One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.224716_2025-12-18.224716_XiuaJ3/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.224716_2025-12-18.224716_XiuaJ3/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---csCCGCCTCCss ; Alignment reference a 0 0 0 122 107 17 32 45 22 7 43 6 18 166 100 c 0 0 0 449 361 826 828 24 849 869 93 864 862 285 368 g 0 0 0 191 281 59 46 818 41 29 128 31 30 289 303 t 0 0 0 169 182 29 25 44 19 26 667 30 21 191 160

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---csCCGCCTCCss ; cor=; Ncor= a 0 0 0 122 107 17 32 45 22 7 43 6 18 166 100 c 0 0 0 449 361 826 828 24 849 869 93 864 862 285 368 g 0 0 0 191 281 59 46 818 41 29 128 31 30 289 303 t 0 0 0 169 182 29 25 44 19 26 667 30 21 191 160

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2; m=2/3; ncol2=15; w=-3; offset=-3; strand=D; shift=0; score=0.674666; ssGCCCCGCCCCCss ; cor=; Ncor= a 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 c 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 g 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 t 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m4; m=3/3; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.53974; cscCCCCACCCCCAs ; cor=; Ncor= a 74 84 60 36 32 24 19 356 20 25 19 29 14 337 73 c 196 151 268 338 381 405 424 7 423 401 385 407 432 46 201 g 117 162 82 60 29 23 19 81 21 25 41 20 21 57 142 t 89 79 66 42 34 24 14 32 12 25 31 20 9 36 60

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----ssGCGGAGCss ; Alignment reference a 0 0 0 0 128 107 25 14 19 18 592 14 28 118 96 c 0 0 0 0 244 320 57 738 46 56 94 28 679 245 244 g 0 0 0 0 302 257 671 15 701 692 57 719 52 284 326 t 0 0 0 0 106 96 27 13 14 14 37 19 21 133 114

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----ssGCGGAGCss ; cor=; Ncor= a 0 0 0 0 128 107 25 14 19 18 592 14 28 118 96 c 0 0 0 0 244 320 57 738 46 56 94 28 679 245 244 g 0 0 0 0 302 257 671 15 701 692 57 719 52 284 326 t 0 0 0 0 106 96 27 13 14 14 37 19 21 133 114

oligos_6nt_mkv3_m2_rc_shift4 (oligos_6nt_mkv3_m2_rc)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2_rc; m=2/3; ncol2=14; w=0; offset=0; strand=R; shift=4; score=0.62915; ----ssGCGGGGCGG ; cor=; Ncor= a 0 0 0 0 97 120 37 52 28 27 33 17 26 24 41 c 0 0 0 0 213 255 103 636 55 69 71 40 744 82 116 g 0 0 0 0 410 329 622 84 699 700 686 733 15 684 587 t 0 0 0 0 90 106 48 38 28 14 20 20 25 20 66

oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2_rc; m=3/3; ncol2=15; w=-4; offset=-4; strand=R; shift=0; score=0.578357; ssGGGGGCGGGGCss ; cor=; Ncor= a 120 130 53 36 56 28 19 39 38 15 53 27 60 95 110 c 256 283 83 53 65 69 69 691 43 49 62 47 583 286 204 g 319 235 626 659 653 670 685 21 689 704 661 687 114 285 344 t 97 144 30 44 18 25 19 41 22 24 16 31 35 126 134

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; stgcCAGGACCTgss ; Alignment reference a 88 166 94 70 47 649 9 10 565 18 13 32 74 112 162 c 331 153 121 439 602 11 18 24 24 660 659 94 117 212 219 g 194 173 355 119 30 38 676 666 26 21 16 50 415 264 198 t 96 217 139 81 30 11 6 9 94 10 21 533 103 121 130

