One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084320_2026-01-22.084320_l9H2rm/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084320_2026-01-22.084320_l9H2rm/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; tsGCCGAACTCGtcs ; Alignment reference a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.923556; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=3/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.859553; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=4/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 0.8581; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=5/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.852163; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=6/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.800557; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.734949; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.731763; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=9/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.708814; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=10/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.691662; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; ssstCCAACTGGcss ; Alignment reference a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=2/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.886817; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.883061; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.829172; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=5/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.805393; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=6/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.801261; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.755007; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.731763; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=9/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.725174; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=10/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.713337; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -sscCCAACTCCCss ; Alignment reference a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.897561; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=3/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.835105; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=4/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.795448; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.78032; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=6/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.758362; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=7/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.725174; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=8/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.691662; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -sscCGAACTGGcss ; Alignment reference a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.92102; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.909956; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=4/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.87959; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.805393; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=6/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.800557; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=7/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.767362; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=8/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.694882; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; sgaCGAGTTCGgss ; Alignment reference a 19 29 106 1 1 209 3 8 10 2 10 28 24 15 c 119 55 47 196 34 8 12 4 8 208 16 41 113 71 g 72 128 50 29 193 7 211 12 3 19 196 139 65 120 t 19 17 26 3 1 5 3 205 208 0 7 21 27 23

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; sgaCGAGTTCGgss ; cor=; Ncor= a 19 29 106 1 1 209 3 8 10 2 10 28 24 15 c 119 55 47 196 34 8 12 4 8 208 16 41 113 71 g 72 128 50 29 193 7 211 12 3 19 196 139 65 120 t 19 17 26 3 1 5 3 205 208 0 7 21 27 23

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=2/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.923556; sgaCGAGTTCGGCs ; cor=; Ncor= a 15 24 117 1 3 178 3 9 8 2 7 16 14 18 c 95 47 28 160 27 7 16 6 7 180 13 30 134 53 g 64 105 34 30 164 3 171 17 4 12 168 136 32 106 t 20 18 15 3 0 6 4 162 175 0 6 12 14 17

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3_rc; m=3/10; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.921573; ssaCGAGTTsGGss ; cor=; Ncor= a 15 15 91 0 1 128 2 6 6 2 4 13 11 12 c 64 40 16 116 11 5 5 12 3 45 11 16 74 45 g 51 73 22 22 126 7 133 11 4 94 124 100 40 69 t 11 13 12 3 3 1 1 112 128 0 2 12 16 15

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/10; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.87959; ssgCCAGTTCGgss ; cor=; Ncor= a 26 21 28 2 0 196 1 3 11 1 3 22 19 17 c 117 72 28 189 190 10 9 11 8 211 19 35 107 78 g 62 124 140 28 38 10 217 18 5 15 200 147 71 114 t 23 11 32 9 0 12 1 196 204 1 6 24 31 19

oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.819769; sgvCGAGTTGGass ; cor=; Ncor= a 15 25 68 1 0 173 1 7 3 0 4 80 10 24 c 83 44 50 155 18 9 6 13 10 45 14 41 119 53 g 76 103 53 30 164 5 180 12 3 141 162 44 53 90 t 14 16 17 2 6 1 1 156 172 2 8 23 6 21

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=6/10; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.807797; sgGCCAGTTsGGss ; cor=; Ncor= a 14 15 8 2 2 108 1 3 2 1 5 3 9 18 c 55 24 17 93 88 3 3 8 0 37 9 13 63 42 g 29 63 78 14 21 1 110 7 2 75 97 83 31 47 t 16 12 11 5 3 2 0 96 110 1 3 15 11 7

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=7/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.793332; ssGCCAGTTCGGCs ; cor=; Ncor= a 14 18 13 3 1 147 2 3 9 1 2 4 3 14 c 97 55 20 139 142 9 9 14 15 160 13 12 144 59 g 45 91 117 20 26 8 158 17 7 8 147 141 16 87 t 14 6 20 8 1 6 1 136 139 1 8 13 7 10

