One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/13/peak-motifs.2025-04-13.004321_2025-04-13.004321_RHGHTx/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/2025/04/13/peak-motifs.2025-04-13.004321_2025-04-13.004321_RHGHTx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift3 ; 5 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=12; shift=3; ncol=15; ---CaCACrCACACa ; Alignment reference a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---CaCACrCACACa ; cor=; Ncor= a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146

oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m4; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.877837; ----acACACACAca ; cor=; Ncor= a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228

oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m5; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.789075; ---cmCACTCACccm ; cor=; Ncor= a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77

dyads_m2_shift0 (dyads_m2)
; oligos_7nt_mkv4_m5 versus dyads_m2; m=4/4; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.724556; aCACACACACACACa ; cor=; Ncor= a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=20; shift=0; ncol=20; gcrGCAGCAGCrGCAGCrrc ; Alignment reference a 60 42 98 16 23 215 22 9 240 16 19 129 26 14 239 22 22 109 78 55 c 48 175 25 29 264 15 7 279 7 8 260 12 12 267 11 15 256 19 52 165 g 151 49 155 245 11 56 271 10 46 278 12 152 259 11 40 258 12 156 141 43 t 48 41 29 17 9 21 7 9 14 5 16 14 10 15 17 12 17 23 36 44

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/1; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; gcrGCAGCAGCrGCAGCrrc ; cor=; Ncor= a 60 42 98 16 23 215 22 9 240 16 19 129 26 14 239 22 22 109 78 55 c 48 175 25 29 264 15 7 279 7 8 260 12 12 267 11 15 256 19 52 165 g 151 49 155 245 11 56 271 10 46 278 12 152 259 11 40 258 12 156 141 43 t 48 41 29 17 9 21 7 9 14 5 16 14 10 15 17 12 17 23 36 44

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift10 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift10 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=12; shift=10; ncol=22; ----------GaGAGmGAGAGa ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 c 0 0 0 0 0 0 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 g 0 0 0 0 0 0 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 t 0 0 0 0 0 0 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63

oligos_7nt_mkv4_m2_shift10 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=10; score= 1; ----------GaGAGmGAGAGa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 c 0 0 0 0 0 0 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 g 0 0 0 0 0 0 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 t 0 0 0 0 0 0 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63

oligos_6nt_mkv3_m1_shift7 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=2/6; ncol2=15; w=-3; offset=-3; strand=D; shift=7; score=0.781071; -------aGAGAGAGmGAGaGa ; cor=; Ncor= a 0 0 0 0 0 0 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 c 0 0 0 0 0 0 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 g 0 0 0 0 0 0 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 t 0 0 0 0 0 0 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91

oligos_6nt_mkv3_m3_rc_shift9 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3_rc; m=3/6; ncol2=14; w=-1; offset=-1; strand=R; shift=9; score=0.768078; ---------aGAGAGAGmGrGa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 490 98 711 10 708 8 741 14 432 20 412 56 490 c 0 0 0 0 0 0 0 0 0 102 82 21 22 19 6 13 3 270 19 28 52 97 g 0 0 0 0 0 0 0 0 0 138 559 40 736 39 764 20 754 55 736 324 625 146 t 0 0 0 0 0 0 0 0 0 56 47 14 18 20 8 12 15 29 11 22 53 53

dyads_m4_shift7 (dyads_m4)
; oligos_7nt_mkv4_m2 versus dyads_m4; m=4/6; ncol2=21; w=-3; offset=-3; strand=D; shift=7; score=0.545773; -------AGAGAGAGAGAGAGA ; cor=; Ncor= a 0 0 0 0 0 0 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 c 0 0 0 0 0 0 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 g 0 0 0 0 0 0 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 t 0 0 0 0 0 0 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15

dyads_m5_shift6 (dyads_m5)
; oligos_7nt_mkv4_m2 versus dyads_m5; m=5/6; ncol2=24; w=-4; offset=-4; strand=D; shift=6; score=0.483197; ------GAGAGAGAGAGAGAGA ; cor=; Ncor= a 0 0 0 0 0 0 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 c 0 0 0 0 0 0 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 g 0 0 0 0 0 0 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 t 0 0 0 0 0 0 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29

dyads_m1_rc_shift0 (dyads_m1_rc)
; oligos_7nt_mkv4_m2 versus dyads_m1_rc; m=6/6; ncol2=24; w=-10; offset=-10; strand=R; shift=0; score=0.476686; GAGAGAGAGAGAGAGaGaGAGA ; cor=; Ncor= a 107 650 60 764 46 778 39 766 41 762 34 792 31 799 33 628 58 628 53 724 56 676 c 81 111 41 80 29 63 30 84 22 84 21 59 26 55 27 184 32 95 64 101 53 115 g 702 118 815 62 846 60 852 59 859 62 868 64 865 59 861 91 826 185 789 81 790 101 t 51 62 25 35 20 40 20 32 19 33 18 26 19 28 20 38 25 33 35 35 42 49

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 2 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; gbCGCAGTCGsc ; Alignment reference a 89 61 16 13 10 357 12 15 14 9 95 101 c 88 110 365 10 396 27 20 25 380 17 147 147 g 146 121 19 389 9 10 370 23 14 387 106 80 t 97 128 20 8 5 26 18 357 12 7 72 92

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; gbCGCAGTCGsc ; cor=; Ncor= a 89 61 16 13 10 357 12 15 14 9 95 101 c 88 110 365 10 396 27 20 25 380 17 147 147 g 146 121 19 389 9 10 370 23 14 387 106 80 t 97 128 20 8 5 26 18 357 12 7 72 92

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----acACACACAca ; Alignment reference a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228

oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----acACACACAca ; cor=; Ncor= a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m5; m=2/4; ncol2=12; w=-1; offset=-1; strand=D; shift=3; score=0.877837; ---CaCACrCACACa ; cor=; Ncor= a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146

dyads_m2_shift0 (dyads_m2)
; oligos_6nt_mkv3_m4 versus dyads_m2; m=3/4; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.668739; aCACACACACACACa ; cor=; Ncor= a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157

oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=12; w=-1; offset=-1; strand=D; shift=3; score=0.663159; ---cmCACTCACccm ; cor=; Ncor= a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; GAGAGAGAGAGAGAGAGaGAGAGa ; Alignment reference a 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 33 579 39 683 45 637 79 540 c 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 23 87 54 76 38 99 74 119 g 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 776 159 733 64 735 77 639 131 t 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29 21 28 27 30 35 40 61 63