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; stgcCAGGACCTgss ; cor=; Ncor= a 88 166 94 70 47 649 9 10 565 18 13 32 74 112 162 c 331 153 121 439 602 11 18 24 24 660 659 94 117 212 219 g 194 173 355 119 30 38 676 666 26 21 16 50 415 264 198 t 96 217 139 81 30 11 6 9 94 10 21 533 103 121 130

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/2; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.924535; -tgcCAGGACCTGss ; cor=; Ncor= a 0 155 132 58 42 584 13 7 506 19 8 18 45 110 143 c 0 155 145 411 551 13 20 30 21 585 599 55 66 193 203 g 0 148 216 113 28 41 607 597 18 26 18 19 482 236 182 t 0 189 154 65 26 9 7 13 102 17 22 555 54 108 119

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=14; shift=2; ncol=16; --ssCCCGCCCCGCss ; Alignment reference a 0 0 112 84 35 66 20 25 20 20 14 28 38 48 106 90 c 0 0 316 358 636 587 684 15 733 686 700 699 84 622 329 410 g 0 0 260 218 90 116 82 744 40 71 69 55 636 103 255 213 t 0 0 122 150 49 41 24 26 17 33 27 28 52 37 120 97

oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --ssCCCGCCCCGCss ; cor=; Ncor= a 0 0 112 84 35 66 20 25 20 20 14 28 38 48 106 90 c 0 0 316 358 636 587 684 15 733 686 700 699 84 622 329 410 g 0 0 260 218 90 116 82 744 40 71 69 55 636 103 255 213 t 0 0 122 150 49 41 24 26 17 33 27 28 52 37 120 97

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.666639; ssGCCCCGCCCCCss- ; cor=; Ncor= a 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 0 c 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 0 g 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 0 t 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120 0

oligos_6nt_mkv3_m3_rc_shift5 (oligos_6nt_mkv3_m3_rc)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3_rc; m=3/4; ncol2=11; w=0; offset=3; strand=R; shift=5; score=0.62915; -----ssGCTCCGCss ; cor=; Ncor= a 0 0 0 0 0 114 133 21 19 37 14 14 13 27 96 106 c 0 0 0 0 0 326 284 52 719 57 692 701 15 671 257 302 g 0 0 0 0 0 244 245 679 28 94 56 46 738 57 320 244 t 0 0 0 0 0 96 118 28 14 592 18 19 14 25 107 128

oligos_7nt_mkv4_m5_rc_shift4 (oligos_7nt_mkv4_m5_rc)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5_rc; m=4/4; ncol2=13; w=0; offset=2; strand=R; shift=4; score=0.587328; ----cvGGCCCTGCCc ; cor=; Ncor= a 0 0 0 0 83 146 27 7 27 16 7 22 6 10 29 80 c 0 0 0 0 262 150 105 19 493 470 520 83 13 490 442 251 g 0 0 0 0 118 158 384 506 9 32 15 34 512 26 49 112 t 0 0 0 0 82 91 29 13 16 27 3 406 14 19 25 102

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 2 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=13; shift=0; ncol=13; rrAAAGAAAGgar ; Alignment reference a 150 128 298 375 374 17 377 385 390 33 79 132 142 c 72 83 34 14 13 14 9 13 7 36 49 89 85 g 118 126 50 16 20 369 16 14 8 319 241 103 111 t 77 80 35 12 10 17 15 5 12 29 48 93 79

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rrAAAGAAAGgar ; cor=; Ncor= a 150 128 298 375 374 17 377 385 390 33 79 132 142 c 72 83 34 14 13 14 9 13 7 36 49 89 85 g 118 126 50 16 20 369 16 14 8 319 241 103 111 t 77 80 35 12 10 17 15 5 12 29 48 93 79

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=11; shift=0; ncol=11; ssGCCAGGCss ; Alignment reference a 73 78 22 18 2 406 6 16 8 75 63 c 153 188 3 432 425 31 38 9 453 130 176 g 159 129 442 12 41 31 424 444 5 186 158 t 93 83 11 16 10 10 10 9 12 87 81

