One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.162114_2026-01-05.162114_sWmD3V/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.162114_2026-01-05.162114_sWmD3V/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift7 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=7; ncol=24; -------wtTACTCATTTTTaaww ; Alignment reference a 0 0 0 0 0 0 0 70 65 21 223 20 18 14 245 6 23 13 27 30 171 171 107 78 c 0 0 0 0 0 0 0 60 42 25 10 190 10 215 6 10 19 15 22 16 25 30 42 55 g 0 0 0 0 0 0 0 54 29 23 6 26 6 8 4 6 13 10 23 18 28 25 40 48 t 0 0 0 0 0 0 0 78 126 193 23 26 228 25 7 240 207 224 190 198 38 36 73 81

oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=7; score= 1; -------wtTACTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 70 65 21 223 20 18 14 245 6 23 13 27 30 171 171 107 78 c 0 0 0 0 0 0 0 60 42 25 10 190 10 215 6 10 19 15 22 16 25 30 42 55 g 0 0 0 0 0 0 0 54 29 23 6 26 6 8 4 6 13 10 23 18 28 25 40 48 t 0 0 0 0 0 0 0 78 126 193 23 26 228 25 7 240 207 224 190 198 38 36 73 81

oligos_6nt_test_vs_ctrl_m3_shift7 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/7; ncol2=17; w=0; offset=0; strand=D; shift=7; score=0.91582; -------wwTAGTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 84 71 24 213 20 11 13 233 7 24 17 27 25 167 153 87 75 c 0 0 0 0 0 0 0 48 33 21 5 17 10 210 7 7 13 13 25 18 29 24 57 52 g 0 0 0 0 0 0 0 50 36 27 13 192 7 7 4 7 11 11 18 18 18 29 39 48 t 0 0 0 0 0 0 0 71 113 181 22 24 225 23 9 232 205 212 183 192 39 47 70 78

oligos_7nt_test_vs_ctrl_m3_rc_shift6 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=3/7; ncol2=18; w=-1; offset=-1; strand=R; shift=6; score=0.808327; ------wwTTACTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 97 71 16 16 215 17 14 15 226 9 19 14 28 16 17 20 70 68 c 0 0 0 0 0 0 35 64 10 18 10 188 8 211 5 10 21 17 25 25 26 32 46 61 g 0 0 0 0 0 0 40 44 10 28 10 23 2 14 4 12 19 11 19 19 35 18 52 40 t 0 0 0 0 0 0 90 83 226 200 27 34 238 22 27 231 203 220 190 202 184 192 94 93

oligos_7nt_test_vs_ctrl_m4_rc_shift6 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/7; ncol2=18; w=-1; offset=-1; strand=R; shift=6; score=0.761913; ------wwTTAgTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 69 69 19 21 206 17 13 16 204 8 23 17 28 12 18 28 73 70 c 0 0 0 0 0 0 34 44 5 13 4 32 3 200 7 12 15 14 15 25 29 28 51 43 g 0 0 0 0 0 0 45 49 13 28 10 159 4 6 6 6 8 8 17 17 25 17 38 34 t 0 0 0 0 0 0 94 80 205 180 22 34 222 20 25 216 196 203 182 188 170 169 80 95

oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/7; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.578007; ttTAAAAATgAaTcATTTTTAAaw ; cor=; Ncor= a 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 3 4 6 37 38 17 16 c 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 3 4 4 4 5 12 9 g 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 4 2 1 3 3 12 9 t 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36 42 42 41 8 6 11 18

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=6/7; ncol2=24; w=-7; offset=-7; strand=D; shift=0; score=0.543509; dwaaAAAATGACTCATTTttttww ; cor=; Ncor= a 29 41 60 65 78 77 86 85 4 5 101 5 14 9 96 11 12 14 13 16 9 21 37 34 c 16 18 13 11 7 4 5 7 2 3 1 84 0 88 2 10 11 7 11 19 17 14 21 22 g 36 18 20 18 13 10 7 6 2 85 0 15 2 6 1 4 7 5 13 5 16 6 18 19 t 29 33 17 16 12 19 12 12 102 17 8 6 94 7 11 85 80 84 73 70 68 69 34 35

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=7/7; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.526071; wwAtTywTATTTTCATTTTTAAww ; cor=; Ncor= a 15 13 39 8 10 7 29 3 36 2 5 4 5 3 36 2 5 5 3 3 34 32 16 17 c 9 5 3 6 1 27 4 3 0 6 2 2 1 35 5 2 2 1 7 7 5 5 9 9 g 7 11 0 8 1 1 2 4 4 3 3 2 1 3 0 0 1 3 2 2 2 1 7 8 t 16 18 5 25 35 12 12 37 7 36 37 39 40 6 6 43 39 38 35 35 6 9 15 13

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift8 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift8 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=17; shift=8; ncol=25; --------wwTAGTCATTTTTaaww ; Alignment reference a 0 0 0 0 0 0 0 0 84 71 24 213 20 11 13 233 7 24 17 27 25 167 153 87 75 c 0 0 0 0 0 0 0 0 48 33 21 5 17 10 210 7 7 13 13 25 18 29 24 57 52 g 0 0 0 0 0 0 0 0 50 36 27 13 192 7 7 4 7 11 11 18 18 18 29 39 48 t 0 0 0 0 0 0 0 0 71 113 181 22 24 225 23 9 232 205 212 183 192 39 47 70 78

oligos_6nt_test_vs_ctrl_m3_shift8 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=8; score= 1; --------wwTAGTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 84 71 24 213 20 11 13 233 7 24 17 27 25 167 153 87 75 c 0 0 0 0 0 0 0 0 48 33 21 5 17 10 210 7 7 13 13 25 18 29 24 57 52 g 0 0 0 0 0 0 0 0 50 36 27 13 192 7 7 4 7 11 11 18 18 18 29 39 48 t 0 0 0 0 0 0 0 0 71 113 181 22 24 225 23 9 232 205 212 183 192 39 47 70 78

oligos_6nt_test_vs_ctrl_m2_shift8 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=2/7; ncol2=17; w=0; offset=0; strand=D; shift=8; score=0.91582; --------wtTACTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 70 65 21 223 20 18 14 245 6 23 13 27 30 171 171 107 78 c 0 0 0 0 0 0 0 0 60 42 25 10 190 10 215 6 10 19 15 22 16 25 30 42 55 g 0 0 0 0 0 0 0 0 54 29 23 6 26 6 8 4 6 13 10 23 18 28 25 40 48 t 0 0 0 0 0 0 0 0 78 126 193 23 26 228 25 7 240 207 224 190 198 38 36 73 81

oligos_7nt_test_vs_ctrl_m4_rc_shift7 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/7; ncol2=18; w=-1; offset=-1; strand=R; shift=7; score=0.82368; -------wwTTAgTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 0 69 69 19 21 206 17 13 16 204 8 23 17 28 12 18 28 73 70 c 0 0 0 0 0 0 0 34 44 5 13 4 32 3 200 7 12 15 14 15 25 29 28 51 43 g 0 0 0 0 0 0 0 45 49 13 28 10 159 4 6 6 6 8 8 17 17 25 17 38 34 t 0 0 0 0 0 0 0 94 80 205 180 22 34 222 20 25 216 196 203 182 188 170 169 80 95

oligos_7nt_test_vs_ctrl_m3_rc_shift7 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3_rc; m=4/7; ncol2=18; w=-1; offset=-1; strand=R; shift=7; score=0.739503; -------wwTTACTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 0 97 71 16 16 215 17 14 15 226 9 19 14 28 16 17 20 70 68 c 0 0 0 0 0 0 0 35 64 10 18 10 188 8 211 5 10 21 17 25 25 26 32 46 61 g 0 0 0 0 0 0 0 40 44 10 28 10 23 2 14 4 12 19 11 19 19 35 18 52 40 t 0 0 0 0 0 0 0 90 83 226 200 27 34 238 22 27 231 203 220 190 202 184 192 94 93