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; GAGAGAGAGAGAGAGAGaGAGAGa ; cor=; Ncor= a 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 33 579 39 683 45 637 79 540 c 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 23 87 54 76 38 99 74 119 g 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 776 159 733 64 735 77 639 131 t 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29 21 28 27 30 35 40 61 63

dyads_m1_rc_shift0 (dyads_m1_rc)
; dyads_m5 versus dyads_m1_rc; m=2/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.998295; GAGAGAGAGAGAGAGaGaGAGAGa ; cor=; Ncor= a 107 650 60 764 46 778 39 766 41 762 34 792 31 799 33 628 58 628 53 724 56 676 91 581 c 81 111 41 80 29 63 30 84 22 84 21 59 26 55 27 184 32 95 64 101 53 115 90 132 g 702 118 815 62 846 60 852 59 859 62 868 64 865 59 861 91 826 185 789 81 790 101 681 157 t 51 62 25 35 20 40 20 32 19 33 18 26 19 28 20 38 25 33 35 35 42 49 79 71

dyads_m4_shift1 (dyads_m4)
; dyads_m5 versus dyads_m4; m=3/6; ncol2=21; w=0; offset=1; strand=D; shift=1; score=0.864758; -AGAGAGAGAGAGAGAGaGaGa-- ; cor=; Ncor= a 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 17 457 38 453 70 450 0 0 c 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 11 143 28 53 54 92 0 0 g 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 653 59 600 160 521 109 0 0 t 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15 13 35 28 28 49 43 0 0

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; dyads_m5 versus oligos_6nt_mkv3_m1; m=4/6; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.615496; -aGAGAGAGmGAGaGa-------- ; cor=; Ncor= a 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 0 0 0 0 0 0 0 0 c 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 0 0 0 0 0 0 0 0 g 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 0 0 0 0 0 0 0 0 t 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91 0 0 0 0 0 0 0 0

oligos_6nt_mkv3_m3_rc_shift7 (oligos_6nt_mkv3_m3_rc)
; dyads_m5 versus oligos_6nt_mkv3_m3_rc; m=5/6; ncol2=14; w=0; offset=7; strand=R; shift=7; score=0.563635; -------aGAGAGAGmGrGag--- ; cor=; Ncor= a 0 0 0 0 0 0 0 490 98 711 10 708 8 741 14 432 20 412 56 490 101 0 0 0 c 0 0 0 0 0 0 0 102 82 21 22 19 6 13 3 270 19 28 52 97 100 0 0 0 g 0 0 0 0 0 0 0 138 559 40 736 39 764 20 754 55 736 324 625 146 526 0 0 0 t 0 0 0 0 0 0 0 56 47 14 18 20 8 12 15 29 11 22 53 53 59 0 0 0

oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)
; dyads_m5 versus oligos_7nt_mkv4_m2; m=6/6; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.483197; ----GaGAGmGAGAGa-------- ; cor=; Ncor= a 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 0 0 0 0 0 0 0 0 c 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 0 0 0 0 0 0 0 0 g 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 0 0 0 0 0 0 0 0 t 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; aCACACACACACACac ; Alignment reference a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 192 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 977 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 187 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157 162

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; aCACACACACACACac ; cor=; Ncor= a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 192 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 977 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 187 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157 162

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; dyads_m2 versus oligos_7nt_mkv4_m5; m=2/4; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.724556; ---CaCACrCACACa- ; cor=; Ncor= a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 0 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 0 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 0 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146 0

oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)
; dyads_m2 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.668739; ----acACACACAca- ; cor=; Ncor= a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 0 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 0 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 0 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228 0

oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)
; dyads_m2 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.526035; ---cmCACTCACccm- ; cor=; Ncor= a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 0 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 0 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 0 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -aGAGAGAGmGAGaGa ; Alignment reference a 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 c 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 g 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 t 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -aGAGAGAGmGAGaGa ; cor=; Ncor= a 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 c 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 g 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 t 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91

oligos_6nt_mkv3_m3_rc_shift1 (oligos_6nt_mkv3_m3_rc)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=2/6; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.911006; -aGAGAGAGmGrGag- ; cor=; Ncor= a 0 490 98 711 10 708 8 741 14 432 20 412 56 490 101 0 c 0 102 82 21 22 19 6 13 3 270 19 28 52 97 100 0 g 0 138 559 40 736 39 764 20 754 55 736 324 625 146 526 0 t 0 56 47 14 18 20 8 12 15 29 11 22 53 53 59 0

oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/6; ncol2=12; w=0; offset=3; strand=D; shift=4; score=0.781071; ----GaGAGmGAGAGa ; cor=; Ncor= a 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 c 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 g 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 t 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63

dyads_m4_shift1 (dyads_m4)
; oligos_6nt_mkv3_m1 versus dyads_m4; m=4/6; ncol2=21; w=0; offset=0; strand=D; shift=1; score=0.69596; -AGAGAGAGAGAGAGA ; cor=; Ncor= a 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 c 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 g 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 t 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15

dyads_m5_shift0 (dyads_m5)
; oligos_6nt_mkv3_m1 versus dyads_m5; m=5/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.615496; GAGAGAGAGAGAGAGA ; cor=; Ncor= a 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 c 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 g 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 t 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29

dyads_m1_rc_shift0 (dyads_m1_rc)
; oligos_6nt_mkv3_m1 versus dyads_m1_rc; m=6/6; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.610962; GAGAGAGAGAGAGAGa ; cor=; Ncor= a 107 650 60 764 46 778 39 766 41 762 34 792 31 799 33 628 c 81 111 41 80 29 63 30 84 22 84 21 59 26 55 27 184 g 702 118 815 62 846 60 852 59 859 62 868 64 865 59 861 91 t 51 62 25 35 20 40 20 32 19 33 18 26 19 28 20 38

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; tCTCTCtCtCTCTCTCTCTCTCTC ; Alignment reference a 71 79 49 42 35 35 33 25 38 20 28 19 26 18 33 19 32 20 40 20 35 25 62 51 c 157 681 101 790 81 789 185 826 91 861 59 865 64 868 62 859 59 852 60 846 62 815 118 702 g 132 90 115 53 101 64 95 32 184 27 55 26 59 21 84 22 84 30 63 29 80 41 111 81 t 581 91 676 56 724 53 628 58 628 33 799 31 792 34 762 41 766 39 778 46 764 60 650 107