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=8/10; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.758362; ssGGGAGTTGGgss ; cor=; Ncor= a 26 18 16 1 5 129 1 2 4 2 10 17 13 22 c 53 46 16 16 12 4 4 4 5 30 13 16 58 36 g 47 65 94 114 114 1 129 11 1 103 105 88 52 66 t 10 7 10 5 5 2 2 119 126 1 8 15 13 12

oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=9/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.713337; ssgCCAGTTGGass ; cor=; Ncor= a 18 16 17 2 1 151 1 8 2 1 7 75 9 22 c 76 49 33 131 125 7 6 11 6 36 15 21 95 55 g 56 83 98 27 32 4 157 10 2 126 137 40 50 74 t 14 16 16 4 6 2 0 135 154 1 5 28 10 13

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=10/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.681075; ssgGGAGTTGGass ; cor=; Ncor= a 22 23 23 1 5 161 1 3 3 0 15 79 8 28 c 80 62 32 24 12 9 7 10 6 33 11 35 101 49 g 66 76 98 150 151 2 167 13 6 145 140 40 56 80 t 10 17 25 3 10 6 3 152 163 0 12 24 13 21

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; ksstCCAACTCCcss ; Alignment reference a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=2/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.897561; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.878848; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=4/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.801261; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=5/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.756084; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=6/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.708814; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=7/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.693294; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=8/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.681075; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ssstCCAACTCGbcs ; Alignment reference a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=2/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.884003; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.883061; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=4/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.878848; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=5/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 0.8581; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=6/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.819769; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.78032; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=8/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.773926; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=9/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.711659; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=10/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.694882; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift1 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssCCsAACTGGCcs ; Alignment reference a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=2/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.92102; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=3/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.886817; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.847844; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.83494; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=6/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.807797; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=7/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.795448; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=8/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.773926; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=9/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.734949; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=10/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.693294; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift1 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssCCsAACTCGtss ; Alignment reference a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.921573; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.884003; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=4/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.859553; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.835105; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=6/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.83494; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=7/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.767362; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=8/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.756084; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=9/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.755007; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18

oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=10/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.69538; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; ssGCCAGTTCGGCsr ; Alignment reference a 14 18 13 3 1 147 2 3 9 1 2 4 3 14 58 c 97 55 20 139 142 9 9 14 15 160 13 12 144 59 40 g 45 91 117 20 26 8 158 17 7 8 147 141 16 87 43 t 14 6 20 8 1 6 1 136 139 1 8 13 7 10 29

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssGCCAGTTCGGCsr ; cor=; Ncor= a 14 18 13 3 1 147 2 3 9 1 2 4 3 14 58 c 97 55 20 139 142 9 9 14 15 160 13 12 144 59 40 g 45 91 117 20 26 8 158 17 7 8 147 141 16 87 43 t 14 6 20 8 1 6 1 136 139 1 8 13 7 10 29

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4_rc; m=2/8; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.909956; ssgCCAGTTCGgss- ; cor=; Ncor= a 26 21 28 2 0 196 1 3 11 1 3 22 19 17 0 c 117 72 28 189 190 10 9 11 8 211 19 35 107 78 0 g 62 124 140 28 38 10 217 18 5 15 200 147 71 114 0 t 23 11 32 9 0 12 1 196 204 1 6 24 31 19 0

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.852163; sgaCGAGTTCGGCsa ; cor=; Ncor= a 15 24 117 1 3 178 3 9 8 2 7 16 14 18 65 c 95 47 28 160 27 7 16 6 7 180 13 30 134 53 42 g 64 105 34 30 164 3 171 17 4 12 168 136 32 106 43 t 20 18 15 3 0 6 4 162 175 0 6 12 14 17 44