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/7; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.578818; -ttTAAAAATgAaTcATTTTTAAaw ; cor=; Ncor= a 0 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 3 4 6 37 38 17 16 c 0 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 3 4 4 4 5 12 9 g 0 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 4 2 1 3 3 12 9 t 0 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36 42 42 41 8 6 11 18

oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/7; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.525473; -wwAtTywTATTTTCATTTTTAAww ; cor=; Ncor= a 0 15 13 39 8 10 7 29 3 36 2 5 4 5 3 36 2 5 5 3 3 34 32 16 17 c 0 9 5 3 6 1 27 4 3 0 6 2 2 1 35 5 2 2 1 7 7 5 5 9 9 g 0 7 11 0 8 1 1 2 4 4 3 3 2 1 3 0 0 1 3 2 2 2 1 7 8 t 0 16 18 5 25 35 12 12 37 7 36 37 39 40 6 6 43 39 38 35 35 6 9 15 13

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=7/7; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.514649; wwaaaaAAATGAGTCATTTTttwh- ; cor=; Ncor= a 35 34 69 68 70 73 84 80 85 11 7 94 6 8 17 102 12 12 19 12 16 17 33 29 0 c 19 18 6 16 5 13 5 7 4 1 6 2 15 0 85 2 6 7 10 13 18 20 18 36 0 g 22 21 14 17 19 11 7 11 10 2 88 0 84 1 3 2 7 5 4 7 11 13 18 16 0 t 34 37 21 9 16 13 14 12 11 96 9 14 5 101 5 4 85 86 77 78 65 60 41 29 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift1 ; 7 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=24; shift=1; ncol=25; -dwaaAAAATGACTCATTTttttww ; Alignment reference a 0 29 41 60 65 78 77 86 85 4 5 101 5 14 9 96 11 12 14 13 16 9 21 37 34 c 0 16 18 13 11 7 4 5 7 2 3 1 84 0 88 2 10 11 7 11 19 17 14 21 22 g 0 36 18 20 18 13 10 7 6 2 85 0 15 2 6 1 4 7 5 13 5 16 6 18 19 t 0 29 33 17 16 12 19 12 12 102 17 8 6 94 7 11 85 80 84 73 70 68 69 34 35

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=1/6; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -dwaaAAAATGACTCATTTttttww ; cor=; Ncor= a 0 29 41 60 65 78 77 86 85 4 5 101 5 14 9 96 11 12 14 13 16 9 21 37 34 c 0 16 18 13 11 7 4 5 7 2 3 1 84 0 88 2 10 11 7 11 19 17 14 21 22 g 0 36 18 20 18 13 10 7 6 2 85 0 15 2 6 1 4 7 5 13 5 16 6 18 19 t 0 29 33 17 16 12 19 12 12 102 17 8 6 94 7 11 85 80 84 73 70 68 69 34 35

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1_rc; m=2/6; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.822789; -ttTAAAAATgAaTcATTTTTAAaw ; cor=; Ncor= a 0 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 3 4 6 37 38 17 16 c 0 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 3 4 4 4 5 12 9 g 0 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 4 2 1 3 3 12 9 t 0 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36 42 42 41 8 6 11 18

oligos_7nt_test_vs_ctrl_m3_rc_shift7 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3_rc; m=3/6; ncol2=18; w=0; offset=6; strand=R; shift=7; score=0.651013; -------wwTTACTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 0 97 71 16 16 215 17 14 15 226 9 19 14 28 16 17 20 70 68 c 0 0 0 0 0 0 0 35 64 10 18 10 188 8 211 5 10 21 17 25 25 26 32 46 61 g 0 0 0 0 0 0 0 40 44 10 28 10 23 2 14 4 12 19 11 19 19 35 18 52 40 t 0 0 0 0 0 0 0 90 83 226 200 27 34 238 22 27 231 203 220 190 202 184 192 94 93

oligos_7nt_test_vs_ctrl_m4_rc_shift7 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/6; ncol2=18; w=0; offset=6; strand=R; shift=7; score=0.605624; -------wwTTAgTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 0 69 69 19 21 206 17 13 16 204 8 23 17 28 12 18 28 73 70 c 0 0 0 0 0 0 0 34 44 5 13 4 32 3 200 7 12 15 14 15 25 29 28 51 43 g 0 0 0 0 0 0 0 45 49 13 28 10 159 4 6 6 6 8 8 17 17 25 17 38 34 t 0 0 0 0 0 0 0 94 80 205 180 22 34 222 20 25 216 196 203 182 188 170 169 80 95

oligos_6nt_test_vs_ctrl_m2_shift8 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=5/6; ncol2=17; w=0; offset=7; strand=D; shift=8; score=0.543509; --------wtTACTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 70 65 21 223 20 18 14 245 6 23 13 27 30 171 171 107 78 c 0 0 0 0 0 0 0 0 60 42 25 10 190 10 215 6 10 19 15 22 16 25 30 42 55 g 0 0 0 0 0 0 0 0 54 29 23 6 26 6 8 4 6 13 10 23 18 28 25 40 48 t 0 0 0 0 0 0 0 0 78 126 193 23 26 228 25 7 240 207 224 190 198 38 36 73 81

oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=6/6; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.514649; wwttAAAAATGACTAww-------- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 0 0 0 0 0 0 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 0 0 0 0 0 0 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 0 0 0 0 0 0 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; wwAAAAAAATGAGTAAww ; Alignment reference a 93 94 192 184 202 190 220 203 231 27 22 238 34 27 200 226 83 90 c 40 52 18 35 19 19 11 19 12 4 14 2 23 10 28 10 44 40 g 61 46 32 26 25 25 17 21 10 5 211 8 188 10 18 10 64 35 t 68 70 20 17 16 28 14 19 9 226 15 14 17 215 16 16 71 97

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/6; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAAAAATGAGTAAww ; cor=; Ncor= a 93 94 192 184 202 190 220 203 231 27 22 238 34 27 200 226 83 90 c 40 52 18 35 19 19 11 19 12 4 14 2 23 10 28 10 44 40 g 61 46 32 26 25 25 17 21 10 5 211 8 188 10 18 10 64 35 t 68 70 20 17 16 28 14 19 9 226 15 14 17 215 16 16 71 97