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; tCTCTCtCtCTCTCTCTCTCTCTC ; cor=; Ncor= a 71 79 49 42 35 35 33 25 38 20 28 19 26 18 33 19 32 20 40 20 35 25 62 51 c 157 681 101 790 81 789 185 826 91 861 59 865 64 868 62 859 59 852 60 846 62 815 118 702 g 132 90 115 53 101 64 95 32 184 27 55 26 59 21 84 22 84 30 63 29 80 41 111 81 t 581 91 676 56 724 53 628 58 628 33 799 31 792 34 762 41 766 39 778 46 764 60 650 107

dyads_m5_rc_shift0 (dyads_m5_rc)
; dyads_m1 versus dyads_m5_rc; m=2/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.998295; tCTCTCtCTCTCTCTCTCTCTCTC ; cor=; Ncor= a 63 61 40 35 30 27 28 21 29 23 25 17 12 15 38 15 38 17 28 17 30 25 62 47 c 131 639 77 735 64 733 159 776 69 780 42 795 62 791 68 782 44 786 52 772 60 731 109 641 g 119 74 99 38 76 54 87 23 171 23 52 18 44 19 162 18 52 17 67 26 73 41 96 70 t 540 79 637 45 683 39 579 33 584 27 734 23 735 28 585 38 719 33 706 38 690 56 586 95

dyads_m4_rc_shift2 (dyads_m4_rc)
; dyads_m1 versus dyads_m4_rc; m=3/6; ncol2=21; w=0; offset=2; strand=R; shift=2; score=0.864307; --tCtCtCTCTCTCTCTCTCTCT- ; cor=; Ncor= a 0 0 43 49 28 28 35 13 15 8 19 13 18 10 27 11 21 6 16 14 26 37 44 0 c 0 0 109 521 160 600 59 653 50 653 27 656 33 656 117 655 24 657 29 624 145 531 97 0 g 0 0 92 54 53 28 143 11 39 17 39 10 31 14 64 13 31 10 32 24 49 58 75 0 t 0 0 450 70 453 38 457 17 590 16 609 15 612 14 486 15 618 21 617 32 474 68 478 0

oligos_6nt_mkv3_m1_rc_shift8 (oligos_6nt_mkv3_m1_rc)
; dyads_m1 versus oligos_6nt_mkv3_m1_rc; m=4/6; ncol2=15; w=0; offset=8; strand=R; shift=8; score=0.610962; --------tCtCTCkCTCTCTCt- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 91 87 70 24 21 9 39 13 39 9 36 18 54 56 96 0 c 0 0 0 0 0 0 0 0 204 778 146 985 65 1027 72 1035 39 1049 41 1013 64 804 179 0 g 0 0 0 0 0 0 0 0 165 117 146 39 46 32 401 16 45 22 89 32 71 112 166 0 t 0 0 0 0 0 0 0 0 640 118 738 52 968 32 588 36 977 20 934 37 911 128 659 0

oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; dyads_m1 versus oligos_6nt_mkv3_m3; m=5/6; ncol2=14; w=0; offset=3; strand=D; shift=3; score=0.568101; ---ctCyCkCTCTCTCt------- ; cor=; Ncor= a 0 0 0 59 53 53 22 11 29 15 12 8 20 18 14 47 56 0 0 0 0 0 0 0 c 0 0 0 526 146 625 324 736 55 754 20 764 39 736 40 559 138 0 0 0 0 0 0 0 g 0 0 0 100 97 52 28 19 270 3 13 6 19 22 21 82 102 0 0 0 0 0 0 0 t 0 0 0 101 490 56 412 20 432 14 741 8 708 10 711 98 490 0 0 0 0 0 0 0

oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)
; dyads_m1 versus oligos_7nt_mkv4_m2_rc; m=6/6; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.476686; --tCTCTCkCTCtC---------- ; cor=; Ncor= a 0 0 63 75 16 7 3 4 26 3 15 5 78 64 0 0 0 0 0 0 0 0 0 0 c 0 0 178 616 14 836 40 860 29 867 16 853 111 621 0 0 0 0 0 0 0 0 0 0 g 0 0 140 103 51 20 20 12 435 3 17 12 160 98 0 0 0 0 0 0 0 0 0 0 t 0 0 512 99 812 30 830 17 403 20 845 23 544 110 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 2 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=11; shift=0; ncol=11; ahAAACAAAha ; Alignment reference a 437 337 1076 1023 1079 3 1021 994 949 337 415 c 200 292 16 43 21 957 27 62 68 297 239 g 245 207 9 36 10 44 35 41 55 194 226 t 265 311 46 45 37 143 64 50 75 319 267

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ahAAACAAAha ; cor=; Ncor= a 437 337 1076 1023 1079 3 1021 994 949 337 415 c 200 292 16 43 21 957 27 62 68 297 239 g 245 207 9 36 10 44 35 41 55 194 226 t 265 311 46 45 37 143 64 50 75 319 267

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=12; shift=3; ncol=15; ---cmCACTCACccm ; Alignment reference a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77

oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---cmCACTCACccm ; cor=; Ncor= a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77

oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m5; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.789075; ---CaCACrCACACa ; cor=; Ncor= a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146

oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.663159; ----acACACACAca ; cor=; Ncor= a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228

dyads_m2_shift0 (dyads_m2)
; oligos_6nt_mkv3_m5 versus dyads_m2; m=4/4; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.526035; aCACACACACACACa ; cor=; Ncor= a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157

One-to-n matrix alignment; reference matrix: dyads_m4_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift1 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=21; shift=1; ncol=22; -AGAGAGAGAGAGAGAGaGaGa ; Alignment reference a 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 17 457 38 453 70 450 c 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 11 143 28 53 54 92 g 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 653 59 600 160 521 109 t 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15 13 35 28 28 49 43

dyads_m4_shift1 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/6; ncol2=21; w=0; offset=0; strand=D; shift=1; score= 1; -AGAGAGAGAGAGAGAGaGaGa ; cor=; Ncor= a 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 17 457 38 453 70 450 c 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 11 143 28 53 54 92 g 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 653 59 600 160 521 109 t 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15 13 35 28 28 49 43

dyads_m5_shift0 (dyads_m5)
; dyads_m4 versus dyads_m5; m=2/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.864758; GAGAGAGAGAGAGAGAGaGAGA ; cor=; Ncor= a 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 33 579 39 683 45 637 c 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 23 87 54 76 38 99 g 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 776 159 733 64 735 77 t 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29 21 28 27 30 35 40

dyads_m1_rc_shift0 (dyads_m1_rc)
; dyads_m4 versus dyads_m1_rc; m=3/6; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.864307; GAGAGAGAGAGAGAGaGaGAGA ; cor=; Ncor= a 107 650 60 764 46 778 39 766 41 762 34 792 31 799 33 628 58 628 53 724 56 676 c 81 111 41 80 29 63 30 84 22 84 21 59 26 55 27 184 32 95 64 101 53 115 g 702 118 815 62 846 60 852 59 859 62 868 64 865 59 861 91 826 185 789 81 790 101 t 51 62 25 35 20 40 20 32 19 33 18 26 19 28 20 38 25 33 35 35 42 49

