One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/09/03/peak-motifs.2025-09-03.113949_2025-09-03.113949_eRwEjV/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/09/03/peak-motifs.2025-09-03.113949_2025-09-03.113949_eRwEjV/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; aaAAArAAAAArAaa ; Alignment reference a 194 201 290 299 310 156 313 313 305 310 303 144 294 196 178 c 40 37 9 10 9 10 4 6 5 7 4 16 12 43 56 g 60 70 30 14 8 159 13 12 21 13 24 166 18 63 57 t 42 28 7 13 9 11 6 5 5 6 5 10 12 34 45

oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; aaAAArAAAAArAaa ; cor=; Ncor= a 194 201 290 299 310 156 313 313 305 310 303 144 294 196 178 c 40 37 9 10 9 10 4 6 5 7 4 16 12 43 56 g 60 70 30 14 8 159 13 12 21 13 24 166 18 63 57 t 42 28 7 13 9 11 6 5 5 6 5 10 12 34 45

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m3; m=2/2; ncol2=18; w=0; offset=0; strand=D; shift=0; score=0.790328; aaAAArAAAAAAArA ; cor=; Ncor= a 216 228 292 300 306 192 303 301 308 311 300 309 306 203 306 c 32 32 8 8 8 12 11 6 6 4 9 10 10 8 8 g 69 61 29 23 21 126 21 28 23 20 25 19 18 123 20 t 26 22 14 12 8 13 8 8 6 8 9 5 9 9 9

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

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; vmCGGGCCgg ; Alignment reference a 45 46 0 0 0 0 0 0 38 33 c 47 56 172 0 0 0 172 172 39 37 g 55 37 0 172 172 172 0 0 60 70 t 25 33 0 0 0 0 0 0 35 32

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; vmCGGGCCgg ; cor=; Ncor= a 45 46 0 0 0 0 0 0 38 33 c 47 56 172 0 0 0 172 172 39 37 g 55 37 0 172 172 172 0 0 60 70 t 25 33 0 0 0 0 0 0 35 32

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; aaAAArAAAAAAArAAAa ; Alignment reference a 216 228 292 300 306 192 303 301 308 311 300 309 306 203 306 296 234 207 c 32 32 8 8 8 12 11 6 6 4 9 10 10 8 8 18 33 38 g 69 61 29 23 21 126 21 28 23 20 25 19 18 123 20 19 54 59 t 26 22 14 12 8 13 8 8 6 8 9 5 9 9 9 10 22 39

oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/2; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; aaAAArAAAAAAArAAAa ; cor=; Ncor= a 216 228 292 300 306 192 303 301 308 311 300 309 306 203 306 296 234 207 c 32 32 8 8 8 12 11 6 6 4 9 10 10 8 8 18 33 38 g 69 61 29 23 21 126 21 28 23 20 25 19 18 123 20 19 54 59 t 26 22 14 12 8 13 8 8 6 8 9 5 9 9 9 10 22 39

oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m4; m=2/2; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.790328; aaAAArAAAAArAaa--- ; cor=; Ncor= a 194 201 290 299 310 156 313 313 305 310 303 144 294 196 178 0 0 0 c 40 37 9 10 9 10 4 6 5 7 4 16 12 43 56 0 0 0 g 60 70 30 14 8 159 13 12 21 13 24 166 18 63 57 0 0 0 t 42 28 7 13 9 11 6 5 5 6 5 10 12 34 45 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift9 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m5_shift9 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=12; shift=9; ncol=21; ---------ysTACAsTAcmy ; Alignment reference a 0 0 0 0 0 0 0 0 0 92 87 6 363 13 284 14 1 362 49 114 87 c 0 0 0 0 0 0 0 0 0 96 107 15 4 349 26 110 3 7 174 103 97 g 0 0 0 0 0 0 0 0 0 91 137 5 10 7 28 244 3 9 88 78 91 t 0 0 0 0 0 0 0 0 0 102 50 355 4 12 43 13 374 3 70 86 106

oligos_7nt_mkv1_m5_shift9 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=9; score= 1; ---------ysTACAsTAcmy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 92 87 6 363 13 284 14 1 362 49 114 87 c 0 0 0 0 0 0 0 0 0 96 107 15 4 349 26 110 3 7 174 103 97 g 0 0 0 0 0 0 0 0 0 91 137 5 10 7 28 244 3 9 88 78 91 t 0 0 0 0 0 0 0 0 0 102 50 355 4 12 43 13 374 3 70 86 106

oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_7nt_mkv1_m5 versus oligos_6nt_mkv1_m2; m=2/3; ncol2=19; w=-5; offset=-5; strand=D; shift=4; score=0.528639; ----hkgTATGTACACTAcac ; cor=; Ncor= a 0 0 0 0 42 37 21 20 109 3 12 2 145 11 119 10 13 119 21 90 26 c 0 0 0 0 42 30 30 16 12 24 8 7 2 122 12 107 11 3 78 18 57 g 0 0 0 0 25 47 81 11 19 14 126 3 5 5 15 21 11 24 26 23 37 t 0 0 0 0 46 41 23 108 15 114 9 143 3 17 9 17 120 9 30 24 35

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m1; m=3/3; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.428598; wtagtgTAGTGTACAcTAcac ; cor=; Ncor= a 25 19 44 16 16 13 5 72 5 11 3 2 79 5 67 6 5 71 11 45 17 c 17 20 11 15 11 17 6 2 16 2 15 3 1 61 5 57 6 3 43 12 36 g 21 16 14 37 12 44 3 6 58 5 62 1 3 16 1 17 2 6 18 11 16 t 22 30 16 17 46 11 71 5 6 67 5 79 2 3 12 5 72 5 13 17 16