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=2/6; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.938824; wwAAAAAAATGAcTAAww ; cor=; Ncor= a 95 80 169 170 188 182 203 196 216 25 20 222 34 22 180 205 80 94 c 34 38 17 25 17 17 8 8 6 6 6 4 159 10 28 13 49 45 g 43 51 28 29 25 15 14 15 12 7 200 3 32 4 13 5 44 34 t 70 73 28 18 12 28 17 23 8 204 16 13 17 206 21 19 69 69

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=3/6; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.808327; wwttAAAAATGAGTAaw- ; cor=; Ncor= a 81 73 36 38 198 190 224 207 240 7 25 228 26 23 193 126 78 0 c 48 40 25 28 18 23 10 13 6 4 8 6 26 6 23 29 54 0 g 55 42 30 25 16 22 15 19 10 6 215 10 190 10 25 42 60 0 t 78 107 171 171 30 27 13 23 6 245 14 18 20 223 21 65 70 0

oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3_rc; m=4/6; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.739503; wwttAAAAATGACTAww- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=5/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.651013; wwaaaaAAATGAGTCATT ; cor=; Ncor= a 35 34 69 68 70 73 84 80 85 11 7 94 6 8 17 102 12 12 c 19 18 6 16 5 13 5 7 4 1 6 2 15 0 85 2 6 7 g 22 21 14 17 19 11 7 11 10 2 88 0 84 1 3 2 7 5 t 34 37 21 9 16 13 14 12 11 96 9 14 5 101 5 4 85 86

oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=6/6; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.510353; -ttTAAAAATgAaTcATT ; cor=; Ncor= a 0 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 c 0 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 g 0 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 t 0 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; wwTTAAAAATGAAAATAwrAaTww ; Alignment reference a 13 15 9 6 35 35 38 39 43 6 6 40 39 37 36 7 37 12 12 35 25 5 18 16 c 8 7 1 2 2 2 3 1 0 0 3 1 2 3 3 4 4 2 1 1 8 0 11 7 g 9 9 5 5 7 7 1 2 2 5 35 1 2 2 6 0 3 4 27 1 6 3 5 9 t 17 16 32 34 3 3 5 5 2 36 3 5 4 5 2 36 3 29 7 10 8 39 13 15

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAATGAAAATAwrAaTww ; cor=; Ncor= a 13 15 9 6 35 35 38 39 43 6 6 40 39 37 36 7 37 12 12 35 25 5 18 16 c 8 7 1 2 2 2 3 1 0 0 3 1 2 3 3 4 4 2 1 1 8 0 11 7 g 9 9 5 5 7 7 1 2 2 5 35 1 2 2 6 0 3 4 27 1 6 3 5 9 t 17 16 32 34 3 3 5 5 2 36 3 5 4 5 2 36 3 29 7 10 8 39 13 15

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/4; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.526071; wwttAAAAATGAGTAaw------- ; cor=; Ncor= a 81 73 36 38 198 190 224 207 240 7 25 228 26 23 193 126 78 0 0 0 0 0 0 0 c 48 40 25 28 18 23 10 13 6 4 8 6 26 6 23 29 54 0 0 0 0 0 0 0 g 55 42 30 25 16 22 15 19 10 6 215 10 190 10 25 42 60 0 0 0 0 0 0 0 t 78 107 171 171 30 27 13 23 6 245 14 18 20 223 21 65 70 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/4; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.525473; wwttAAAAATGACTAww------- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 0 0 0 0 0 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 0 0 0 0 0 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 0 0 0 0 0 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=4/4; ncol2=24; w=0; offset=4; strand=D; shift=4; score=0.502602; ----aaAAAAmAAAAtAtgAAAAT ; cor=; Ncor= a 0 0 0 0 35 38 68 65 63 67 24 67 69 72 66 19 61 18 19 67 71 76 65 8 c 0 0 0 0 18 12 5 5 5 5 38 5 5 2 5 6 9 3 9 3 2 1 6 3 g 0 0 0 0 11 17 4 4 8 3 9 6 7 6 3 7 5 8 42 8 9 2 8 6 t 0 0 0 0 19 16 6 9 7 8 12 5 2 3 9 51 8 54 13 5 1 4 4 66

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 7 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=18; shift=0; ncol=18; wwAAAAAAATGAcTAAww ; Alignment reference a 95 80 169 170 188 182 203 196 216 25 20 222 34 22 180 205 80 94 c 34 38 17 25 17 17 8 8 6 6 6 4 159 10 28 13 49 45 g 43 51 28 29 25 15 14 15 12 7 200 3 32 4 13 5 44 34 t 70 73 28 18 12 28 17 23 8 204 16 13 17 206 21 19 69 69

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=1/6; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAAAAATGAcTAAww ; cor=; Ncor= a 95 80 169 170 188 182 203 196 216 25 20 222 34 22 180 205 80 94 c 34 38 17 25 17 17 8 8 6 6 6 4 159 10 28 13 49 45 g 43 51 28 29 25 15 14 15 12 7 200 3 32 4 13 5 44 34 t 70 73 28 18 12 28 17 23 8 204 16 13 17 206 21 19 69 69

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=2/6; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.938824; wwAAAAAAATGAGTAAww ; cor=; Ncor= a 93 94 192 184 202 190 220 203 231 27 22 238 34 27 200 226 83 90 c 40 52 18 35 19 19 11 19 12 4 14 2 23 10 28 10 44 40 g 61 46 32 26 25 25 17 21 10 5 211 8 188 10 18 10 64 35 t 68 70 20 17 16 28 14 19 9 226 15 14 17 215 16 16 71 97

oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/6; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.82368; wwttAAAAATGACTAww- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=4/6; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.761913; wwttAAAAATGAGTAaw- ; cor=; Ncor= a 81 73 36 38 198 190 224 207 240 7 25 228 26 23 193 126 78 0 c 48 40 25 28 18 23 10 13 6 4 8 6 26 6 23 29 54 0 g 55 42 30 25 16 22 15 19 10 6 215 10 190 10 25 42 60 0 t 78 107 171 171 30 27 13 23 6 245 14 18 20 223 21 65 70 0

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=5/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.605624; wwaaaaAAATGAGTCATT ; cor=; Ncor= a 35 34 69 68 70 73 84 80 85 11 7 94 6 8 17 102 12 12 c 19 18 6 16 5 13 5 7 4 1 6 2 15 0 85 2 6 7 g 22 21 14 17 19 11 7 11 10 2 88 0 84 1 3 2 7 5 t 34 37 21 9 16 13 14 12 11 96 9 14 5 101 5 4 85 86

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=6/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.530727; wtTTAAAAATgAtTcATT ; cor=; Ncor= a 18 11 6 8 41 42 42 36 41 6 7 43 6 6 6 46 6 5 c 9 12 3 3 1 2 4 1 1 2 1 0 10 0 35 1 1 5 g 9 12 5 4 4 4 3 8 1 1 35 1 11 2 3 1 2 3 t 16 17 38 37 6 4 3 7 9 43 9 8 25 44 8 4 43 39

