16 2 17 16 320 1 7 38 46 g 0 42 38 15 3 300 0 1 330 10 206 89 t 0 102 170 303 33 4 5 5 4 7 56 50
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m2; m=8/11; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.717489; wwtTACACGACc ; cor=; Ncor= a 110 107 57 16 285 15 291 7 16 280 42 73 c 54 39 26 17 10 258 4 300 13 11 213 173 g 61 37 41 16 10 27 10 2 262 7 31 29 t 88 130 189 264 8 13 8 4 22 15 27 38
positions_6nt_m4_shift1 (positions_6nt_m4)				; oligos_7nt_mkv4_m4 versus positions_6nt_m4; m=9/11; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.699844; -wwTAGACGAca ; cor=; Ncor= a 0 172 115 18 360 18 380 0 11 384 49 227 c 0 52 46 14 10 56 15 401 6 5 216 57 g 0 61 59 21 3 320 4 2 385 15 62 79 t 0 122 187 354 34 13 8 4 5 3 80 44
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)				; oligos_7nt_mkv4_m4 versus positions_7nt_m2_rc; m=10/11; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.691856; -wwTTGACGAtr ; cor=; Ncor= a 0 224 201 35 154 24 577 12 4 584 127 216 c 0 105 66 18 12 7 32 599 6 18 142 79 g 0 106 125 16 10 608 22 3 617 19 139 204 t 0 219 262 585 478 15 23 40 27 33 246 155
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m2_rc; m=11/11; ncol2=15; w=0; offset=1; strand=R; shift=1; score=0.564874; -wwTACACGACA ; cor=; Ncor= a 0 121 80 43 282 19 291 3 14 292 36 231 c 0 45 47 27 15 243 8 305 7 8 231 50 g 0 43 73 20 10 38 9 7 282 8 26 7 t 0 108 117 227 10 17 9 2 14 9 24 29