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=19; shift=4; ncol=23; ----hkgTATGTACACTAcactr ; Alignment reference a 0 0 0 0 42 37 21 20 109 3 12 2 145 11 119 10 13 119 21 90 26 38 45 c 0 0 0 0 42 30 30 16 12 24 8 7 2 122 12 107 11 3 78 18 57 32 32 g 0 0 0 0 25 47 81 11 19 14 126 3 5 5 15 21 11 24 26 23 37 31 44 t 0 0 0 0 46 41 23 108 15 114 9 143 3 17 9 17 120 9 30 24 35 54 34

oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=4; score= 1; ----hkgTATGTACACTAcactr ; cor=; Ncor= a 0 0 0 0 42 37 21 20 109 3 12 2 145 11 119 10 13 119 21 90 26 38 45 c 0 0 0 0 42 30 30 16 12 24 8 7 2 122 12 107 11 3 78 18 57 32 32 g 0 0 0 0 25 47 81 11 19 14 126 3 5 5 15 21 11 24 26 23 37 31 44 t 0 0 0 0 46 41 23 108 15 114 9 143 3 17 9 17 120 9 30 24 35 54 34

oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1_rc; m=2/3; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.582608; wtagtgTAgTGTACACTAcacta ; cor=; Ncor= a 25 19 44 16 17 13 5 72 5 12 3 2 79 5 67 6 5 71 11 46 17 16 30 c 17 21 11 16 11 18 6 2 17 1 16 3 1 62 5 58 6 3 44 12 37 14 16 g 21 16 14 36 12 43 3 6 57 5 61 1 3 15 2 16 2 6 17 11 15 11 20 t 22 29 16 17 45 11 71 5 6 67 5 79 2 3 11 5 72 5 13 16 16 44 19

oligos_7nt_mkv1_m5_shift9 (oligos_7nt_mkv1_m5)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m5; m=3/3; ncol2=12; w=0; offset=5; strand=D; shift=9; score=0.528639; ---------ysTACAsTAcmy-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 92 87 6 363 13 284 14 1 362 49 114 87 0 0 c 0 0 0 0 0 0 0 0 0 96 107 15 4 349 26 110 3 7 174 103 97 0 0 g 0 0 0 0 0 0 0 0 0 91 137 5 10 7 28 244 3 9 88 78 91 0 0 t 0 0 0 0 0 0 0 0 0 102 50 355 4 12 43 13 374 3 70 86 106 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=16; shift=4; ncol=20; ----aggTAtGTACaTAcmk ; Alignment reference a 0 0 0 0 51 40 33 10 147 14 20 1 163 9 108 4 142 16 43 40 c 0 0 0 0 42 39 26 13 8 25 14 3 5 128 25 13 7 96 51 37 g 0 0 0 0 37 51 96 7 13 25 130 5 3 14 26 8 13 26 39 43 t 0 0 0 0 42 42 17 142 4 108 8 163 1 21 13 147 10 34 39 52

oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score= 1; ----aggTAtGTACaTAcmk ; cor=; Ncor= a 0 0 0 0 51 40 33 10 147 14 20 1 163 9 108 4 142 16 43 40 c 0 0 0 0 42 39 26 13 8 25 14 3 5 128 25 13 7 96 51 37 g 0 0 0 0 37 51 96 7 13 25 130 5 3 14 26 8 13 26 39 43 t 0 0 0 0 42 42 17 142 4 108 8 163 1 21 13 147 10 34 39 52

oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m3; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.874894; ----mbgTAgGTACcTAcvk ; cor=; Ncor= a 0 0 0 0 55 34 21 12 135 11 12 6 151 5 20 11 124 20 42 29 c 0 0 0 0 46 42 27 12 8 21 14 2 2 129 109 8 13 93 44 30 g 0 0 0 0 30 43 93 12 8 109 130 2 2 15 21 8 12 27 41 46 t 0 0 0 0 30 42 20 125 10 20 5 151 6 12 11 134 12 21 34 56

oligos_6nt_mkv1_m5_rc_shift4 (oligos_6nt_mkv1_m5_rc)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m5_rc; m=3/4; ncol2=15; w=0; offset=0; strand=R; shift=4; score=0.689815; ----mggTAGGTACCgaag- ; cor=; Ncor= a 0 0 0 0 68 49 28 14 191 9 3 3 197 14 23 22 114 67 47 0 c 0 0 0 0 64 46 32 12 5 32 12 2 6 158 149 11 22 49 53 0 g 0 0 0 0 44 75 130 13 8 152 196 5 4 33 28 135 34 53 74 0 t 0 0 0 0 38 44 24 175 10 21 3 204 7 9 14 46 44 45 40 0

oligos_7nt_mkv1_m2_rc_shift0 (oligos_7nt_mkv1_m2_rc)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2_rc; m=4/4; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.587289; atsTAggTAgGTAcrTAcaT ; cor=; Ncor= a 19 9 9 7 36 2 5 2 37 4 6 2 44 2 27 1 36 5 25 3 c 7 11 13 3 3 7 5 3 2 8 2 1 0 29 4 3 1 27 6 4 g 11 10 12 3 4 26 30 3 3 23 35 2 0 6 12 1 6 7 10 6 t 8 15 11 32 2 10 5 37 3 10 2 40 1 8 2 40 2 6 4 32

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; ssACCCGGGTss ; Alignment reference a 20 33 127 8 1 9 5 7 8 8 22 23 c 54 44 8 134 147 140 2 1 6 13 57 59 g 59 57 13 6 1 2 140 147 134 8 44 54 t 23 22 8 8 7 5 9 1 8 127 33 20