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift4 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=24; shift=4; ncol=28; ----aaAAAAmAAAAtAtgAAAATGAaw ; Alignment reference a 0 0 0 0 35 38 68 65 63 67 24 67 69 72 66 19 61 18 19 67 71 76 65 8 15 63 33 34 c 0 0 0 0 18 12 5 5 5 5 38 5 5 2 5 6 9 3 9 3 2 1 6 3 5 4 18 14 g 0 0 0 0 11 17 4 4 8 3 9 6 7 6 3 7 5 8 42 8 9 2 8 6 61 5 13 12 t 0 0 0 0 19 16 6 9 7 8 12 5 2 3 9 51 8 54 13 5 1 4 4 66 2 11 19 23

oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/2; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----aaAAAAmAAAAtAtgAAAATGAaw ; cor=; Ncor= a 0 0 0 0 35 38 68 65 63 67 24 67 69 72 66 19 61 18 19 67 71 76 65 8 15 63 33 34 c 0 0 0 0 18 12 5 5 5 5 38 5 5 2 5 6 9 3 9 3 2 1 6 3 5 4 18 14 g 0 0 0 0 11 17 4 4 8 3 9 6 7 6 3 7 5 8 42 8 9 2 8 6 61 5 13 12 t 0 0 0 0 19 16 6 9 7 8 12 5 2 3 9 51 8 54 13 5 1 4 4 66 2 11 19 23

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=2/2; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.502602; wwTTAAAAATGAAAATAwrAaTww---- ; cor=; Ncor= a 13 15 9 6 35 35 38 39 43 6 6 40 39 37 36 7 37 12 12 35 25 5 18 16 0 0 0 0 c 8 7 1 2 2 2 3 1 0 0 3 1 2 3 3 4 4 2 1 1 8 0 11 7 0 0 0 0 g 9 9 5 5 7 7 1 2 2 5 35 1 2 2 6 0 3 4 27 1 6 3 5 9 0 0 0 0 t 17 16 32 34 3 3 5 5 2 36 3 5 4 5 2 36 3 29 7 10 8 39 13 15 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift4 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift4 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=15; shift=4; ncol=19; ----wwTATGAATCATgww ; Alignment reference a 0 0 0 0 121 125 58 283 20 20 364 290 24 30 372 30 40 102 108 c 0 0 0 0 74 74 29 38 8 11 14 44 7 335 6 17 40 88 85 g 0 0 0 0 92 81 34 48 12 343 3 32 13 17 11 23 268 83 84 t 0 0 0 0 109 116 275 27 356 22 15 30 352 14 7 326 48 123 119

oligos_7nt_test_vs_ctrl_m2_shift4 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=4; score= 1; ----wwTATGAATCATgww ; cor=; Ncor= a 0 0 0 0 121 125 58 283 20 20 364 290 24 30 372 30 40 102 108 c 0 0 0 0 74 74 29 38 8 11 14 44 7 335 6 17 40 88 85 g 0 0 0 0 92 81 34 48 12 343 3 32 13 17 11 23 268 83 84 t 0 0 0 0 109 116 275 27 356 22 15 30 352 14 7 326 48 123 119

oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=2/2; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.442572; ttTAAAAATgAaTcATTTT ; cor=; Ncor= a 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 3 4 c 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 3 4 g 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 4 2 t 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36 42 42

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 8 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=24; shift=0; ncol=24; wtTTAAAAATgAtTcATTTTTAaa ; Alignment reference a 18 11 6 8 41 42 42 36 41 6 7 43 6 6 6 46 6 5 1 2 3 37 23 17 c 9 12 3 3 1 2 4 1 1 2 1 0 10 0 35 1 1 5 2 7 1 2 12 11 g 9 12 5 4 4 4 3 8 1 1 35 1 11 2 3 1 2 3 7 4 7 3 5 12 t 16 17 38 37 6 4 3 7 9 43 9 8 25 44 8 4 43 39 42 39 41 10 12 12

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=1/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wtTTAAAAATgAtTcATTTTTAaa ; cor=; Ncor= a 18 11 6 8 41 42 42 36 41 6 7 43 6 6 6 46 6 5 1 2 3 37 23 17 c 9 12 3 3 1 2 4 1 1 2 1 0 10 0 35 1 1 5 2 7 1 2 12 11 g 9 12 5 4 4 4 3 8 1 1 35 1 11 2 3 1 2 3 7 4 7 3 5 12 t 16 17 38 37 6 4 3 7 9 43 9 8 25 44 8 4 43 39 42 39 41 10 12 12

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/7; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.822789; wwaaaaAAATGAGTCATTTTttwh ; cor=; Ncor= a 35 34 69 68 70 73 84 80 85 11 7 94 6 8 17 102 12 12 19 12 16 17 33 29 c 19 18 6 16 5 13 5 7 4 1 6 2 15 0 85 2 6 7 10 13 18 20 18 36 g 22 21 14 17 19 11 7 11 10 2 88 0 84 1 3 2 7 5 4 7 11 13 18 16 t 34 37 21 9 16 13 14 12 11 96 9 14 5 101 5 4 85 86 77 78 65 60 41 29

oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/7; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.578818; wwttAAAAATGACTAww------- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 0 0 0 0 0 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 0 0 0 0 0 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 0 0 0 0 0 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=4/7; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.578007; wwttAAAAATGAGTAaw------- ; cor=; Ncor= a 81 73 36 38 198 190 224 207 240 7 25 228 26 23 193 126 78 0 0 0 0 0 0 0 c 48 40 25 28 18 23 10 13 6 4 8 6 26 6 23 29 54 0 0 0 0 0 0 0 g 55 42 30 25 16 22 15 19 10 6 215 10 190 10 25 42 60 0 0 0 0 0 0 0 t 78 107 171 171 30 27 13 23 6 245 14 18 20 223 21 65 70 0 0 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=5/7; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.530727; wwAAAAAAATGAcTAAww------ ; cor=; Ncor= a 95 80 169 170 188 182 203 196 216 25 20 222 34 22 180 205 80 94 0 0 0 0 0 0 c 34 38 17 25 17 17 8 8 6 6 6 4 159 10 28 13 49 45 0 0 0 0 0 0 g 43 51 28 29 25 15 14 15 12 7 200 3 32 4 13 5 44 34 0 0 0 0 0 0 t 70 73 28 18 12 28 17 23 8 204 16 13 17 206 21 19 69 69 0 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m3_rc_shift7 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3_rc; m=6/7; ncol2=18; w=0; offset=7; strand=R; shift=7; score=0.510353; -------wwTTACTCATTTTTTTw ; cor=; Ncor= a 0 0 0 0 0 0 0 97 71 16 16 215 17 14 15 226 9 19 14 28 16 17 20 70 c 0 0 0 0 0 0 0 35 64 10 18 10 188 8 211 5 10 21 17 25 25 26 32 46 g 0 0 0 0 0 0 0 40 44 10 28 10 23 2 14 4 12 19 11 19 19 35 18 52 t 0 0 0 0 0 0 0 90 83 226 200 27 34 238 22 27 231 203 220 190 202 184 192 94

oligos_7nt_test_vs_ctrl_m2_rc_shift5 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2_rc; m=7/7; ncol2=15; w=0; offset=5; strand=R; shift=5; score=0.442572; -----wwcATGATTCATAww---- ; cor=; Ncor= a 0 0 0 0 0 119 123 48 326 7 14 352 30 15 22 356 27 275 116 109 0 0 0 0 c 0 0 0 0 0 84 83 268 23 11 17 13 32 3 343 12 48 34 81 92 0 0 0 0 g 0 0 0 0 0 85 88 40 17 6 335 7 44 14 11 8 38 29 74 74 0 0 0 0 t 0 0 0 0 0 108 102 40 30 372 30 24 290 364 20 20 283 58 125 121 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; amTATGACACAkw ; Alignment reference a 117 93 38 312 10 10 344 17 297 20 333 83 111 c 80 113 26 18 13 9 8 328 11 319 8 88 68 g 83 72 25 26 6 335 2 12 13 15 14 94 82 t 90 92 281 14 341 16 16 13 49 16 15 105 109