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=4/8; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.847844; sgGCCAGTTsGGss- ; cor=; Ncor= a 14 15 8 2 2 108 1 3 2 1 5 3 9 18 0 c 55 24 17 93 88 3 3 8 0 37 9 13 63 42 0 g 29 63 78 14 21 1 110 7 2 75 97 83 31 47 0 t 16 12 11 5 3 2 0 96 110 1 3 15 11 7 0

oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=5/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.829172; ssgCCAGTTGGasss ; cor=; Ncor= a 18 16 17 2 1 151 1 8 2 1 7 75 9 22 38 c 76 49 33 131 125 7 6 11 6 36 15 21 95 55 47 g 56 83 98 27 32 4 157 10 2 126 137 40 50 74 50 t 14 16 16 4 6 2 0 135 154 1 5 28 10 13 29

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=6/8; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.793332; sgaCGAGTTCGgss- ; cor=; Ncor= a 19 29 106 1 1 209 3 8 10 2 10 28 24 15 0 c 119 55 47 196 34 8 12 4 8 208 16 41 113 71 0 g 72 128 50 29 193 7 211 12 3 19 196 139 65 120 0 t 19 17 26 3 1 5 3 205 208 0 7 21 27 23 0

oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=7/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.711659; sgvCGAGTTGGasss ; cor=; Ncor= a 15 25 68 1 0 173 1 7 3 0 4 80 10 24 41 c 83 44 50 155 18 9 6 13 10 45 14 41 119 53 52 g 76 103 53 30 164 5 180 12 3 141 162 44 53 90 53 t 14 16 17 2 6 1 1 156 172 2 8 23 6 21 42