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssACCCGGGTss ; cor=; Ncor= a 20 33 127 8 1 9 5 7 8 8 22 23 c 54 44 8 134 147 140 2 1 6 13 57 59 g 59 57 13 6 1 2 140 147 134 8 44 54 t 23 22 8 8 7 5 9 1 8 127 33 20

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.71376; ssCCCCGGGGss ; cor=; Ncor= a 24 33 8 6 4 6 5 6 6 8 35 40 c 56 57 160 166 171 166 11 7 10 12 63 68 g 68 63 12 10 7 11 166 171 166 160 57 56 t 40 35 8 6 6 5 6 4 6 8 33 24

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=16; shift=4; ncol=20; ----mbgTAgGTACcTAcvk ; Alignment reference a 0 0 0 0 55 34 21 12 135 11 12 6 151 5 20 11 124 20 42 29 c 0 0 0 0 46 42 27 12 8 21 14 2 2 129 109 8 13 93 44 30 g 0 0 0 0 30 43 93 12 8 109 130 2 2 15 21 8 12 27 41 46 t 0 0 0 0 30 42 20 125 10 20 5 151 6 12 11 134 12 21 34 56

oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score= 1; ----mbgTAgGTACcTAcvk ; cor=; Ncor= a 0 0 0 0 55 34 21 12 135 11 12 6 151 5 20 11 124 20 42 29 c 0 0 0 0 46 42 27 12 8 21 14 2 2 129 109 8 13 93 44 30 g 0 0 0 0 30 43 93 12 8 109 130 2 2 15 21 8 12 27 41 46 t 0 0 0 0 30 42 20 125 10 20 5 151 6 12 11 134 12 21 34 56

oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.874894; ----aggTAtGTACaTAcmk ; cor=; Ncor= a 0 0 0 0 51 40 33 10 147 14 20 1 163 9 108 4 142 16 43 40 c 0 0 0 0 42 39 26 13 8 25 14 3 5 128 25 13 7 96 51 37 g 0 0 0 0 37 51 96 7 13 25 130 5 3 14 26 8 13 26 39 43 t 0 0 0 0 42 42 17 142 4 108 8 163 1 21 13 147 10 34 39 52

oligos_6nt_mkv1_m5_rc_shift4 (oligos_6nt_mkv1_m5_rc)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m5_rc; m=3/4; ncol2=15; w=0; offset=0; strand=R; shift=4; score=0.827407; ----mggTAGGTACCgaag- ; cor=; Ncor= a 0 0 0 0 68 49 28 14 191 9 3 3 197 14 23 22 114 67 47 0 c 0 0 0 0 64 46 32 12 5 32 12 2 6 158 149 11 22 49 53 0 g 0 0 0 0 44 75 130 13 8 152 196 5 4 33 28 135 34 53 74 0 t 0 0 0 0 38 44 24 175 10 21 3 204 7 9 14 46 44 45 40 0

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=4/4; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.572198; ryatAtgTAygTACcTAccT ; cor=; Ncor= a 21 10 21 3 32 4 6 2 40 2 8 1 40 2 10 3 37 5 10 2 c 5 15 9 5 6 10 7 6 1 12 6 0 2 35 23 3 3 30 26 4 g 12 8 11 8 4 6 27 1 3 4 29 0 1 2 8 2 3 5 7 3 t 7 12 4 29 3 25 5 36 1 27 2 44 2 6 4 37 2 5 2 36

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; rrcgGGACGGGAms ; Alignment reference a 75 86 39 34 24 14 260 10 2 7 7 266 77 58 c 63 70 171 44 29 9 14 262 12 9 17 12 93 80 g 107 82 57 185 215 258 11 11 268 273 260 12 71 103 t 52 59 30 34 29 16 12 14 15 8 13 7 56 56

oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; rrcgGGACGGGAms ; cor=; Ncor= a 75 86 39 34 24 14 260 10 2 7 7 266 77 58 c 63 70 171 44 29 9 14 262 12 9 17 12 93 80 g 107 82 57 185 215 258 11 11 268 273 260 12 71 103 t 52 59 30 34 29 16 12 14 15 8 13 7 56 56

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m5_shift5 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=15; shift=5; ncol=20; -----cttcGGTACCTAcck ; Alignment reference a 0 0 0 0 0 40 45 44 46 14 9 7 204 3 21 10 175 24 44 38 c 0 0 0 0 0 74 53 34 135 28 33 4 5 196 152 8 13 130 75 44 g 0 0 0 0 0 53 49 22 11 149 158 6 2 12 32 5 12 32 46 64 t 0 0 0 0 0 47 67 114 22 23 14 197 3 3 9 191 14 28 49 68

oligos_6nt_mkv1_m5_shift5 (oligos_6nt_mkv1_m5)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=5; score= 1; -----cttcGGTACCTAcck ; cor=; Ncor= a 0 0 0 0 0 40 45 44 46 14 9 7 204 3 21 10 175 24 44 38 c 0 0 0 0 0 74 53 34 135 28 33 4 5 196 152 8 13 130 75 44 g 0 0 0 0 0 53 49 22 11 149 158 6 2 12 32 5 12 32 46 64 t 0 0 0 0 0 47 67 114 22 23 14 197 3 3 9 191 14 28 49 68

oligos_6nt_mkv1_m3_rc_shift4 (oligos_6nt_mkv1_m3_rc)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m3_rc; m=2/4; ncol2=16; w=-1; offset=-1; strand=R; shift=4; score=0.827407; ----mbgTAgGTACcTAcvk ; cor=; Ncor= a 0 0 0 0 56 34 21 12 134 11 12 6 151 5 20 10 125 20 42 30 c 0 0 0 0 46 41 27 12 8 21 15 2 2 130 109 8 12 93 43 30 g 0 0 0 0 30 44 93 13 8 109 129 2 2 14 21 8 12 27 42 46 t 0 0 0 0 29 42 20 124 11 20 5 151 6 12 11 135 12 21 34 55