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssGCCAGGCss ; cor=; Ncor= a 73 78 22 18 2 406 6 16 8 75 63 c 153 188 3 432 425 31 38 9 453 130 176 g 159 129 442 12 41 31 424 444 5 186 158 t 93 83 11 16 10 10 10 9 12 87 81

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 4 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=16; shift=0; ncol=16; cscCCCCACCCCCAsc ; Alignment reference a 74 84 60 36 32 24 19 356 20 25 19 29 14 337 73 89 c 196 151 268 338 381 405 424 7 423 401 385 407 432 46 201 218 g 117 162 82 60 29 23 19 81 21 25 41 20 21 57 142 110 t 89 79 66 42 34 24 14 32 12 25 31 20 9 36 60 59

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cscCCCCACCCCCAsc ; cor=; Ncor= a 74 84 60 36 32 24 19 356 20 25 19 29 14 337 73 89 c 196 151 268 338 381 405 424 7 423 401 385 407 432 46 201 218 g 117 162 82 60 29 23 19 81 21 25 41 20 21 57 142 110 t 89 79 66 42 34 24 14 32 12 25 31 20 9 36 60 59

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m2; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.762648; ssGCCCCGCCCCCss- ; cor=; Ncor= a 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 0 c 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 0 g 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 0 t 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120 0

oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m3; m=3/3; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.53974; ---csCCGCCTCCss- ; cor=; Ncor= a 0 0 0 122 107 17 32 45 22 7 43 6 18 166 100 0 c 0 0 0 449 361 826 828 24 849 869 93 864 862 285 368 0 g 0 0 0 191 281 59 46 818 41 29 128 31 30 289 303 0 t 0 0 0 169 182 29 25 44 19 26 667 30 21 191 160 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -tgcCAGGACCTGss ; Alignment reference a 0 155 132 58 42 584 13 7 506 19 8 18 45 110 143 c 0 155 145 411 551 13 20 30 21 585 599 55 66 193 203 g 0 148 216 113 28 41 607 597 18 26 18 19 482 236 182 t 0 189 154 65 26 9 7 13 102 17 22 555 54 108 119

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -tgcCAGGACCTGss ; cor=; Ncor= a 0 155 132 58 42 584 13 7 506 19 8 18 45 110 143 c 0 155 145 411 551 13 20 30 21 585 599 55 66 193 203 g 0 148 216 113 28 41 607 597 18 26 18 19 482 236 182 t 0 189 154 65 26 9 7 13 102 17 22 555 54 108 119

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=2/2; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.924535; stgcCAGGACCTgss ; cor=; Ncor= a 88 166 94 70 47 649 9 10 565 18 13 32 74 112 162 c 331 153 121 439 602 11 18 24 24 660 659 94 117 212 219 g 194 173 355 119 30 38 676 666 26 21 16 50 415 264 198 t 96 217 139 81 30 11 6 9 94 10 21 533 103 121 130

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=13; shift=3; ncol=16; ---sgGGCAGGGCCbg ; Alignment reference a 0 0 0 82 102 25 19 14 406 3 27 16 13 29 91 82 c 0 0 0 161 112 49 26 512 34 15 32 9 506 384 158 118 g 0 0 0 217 251 442 490 13 83 520 470 493 19 105 150 262 t 0 0 0 85 80 29 10 6 22 7 16 27 7 27 146 83