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3_rc; m=8/8; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.69538; ssaCGAGTTsGGss- ; cor=; Ncor= a 15 15 91 0 1 128 2 6 6 2 4 13 11 12 0 c 64 40 16 116 11 5 5 12 3 45 11 16 74 45 0 g 51 73 22 22 126 7 133 11 4 94 124 100 40 69 0 t 11 13 12 3 3 1 1 112 128 0 2 12 16 15 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; tsGCCGAACTCGtcs ; Alignment reference a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.923556; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=3/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.859553; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=4/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 0.8581; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=5/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.852163; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=6/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.800557; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.734949; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.731763; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=9/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.708814; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=10/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.691662; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; ssstCCAACTGGcss ; Alignment reference a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=2/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.886817; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.883061; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.829172; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=5/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.805393; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=6/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.801261; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.755007; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=8/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.731763; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=9/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.725174; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=10/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.713337; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -sscCCAACTCCCss ; Alignment reference a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.897561; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=3/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.835105; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=4/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.795448; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.78032; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=6/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.758362; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=7/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.725174; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=8/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.691662; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -sscCGAACTGGcss ; Alignment reference a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5; m=2/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.92102; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/8; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.909956; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=4/8; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.87959; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=5/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.805393; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=6/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.800557; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=7/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.767362; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=8/8; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.694882; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; sgaCGAGTTCGgss ; Alignment reference a 19 29 106 1 1 209 3 8 10 2 10 28 24 15 c 119 55 47 196 34 8 12 4 8 208 16 41 113 71 g 72 128 50 29 193 7 211 12 3 19 196 139 65 120 t 19 17 26 3 1 5 3 205 208 0 7 21 27 23
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; sgaCGAGTTCGgss ; cor=; Ncor= a 19 29 106 1 1 209 3 8 10 2 10 28 24 15 c 119 55 47 196 34 8 12 4 8 208 16 41 113 71 g 72 128 50 29 193 7 211 12 3 19 196 139 65 120 t 19 17 26 3 1 5 3 205 208 0 7 21 27 23
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=2/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.923556; sgaCGAGTTCGGCs ; cor=; Ncor= a 15 24 117 1 3 178 3 9 8 2 7 16 14 18 c 95 47 28 160 27 7 16 6 7 180 13 30 134 53 g 64 105 34 30 164 3 171 17 4 12 168 136 32 106 t 20 18 15 3 0 6 4 162 175 0 6 12 14 17
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3_rc; m=3/10; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.921573; ssaCGAGTTsGGss ; cor=; Ncor= a 15 15 91 0 1 128 2 6 6 2 4 13 11 12 c 64 40 16 116 11 5 5 12 3 45 11 16 74 45 g 51 73 22 22 126 7 133 11 4 94 124 100 40 69 t 11 13 12 3 3 1 1 112 128 0 2 12 16 15
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/10; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.87959; ssgCCAGTTCGgss ; cor=; Ncor= a 26 21 28 2 0 196 1 3 11 1 3 22 19 17 c 117 72 28 189 190 10 9 11 8 211 19 35 107 78 g 62 124 140 28 38 10 217 18 5 15 200 147 71 114 t 23 11 32 9 0 12 1 196 204 1 6 24 31 19
oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.819769; sgvCGAGTTGGass ; cor=; Ncor= a 15 25 68 1 0 173 1 7 3 0 4 80 10 24 c 83 44 50 155 18 9 6 13 10 45 14 41 119 53 g 76 103 53 30 164 5 180 12 3 141 162 44 53 90 t 14 16 17 2 6 1 1 156 172 2 8 23 6 21
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5_rc; m=6/10; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.807797; sgGCCAGTTsGGss ; cor=; Ncor= a 14 15 8 2 2 108 1 3 2 1 5 3 9 18 c 55 24 17 93 88 3 3 8 0 37 9 13 63 42 g 29 63 78 14 21 1 110 7 2 75 97 83 31 47 t 16 12 11 5 3 2 0 96 110 1 3 15 11 7
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=7/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.793332; ssGCCAGTTCGGCs ; cor=; Ncor= a 14 18 13 3 1 147 2 3 9 1 2 4 3 14 c 97 55 20 139 142 9 9 14 15 160 13 12 144 59 g 45 91 117 20 26 8 158 17 7 8 147 141 16 87 t 14 6 20 8 1 6 1 136 139 1 8 13 7 10
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=8/10; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.758362; ssGGGAGTTGGgss ; cor=; Ncor= a 26 18 16 1 5 129 1 2 4 2 10 17 13 22 c 53 46 16 16 12 4 4 4 5 30 13 16 58 36 g 47 65 94 114 114 1 129 11 1 103 105 88 52 66 t 10 7 10 5 5 2 2 119 126 1 8 15 13 12
oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5_rc; m=9/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.713337; ssgCCAGTTGGass ; cor=; Ncor= a 18 16 17 2 1 151 1 8 2 1 7 75 9 22 c 76 49 33 131 125 7 6 11 6 36 15 21 95 55 g 56 83 98 27 32 4 157 10 2 126 137 40 50 74 t 14 16 16 4 6 2 0 135 154 1 5 28 10 13
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=10/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.681075; ssgGGAGTTGGass ; cor=; Ncor= a 22 23 23 1 5 161 1 3 3 0 15 79 8 28 c 80 62 32 24 12 9 7 10 6 33 11 35 101 49 g 66 76 98 150 151 2 167 13 6 145 140 40 56 80 t 10 17 25 3 10 6 3 152 163 0 12 24 13 21