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; dyads_m4 versus oligos_6nt_mkv3_m1; m=4/6; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.69596; -aGAGAGAGmGAGaGa------ ; cor=; Ncor= a 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 0 0 0 0 0 0 c 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 0 0 0 0 0 0 g 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 0 0 0 0 0 0 t 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91 0 0 0 0 0 0

oligos_6nt_mkv3_m3_rc_shift7 (oligos_6nt_mkv3_m3_rc)
; dyads_m4 versus oligos_6nt_mkv3_m3_rc; m=5/6; ncol2=14; w=0; offset=6; strand=R; shift=7; score=0.637359; -------aGAGAGAGmGrGag- ; cor=; Ncor= a 0 0 0 0 0 0 0 490 98 711 10 708 8 741 14 432 20 412 56 490 101 0 c 0 0 0 0 0 0 0 102 82 21 22 19 6 13 3 270 19 28 52 97 100 0 g 0 0 0 0 0 0 0 138 559 40 736 39 764 20 754 55 736 324 625 146 526 0 t 0 0 0 0 0 0 0 56 47 14 18 20 8 12 15 29 11 22 53 53 59 0

oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)
; dyads_m4 versus oligos_7nt_mkv4_m2; m=6/6; ncol2=12; w=0; offset=3; strand=D; shift=4; score=0.545773; ----GaGAGmGAGAGa------ ; cor=; Ncor= a 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 0 0 0 0 0 0 c 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 0 0 0 0 0 0 g 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 0 0 0 0 0 0 t 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; gsgCACAGTGGgs ; Alignment reference a 69 57 31 24 281 6 266 4 11 12 8 71 63 c 72 103 37 211 14 284 7 20 6 7 9 60 104 g 102 86 201 36 9 11 19 280 9 282 281 118 97 t 65 62 39 37 4 7 16 4 282 7 10 59 44

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; gsgCACAGTGGgs ; cor=; Ncor= a 69 57 31 24 281 6 266 4 11 12 8 71 63 c 72 103 37 211 14 284 7 20 6 7 9 60 104 g 102 86 201 36 9 11 19 280 9 282 281 118 97 t 65 62 39 37 4 7 16 4 282 7 10 59 44

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 2 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=13; shift=0; ncol=13; cygCCTCTGCCks ; Alignment reference a 51 50 26 17 3 11 6 6 6 8 7 60 56 c 131 100 43 223 280 16 277 14 20 265 274 63 122 g 66 48 190 21 8 25 7 12 263 10 5 92 75 t 51 101 40 38 8 247 9 267 10 16 13 84 46

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; cygCCTCTGCCks ; cor=; Ncor= a 51 50 26 17 3 11 6 6 6 8 7 60 56 c 131 100 43 223 280 16 277 14 20 265 274 63 122 g 66 48 190 21 8 25 7 12 263 10 5 92 75 t 51 101 40 38 8 247 9 267 10 16 13 84 46

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift3 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=14; shift=3; ncol=17; ---ctCyCkCTCTCTCt ; Alignment reference a 0 0 0 59 53 53 22 11 29 15 12 8 20 18 14 47 56 c 0 0 0 526 146 625 324 736 55 754 20 764 39 736 40 559 138 g 0 0 0 100 97 52 28 19 270 3 13 6 19 22 21 82 102 t 0 0 0 101 490 56 412 20 432 14 741 8 708 10 711 98 490

oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCyCkCTCTCTCt ; cor=; Ncor= a 0 0 0 59 53 53 22 11 29 15 12 8 20 18 14 47 56 c 0 0 0 526 146 625 324 736 55 754 20 764 39 736 40 559 138 g 0 0 0 100 97 52 28 19 270 3 13 6 19 22 21 82 102 t 0 0 0 101 490 56 412 20 432 14 741 8 708 10 711 98 490

oligos_6nt_mkv3_m1_rc_shift2 (oligos_6nt_mkv3_m1_rc)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1_rc; m=2/6; ncol2=15; w=-1; offset=-1; strand=R; shift=2; score=0.911006; --tCtCTCkCTCTCTCt ; cor=; Ncor= a 0 0 91 87 70 24 21 9 39 13 39 9 36 18 54 56 96 c 0 0 204 778 146 985 65 1027 72 1035 39 1049 41 1013 64 804 179 g 0 0 165 117 146 39 46 32 401 16 45 22 89 32 71 112 166 t 0 0 640 118 738 52 968 32 588 36 977 20 934 37 911 128 659

oligos_7nt_mkv4_m2_rc_shift4 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2_rc; m=3/6; ncol2=12; w=0; offset=1; strand=R; shift=4; score=0.768078; ----tCTCTCkCTCtC- ; cor=; Ncor= a 0 0 0 0 63 75 16 7 3 4 26 3 15 5 78 64 0 c 0 0 0 0 178 616 14 836 40 860 29 867 16 853 111 621 0 g 0 0 0 0 140 103 51 20 20 12 435 3 17 12 160 98 0 t 0 0 0 0 512 99 812 30 830 17 403 20 845 23 544 110 0

dyads_m4_rc_shift2 (dyads_m4_rc)
; oligos_6nt_mkv3_m3 versus dyads_m4_rc; m=4/6; ncol2=21; w=-1; offset=-1; strand=R; shift=2; score=0.637359; --tCtCtCTCTCTCTCT ; cor=; Ncor= a 0 0 43 49 28 28 35 13 15 8 19 13 18 10 27 11 21 c 0 0 109 521 160 600 59 653 50 653 27 656 33 656 117 655 24 g 0 0 92 54 53 28 143 11 39 17 39 10 31 14 64 13 31 t 0 0 450 70 453 38 457 17 590 16 609 15 612 14 486 15 618

dyads_m1_shift0 (dyads_m1)
; oligos_6nt_mkv3_m3 versus dyads_m1; m=5/6; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.568101; tCTCTCtCtCTCTCTCT ; cor=; Ncor= a 71 79 49 42 35 35 33 25 38 20 28 19 26 18 33 19 32 c 157 681 101 790 81 789 185 826 91 861 59 865 64 868 62 859 59 g 132 90 115 53 101 64 95 32 184 27 55 26 59 21 84 22 84 t 581 91 676 56 724 53 628 58 628 33 799 31 792 34 762 41 766

dyads_m5_rc_shift0 (dyads_m5_rc)
; oligos_6nt_mkv3_m3 versus dyads_m5_rc; m=6/6; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.563635; tCTCTCtCTCTCTCTCT ; cor=; Ncor= a 63 61 40 35 30 27 28 21 29 23 25 17 12 15 38 15 38 c 131 639 77 735 64 733 159 776 69 780 42 795 62 791 68 782 44 g 119 74 99 38 76 54 87 23 171 23 52 18 44 19 162 18 52 t 540 79 637 45 683 39 579 33 584 27 734 23 735 28 585 38 719