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---sgGGCAGGGCCbg ; cor=; Ncor= a 0 0 0 82 102 25 19 14 406 3 27 16 13 29 91 82 c 0 0 0 161 112 49 26 512 34 15 32 9 506 384 158 118 g 0 0 0 217 251 442 490 13 83 520 470 493 19 105 150 262 t 0 0 0 85 80 29 10 6 22 7 16 27 7 27 146 83

oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.615379; ssGGGGGCGGGGCss- ; cor=; Ncor= a 120 130 53 36 56 28 19 39 38 15 53 27 60 95 110 0 c 256 283 83 53 65 69 69 691 43 49 62 47 583 286 204 0 g 319 235 626 659 653 670 685 21 689 704 661 687 114 285 344 0 t 97 144 30 44 18 25 19 41 22 24 16 31 35 126 134 0

oligos_6nt_mkv3_m2_rc_shift4 (oligos_6nt_mkv3_m2_rc)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2_rc; m=3/3; ncol2=14; w=0; offset=1; strand=R; shift=4; score=0.587328; ----ssGCGGGGCGGG ; cor=; Ncor= a 0 0 0 0 97 120 37 52 28 27 33 17 26 24 41 49 c 0 0 0 0 213 255 103 636 55 69 71 40 744 82 116 90 g 0 0 0 0 410 329 622 84 699 700 686 733 15 684 587 636 t 0 0 0 0 90 106 48 38 28 14 20 20 25 20 66 35

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssGCCCCGCCCCCss ; Alignment reference a 0 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 c 0 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 g 0 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 t 0 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120

oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCCCGCCCCCss ; cor=; Ncor= a 0 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 c 0 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 g 0 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 t 0 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120

oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m4; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.762648; -cscCCCCACCCCCAs ; cor=; Ncor= a 0 74 84 60 36 32 24 19 356 20 25 19 29 14 337 73 c 0 196 151 268 338 381 405 424 7 423 401 385 407 432 46 201 g 0 117 162 82 60 29 23 19 81 21 25 41 20 21 57 142 t 0 89 79 66 42 34 24 14 32 12 25 31 20 9 36 60

oligos_7nt_mkv4_m3_shift4 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=3/6; ncol2=12; w=0; offset=3; strand=D; shift=4; score=0.674666; ----csCCGCCTCCss ; cor=; Ncor= a 0 0 0 0 122 107 17 32 45 22 7 43 6 18 166 100 c 0 0 0 0 449 361 826 828 24 849 869 93 864 862 285 368 g 0 0 0 0 191 281 59 46 818 41 29 128 31 30 289 303 t 0 0 0 0 169 182 29 25 44 19 26 667 30 21 191 160

oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2; m=4/6; ncol2=14; w=0; offset=2; strand=D; shift=3; score=0.666639; ---ssCCCGCCCCGCs ; cor=; Ncor= a 0 0 0 112 84 35 66 20 25 20 20 14 28 38 48 106 c 0 0 0 316 358 636 587 684 15 733 686 700 699 84 622 329 g 0 0 0 260 218 90 116 82 744 40 71 69 55 636 103 255 t 0 0 0 122 150 49 41 24 26 17 33 27 28 52 37 120

oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5_rc; m=5/6; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.615379; cvGGCCCTGCCcs--- ; cor=; Ncor= a 83 146 27 7 27 16 7 22 6 10 29 80 85 0 0 0 c 262 150 105 19 493 470 520 83 13 490 442 251 217 0 0 0 g 118 158 384 506 9 32 15 34 512 26 49 112 161 0 0 0 t 82 91 29 13 16 27 3 406 14 19 25 102 82 0 0 0