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; ksstCCAACTCCcss ; Alignment reference a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=2/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.897561; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=3/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.878848; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=4/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.801261; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=5/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.756084; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=6/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.708814; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5; m=7/8; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.693294; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=8/8; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.681075; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ssstCCAACTCGbcs ; Alignment reference a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=2/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.884003; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=3/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.883061; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=4/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.878848; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=5/10; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 0.8581; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=6/10; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.819769; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=7/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.78032; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=8/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.773926; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=9/10; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.711659; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=10/10; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.694882; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssCCsAACTGGCcs ; Alignment reference a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=2/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.92102; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=3/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.886817; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.847844; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.83494; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3_rc; m=6/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.807797; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=7/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.795448; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=8/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.773926; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=9/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.734949; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=10/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.693294; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssCCsAACTCGtss ; Alignment reference a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_7nt_test_vs_ctrl_m3_shift1 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -ssCCsAACTCGtss ; cor=; Ncor= a 0 15 16 12 2 0 128 112 1 1 3 3 12 13 11 c 0 69 40 100 124 94 4 11 133 7 126 22 22 73 51 g 0 45 74 16 11 45 3 12 5 5 11 116 16 40 64 t 0 12 11 13 4 2 6 6 2 128 1 0 91 15 15
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/10; ncol2=14; w=0; offset=0; strand=R; shift=1; score=0.921573; -sscCGAACTCGtcs ; cor=; Ncor= a 0 23 27 21 7 0 208 205 3 5 1 3 26 17 19 c 0 120 65 139 196 19 3 12 211 7 193 29 50 128 72 g 0 71 113 41 16 208 8 4 12 8 34 196 47 55 119 t 0 15 24 28 10 2 10 8 3 209 1 1 106 29 19
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.884003; ssstCCAACTCGbcs ; cor=; Ncor= a 42 21 6 23 8 2 172 156 1 1 6 2 17 16 14 c 53 90 53 44 162 141 3 12 180 5 164 30 53 103 76 g 52 53 119 41 14 45 10 13 6 9 18 155 50 44 83 t 41 24 10 80 4 0 3 7 1 173 0 1 68 25 15
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=4/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.859553; tsGCCGAACTCGtcs ; cor=; Ncor= a 44 17 14 12 6 0 175 162 4 6 0 3 15 18 20 c 43 106 32 136 168 12 4 17 171 3 164 30 34 105 64 g 42 53 134 30 13 180 7 6 16 7 27 160 28 47 95 t 65 18 14 16 7 2 8 9 3 178 3 1 117 24 15