oligos_6nt_mkv1_m1_rc_shift4 (oligos_6nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m1_rc; m=3/4; ncol2=16; w=-1; offset=-1; strand=R; shift=4; score=0.689815; ----mkgTAtGTACaTAcct ; cor=; Ncor= a 0 0 0 0 52 39 34 10 147 13 21 1 163 8 108 4 142 17 42 42 c 0 0 0 0 43 39 26 13 8 26 14 3 5 130 25 13 7 96 51 37 g 0 0 0 0 37 51 96 7 13 25 128 5 3 14 25 8 13 26 39 42 t 0 0 0 0 40 43 16 142 4 108 9 163 1 20 14 147 10 33 40 51

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m2; m=4/4; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.461541; ryatAtgTAygTACcTAccT ; cor=; Ncor= a 21 10 21 3 32 4 6 2 40 2 8 1 40 2 10 3 37 5 10 2 c 5 15 9 5 6 10 7 6 1 12 6 0 2 35 23 3 3 30 26 4 g 12 8 11 8 4 6 27 1 3 4 29 0 1 2 8 2 3 5 7 3 t 7 12 4 29 3 25 5 36 1 27 2 44 2 6 4 37 2 5 2 36

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; ryatAtgTAygTACcTAccTAsat ; Alignment reference a 21 10 21 3 32 4 6 2 40 2 8 1 40 2 10 3 37 5 10 2 32 11 15 8 c 5 15 9 5 6 10 7 6 1 12 6 0 2 35 23 3 3 30 26 4 3 12 10 11 g 12 8 11 8 4 6 27 1 3 4 29 0 1 2 8 2 3 5 7 3 3 13 11 7 t 7 12 4 29 3 25 5 36 1 27 2 44 2 6 4 37 2 5 2 36 7 9 9 19

oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ryatAtgTAygTACcTAccTAsat ; cor=; Ncor= a 21 10 21 3 32 4 6 2 40 2 8 1 40 2 10 3 37 5 10 2 32 11 15 8 c 5 15 9 5 6 10 7 6 1 12 6 0 2 35 23 3 3 30 26 4 3 12 10 11 g 12 8 11 8 4 6 27 1 3 4 29 0 1 2 8 2 3 5 7 3 3 13 11 7 t 7 12 4 29 3 25 5 36 1 27 2 44 2 6 4 37 2 5 2 36 7 9 9 19

oligos_6nt_mkv1_m1_rc_shift4 (oligos_6nt_mkv1_m1_rc)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1_rc; m=2/4; ncol2=16; w=0; offset=4; strand=R; shift=4; score=0.587289; ----mkgTAtGTACaTAcct---- ; cor=; Ncor= a 0 0 0 0 52 39 34 10 147 13 21 1 163 8 108 4 142 17 42 42 0 0 0 0 c 0 0 0 0 43 39 26 13 8 26 14 3 5 130 25 13 7 96 51 37 0 0 0 0 g 0 0 0 0 37 51 96 7 13 25 128 5 3 14 25 8 13 26 39 42 0 0 0 0 t 0 0 0 0 40 43 16 142 4 108 9 163 1 20 14 147 10 33 40 51 0 0 0 0

oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=3/4; ncol2=16; w=0; offset=4; strand=D; shift=4; score=0.572198; ----mbgTAgGTACcTAcvk---- ; cor=; Ncor= a 0 0 0 0 55 34 21 12 135 11 12 6 151 5 20 11 124 20 42 29 0 0 0 0 c 0 0 0 0 46 42 27 12 8 21 14 2 2 129 109 8 13 93 44 30 0 0 0 0 g 0 0 0 0 30 43 93 12 8 109 130 2 2 15 21 8 12 27 41 46 0 0 0 0 t 0 0 0 0 30 42 20 125 10 20 5 151 6 12 11 134 12 21 34 56 0 0 0 0

oligos_6nt_mkv1_m5_shift5 (oligos_6nt_mkv1_m5)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m5; m=4/4; ncol2=15; w=0; offset=5; strand=D; shift=5; score=0.461541; -----cttcGGTACCTAcck---- ; cor=; Ncor= a 0 0 0 0 0 40 45 44 46 14 9 7 204 3 21 10 175 24 44 38 0 0 0 0 c 0 0 0 0 0 74 53 34 135 28 33 4 5 196 152 8 13 130 75 44 0 0 0 0 g 0 0 0 0 0 53 49 22 11 149 158 6 2 12 32 5 12 32 46 64 0 0 0 0 t 0 0 0 0 0 47 67 114 22 23 14 197 3 3 9 191 14 28 49 68 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; hmTCCACAsm ; Alignment reference a 34 40 0 0 0 110 0 110 25 35 c 28 28 0 110 110 0 110 0 34 35 g 17 21 0 0 0 0 0 0 29 26 t 31 21 110 0 0 0 0 0 22 14

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; hmTCCACAsm ; cor=; Ncor= a 34 40 0 0 0 110 0 110 25 35 c 28 28 0 110 110 0 110 0 34 35 g 17 21 0 0 0 0 0 0 29 26 t 31 21 110 0 0 0 0 0 22 14

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCCCCGGGGss ; Alignment reference a 24 33 8 6 4 6 5 6 6 8 35 40 c 56 57 160 166 171 166 11 7 10 12 63 68 g 68 63 12 10 7 11 166 171 166 160 57 56 t 40 35 8 6 6 5 6 4 6 8 33 24