oligos_6nt_mkv3_m3_rc_shift1 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3_rc; m=6/6; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.578357; -ssGCTCCGCss---- ; cor=; Ncor= a 0 114 133 21 19 37 14 14 13 27 96 106 0 0 0 0 c 0 326 284 52 719 57 692 701 15 671 257 302 0 0 0 0 g 0 244 245 679 28 94 56 46 738 57 320 244 0 0 0 0 t 0 96 118 28 14 592 18 19 14 25 107 128 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---csCCGCCTCCss ; Alignment reference a 0 0 0 122 107 17 32 45 22 7 43 6 18 166 100 c 0 0 0 449 361 826 828 24 849 869 93 864 862 285 368 g 0 0 0 191 281 59 46 818 41 29 128 31 30 289 303 t 0 0 0 169 182 29 25 44 19 26 667 30 21 191 160
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---csCCGCCTCCss ; cor=; Ncor= a 0 0 0 122 107 17 32 45 22 7 43 6 18 166 100 c 0 0 0 449 361 826 828 24 849 869 93 864 862 285 368 g 0 0 0 191 281 59 46 818 41 29 128 31 30 289 303 t 0 0 0 169 182 29 25 44 19 26 667 30 21 191 160
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2; m=2/3; ncol2=15; w=-3; offset=-3; strand=D; shift=0; score=0.674666; ssGCCCCGCCCCCss ; cor=; Ncor= a 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 c 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 g 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 t 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m4; m=3/3; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.53974; cscCCCCACCCCCAs ; cor=; Ncor= a 74 84 60 36 32 24 19 356 20 25 19 29 14 337 73 c 196 151 268 338 381 405 424 7 423 401 385 407 432 46 201 g 117 162 82 60 29 23 19 81 21 25 41 20 21 57 142 t 89 79 66 42 34 24 14 32 12 25 31 20 9 36 60

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----ssGCGGAGCss ; Alignment reference a 0 0 0 0 128 107 25 14 19 18 592 14 28 118 96 c 0 0 0 0 244 320 57 738 46 56 94 28 679 245 244 g 0 0 0 0 302 257 671 15 701 692 57 719 52 284 326 t 0 0 0 0 106 96 27 13 14 14 37 19 21 133 114
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----ssGCGGAGCss ; cor=; Ncor= a 0 0 0 0 128 107 25 14 19 18 592 14 28 118 96 c 0 0 0 0 244 320 57 738 46 56 94 28 679 245 244 g 0 0 0 0 302 257 671 15 701 692 57 719 52 284 326 t 0 0 0 0 106 96 27 13 14 14 37 19 21 133 114
oligos_6nt_mkv3_m2_rc_shift4 (oligos_6nt_mkv3_m2_rc)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2_rc; m=2/3; ncol2=14; w=0; offset=0; strand=R; shift=4; score=0.62915; ----ssGCGGGGCGG ; cor=; Ncor= a 0 0 0 0 97 120 37 52 28 27 33 17 26 24 41 c 0 0 0 0 213 255 103 636 55 69 71 40 744 82 116 g 0 0 0 0 410 329 622 84 699 700 686 733 15 684 587 t 0 0 0 0 90 106 48 38 28 14 20 20 25 20 66
oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2_rc; m=3/3; ncol2=15; w=-4; offset=-4; strand=R; shift=0; score=0.578357; ssGGGGGCGGGGCss ; cor=; Ncor= a 120 130 53 36 56 28 19 39 38 15 53 27 60 95 110 c 256 283 83 53 65 69 69 691 43 49 62 47 583 286 204 g 319 235 626 659 653 670 685 21 689 704 661 687 114 285 344 t 97 144 30 44 18 25 19 41 22 24 16 31 35 126 134