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=12; shift=3; ncol=15; ---CaCACrCACACa ; Alignment reference a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---CaCACrCACACa ; cor=; Ncor= a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m4; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.877837; ----acACACACAca ; cor=; Ncor= a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m5; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.789075; ---cmCACTCACccm ; cor=; Ncor= a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77
dyads_m2_shift0 (dyads_m2)				; oligos_7nt_mkv4_m5 versus dyads_m2; m=4/4; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.724556; aCACACACACACACa ; cor=; Ncor= a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift10 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=12; shift=10; ncol=22; ----------GaGAGmGAGAGa ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 c 0 0 0 0 0 0 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 g 0 0 0 0 0 0 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 t 0 0 0 0 0 0 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63
oligos_7nt_mkv4_m2_shift10 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/6; ncol2=12; w=0; offset=0; strand=D; shift=10; score= 1; ----------GaGAGmGAGAGa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 c 0 0 0 0 0 0 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 g 0 0 0 0 0 0 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 t 0 0 0 0 0 0 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63
oligos_6nt_mkv3_m1_shift7 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=2/6; ncol2=15; w=-3; offset=-3; strand=D; shift=7; score=0.781071; -------aGAGAGAGmGAGaGa ; cor=; Ncor= a 0 0 0 0 0 0 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 c 0 0 0 0 0 0 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 g 0 0 0 0 0 0 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 t 0 0 0 0 0 0 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91
oligos_6nt_mkv3_m3_rc_shift9 (oligos_6nt_mkv3_m3_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3_rc; m=3/6; ncol2=14; w=-1; offset=-1; strand=R; shift=9; score=0.768078; ---------aGAGAGAGmGrGa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 490 98 711 10 708 8 741 14 432 20 412 56 490 c 0 0 0 0 0 0 0 0 0 102 82 21 22 19 6 13 3 270 19 28 52 97 g 0 0 0 0 0 0 0 0 0 138 559 40 736 39 764 20 754 55 736 324 625 146 t 0 0 0 0 0 0 0 0 0 56 47 14 18 20 8 12 15 29 11 22 53 53
dyads_m4_shift7 (dyads_m4)				; oligos_7nt_mkv4_m2 versus dyads_m4; m=4/6; ncol2=21; w=-3; offset=-3; strand=D; shift=7; score=0.545773; -------AGAGAGAGAGAGAGA ; cor=; Ncor= a 0 0 0 0 0 0 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 c 0 0 0 0 0 0 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 g 0 0 0 0 0 0 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 t 0 0 0 0 0 0 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15
dyads_m5_shift6 (dyads_m5)				; oligos_7nt_mkv4_m2 versus dyads_m5; m=5/6; ncol2=24; w=-4; offset=-4; strand=D; shift=6; score=0.483197; ------GAGAGAGAGAGAGAGA ; cor=; Ncor= a 0 0 0 0 0 0 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 c 0 0 0 0 0 0 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 g 0 0 0 0 0 0 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 t 0 0 0 0 0 0 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29
dyads_m1_rc_shift0 (dyads_m1_rc)				; oligos_7nt_mkv4_m2 versus dyads_m1_rc; m=6/6; ncol2=24; w=-10; offset=-10; strand=R; shift=0; score=0.476686; GAGAGAGAGAGAGAGaGaGAGA ; cor=; Ncor= a 107 650 60 764 46 778 39 766 41 762 34 792 31 799 33 628 58 628 53 724 56 676 c 81 111 41 80 29 63 30 84 22 84 21 59 26 55 27 184 32 95 64 101 53 115 g 702 118 815 62 846 60 852 59 859 62 868 64 865 59 861 91 826 185 789 81 790 101 t 51 62 25 35 20 40 20 32 19 33 18 26 19 28 20 38 25 33 35 35 42 49