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=5/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.835105; -sscCCAACTCCCss ; cor=; Ncor= a 0 12 13 15 8 1 126 119 2 2 5 5 10 7 10 c 0 66 52 88 105 103 1 11 129 1 114 114 94 65 47 g 0 36 58 16 13 30 5 4 4 4 12 16 16 46 53 t 0 22 13 17 10 2 4 2 1 129 5 1 16 18 26
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=6/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.83494; -ssCCsAACTGGCcs ; cor=; Ncor= a 0 7 11 15 3 1 110 96 0 2 3 5 11 12 16 c 0 47 31 83 97 75 2 7 110 1 21 14 78 63 29 g 0 42 63 13 9 37 0 8 3 3 88 93 17 24 55 t 0 18 9 3 5 1 2 3 1 108 2 2 8 15 14
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=7/10; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.767362; -sscCGAACTGGcss ; cor=; Ncor= a 0 19 31 24 6 1 204 196 1 12 0 9 32 11 23 c 0 114 71 147 200 15 5 18 217 10 38 28 140 124 62 g 0 78 107 35 19 211 8 11 9 10 190 189 28 72 117 t 0 17 19 22 3 1 11 3 1 196 0 2 28 21 26
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=8/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.756084; ksstCCAACTCCcss ; cor=; Ncor= a 38 21 13 24 12 0 163 152 3 6 10 3 25 17 10 c 38 80 56 40 140 145 6 13 167 2 151 150 98 76 66 g 54 49 101 35 11 33 6 10 7 9 12 24 32 62 80 t 48 28 8 79 15 0 3 3 1 161 5 1 23 23 22
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=9/10; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.755007; ssstCCAACTGGcss ; cor=; Ncor= a 29 13 10 28 5 1 154 135 0 2 6 4 16 16 14 c 50 74 50 40 137 126 2 10 157 4 32 27 98 83 56 g 47 55 95 21 15 36 6 11 6 7 125 131 33 49 76 t 38 22 9 75 7 1 2 8 1 151 1 2 17 16 18
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=10/10; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.69538; ysGCCGAACTGGCss ; cor=; Ncor= a 29 10 7 13 8 1 139 136 1 6 1 8 20 6 14 c 43 87 16 141 147 8 7 17 158 8 26 20 117 91 45 g 40 59 144 12 13 160 15 14 9 9 142 139 20 55 97 t 58 14 3 4 2 1 9 3 2 147 1 3 13 18 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; ssGCCAGTTCGGCsr ; Alignment reference a 14 18 13 3 1 147 2 3 9 1 2 4 3 14 58 c 97 55 20 139 142 9 9 14 15 160 13 12 144 59 40 g 45 91 117 20 26 8 158 17 7 8 147 141 16 87 43 t 14 6 20 8 1 6 1 136 139 1 8 13 7 10 29
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; ssGCCAGTTCGGCsr ; cor=; Ncor= a 14 18 13 3 1 147 2 3 9 1 2 4 3 14 58 c 97 55 20 139 142 9 9 14 15 160 13 12 144 59 40 g 45 91 117 20 26 8 158 17 7 8 147 141 16 87 43 t 14 6 20 8 1 6 1 136 139 1 8 13 7 10 29
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4_rc; m=2/8; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.909956; ssgCCAGTTCGgss- ; cor=; Ncor= a 26 21 28 2 0 196 1 3 11 1 3 22 19 17 0 c 117 72 28 189 190 10 9 11 8 211 19 35 107 78 0 g 62 124 140 28 38 10 217 18 5 15 200 147 71 114 0 t 23 11 32 9 0 12 1 196 204 1 6 24 31 19 0
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.852163; sgaCGAGTTCGGCsa ; cor=; Ncor= a 15 24 117 1 3 178 3 9 8 2 7 16 14 18 65 c 95 47 28 160 27 7 16 6 7 180 13 30 134 53 42 g 64 105 34 30 164 3 171 17 4 12 168 136 32 106 43 t 20 18 15 3 0 6 4 162 175 0 6 12 14 17 44
oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=4/8; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.847844; sgGCCAGTTsGGss- ; cor=; Ncor= a 14 15 8 2 2 108 1 3 2 1 5 3 9 18 0 c 55 24 17 93 88 3 3 8 0 37 9 13 63 42 0 g 29 63 78 14 21 1 110 7 2 75 97 83 31 47 0 t 16 12 11 5 3 2 0 96 110 1 3 15 11 7 0
oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=5/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.829172; ssgCCAGTTGGasss ; cor=; Ncor= a 18 16 17 2 1 151 1 8 2 1 7 75 9 22 38 c 76 49 33 131 125 7 6 11 6 36 15 21 95 55 47 g 56 83 98 27 32 4 157 10 2 126 137 40 50 74 50 t 14 16 16 4 6 2 0 135 154 1 5 28 10 13 29
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=6/8; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.793332; sgaCGAGTTCGgss- ; cor=; Ncor= a 19 29 106 1 1 209 3 8 10 2 10 28 24 15 0 c 119 55 47 196 34 8 12 4 8 208 16 41 113 71 0 g 72 128 50 29 193 7 211 12 3 19 196 139 65 120 0 t 19 17 26 3 1 5 3 205 208 0 7 21 27 23 0
oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=7/8; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.711659; sgvCGAGTTGGasss ; cor=; Ncor= a 15 25 68 1 0 173 1 7 3 0 4 80 10 24 41 c 83 44 50 155 18 9 6 13 10 45 14 41 119 53 52 g 76 103 53 30 164 5 180 12 3 141 162 44 53 90 53 t 14 16 17 2 6 1 1 156 172 2 8 23 6 21 42
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3_rc; m=8/8; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.69538; ssaCGAGTTsGGss- ; cor=; Ncor= a 15 15 91 0 1 128 2 6 6 2 4 13 11 12 0 c 64 40 16 116 11 5 5 12 3 45 11 16 74 45 0 g 51 73 22 22 126 7 133 11 4 94 124 100 40 69 0 t 11 13 12 3 3 1 1 112 128 0 2 12 16 15 0