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; amTATGACACAkw ; cor=; Ncor= a 117 93 38 312 10 10 344 17 297 20 333 83 111 c 80 113 26 18 13 9 8 328 11 319 8 88 68 g 83 72 25 26 6 335 2 12 13 15 14 94 82 t 90 92 281 14 341 16 16 13 49 16 15 105 109

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=7; ncol=24; -------wtTACTCATTTTTaaww ; Alignment reference a 0 0 0 0 0 0 0 70 65 21 223 20 18 14 245 6 23 13 27 30 171 171 107 78 c 0 0 0 0 0 0 0 60 42 25 10 190 10 215 6 10 19 15 22 16 25 30 42 55 g 0 0 0 0 0 0 0 54 29 23 6 26 6 8 4 6 13 10 23 18 28 25 40 48 t 0 0 0 0 0 0 0 78 126 193 23 26 228 25 7 240 207 224 190 198 38 36 73 81
oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=7; score= 1; -------wtTACTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 70 65 21 223 20 18 14 245 6 23 13 27 30 171 171 107 78 c 0 0 0 0 0 0 0 60 42 25 10 190 10 215 6 10 19 15 22 16 25 30 42 55 g 0 0 0 0 0 0 0 54 29 23 6 26 6 8 4 6 13 10 23 18 28 25 40 48 t 0 0 0 0 0 0 0 78 126 193 23 26 228 25 7 240 207 224 190 198 38 36 73 81
oligos_6nt_test_vs_ctrl_m3_shift7 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/7; ncol2=17; w=0; offset=0; strand=D; shift=7; score=0.91582; -------wwTAGTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 84 71 24 213 20 11 13 233 7 24 17 27 25 167 153 87 75 c 0 0 0 0 0 0 0 48 33 21 5 17 10 210 7 7 13 13 25 18 29 24 57 52 g 0 0 0 0 0 0 0 50 36 27 13 192 7 7 4 7 11 11 18 18 18 29 39 48 t 0 0 0 0 0 0 0 71 113 181 22 24 225 23 9 232 205 212 183 192 39 47 70 78
oligos_7nt_test_vs_ctrl_m3_rc_shift6 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=3/7; ncol2=18; w=-1; offset=-1; strand=R; shift=6; score=0.808327; ------wwTTACTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 97 71 16 16 215 17 14 15 226 9 19 14 28 16 17 20 70 68 c 0 0 0 0 0 0 35 64 10 18 10 188 8 211 5 10 21 17 25 25 26 32 46 61 g 0 0 0 0 0 0 40 44 10 28 10 23 2 14 4 12 19 11 19 19 35 18 52 40 t 0 0 0 0 0 0 90 83 226 200 27 34 238 22 27 231 203 220 190 202 184 192 94 93
oligos_7nt_test_vs_ctrl_m4_rc_shift6 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/7; ncol2=18; w=-1; offset=-1; strand=R; shift=6; score=0.761913; ------wwTTAgTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 69 69 19 21 206 17 13 16 204 8 23 17 28 12 18 28 73 70 c 0 0 0 0 0 0 34 44 5 13 4 32 3 200 7 12 15 14 15 25 29 28 51 43 g 0 0 0 0 0 0 45 49 13 28 10 159 4 6 6 6 8 8 17 17 25 17 38 34 t 0 0 0 0 0 0 94 80 205 180 22 34 222 20 25 216 196 203 182 188 170 169 80 95
oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/7; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.578007; ttTAAAAATgAaTcATTTTTAAaw ; cor=; Ncor= a 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 3 4 6 37 38 17 16 c 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 3 4 4 4 5 12 9 g 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 4 2 1 3 3 12 9 t 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36 42 42 41 8 6 11 18
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=6/7; ncol2=24; w=-7; offset=-7; strand=D; shift=0; score=0.543509; dwaaAAAATGACTCATTTttttww ; cor=; Ncor= a 29 41 60 65 78 77 86 85 4 5 101 5 14 9 96 11 12 14 13 16 9 21 37 34 c 16 18 13 11 7 4 5 7 2 3 1 84 0 88 2 10 11 7 11 19 17 14 21 22 g 36 18 20 18 13 10 7 6 2 85 0 15 2 6 1 4 7 5 13 5 16 6 18 19 t 29 33 17 16 12 19 12 12 102 17 8 6 94 7 11 85 80 84 73 70 68 69 34 35
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=7/7; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.526071; wwAtTywTATTTTCATTTTTAAww ; cor=; Ncor= a 15 13 39 8 10 7 29 3 36 2 5 4 5 3 36 2 5 5 3 3 34 32 16 17 c 9 5 3 6 1 27 4 3 0 6 2 2 1 35 5 2 2 1 7 7 5 5 9 9 g 7 11 0 8 1 1 2 4 4 3 3 2 1 3 0 0 1 3 2 2 2 1 7 8 t 16 18 5 25 35 12 12 37 7 36 37 39 40 6 6 43 39 38 35 35 6 9 15 13