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCCCCGGGGss ; cor=; Ncor= a 24 33 8 6 4 6 5 6 6 8 35 40 c 56 57 160 166 171 166 11 7 10 12 63 68 g 68 63 12 10 7 11 166 171 166 160 57 56 t 40 35 8 6 6 5 6 4 6 8 33 24

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.71376; ssACCCGGGTss ; cor=; Ncor= a 20 33 127 8 1 9 5 7 8 8 22 23 c 54 44 8 134 147 140 2 1 6 13 57 59 g 59 57 13 6 1 2 140 147 134 8 44 54 t 23 22 8 8 7 5 9 1 8 127 33 20

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; wtagtgTAGTGTACAcTAcactaw ; Alignment reference a 25 19 44 16 16 13 5 72 5 11 3 2 79 5 67 6 5 71 11 45 17 16 29 22 c 17 20 11 15 11 17 6 2 16 2 15 3 1 61 5 57 6 3 43 12 36 14 16 21 g 21 16 14 37 12 44 3 6 58 5 62 1 3 16 1 17 2 6 18 11 16 11 21 17 t 22 30 16 17 46 11 71 5 6 67 5 79 2 3 12 5 72 5 13 17 16 44 19 25

oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wtagtgTAGTGTACAcTAcactaw ; cor=; Ncor= a 25 19 44 16 16 13 5 72 5 11 3 2 79 5 67 6 5 71 11 45 17 16 29 22 c 17 20 11 15 11 17 6 2 16 2 15 3 1 61 5 57 6 3 43 12 36 14 16 21 g 21 16 14 37 12 44 3 6 58 5 62 1 3 16 1 17 2 6 18 11 16 11 21 17 t 22 30 16 17 46 11 71 5 6 67 5 79 2 3 12 5 72 5 13 17 16 44 19 25

oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=19; w=0; offset=1; strand=R; shift=1; score=0.582608; -yagtgTAGTGTACATAcmd---- ; cor=; Ncor= a 0 34 54 35 24 30 9 120 17 9 17 3 143 9 114 15 108 23 41 46 0 0 0 0 c 0 44 31 37 23 26 24 11 21 15 5 5 3 126 14 19 11 81 47 25 0 0 0 0 g 0 32 32 57 18 78 3 11 107 12 122 2 7 8 24 12 16 30 30 42 0 0 0 0 t 0 45 38 26 90 21 119 13 10 119 11 145 2 12 3 109 20 21 37 42 0 0 0 0

oligos_7nt_mkv1_m5_shift9 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m5; m=3/3; ncol2=12; w=0; offset=9; strand=D; shift=9; score=0.428598; ---------ysTACAsTAcmy--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 92 87 6 363 13 284 14 1 362 49 114 87 0 0 0 c 0 0 0 0 0 0 0 0 0 96 107 15 4 349 26 110 3 7 174 103 97 0 0 0 g 0 0 0 0 0 0 0 0 0 91 137 5 10 7 28 244 3 9 88 78 91 0 0 0 t 0 0 0 0 0 0 0 0 0 102 50 355 4 12 43 13 374 3 70 86 106 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m5_shift9 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=12; shift=9; ncol=21; ---------ysTACAsTAcmy ; Alignment reference a 0 0 0 0 0 0 0 0 0 92 87 6 363 13 284 14 1 362 49 114 87 c 0 0 0 0 0 0 0 0 0 96 107 15 4 349 26 110 3 7 174 103 97 g 0 0 0 0 0 0 0 0 0 91 137 5 10 7 28 244 3 9 88 78 91 t 0 0 0 0 0 0 0 0 0 102 50 355 4 12 43 13 374 3 70 86 106
oligos_7nt_mkv1_m5_shift9 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=9; score= 1; ---------ysTACAsTAcmy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 92 87 6 363 13 284 14 1 362 49 114 87 c 0 0 0 0 0 0 0 0 0 96 107 15 4 349 26 110 3 7 174 103 97 g 0 0 0 0 0 0 0 0 0 91 137 5 10 7 28 244 3 9 88 78 91 t 0 0 0 0 0 0 0 0 0 102 50 355 4 12 43 13 374 3 70 86 106
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)				; oligos_7nt_mkv1_m5 versus oligos_6nt_mkv1_m2; m=2/3; ncol2=19; w=-5; offset=-5; strand=D; shift=4; score=0.528639; ----hkgTATGTACACTAcac ; cor=; Ncor= a 0 0 0 0 42 37 21 20 109 3 12 2 145 11 119 10 13 119 21 90 26 c 0 0 0 0 42 30 30 16 12 24 8 7 2 122 12 107 11 3 78 18 57 g 0 0 0 0 25 47 81 11 19 14 126 3 5 5 15 21 11 24 26 23 37 t 0 0 0 0 46 41 23 108 15 114 9 143 3 17 9 17 120 9 30 24 35
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m1; m=3/3; ncol2=24; w=-9; offset=-9; strand=D; shift=0; score=0.428598; wtagtgTAGTGTACAcTAcac ; cor=; Ncor= a 25 19 44 16 16 13 5 72 5 11 3 2 79 5 67 6 5 71 11 45 17 c 17 20 11 15 11 17 6 2 16 2 15 3 1 61 5 57 6 3 43 12 36 g 21 16 14 37 12 44 3 6 58 5 62 1 3 16 1 17 2 6 18 11 16 t 22 30 16 17 46 11 71 5 6 67 5 79 2 3 12 5 72 5 13 17 16