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=14; shift=2; ncol=16; --ssCCCGCCCCGCss ; Alignment reference a 0 0 112 84 35 66 20 25 20 20 14 28 38 48 106 90 c 0 0 316 358 636 587 684 15 733 686 700 699 84 622 329 410 g 0 0 260 218 90 116 82 744 40 71 69 55 636 103 255 213 t 0 0 122 150 49 41 24 26 17 33 27 28 52 37 120 97
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --ssCCCGCCCCGCss ; cor=; Ncor= a 0 0 112 84 35 66 20 25 20 20 14 28 38 48 106 90 c 0 0 316 358 636 587 684 15 733 686 700 699 84 622 329 410 g 0 0 260 218 90 116 82 744 40 71 69 55 636 103 255 213 t 0 0 122 150 49 41 24 26 17 33 27 28 52 37 120 97
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.666639; ssGCCCCGCCCCCss- ; cor=; Ncor= a 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 0 c 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 0 g 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 0 t 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120 0
oligos_6nt_mkv3_m3_rc_shift5 (oligos_6nt_mkv3_m3_rc)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3_rc; m=3/4; ncol2=11; w=0; offset=3; strand=R; shift=5; score=0.62915; -----ssGCTCCGCss ; cor=; Ncor= a 0 0 0 0 0 114 133 21 19 37 14 14 13 27 96 106 c 0 0 0 0 0 326 284 52 719 57 692 701 15 671 257 302 g 0 0 0 0 0 244 245 679 28 94 56 46 738 57 320 244 t 0 0 0 0 0 96 118 28 14 592 18 19 14 25 107 128
oligos_7nt_mkv4_m5_rc_shift4 (oligos_7nt_mkv4_m5_rc)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5_rc; m=4/4; ncol2=13; w=0; offset=2; strand=R; shift=4; score=0.587328; ----cvGGCCCTGCCc ; cor=; Ncor= a 0 0 0 0 83 146 27 7 27 16 7 22 6 10 29 80 c 0 0 0 0 262 150 105 19 493 470 520 83 13 490 442 251 g 0 0 0 0 118 158 384 506 9 32 15 34 512 26 49 112 t 0 0 0 0 82 91 29 13 16 27 3 406 14 19 25 102

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=16; shift=0; ncol=16; cscCCCCACCCCCAsc ; Alignment reference a 74 84 60 36 32 24 19 356 20 25 19 29 14 337 73 89 c 196 151 268 338 381 405 424 7 423 401 385 407 432 46 201 218 g 117 162 82 60 29 23 19 81 21 25 41 20 21 57 142 110 t 89 79 66 42 34 24 14 32 12 25 31 20 9 36 60 59
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cscCCCCACCCCCAsc ; cor=; Ncor= a 74 84 60 36 32 24 19 356 20 25 19 29 14 337 73 89 c 196 151 268 338 381 405 424 7 423 401 385 407 432 46 201 218 g 117 162 82 60 29 23 19 81 21 25 41 20 21 57 142 110 t 89 79 66 42 34 24 14 32 12 25 31 20 9 36 60 59
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m2; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.762648; ssGCCCCGCCCCCss- ; cor=; Ncor= a 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 0 c 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 0 g 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 0 t 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120 0
oligos_7nt_mkv4_m3_shift3 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m3; m=3/3; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.53974; ---csCCGCCTCCss- ; cor=; Ncor= a 0 0 0 122 107 17 32 45 22 7 43 6 18 166 100 0 c 0 0 0 449 361 826 828 24 849 869 93 864 862 285 368 0 g 0 0 0 191 281 59 46 818 41 29 128 31 30 289 303 0 t 0 0 0 169 182 29 25 44 19 26 667 30 21 191 160 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=13; shift=3; ncol=16; ---sgGGCAGGGCCbg ; Alignment reference a 0 0 0 82 102 25 19 14 406 3 27 16 13 29 91 82 c 0 0 0 161 112 49 26 512 34 15 32 9 506 384 158 118 g 0 0 0 217 251 442 490 13 83 520 470 493 19 105 150 262 t 0 0 0 85 80 29 10 6 22 7 16 27 7 27 146 83
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---sgGGCAGGGCCbg ; cor=; Ncor= a 0 0 0 82 102 25 19 14 406 3 27 16 13 29 91 82 c 0 0 0 161 112 49 26 512 34 15 32 9 506 384 158 118 g 0 0 0 217 251 442 490 13 83 520 470 493 19 105 150 262 t 0 0 0 85 80 29 10 6 22 7 16 27 7 27 146 83
oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.615379; ssGGGGGCGGGGCss- ; cor=; Ncor= a 120 130 53 36 56 28 19 39 38 15 53 27 60 95 110 0 c 256 283 83 53 65 69 69 691 43 49 62 47 583 286 204 0 g 319 235 626 659 653 670 685 21 689 704 661 687 114 285 344 0 t 97 144 30 44 18 25 19 41 22 24 16 31 35 126 134 0
oligos_6nt_mkv3_m2_rc_shift4 (oligos_6nt_mkv3_m2_rc)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2_rc; m=3/3; ncol2=14; w=0; offset=1; strand=R; shift=4; score=0.587328; ----ssGCGGGGCGGG ; cor=; Ncor= a 0 0 0 0 97 120 37 52 28 27 33 17 26 24 41 49 c 0 0 0 0 213 255 103 636 55 69 71 40 744 82 116 90 g 0 0 0 0 410 329 622 84 699 700 686 733 15 684 587 636 t 0 0 0 0 90 106 48 38 28 14 20 20 25 20 66 35