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift8 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=17; shift=8; ncol=25; --------wwTAGTCATTTTTaaww ; Alignment reference a 0 0 0 0 0 0 0 0 84 71 24 213 20 11 13 233 7 24 17 27 25 167 153 87 75 c 0 0 0 0 0 0 0 0 48 33 21 5 17 10 210 7 7 13 13 25 18 29 24 57 52 g 0 0 0 0 0 0 0 0 50 36 27 13 192 7 7 4 7 11 11 18 18 18 29 39 48 t 0 0 0 0 0 0 0 0 71 113 181 22 24 225 23 9 232 205 212 183 192 39 47 70 78
oligos_6nt_test_vs_ctrl_m3_shift8 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/7; ncol2=17; w=0; offset=0; strand=D; shift=8; score= 1; --------wwTAGTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 84 71 24 213 20 11 13 233 7 24 17 27 25 167 153 87 75 c 0 0 0 0 0 0 0 0 48 33 21 5 17 10 210 7 7 13 13 25 18 29 24 57 52 g 0 0 0 0 0 0 0 0 50 36 27 13 192 7 7 4 7 11 11 18 18 18 29 39 48 t 0 0 0 0 0 0 0 0 71 113 181 22 24 225 23 9 232 205 212 183 192 39 47 70 78
oligos_6nt_test_vs_ctrl_m2_shift8 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=2/7; ncol2=17; w=0; offset=0; strand=D; shift=8; score=0.91582; --------wtTACTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 70 65 21 223 20 18 14 245 6 23 13 27 30 171 171 107 78 c 0 0 0 0 0 0 0 0 60 42 25 10 190 10 215 6 10 19 15 22 16 25 30 42 55 g 0 0 0 0 0 0 0 0 54 29 23 6 26 6 8 4 6 13 10 23 18 28 25 40 48 t 0 0 0 0 0 0 0 0 78 126 193 23 26 228 25 7 240 207 224 190 198 38 36 73 81
oligos_7nt_test_vs_ctrl_m4_rc_shift7 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/7; ncol2=18; w=-1; offset=-1; strand=R; shift=7; score=0.82368; -------wwTTAgTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 0 69 69 19 21 206 17 13 16 204 8 23 17 28 12 18 28 73 70 c 0 0 0 0 0 0 0 34 44 5 13 4 32 3 200 7 12 15 14 15 25 29 28 51 43 g 0 0 0 0 0 0 0 45 49 13 28 10 159 4 6 6 6 8 8 17 17 25 17 38 34 t 0 0 0 0 0 0 0 94 80 205 180 22 34 222 20 25 216 196 203 182 188 170 169 80 95
oligos_7nt_test_vs_ctrl_m3_rc_shift7 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3_rc; m=4/7; ncol2=18; w=-1; offset=-1; strand=R; shift=7; score=0.739503; -------wwTTACTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 0 97 71 16 16 215 17 14 15 226 9 19 14 28 16 17 20 70 68 c 0 0 0 0 0 0 0 35 64 10 18 10 188 8 211 5 10 21 17 25 25 26 32 46 61 g 0 0 0 0 0 0 0 40 44 10 28 10 23 2 14 4 12 19 11 19 19 35 18 52 40 t 0 0 0 0 0 0 0 90 83 226 200 27 34 238 22 27 231 203 220 190 202 184 192 94 93
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=5/7; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.578818; -ttTAAAAATgAaTcATTTTTAAaw ; cor=; Ncor= a 0 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 3 4 6 37 38 17 16 c 0 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 3 4 4 4 5 12 9 g 0 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 4 2 1 3 3 12 9 t 0 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36 42 42 41 8 6 11 18
oligos_6nt_test_vs_ctrl_m4_rc_shift1 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/7; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.525473; -wwAtTywTATTTTCATTTTTAAww ; cor=; Ncor= a 0 15 13 39 8 10 7 29 3 36 2 5 4 5 3 36 2 5 5 3 3 34 32 16 17 c 0 9 5 3 6 1 27 4 3 0 6 2 2 1 35 5 2 2 1 7 7 5 5 9 9 g 0 7 11 0 8 1 1 2 4 4 3 3 2 1 3 0 0 1 3 2 2 2 1 7 8 t 0 16 18 5 25 35 12 12 37 7 36 37 39 40 6 6 43 39 38 35 35 6 9 15 13
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=7/7; ncol2=24; w=-8; offset=-8; strand=R; shift=0; score=0.514649; wwaaaaAAATGAGTCATTTTttwh- ; cor=; Ncor= a 35 34 69 68 70 73 84 80 85 11 7 94 6 8 17 102 12 12 19 12 16 17 33 29 0 c 19 18 6 16 5 13 5 7 4 1 6 2 15 0 85 2 6 7 10 13 18 20 18 36 0 g 22 21 14 17 19 11 7 11 10 2 88 0 84 1 3 2 7 5 4 7 11 13 18 16 0 t 34 37 21 9 16 13 14 12 11 96 9 14 5 101 5 4 85 86 77 78 65 60 41 29 0