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=19; shift=4; ncol=23; ----hkgTATGTACACTAcactr ; Alignment reference a 0 0 0 0 42 37 21 20 109 3 12 2 145 11 119 10 13 119 21 90 26 38 45 c 0 0 0 0 42 30 30 16 12 24 8 7 2 122 12 107 11 3 78 18 57 32 32 g 0 0 0 0 25 47 81 11 19 14 126 3 5 5 15 21 11 24 26 23 37 31 44 t 0 0 0 0 46 41 23 108 15 114 9 143 3 17 9 17 120 9 30 24 35 54 34
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=19; w=0; offset=0; strand=D; shift=4; score= 1; ----hkgTATGTACACTAcactr ; cor=; Ncor= a 0 0 0 0 42 37 21 20 109 3 12 2 145 11 119 10 13 119 21 90 26 38 45 c 0 0 0 0 42 30 30 16 12 24 8 7 2 122 12 107 11 3 78 18 57 32 32 g 0 0 0 0 25 47 81 11 19 14 126 3 5 5 15 21 11 24 26 23 37 31 44 t 0 0 0 0 46 41 23 108 15 114 9 143 3 17 9 17 120 9 30 24 35 54 34
oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1_rc; m=2/3; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.582608; wtagtgTAgTGTACACTAcacta ; cor=; Ncor= a 25 19 44 16 17 13 5 72 5 12 3 2 79 5 67 6 5 71 11 46 17 16 30 c 17 21 11 16 11 18 6 2 17 1 16 3 1 62 5 58 6 3 44 12 37 14 16 g 21 16 14 36 12 43 3 6 57 5 61 1 3 15 2 16 2 6 17 11 15 11 20 t 22 29 16 17 45 11 71 5 6 67 5 79 2 3 11 5 72 5 13 16 16 44 19
oligos_7nt_mkv1_m5_shift9 (oligos_7nt_mkv1_m5)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m5; m=3/3; ncol2=12; w=0; offset=5; strand=D; shift=9; score=0.528639; ---------ysTACAsTAcmy-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 92 87 6 363 13 284 14 1 362 49 114 87 0 0 c 0 0 0 0 0 0 0 0 0 96 107 15 4 349 26 110 3 7 174 103 97 0 0 g 0 0 0 0 0 0 0 0 0 91 137 5 10 7 28 244 3 9 88 78 91 0 0 t 0 0 0 0 0 0 0 0 0 102 50 355 4 12 43 13 374 3 70 86 106 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=16; shift=4; ncol=20; ----aggTAtGTACaTAcmk ; Alignment reference a 0 0 0 0 51 40 33 10 147 14 20 1 163 9 108 4 142 16 43 40 c 0 0 0 0 42 39 26 13 8 25 14 3 5 128 25 13 7 96 51 37 g 0 0 0 0 37 51 96 7 13 25 130 5 3 14 26 8 13 26 39 43 t 0 0 0 0 42 42 17 142 4 108 8 163 1 21 13 147 10 34 39 52
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score= 1; ----aggTAtGTACaTAcmk ; cor=; Ncor= a 0 0 0 0 51 40 33 10 147 14 20 1 163 9 108 4 142 16 43 40 c 0 0 0 0 42 39 26 13 8 25 14 3 5 128 25 13 7 96 51 37 g 0 0 0 0 37 51 96 7 13 25 130 5 3 14 26 8 13 26 39 43 t 0 0 0 0 42 42 17 142 4 108 8 163 1 21 13 147 10 34 39 52
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m3; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.874894; ----mbgTAgGTACcTAcvk ; cor=; Ncor= a 0 0 0 0 55 34 21 12 135 11 12 6 151 5 20 11 124 20 42 29 c 0 0 0 0 46 42 27 12 8 21 14 2 2 129 109 8 13 93 44 30 g 0 0 0 0 30 43 93 12 8 109 130 2 2 15 21 8 12 27 41 46 t 0 0 0 0 30 42 20 125 10 20 5 151 6 12 11 134 12 21 34 56
oligos_6nt_mkv1_m5_rc_shift4 (oligos_6nt_mkv1_m5_rc)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m5_rc; m=3/4; ncol2=15; w=0; offset=0; strand=R; shift=4; score=0.689815; ----mggTAGGTACCgaag- ; cor=; Ncor= a 0 0 0 0 68 49 28 14 191 9 3 3 197 14 23 22 114 67 47 0 c 0 0 0 0 64 46 32 12 5 32 12 2 6 158 149 11 22 49 53 0 g 0 0 0 0 44 75 130 13 8 152 196 5 4 33 28 135 34 53 74 0 t 0 0 0 0 38 44 24 175 10 21 3 204 7 9 14 46 44 45 40 0
oligos_7nt_mkv1_m2_rc_shift0 (oligos_7nt_mkv1_m2_rc)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2_rc; m=4/4; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.587289; atsTAggTAgGTAcrTAcaT ; cor=; Ncor= a 19 9 9 7 36 2 5 2 37 4 6 2 44 2 27 1 36 5 25 3 c 7 11 13 3 3 7 5 3 2 8 2 1 0 29 4 3 1 27 6 4 g 11 10 12 3 4 26 30 3 3 23 35 2 0 6 12 1 6 7 10 6 t 8 15 11 32 2 10 5 37 3 10 2 40 1 8 2 40 2 6 4 32