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -ssGCCCCGCCCCCss ; Alignment reference a 0 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 c 0 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 g 0 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 t 0 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120
oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCCCCGCCCCCss ; cor=; Ncor= a 0 134 126 35 31 16 24 22 41 19 25 18 44 30 144 97 c 0 344 285 114 687 661 704 689 21 685 670 653 659 626 235 319 g 0 204 286 583 47 62 49 43 691 69 69 65 53 83 283 256 t 0 110 95 60 27 53 15 38 39 19 28 56 36 53 130 120
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m4; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=1; score=0.762648; -cscCCCCACCCCCAs ; cor=; Ncor= a 0 74 84 60 36 32 24 19 356 20 25 19 29 14 337 73 c 0 196 151 268 338 381 405 424 7 423 401 385 407 432 46 201 g 0 117 162 82 60 29 23 19 81 21 25 41 20 21 57 142 t 0 89 79 66 42 34 24 14 32 12 25 31 20 9 36 60
oligos_7nt_mkv4_m3_shift4 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=3/6; ncol2=12; w=0; offset=3; strand=D; shift=4; score=0.674666; ----csCCGCCTCCss ; cor=; Ncor= a 0 0 0 0 122 107 17 32 45 22 7 43 6 18 166 100 c 0 0 0 0 449 361 826 828 24 849 869 93 864 862 285 368 g 0 0 0 0 191 281 59 46 818 41 29 128 31 30 289 303 t 0 0 0 0 169 182 29 25 44 19 26 667 30 21 191 160
oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2; m=4/6; ncol2=14; w=0; offset=2; strand=D; shift=3; score=0.666639; ---ssCCCGCCCCGCs ; cor=; Ncor= a 0 0 0 112 84 35 66 20 25 20 20 14 28 38 48 106 c 0 0 0 316 358 636 587 684 15 733 686 700 699 84 622 329 g 0 0 0 260 218 90 116 82 744 40 71 69 55 636 103 255 t 0 0 0 122 150 49 41 24 26 17 33 27 28 52 37 120
oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5_rc; m=5/6; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.615379; cvGGCCCTGCCcs--- ; cor=; Ncor= a 83 146 27 7 27 16 7 22 6 10 29 80 85 0 0 0 c 262 150 105 19 493 470 520 83 13 490 442 251 217 0 0 0 g 118 158 384 506 9 32 15 34 512 26 49 112 161 0 0 0 t 82 91 29 13 16 27 3 406 14 19 25 102 82 0 0 0
oligos_6nt_mkv3_m3_rc_shift1 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3_rc; m=6/6; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.578357; -ssGCTCCGCss---- ; cor=; Ncor= a 0 114 133 21 19 37 14 14 13 27 96 106 0 0 0 0 c 0 326 284 52 719 57 692 701 15 671 257 302 0 0 0 0 g 0 244 245 679 28 94 56 46 738 57 320 244 0 0 0 0 t 0 96 118 28 14 592 18 19 14 25 107 128 0 0 0 0