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=24; shift=1; ncol=25; -dwaaAAAATGACTCATTTttttww ; Alignment reference a 0 29 41 60 65 78 77 86 85 4 5 101 5 14 9 96 11 12 14 13 16 9 21 37 34 c 0 16 18 13 11 7 4 5 7 2 3 1 84 0 88 2 10 11 7 11 19 17 14 21 22 g 0 36 18 20 18 13 10 7 6 2 85 0 15 2 6 1 4 7 5 13 5 16 6 18 19 t 0 29 33 17 16 12 19 12 12 102 17 8 6 94 7 11 85 80 84 73 70 68 69 34 35
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=1/6; ncol2=24; w=0; offset=0; strand=D; shift=1; score= 1; -dwaaAAAATGACTCATTTttttww ; cor=; Ncor= a 0 29 41 60 65 78 77 86 85 4 5 101 5 14 9 96 11 12 14 13 16 9 21 37 34 c 0 16 18 13 11 7 4 5 7 2 3 1 84 0 88 2 10 11 7 11 19 17 14 21 22 g 0 36 18 20 18 13 10 7 6 2 85 0 15 2 6 1 4 7 5 13 5 16 6 18 19 t 0 29 33 17 16 12 19 12 12 102 17 8 6 94 7 11 85 80 84 73 70 68 69 34 35
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1_rc; m=2/6; ncol2=24; w=0; offset=0; strand=R; shift=1; score=0.822789; -ttTAAAAATgAaTcATTTTTAAaw ; cor=; Ncor= a 0 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 3 4 6 37 38 17 16 c 0 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 3 4 4 4 5 12 9 g 0 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 4 2 1 3 3 12 9 t 0 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36 42 42 41 8 6 11 18
oligos_7nt_test_vs_ctrl_m3_rc_shift7 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3_rc; m=3/6; ncol2=18; w=0; offset=6; strand=R; shift=7; score=0.651013; -------wwTTACTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 0 97 71 16 16 215 17 14 15 226 9 19 14 28 16 17 20 70 68 c 0 0 0 0 0 0 0 35 64 10 18 10 188 8 211 5 10 21 17 25 25 26 32 46 61 g 0 0 0 0 0 0 0 40 44 10 28 10 23 2 14 4 12 19 11 19 19 35 18 52 40 t 0 0 0 0 0 0 0 90 83 226 200 27 34 238 22 27 231 203 220 190 202 184 192 94 93
oligos_7nt_test_vs_ctrl_m4_rc_shift7 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/6; ncol2=18; w=0; offset=6; strand=R; shift=7; score=0.605624; -------wwTTAgTCATTTTTTTww ; cor=; Ncor= a 0 0 0 0 0 0 0 69 69 19 21 206 17 13 16 204 8 23 17 28 12 18 28 73 70 c 0 0 0 0 0 0 0 34 44 5 13 4 32 3 200 7 12 15 14 15 25 29 28 51 43 g 0 0 0 0 0 0 0 45 49 13 28 10 159 4 6 6 6 8 8 17 17 25 17 38 34 t 0 0 0 0 0 0 0 94 80 205 180 22 34 222 20 25 216 196 203 182 188 170 169 80 95
oligos_6nt_test_vs_ctrl_m2_shift8 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=5/6; ncol2=17; w=0; offset=7; strand=D; shift=8; score=0.543509; --------wtTACTCATTTTTaaww ; cor=; Ncor= a 0 0 0 0 0 0 0 0 70 65 21 223 20 18 14 245 6 23 13 27 30 171 171 107 78 c 0 0 0 0 0 0 0 0 60 42 25 10 190 10 215 6 10 19 15 22 16 25 30 42 55 g 0 0 0 0 0 0 0 0 54 29 23 6 26 6 8 4 6 13 10 23 18 28 25 40 48 t 0 0 0 0 0 0 0 0 78 126 193 23 26 228 25 7 240 207 224 190 198 38 36 73 81
oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=6/6; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score=0.514649; wwttAAAAATGACTAww-------- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 0 0 0 0 0 0 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 0 0 0 0 0 0 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 0 0 0 0 0 0 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; wwAAAAAAATGAGTAAww ; Alignment reference a 93 94 192 184 202 190 220 203 231 27 22 238 34 27 200 226 83 90 c 40 52 18 35 19 19 11 19 12 4 14 2 23 10 28 10 44 40 g 61 46 32 26 25 25 17 21 10 5 211 8 188 10 18 10 64 35 t 68 70 20 17 16 28 14 19 9 226 15 14 17 215 16 16 71 97
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/6; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAAAAATGAGTAAww ; cor=; Ncor= a 93 94 192 184 202 190 220 203 231 27 22 238 34 27 200 226 83 90 c 40 52 18 35 19 19 11 19 12 4 14 2 23 10 28 10 44 40 g 61 46 32 26 25 25 17 21 10 5 211 8 188 10 18 10 64 35 t 68 70 20 17 16 28 14 19 9 226 15 14 17 215 16 16 71 97
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4; m=2/6; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.938824; wwAAAAAAATGAcTAAww ; cor=; Ncor= a 95 80 169 170 188 182 203 196 216 25 20 222 34 22 180 205 80 94 c 34 38 17 25 17 17 8 8 6 6 6 4 159 10 28 13 49 45 g 43 51 28 29 25 15 14 15 12 7 200 3 32 4 13 5 44 34 t 70 73 28 18 12 28 17 23 8 204 16 13 17 206 21 19 69 69
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=3/6; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.808327; wwttAAAAATGAGTAaw- ; cor=; Ncor= a 81 73 36 38 198 190 224 207 240 7 25 228 26 23 193 126 78 0 c 48 40 25 28 18 23 10 13 6 4 8 6 26 6 23 29 54 0 g 55 42 30 25 16 22 15 19 10 6 215 10 190 10 25 42 60 0 t 78 107 171 171 30 27 13 23 6 245 14 18 20 223 21 65 70 0
oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3_rc; m=4/6; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.739503; wwttAAAAATGACTAww- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=5/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.651013; wwaaaaAAATGAGTCATT ; cor=; Ncor= a 35 34 69 68 70 73 84 80 85 11 7 94 6 8 17 102 12 12 c 19 18 6 16 5 13 5 7 4 1 6 2 15 0 85 2 6 7 g 22 21 14 17 19 11 7 11 10 2 88 0 84 1 3 2 7 5 t 34 37 21 9 16 13 14 12 11 96 9 14 5 101 5 4 85 86
oligos_6nt_test_vs_ctrl_m1_rc_shift1 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=6/6; ncol2=24; w=0; offset=1; strand=R; shift=1; score=0.510353; -ttTAAAAATgAaTcATT ; cor=; Ncor= a 0 12 12 10 41 39 42 39 43 4 8 44 25 8 9 43 9 7 c 0 12 5 3 7 4 7 3 2 1 3 2 11 1 35 1 1 8 g 0 11 12 2 1 7 2 5 1 1 35 0 10 0 1 2 1 1 t 0 17 23 37 3 2 1 5 6 46 6 6 6 43 7 6 41 36

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; wwTTAAAAATGAAAATAwrAaTww ; Alignment reference a 13 15 9 6 35 35 38 39 43 6 6 40 39 37 36 7 37 12 12 35 25 5 18 16 c 8 7 1 2 2 2 3 1 0 0 3 1 2 3 3 4 4 2 1 1 8 0 11 7 g 9 9 5 5 7 7 1 2 2 5 35 1 2 2 6 0 3 4 27 1 6 3 5 9 t 17 16 32 34 3 3 5 5 2 36 3 5 4 5 2 36 3 29 7 10 8 39 13 15
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAATGAAAATAwrAaTww ; cor=; Ncor= a 13 15 9 6 35 35 38 39 43 6 6 40 39 37 36 7 37 12 12 35 25 5 18 16 c 8 7 1 2 2 2 3 1 0 0 3 1 2 3 3 4 4 2 1 1 8 0 11 7 g 9 9 5 5 7 7 1 2 2 5 35 1 2 2 6 0 3 4 27 1 6 3 5 9 t 17 16 32 34 3 3 5 5 2 36 3 5 4 5 2 36 3 29 7 10 8 39 13 15
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/4; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.526071; wwttAAAAATGAGTAaw------- ; cor=; Ncor= a 81 73 36 38 198 190 224 207 240 7 25 228 26 23 193 126 78 0 0 0 0 0 0 0 c 48 40 25 28 18 23 10 13 6 4 8 6 26 6 23 29 54 0 0 0 0 0 0 0 g 55 42 30 25 16 22 15 19 10 6 215 10 190 10 25 42 60 0 0 0 0 0 0 0 t 78 107 171 171 30 27 13 23 6 245 14 18 20 223 21 65 70 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/4; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.525473; wwttAAAAATGACTAww------- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 0 0 0 0 0 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 0 0 0 0 0 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 0 0 0 0 0 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=4/4; ncol2=24; w=0; offset=4; strand=D; shift=4; score=0.502602; ----aaAAAAmAAAAtAtgAAAAT ; cor=; Ncor= a 0 0 0 0 35 38 68 65 63 67 24 67 69 72 66 19 61 18 19 67 71 76 65 8 c 0 0 0 0 18 12 5 5 5 5 38 5 5 2 5 6 9 3 9 3 2 1 6 3 g 0 0 0 0 11 17 4 4 8 3 9 6 7 6 3 7 5 8 42 8 9 2 8 6 t 0 0 0 0 19 16 6 9 7 8 12 5 2 3 9 51 8 54 13 5 1 4 4 66