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----acACACACAca ; Alignment reference a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----acACACACAca ; cor=; Ncor= a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m5; m=2/4; ncol2=12; w=-1; offset=-1; strand=D; shift=3; score=0.877837; ---CaCACrCACACa ; cor=; Ncor= a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146
dyads_m2_shift0 (dyads_m2)				; oligos_6nt_mkv3_m4 versus dyads_m2; m=3/4; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.668739; aCACACACACACACa ; cor=; Ncor= a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=12; w=-1; offset=-1; strand=D; shift=3; score=0.663159; ---cmCACTCACccm ; cor=; Ncor= a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift0 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; GAGAGAGAGAGAGAGAGaGAGAGa ; Alignment reference a 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 33 579 39 683 45 637 79 540 c 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 23 87 54 76 38 99 74 119 g 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 776 159 733 64 735 77 639 131 t 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29 21 28 27 30 35 40 61 63
dyads_m5_shift0 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; GAGAGAGAGAGAGAGAGaGAGAGa ; cor=; Ncor= a 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 33 579 39 683 45 637 79 540 c 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 23 87 54 76 38 99 74 119 g 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 776 159 733 64 735 77 639 131 t 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29 21 28 27 30 35 40 61 63
dyads_m1_rc_shift0 (dyads_m1_rc)				; dyads_m5 versus dyads_m1_rc; m=2/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.998295; GAGAGAGAGAGAGAGaGaGAGAGa ; cor=; Ncor= a 107 650 60 764 46 778 39 766 41 762 34 792 31 799 33 628 58 628 53 724 56 676 91 581 c 81 111 41 80 29 63 30 84 22 84 21 59 26 55 27 184 32 95 64 101 53 115 90 132 g 702 118 815 62 846 60 852 59 859 62 868 64 865 59 861 91 826 185 789 81 790 101 681 157 t 51 62 25 35 20 40 20 32 19 33 18 26 19 28 20 38 25 33 35 35 42 49 79 71
dyads_m4_shift1 (dyads_m4)				; dyads_m5 versus dyads_m4; m=3/6; ncol2=21; w=0; offset=1; strand=D; shift=1; score=0.864758; -AGAGAGAGAGAGAGAGaGaGa-- ; cor=; Ncor= a 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 17 457 38 453 70 450 0 0 c 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 11 143 28 53 54 92 0 0 g 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 653 59 600 160 521 109 0 0 t 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15 13 35 28 28 49 43 0 0
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; dyads_m5 versus oligos_6nt_mkv3_m1; m=4/6; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.615496; -aGAGAGAGmGAGaGa-------- ; cor=; Ncor= a 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 0 0 0 0 0 0 0 0 c 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 0 0 0 0 0 0 0 0 g 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 0 0 0 0 0 0 0 0 t 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91 0 0 0 0 0 0 0 0
oligos_6nt_mkv3_m3_rc_shift7 (oligos_6nt_mkv3_m3_rc)				; dyads_m5 versus oligos_6nt_mkv3_m3_rc; m=5/6; ncol2=14; w=0; offset=7; strand=R; shift=7; score=0.563635; -------aGAGAGAGmGrGag--- ; cor=; Ncor= a 0 0 0 0 0 0 0 490 98 711 10 708 8 741 14 432 20 412 56 490 101 0 0 0 c 0 0 0 0 0 0 0 102 82 21 22 19 6 13 3 270 19 28 52 97 100 0 0 0 g 0 0 0 0 0 0 0 138 559 40 736 39 764 20 754 55 736 324 625 146 526 0 0 0 t 0 0 0 0 0 0 0 56 47 14 18 20 8 12 15 29 11 22 53 53 59 0 0 0
oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)				; dyads_m5 versus oligos_7nt_mkv4_m2; m=6/6; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.483197; ----GaGAGmGAGAGa-------- ; cor=; Ncor= a 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 0 0 0 0 0 0 0 0 c 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 0 0 0 0 0 0 0 0 g 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 0 0 0 0 0 0 0 0 t 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift0 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; aCACACACACACACac ; Alignment reference a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 192 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 977 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 187 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157 162
dyads_m2_shift0 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; aCACACACACACACac ; cor=; Ncor= a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 192 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 977 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 187 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157 162
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; dyads_m2 versus oligos_7nt_mkv4_m5; m=2/4; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.724556; ---CaCACrCACACa- ; cor=; Ncor= a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 0 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 0 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 0 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146 0
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)				; dyads_m2 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.668739; ----acACACACAca- ; cor=; Ncor= a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 0 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 0 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 0 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228 0
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)				; dyads_m2 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.526035; ---cmCACTCACccm- ; cor=; Ncor= a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 0 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 0 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 0 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -aGAGAGAGmGAGaGa ; Alignment reference a 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 c 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 g 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 t 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/6; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -aGAGAGAGmGAGaGa ; cor=; Ncor= a 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 c 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 g 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 t 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91
oligos_6nt_mkv3_m3_rc_shift1 (oligos_6nt_mkv3_m3_rc)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3_rc; m=2/6; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.911006; -aGAGAGAGmGrGag- ; cor=; Ncor= a 0 490 98 711 10 708 8 741 14 432 20 412 56 490 101 0 c 0 102 82 21 22 19 6 13 3 270 19 28 52 97 100 0 g 0 138 559 40 736 39 764 20 754 55 736 324 625 146 526 0 t 0 56 47 14 18 20 8 12 15 29 11 22 53 53 59 0
oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/6; ncol2=12; w=0; offset=3; strand=D; shift=4; score=0.781071; ----GaGAGmGAGAGa ; cor=; Ncor= a 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 c 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 g 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 t 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63
dyads_m4_shift1 (dyads_m4)				; oligos_6nt_mkv3_m1 versus dyads_m4; m=4/6; ncol2=21; w=0; offset=0; strand=D; shift=1; score=0.69596; -AGAGAGAGAGAGAGA ; cor=; Ncor= a 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 c 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 g 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 t 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15
dyads_m5_shift0 (dyads_m5)				; oligos_6nt_mkv3_m1 versus dyads_m5; m=5/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.615496; GAGAGAGAGAGAGAGA ; cor=; Ncor= a 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 c 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 g 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 t 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29
dyads_m1_rc_shift0 (dyads_m1_rc)				; oligos_6nt_mkv3_m1 versus dyads_m1_rc; m=6/6; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.610962; GAGAGAGAGAGAGAGa ; cor=; Ncor= a 107 650 60 764 46 778 39 766 41 762 34 792 31 799 33 628 c 81 111 41 80 29 63 30 84 22 84 21 59 26 55 27 184 g 702 118 815 62 846 60 852 59 859 62 868 64 865 59 861 91 t 51 62 25 35 20 40 20 32 19 33 18 26 19 28 20 38