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=16; shift=4; ncol=20; ----mbgTAgGTACcTAcvk ; Alignment reference a 0 0 0 0 55 34 21 12 135 11 12 6 151 5 20 11 124 20 42 29 c 0 0 0 0 46 42 27 12 8 21 14 2 2 129 109 8 13 93 44 30 g 0 0 0 0 30 43 93 12 8 109 130 2 2 15 21 8 12 27 41 46 t 0 0 0 0 30 42 20 125 10 20 5 151 6 12 11 134 12 21 34 56
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score= 1; ----mbgTAgGTACcTAcvk ; cor=; Ncor= a 0 0 0 0 55 34 21 12 135 11 12 6 151 5 20 11 124 20 42 29 c 0 0 0 0 46 42 27 12 8 21 14 2 2 129 109 8 13 93 44 30 g 0 0 0 0 30 43 93 12 8 109 130 2 2 15 21 8 12 27 41 46 t 0 0 0 0 30 42 20 125 10 20 5 151 6 12 11 134 12 21 34 56
oligos_6nt_mkv1_m1_shift4 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=4; score=0.874894; ----aggTAtGTACaTAcmk ; cor=; Ncor= a 0 0 0 0 51 40 33 10 147 14 20 1 163 9 108 4 142 16 43 40 c 0 0 0 0 42 39 26 13 8 25 14 3 5 128 25 13 7 96 51 37 g 0 0 0 0 37 51 96 7 13 25 130 5 3 14 26 8 13 26 39 43 t 0 0 0 0 42 42 17 142 4 108 8 163 1 21 13 147 10 34 39 52
oligos_6nt_mkv1_m5_rc_shift4 (oligos_6nt_mkv1_m5_rc)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m5_rc; m=3/4; ncol2=15; w=0; offset=0; strand=R; shift=4; score=0.827407; ----mggTAGGTACCgaag- ; cor=; Ncor= a 0 0 0 0 68 49 28 14 191 9 3 3 197 14 23 22 114 67 47 0 c 0 0 0 0 64 46 32 12 5 32 12 2 6 158 149 11 22 49 53 0 g 0 0 0 0 44 75 130 13 8 152 196 5 4 33 28 135 34 53 74 0 t 0 0 0 0 38 44 24 175 10 21 3 204 7 9 14 46 44 45 40 0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=4/4; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.572198; ryatAtgTAygTACcTAccT ; cor=; Ncor= a 21 10 21 3 32 4 6 2 40 2 8 1 40 2 10 3 37 5 10 2 c 5 15 9 5 6 10 7 6 1 12 6 0 2 35 23 3 3 30 26 4 g 12 8 11 8 4 6 27 1 3 4 29 0 1 2 8 2 3 5 7 3 t 7 12 4 29 3 25 5 36 1 27 2 44 2 6 4 37 2 5 2 36

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m5_shift5 (oligos_6nt_mkv1_m5)				; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=15; shift=5; ncol=20; -----cttcGGTACCTAcck ; Alignment reference a 0 0 0 0 0 40 45 44 46 14 9 7 204 3 21 10 175 24 44 38 c 0 0 0 0 0 74 53 34 135 28 33 4 5 196 152 8 13 130 75 44 g 0 0 0 0 0 53 49 22 11 149 158 6 2 12 32 5 12 32 46 64 t 0 0 0 0 0 47 67 114 22 23 14 197 3 3 9 191 14 28 49 68
oligos_6nt_mkv1_m5_shift5 (oligos_6nt_mkv1_m5)				; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=5; score= 1; -----cttcGGTACCTAcck ; cor=; Ncor= a 0 0 0 0 0 40 45 44 46 14 9 7 204 3 21 10 175 24 44 38 c 0 0 0 0 0 74 53 34 135 28 33 4 5 196 152 8 13 130 75 44 g 0 0 0 0 0 53 49 22 11 149 158 6 2 12 32 5 12 32 46 64 t 0 0 0 0 0 47 67 114 22 23 14 197 3 3 9 191 14 28 49 68
oligos_6nt_mkv1_m3_rc_shift4 (oligos_6nt_mkv1_m3_rc)				; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m3_rc; m=2/4; ncol2=16; w=-1; offset=-1; strand=R; shift=4; score=0.827407; ----mbgTAgGTACcTAcvk ; cor=; Ncor= a 0 0 0 0 56 34 21 12 134 11 12 6 151 5 20 10 125 20 42 30 c 0 0 0 0 46 41 27 12 8 21 15 2 2 130 109 8 12 93 43 30 g 0 0 0 0 30 44 93 13 8 109 129 2 2 14 21 8 12 27 42 46 t 0 0 0 0 29 42 20 124 11 20 5 151 6 12 11 135 12 21 34 55
oligos_6nt_mkv1_m1_rc_shift4 (oligos_6nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m1_rc; m=3/4; ncol2=16; w=-1; offset=-1; strand=R; shift=4; score=0.689815; ----mkgTAtGTACaTAcct ; cor=; Ncor= a 0 0 0 0 52 39 34 10 147 13 21 1 163 8 108 4 142 17 42 42 c 0 0 0 0 43 39 26 13 8 26 14 3 5 130 25 13 7 96 51 37 g 0 0 0 0 37 51 96 7 13 25 128 5 3 14 25 8 13 26 39 42 t 0 0 0 0 40 43 16 142 4 108 9 163 1 20 14 147 10 33 40 51
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m2; m=4/4; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.461541; ryatAtgTAygTACcTAccT ; cor=; Ncor= a 21 10 21 3 32 4 6 2 40 2 8 1 40 2 10 3 37 5 10 2 c 5 15 9 5 6 10 7 6 1 12 6 0 2 35 23 3 3 30 26 4 g 12 8 11 8 4 6 27 1 3 4 29 0 1 2 8 2 3 5 7 3 t 7 12 4 29 3 25 5 36 1 27 2 44 2 6 4 37 2 5 2 36