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=18; shift=0; ncol=18; wwAAAAAAATGAcTAAww ; Alignment reference a 95 80 169 170 188 182 203 196 216 25 20 222 34 22 180 205 80 94 c 34 38 17 25 17 17 8 8 6 6 6 4 159 10 28 13 49 45 g 43 51 28 29 25 15 14 15 12 7 200 3 32 4 13 5 44 34 t 70 73 28 18 12 28 17 23 8 204 16 13 17 206 21 19 69 69
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=1/6; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAAAAATGAcTAAww ; cor=; Ncor= a 95 80 169 170 188 182 203 196 216 25 20 222 34 22 180 205 80 94 c 34 38 17 25 17 17 8 8 6 6 6 4 159 10 28 13 49 45 g 43 51 28 29 25 15 14 15 12 7 200 3 32 4 13 5 44 34 t 70 73 28 18 12 28 17 23 8 204 16 13 17 206 21 19 69 69
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=2/6; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.938824; wwAAAAAAATGAGTAAww ; cor=; Ncor= a 93 94 192 184 202 190 220 203 231 27 22 238 34 27 200 226 83 90 c 40 52 18 35 19 19 11 19 12 4 14 2 23 10 28 10 44 40 g 61 46 32 26 25 25 17 21 10 5 211 8 188 10 18 10 64 35 t 68 70 20 17 16 28 14 19 9 226 15 14 17 215 16 16 71 97
oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/6; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.82368; wwttAAAAATGACTAww- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=4/6; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.761913; wwttAAAAATGAGTAaw- ; cor=; Ncor= a 81 73 36 38 198 190 224 207 240 7 25 228 26 23 193 126 78 0 c 48 40 25 28 18 23 10 13 6 4 8 6 26 6 23 29 54 0 g 55 42 30 25 16 22 15 19 10 6 215 10 190 10 25 42 60 0 t 78 107 171 171 30 27 13 23 6 245 14 18 20 223 21 65 70 0
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=5/6; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.605624; wwaaaaAAATGAGTCATT ; cor=; Ncor= a 35 34 69 68 70 73 84 80 85 11 7 94 6 8 17 102 12 12 c 19 18 6 16 5 13 5 7 4 1 6 2 15 0 85 2 6 7 g 22 21 14 17 19 11 7 11 10 2 88 0 84 1 3 2 7 5 t 34 37 21 9 16 13 14 12 11 96 9 14 5 101 5 4 85 86
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=6/6; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.530727; wtTTAAAAATgAtTcATT ; cor=; Ncor= a 18 11 6 8 41 42 42 36 41 6 7 43 6 6 6 46 6 5 c 9 12 3 3 1 2 4 1 1 2 1 0 10 0 35 1 1 5 g 9 12 5 4 4 4 3 8 1 1 35 1 11 2 3 1 2 3 t 16 17 38 37 6 4 3 7 9 43 9 8 25 44 8 4 43 39

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=24; shift=0; ncol=24; wtTTAAAAATgAtTcATTTTTAaa ; Alignment reference a 18 11 6 8 41 42 42 36 41 6 7 43 6 6 6 46 6 5 1 2 3 37 23 17 c 9 12 3 3 1 2 4 1 1 2 1 0 10 0 35 1 1 5 2 7 1 2 12 11 g 9 12 5 4 4 4 3 8 1 1 35 1 11 2 3 1 2 3 7 4 7 3 5 12 t 16 17 38 37 6 4 3 7 9 43 9 8 25 44 8 4 43 39 42 39 41 10 12 12
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=1/7; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wtTTAAAAATgAtTcATTTTTAaa ; cor=; Ncor= a 18 11 6 8 41 42 42 36 41 6 7 43 6 6 6 46 6 5 1 2 3 37 23 17 c 9 12 3 3 1 2 4 1 1 2 1 0 10 0 35 1 1 5 2 7 1 2 12 11 g 9 12 5 4 4 4 3 8 1 1 35 1 11 2 3 1 2 3 7 4 7 3 5 12 t 16 17 38 37 6 4 3 7 9 43 9 8 25 44 8 4 43 39 42 39 41 10 12 12
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/7; ncol2=24; w=0; offset=0; strand=R; shift=0; score=0.822789; wwaaaaAAATGAGTCATTTTttwh ; cor=; Ncor= a 35 34 69 68 70 73 84 80 85 11 7 94 6 8 17 102 12 12 19 12 16 17 33 29 c 19 18 6 16 5 13 5 7 4 1 6 2 15 0 85 2 6 7 10 13 18 20 18 36 g 22 21 14 17 19 11 7 11 10 2 88 0 84 1 3 2 7 5 4 7 11 13 18 16 t 34 37 21 9 16 13 14 12 11 96 9 14 5 101 5 4 85 86 77 78 65 60 41 29
oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/7; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.578818; wwttAAAAATGACTAww------- ; cor=; Ncor= a 78 70 47 39 192 183 212 205 232 9 23 225 24 22 181 113 71 0 0 0 0 0 0 0 c 48 39 29 18 18 18 11 11 7 4 7 7 192 13 27 36 50 0 0 0 0 0 0 0 g 52 57 24 29 18 25 13 13 7 7 210 10 17 5 21 33 48 0 0 0 0 0 0 0 t 75 87 153 167 25 27 17 24 7 233 13 11 20 213 24 71 84 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=4/7; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.578007; wwttAAAAATGAGTAaw------- ; cor=; Ncor= a 81 73 36 38 198 190 224 207 240 7 25 228 26 23 193 126 78 0 0 0 0 0 0 0 c 48 40 25 28 18 23 10 13 6 4 8 6 26 6 23 29 54 0 0 0 0 0 0 0 g 55 42 30 25 16 22 15 19 10 6 215 10 190 10 25 42 60 0 0 0 0 0 0 0 t 78 107 171 171 30 27 13 23 6 245 14 18 20 223 21 65 70 0 0 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=5/7; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.530727; wwAAAAAAATGAcTAAww------ ; cor=; Ncor= a 95 80 169 170 188 182 203 196 216 25 20 222 34 22 180 205 80 94 0 0 0 0 0 0 c 34 38 17 25 17 17 8 8 6 6 6 4 159 10 28 13 49 45 0 0 0 0 0 0 g 43 51 28 29 25 15 14 15 12 7 200 3 32 4 13 5 44 34 0 0 0 0 0 0 t 70 73 28 18 12 28 17 23 8 204 16 13 17 206 21 19 69 69 0 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m3_rc_shift7 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3_rc; m=6/7; ncol2=18; w=0; offset=7; strand=R; shift=7; score=0.510353; -------wwTTACTCATTTTTTTw ; cor=; Ncor= a 0 0 0 0 0 0 0 97 71 16 16 215 17 14 15 226 9 19 14 28 16 17 20 70 c 0 0 0 0 0 0 0 35 64 10 18 10 188 8 211 5 10 21 17 25 25 26 32 46 g 0 0 0 0 0 0 0 40 44 10 28 10 23 2 14 4 12 19 11 19 19 35 18 52 t 0 0 0 0 0 0 0 90 83 226 200 27 34 238 22 27 231 203 220 190 202 184 192 94
oligos_7nt_test_vs_ctrl_m2_rc_shift5 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2_rc; m=7/7; ncol2=15; w=0; offset=5; strand=R; shift=5; score=0.442572; -----wwcATGATTCATAww---- ; cor=; Ncor= a 0 0 0 0 0 119 123 48 326 7 14 352 30 15 22 356 27 275 116 109 0 0 0 0 c 0 0 0 0 0 84 83 268 23 11 17 13 32 3 343 12 48 34 81 92 0 0 0 0 g 0 0 0 0 0 85 88 40 17 6 335 7 44 14 11 8 38 29 74 74 0 0 0 0 t 0 0 0 0 0 108 102 40 30 372 30 24 290 364 20 20 283 58 125 121 0 0 0 0