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift0 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; tCTCTCtCtCTCTCTCTCTCTCTC ; Alignment reference a 71 79 49 42 35 35 33 25 38 20 28 19 26 18 33 19 32 20 40 20 35 25 62 51 c 157 681 101 790 81 789 185 826 91 861 59 865 64 868 62 859 59 852 60 846 62 815 118 702 g 132 90 115 53 101 64 95 32 184 27 55 26 59 21 84 22 84 30 63 29 80 41 111 81 t 581 91 676 56 724 53 628 58 628 33 799 31 792 34 762 41 766 39 778 46 764 60 650 107
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; tCTCTCtCtCTCTCTCTCTCTCTC ; cor=; Ncor= a 71 79 49 42 35 35 33 25 38 20 28 19 26 18 33 19 32 20 40 20 35 25 62 51 c 157 681 101 790 81 789 185 826 91 861 59 865 64 868 62 859 59 852 60 846 62 815 118 702 g 132 90 115 53 101 64 95 32 184 27 55 26 59 21 84 22 84 30 63 29 80 41 111 81 t 581 91 676 56 724 53 628 58 628 33 799 31 792 34 762 41 766 39 778 46 764 60 650 107
dyads_m5_rc_shift0 (dyads_m5_rc)				; dyads_m1 versus dyads_m5_rc; m=2/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.998295; tCTCTCtCTCTCTCTCTCTCTCTC ; cor=; Ncor= a 63 61 40 35 30 27 28 21 29 23 25 17 12 15 38 15 38 17 28 17 30 25 62 47 c 131 639 77 735 64 733 159 776 69 780 42 795 62 791 68 782 44 786 52 772 60 731 109 641 g 119 74 99 38 76 54 87 23 171 23 52 18 44 19 162 18 52 17 67 26 73 41 96 70 t 540 79 637 45 683 39 579 33 584 27 734 23 735 28 585 38 719 33 706 38 690 56 586 95
dyads_m4_rc_shift2 (dyads_m4_rc)				; dyads_m1 versus dyads_m4_rc; m=3/6; ncol2=21; w=0; offset=2; strand=R; shift=2; score=0.864307; --tCtCtCTCTCTCTCTCTCTCT- ; cor=; Ncor= a 0 0 43 49 28 28 35 13 15 8 19 13 18 10 27 11 21 6 16 14 26 37 44 0 c 0 0 109 521 160 600 59 653 50 653 27 656 33 656 117 655 24 657 29 624 145 531 97 0 g 0 0 92 54 53 28 143 11 39 17 39 10 31 14 64 13 31 10 32 24 49 58 75 0 t 0 0 450 70 453 38 457 17 590 16 609 15 612 14 486 15 618 21 617 32 474 68 478 0
oligos_6nt_mkv3_m1_rc_shift8 (oligos_6nt_mkv3_m1_rc)				; dyads_m1 versus oligos_6nt_mkv3_m1_rc; m=4/6; ncol2=15; w=0; offset=8; strand=R; shift=8; score=0.610962; --------tCtCTCkCTCTCTCt- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 91 87 70 24 21 9 39 13 39 9 36 18 54 56 96 0 c 0 0 0 0 0 0 0 0 204 778 146 985 65 1027 72 1035 39 1049 41 1013 64 804 179 0 g 0 0 0 0 0 0 0 0 165 117 146 39 46 32 401 16 45 22 89 32 71 112 166 0 t 0 0 0 0 0 0 0 0 640 118 738 52 968 32 588 36 977 20 934 37 911 128 659 0
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; dyads_m1 versus oligos_6nt_mkv3_m3; m=5/6; ncol2=14; w=0; offset=3; strand=D; shift=3; score=0.568101; ---ctCyCkCTCTCTCt------- ; cor=; Ncor= a 0 0 0 59 53 53 22 11 29 15 12 8 20 18 14 47 56 0 0 0 0 0 0 0 c 0 0 0 526 146 625 324 736 55 754 20 764 39 736 40 559 138 0 0 0 0 0 0 0 g 0 0 0 100 97 52 28 19 270 3 13 6 19 22 21 82 102 0 0 0 0 0 0 0 t 0 0 0 101 490 56 412 20 432 14 741 8 708 10 711 98 490 0 0 0 0 0 0 0
oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)				; dyads_m1 versus oligos_7nt_mkv4_m2_rc; m=6/6; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.476686; --tCTCTCkCTCtC---------- ; cor=; Ncor= a 0 0 63 75 16 7 3 4 26 3 15 5 78 64 0 0 0 0 0 0 0 0 0 0 c 0 0 178 616 14 836 40 860 29 867 16 853 111 621 0 0 0 0 0 0 0 0 0 0 g 0 0 140 103 51 20 20 12 435 3 17 12 160 98 0 0 0 0 0 0 0 0 0 0 t 0 0 512 99 812 30 830 17 403 20 845 23 544 110 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=12; shift=3; ncol=15; ---cmCACTCACccm ; Alignment reference a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---cmCACTCACccm ; cor=; Ncor= a 0 0 0 81 120 23 353 4 38 3 355 5 75 97 124 c 0 0 0 163 125 315 16 382 19 363 16 369 244 152 117 g 0 0 0 68 93 19 12 3 11 10 13 16 30 65 77 t 0 0 0 83 57 38 14 6 327 19 11 5 46 81 77
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m5; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.789075; ---CaCACrCACACa ; cor=; Ncor= a 0 0 0 128 696 15 1086 12 611 19 1099 16 952 122 676 c 0 0 0 789 168 1106 18 1107 49 1099 28 1126 92 792 182 g 0 0 0 105 181 23 24 23 424 25 18 9 57 131 153 t 0 0 0 135 112 13 29 15 73 14 12 6 56 112 146
oligos_6nt_mkv3_m4_shift4 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m4; m=3/4; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.663159; ----acACACACAca ; cor=; Ncor= a 0 0 0 0 1055 213 1583 44 1713 25 1755 35 1706 240 1114 c 0 0 0 0 294 1232 99 1754 54 1752 37 1734 61 1123 282 g 0 0 0 0 304 191 136 42 57 54 36 59 60 273 266 t 0 0 0 0 237 254 72 50 66 59 62 62 63 254 228
dyads_m2_shift0 (dyads_m2)				; oligos_6nt_mkv3_m5 versus dyads_m2; m=4/4; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.526035; aCACACACACACACa ; cor=; Ncor= a 914 156 1122 63 1278 39 1303 51 1270 48 1335 47 1302 109 980 c 213 1058 125 1358 68 1408 65 1343 72 1345 50 1344 60 1203 178 g 217 138 152 45 93 31 69 51 104 52 75 44 86 113 203 t 174 166 119 52 79 40 81 73 72 73 58 83 70 93 157