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; ryatAtgTAygTACcTAccTAsat ; Alignment reference a 21 10 21 3 32 4 6 2 40 2 8 1 40 2 10 3 37 5 10 2 32 11 15 8 c 5 15 9 5 6 10 7 6 1 12 6 0 2 35 23 3 3 30 26 4 3 12 10 11 g 12 8 11 8 4 6 27 1 3 4 29 0 1 2 8 2 3 5 7 3 3 13 11 7 t 7 12 4 29 3 25 5 36 1 27 2 44 2 6 4 37 2 5 2 36 7 9 9 19
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; ryatAtgTAygTACcTAccTAsat ; cor=; Ncor= a 21 10 21 3 32 4 6 2 40 2 8 1 40 2 10 3 37 5 10 2 32 11 15 8 c 5 15 9 5 6 10 7 6 1 12 6 0 2 35 23 3 3 30 26 4 3 12 10 11 g 12 8 11 8 4 6 27 1 3 4 29 0 1 2 8 2 3 5 7 3 3 13 11 7 t 7 12 4 29 3 25 5 36 1 27 2 44 2 6 4 37 2 5 2 36 7 9 9 19
oligos_6nt_mkv1_m1_rc_shift4 (oligos_6nt_mkv1_m1_rc)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1_rc; m=2/4; ncol2=16; w=0; offset=4; strand=R; shift=4; score=0.587289; ----mkgTAtGTACaTAcct---- ; cor=; Ncor= a 0 0 0 0 52 39 34 10 147 13 21 1 163 8 108 4 142 17 42 42 0 0 0 0 c 0 0 0 0 43 39 26 13 8 26 14 3 5 130 25 13 7 96 51 37 0 0 0 0 g 0 0 0 0 37 51 96 7 13 25 128 5 3 14 25 8 13 26 39 42 0 0 0 0 t 0 0 0 0 40 43 16 142 4 108 9 163 1 20 14 147 10 33 40 51 0 0 0 0
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=3/4; ncol2=16; w=0; offset=4; strand=D; shift=4; score=0.572198; ----mbgTAgGTACcTAcvk---- ; cor=; Ncor= a 0 0 0 0 55 34 21 12 135 11 12 6 151 5 20 11 124 20 42 29 0 0 0 0 c 0 0 0 0 46 42 27 12 8 21 14 2 2 129 109 8 13 93 44 30 0 0 0 0 g 0 0 0 0 30 43 93 12 8 109 130 2 2 15 21 8 12 27 41 46 0 0 0 0 t 0 0 0 0 30 42 20 125 10 20 5 151 6 12 11 134 12 21 34 56 0 0 0 0
oligos_6nt_mkv1_m5_shift5 (oligos_6nt_mkv1_m5)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m5; m=4/4; ncol2=15; w=0; offset=5; strand=D; shift=5; score=0.461541; -----cttcGGTACCTAcck---- ; cor=; Ncor= a 0 0 0 0 0 40 45 44 46 14 9 7 204 3 21 10 175 24 44 38 0 0 0 0 c 0 0 0 0 0 74 53 34 135 28 33 4 5 196 152 8 13 130 75 44 0 0 0 0 g 0 0 0 0 0 53 49 22 11 149 158 6 2 12 32 5 12 32 46 64 0 0 0 0 t 0 0 0 0 0 47 67 114 22 23 14 197 3 3 9 191 14 28 49 68 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; wtagtgTAGTGTACAcTAcactaw ; Alignment reference a 25 19 44 16 16 13 5 72 5 11 3 2 79 5 67 6 5 71 11 45 17 16 29 22 c 17 20 11 15 11 17 6 2 16 2 15 3 1 61 5 57 6 3 43 12 36 14 16 21 g 21 16 14 37 12 44 3 6 58 5 62 1 3 16 1 17 2 6 18 11 16 11 21 17 t 22 30 16 17 46 11 71 5 6 67 5 79 2 3 12 5 72 5 13 17 16 44 19 25
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wtagtgTAGTGTACAcTAcactaw ; cor=; Ncor= a 25 19 44 16 16 13 5 72 5 11 3 2 79 5 67 6 5 71 11 45 17 16 29 22 c 17 20 11 15 11 17 6 2 16 2 15 3 1 61 5 57 6 3 43 12 36 14 16 21 g 21 16 14 37 12 44 3 6 58 5 62 1 3 16 1 17 2 6 18 11 16 11 21 17 t 22 30 16 17 46 11 71 5 6 67 5 79 2 3 12 5 72 5 13 17 16 44 19 25
oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=19; w=0; offset=1; strand=R; shift=1; score=0.582608; -yagtgTAGTGTACATAcmd---- ; cor=; Ncor= a 0 34 54 35 24 30 9 120 17 9 17 3 143 9 114 15 108 23 41 46 0 0 0 0 c 0 44 31 37 23 26 24 11 21 15 5 5 3 126 14 19 11 81 47 25 0 0 0 0 g 0 32 32 57 18 78 3 11 107 12 122 2 7 8 24 12 16 30 30 42 0 0 0 0 t 0 45 38 26 90 21 119 13 10 119 11 145 2 12 3 109 20 21 37 42 0 0 0 0
oligos_7nt_mkv1_m5_shift9 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m5; m=3/3; ncol2=12; w=0; offset=9; strand=D; shift=9; score=0.428598; ---------ysTACAsTAcmy--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 92 87 6 363 13 284 14 1 362 49 114 87 0 0 0 c 0 0 0 0 0 0 0 0 0 96 107 15 4 349 26 110 3 7 174 103 97 0 0 0 g 0 0 0 0 0 0 0 0 0 91 137 5 10 7 28 244 3 9 88 78 91 0 0 0 t 0 0 0 0 0 0 0 0 0 102 50 355 4 12 43 13 374 3 70 86 106 0 0 0