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift1 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=21; shift=1; ncol=22; -AGAGAGAGAGAGAGAGaGaGa ; Alignment reference a 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 17 457 38 453 70 450 c 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 11 143 28 53 54 92 g 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 653 59 600 160 521 109 t 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15 13 35 28 28 49 43
dyads_m4_shift1 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/6; ncol2=21; w=0; offset=0; strand=D; shift=1; score= 1; -AGAGAGAGAGAGAGAGaGaGa ; cor=; Ncor= a 0 478 68 474 32 617 21 618 15 486 14 612 15 609 16 590 17 457 38 453 70 450 c 0 75 58 49 24 32 10 31 13 64 14 31 10 39 17 39 11 143 28 53 54 92 g 0 97 531 145 624 29 657 24 655 117 656 33 656 27 653 50 653 59 600 160 521 109 t 0 44 37 26 14 16 6 21 11 27 10 18 13 19 8 15 13 35 28 28 49 43
dyads_m5_shift0 (dyads_m5)				; dyads_m4 versus dyads_m5; m=2/6; ncol2=24; w=-1; offset=-1; strand=D; shift=0; score=0.864758; GAGAGAGAGAGAGAGAGaGAGA ; cor=; Ncor= a 95 586 56 690 38 706 33 719 38 585 28 735 23 734 27 584 33 579 39 683 45 637 c 70 96 41 73 26 67 17 52 18 162 19 44 18 52 23 171 23 87 54 76 38 99 g 641 109 731 60 772 52 786 44 782 68 791 62 795 42 780 69 776 159 733 64 735 77 t 47 62 25 30 17 28 17 38 15 38 15 12 17 25 23 29 21 28 27 30 35 40
dyads_m1_rc_shift0 (dyads_m1_rc)				; dyads_m4 versus dyads_m1_rc; m=3/6; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.864307; GAGAGAGAGAGAGAGaGaGAGA ; cor=; Ncor= a 107 650 60 764 46 778 39 766 41 762 34 792 31 799 33 628 58 628 53 724 56 676 c 81 111 41 80 29 63 30 84 22 84 21 59 26 55 27 184 32 95 64 101 53 115 g 702 118 815 62 846 60 852 59 859 62 868 64 865 59 861 91 826 185 789 81 790 101 t 51 62 25 35 20 40 20 32 19 33 18 26 19 28 20 38 25 33 35 35 42 49
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; dyads_m4 versus oligos_6nt_mkv3_m1; m=4/6; ncol2=15; w=0; offset=0; strand=D; shift=1; score=0.69596; -aGAGAGAGmGAGaGa------ ; cor=; Ncor= a 0 659 128 911 37 934 20 977 36 588 32 968 52 738 118 640 0 0 0 0 0 0 c 0 166 112 71 32 89 22 45 16 401 32 46 39 146 117 165 0 0 0 0 0 0 g 0 179 804 64 1013 41 1049 39 1035 72 1027 65 985 146 778 204 0 0 0 0 0 0 t 0 96 56 54 18 36 9 39 13 39 9 21 24 70 87 91 0 0 0 0 0 0
oligos_6nt_mkv3_m3_rc_shift7 (oligos_6nt_mkv3_m3_rc)				; dyads_m4 versus oligos_6nt_mkv3_m3_rc; m=5/6; ncol2=14; w=0; offset=6; strand=R; shift=7; score=0.637359; -------aGAGAGAGmGrGag- ; cor=; Ncor= a 0 0 0 0 0 0 0 490 98 711 10 708 8 741 14 432 20 412 56 490 101 0 c 0 0 0 0 0 0 0 102 82 21 22 19 6 13 3 270 19 28 52 97 100 0 g 0 0 0 0 0 0 0 138 559 40 736 39 764 20 754 55 736 324 625 146 526 0 t 0 0 0 0 0 0 0 56 47 14 18 20 8 12 15 29 11 22 53 53 59 0
oligos_7nt_mkv4_m2_shift4 (oligos_7nt_mkv4_m2)				; dyads_m4 versus oligos_7nt_mkv4_m2; m=6/6; ncol2=12; w=0; offset=3; strand=D; shift=4; score=0.545773; ----GaGAGmGAGAGa------ ; cor=; Ncor= a 0 0 0 0 110 544 23 845 20 403 17 830 30 812 99 512 0 0 0 0 0 0 c 0 0 0 0 98 160 12 17 3 435 12 20 20 51 103 140 0 0 0 0 0 0 g 0 0 0 0 621 111 853 16 867 29 860 40 836 14 616 178 0 0 0 0 0 0 t 0 0 0 0 64 78 5 15 3 26 4 3 7 16 75 63 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=14; shift=3; ncol=17; ---ctCyCkCTCTCTCt ; Alignment reference a 0 0 0 59 53 53 22 11 29 15 12 8 20 18 14 47 56 c 0 0 0 526 146 625 324 736 55 754 20 764 39 736 40 559 138 g 0 0 0 100 97 52 28 19 270 3 13 6 19 22 21 82 102 t 0 0 0 101 490 56 412 20 432 14 741 8 708 10 711 98 490
oligos_6nt_mkv3_m3_shift3 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/6; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCyCkCTCTCTCt ; cor=; Ncor= a 0 0 0 59 53 53 22 11 29 15 12 8 20 18 14 47 56 c 0 0 0 526 146 625 324 736 55 754 20 764 39 736 40 559 138 g 0 0 0 100 97 52 28 19 270 3 13 6 19 22 21 82 102 t 0 0 0 101 490 56 412 20 432 14 741 8 708 10 711 98 490
oligos_6nt_mkv3_m1_rc_shift2 (oligos_6nt_mkv3_m1_rc)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1_rc; m=2/6; ncol2=15; w=-1; offset=-1; strand=R; shift=2; score=0.911006; --tCtCTCkCTCTCTCt ; cor=; Ncor= a 0 0 91 87 70 24 21 9 39 13 39 9 36 18 54 56 96 c 0 0 204 778 146 985 65 1027 72 1035 39 1049 41 1013 64 804 179 g 0 0 165 117 146 39 46 32 401 16 45 22 89 32 71 112 166 t 0 0 640 118 738 52 968 32 588 36 977 20 934 37 911 128 659
oligos_7nt_mkv4_m2_rc_shift4 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2_rc; m=3/6; ncol2=12; w=0; offset=1; strand=R; shift=4; score=0.768078; ----tCTCTCkCTCtC- ; cor=; Ncor= a 0 0 0 0 63 75 16 7 3 4 26 3 15 5 78 64 0 c 0 0 0 0 178 616 14 836 40 860 29 867 16 853 111 621 0 g 0 0 0 0 140 103 51 20 20 12 435 3 17 12 160 98 0 t 0 0 0 0 512 99 812 30 830 17 403 20 845 23 544 110 0
dyads_m4_rc_shift2 (dyads_m4_rc)				; oligos_6nt_mkv3_m3 versus dyads_m4_rc; m=4/6; ncol2=21; w=-1; offset=-1; strand=R; shift=2; score=0.637359; --tCtCtCTCTCTCTCT ; cor=; Ncor= a 0 0 43 49 28 28 35 13 15 8 19 13 18 10 27 11 21 c 0 0 109 521 160 600 59 653 50 653 27 656 33 656 117 655 24 g 0 0 92 54 53 28 143 11 39 17 39 10 31 14 64 13 31 t 0 0 450 70 453 38 457 17 590 16 609 15 612 14 486 15 618
dyads_m1_shift0 (dyads_m1)				; oligos_6nt_mkv3_m3 versus dyads_m1; m=5/6; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.568101; tCTCTCtCtCTCTCTCT ; cor=; Ncor= a 71 79 49 42 35 35 33 25 38 20 28 19 26 18 33 19 32 c 157 681 101 790 81 789 185 826 91 861 59 865 64 868 62 859 59 g 132 90 115 53 101 64 95 32 184 27 55 26 59 21 84 22 84 t 581 91 676 56 724 53 628 58 628 33 799 31 792 34 762 41 766
dyads_m5_rc_shift0 (dyads_m5_rc)				; oligos_6nt_mkv3_m3 versus dyads_m5_rc; m=6/6; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.563635; tCTCTCtCTCTCTCTCT ; cor=; Ncor= a 63 61 40 35 30 27 28 21 29 23 25 17 12 15 38 15 38 c 131 639 77 735 64 733 159 776 69 780 42 795 62 791 68 782 44 g 119 74 99 38 76 54 87 23 171 23 52 18 44 19 162 18 52 t 540 79 637 45 683 39 579 33 584 27 734 23 735 28 585 38 719