One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.192302_2025-12-18.192302_HeMbBV/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.192302_2025-12-18.192302_HeMbBV/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; cyCCCACCCmc ; Alignment reference a 46 50 10 11 8 178 4 9 13 69 42 c 76 68 174 192 205 4 197 201 190 67 77 g 54 38 15 8 2 16 10 5 2 37 48 t 46 66 23 11 7 24 11 7 17 49 55

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; cyCCCACCCmc ; cor=; Ncor= a 46 50 10 11 8 178 4 9 13 69 42 c 76 68 174 192 205 4 197 201 190 67 77 g 54 38 15 8 2 16 10 5 2 37 48 t 46 66 23 11 7 24 11 7 17 49 55

oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score= 0.7323; -cwCCACCCCh ; cor=; Ncor= a 0 52 60 6 4 196 8 16 29 15 65 c 0 81 56 224 226 5 209 197 190 205 69 g 0 46 59 5 2 18 8 12 5 6 38 t 0 59 63 3 6 19 13 13 14 12 66

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -cwCCACCCChm ; Alignment reference a 0 52 60 6 4 196 8 16 29 15 65 65 c 0 81 56 224 226 5 209 197 190 205 69 75 g 0 46 59 5 2 18 8 12 5 6 38 49 t 0 59 63 3 6 19 13 13 14 12 66 49

oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -cwCCACCCChm ; cor=; Ncor= a 0 52 60 6 4 196 8 16 29 15 65 65 c 0 81 56 224 226 5 209 197 190 205 69 75 g 0 46 59 5 2 18 8 12 5 6 38 49 t 0 59 63 3 6 19 13 13 14 12 66 49

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score= 0.7323; cyCCCACCCmc- ; cor=; Ncor= a 46 50 10 11 8 178 4 9 13 69 42 0 c 76 68 174 192 205 4 197 201 190 67 77 0 g 54 38 15 8 2 16 10 5 2 37 48 0 t 46 66 23 11 7 24 11 7 17 49 55 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=17; shift=0; ncol=17; maAGTAGCTGGGAytry ; Alignment reference a 16 23 46 7 4 49 1 3 1 3 3 2 53 10 4 28 14 c 24 14 7 1 7 5 2 56 2 2 2 3 6 16 8 6 21 g 14 15 5 53 9 5 59 4 2 54 58 53 3 9 11 19 13 t 10 12 6 3 44 5 2 1 59 5 1 6 2 29 41 11 16

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; maAGTAGCTGGGAytry ; cor=; Ncor= a 16 23 46 7 4 49 1 3 1 3 3 2 53 10 4 28 14 c 24 14 7 1 7 5 2 56 2 2 2 3 6 16 8 6 21 g 14 15 5 53 9 5 59 4 2 54 58 53 3 9 11 19 13 t 10 12 6 3 44 5 2 1 59 5 1 6 2 29 41 11 16

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift4 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift4 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=12; shift=4; ncol=16; ----csAGGCTGGAgd ; Alignment reference a 0 0 0 0 34 22 161 2 7 8 17 2 15 135 36 46 c 0 0 0 0 61 65 4 3 10 156 7 1 11 6 35 19 g 0 0 0 0 39 67 3 163 154 3 6 167 144 13 75 51 t 0 0 0 0 39 19 5 5 2 6 143 3 3 19 27 57

oligos_6nt_mkv2_m3_shift4 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----csAGGCTGGAgd ; cor=; Ncor= a 0 0 0 0 34 22 161 2 7 8 17 2 15 135 36 46 c 0 0 0 0 61 65 4 3 10 156 7 1 11 6 35 19 g 0 0 0 0 39 67 3 163 154 3 6 167 144 13 75 51 t 0 0 0 0 39 19 5 5 2 6 143 3 3 19 27 57

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=2/5; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.700136; -ygcCCAGGCTGGAGy ; cor=; Ncor= a 0 18 16 10 10 6 98 2 2 5 5 3 14 76 9 13 c 0 28 20 54 76 81 1 3 11 94 3 6 7 4 16 27 g 0 24 47 16 10 12 3 97 89 2 12 90 82 8 74 20 t 0 34 21 24 8 5 2 2 2 3 84 5 1 16 5 44

oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.649296; ----rgAGGCAGrr-- ; cor=; Ncor= a 0 0 0 0 44 34 148 0 1 0 132 0 57 55 0 0 c 0 0 0 0 41 35 12 3 0 165 16 2 37 31 0 0 g 0 0 0 0 46 81 5 164 165 1 17 165 57 48 0 0 t 0 0 0 0 36 17 2 0 1 1 2 0 16 33 0 0

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=4/5; ncol2=17; w=-4; offset=-4; strand=R; shift=0; score=0.566971; yttGGGAGGCtGrrGy ; cor=; Ncor= a 13 7 8 1 3 3 62 2 2 3 8 1 32 34 3 8 c 21 17 8 4 5 4 6 1 1 62 10 0 5 3 4 31 g 17 11 10 60 60 63 1 66 67 1 5 67 29 30 64 13 t 20 36 45 6 3 1 2 2 1 5 48 3 5 4 0 19

oligos_6nt_mkv2_m1_rc_shift4 (oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=5/5; ncol2=16; w=0; offset=0; strand=R; shift=4; score=0.528999; ----ysAGgCTGGGaG ; cor=; Ncor= a 0 0 0 0 7 2 44 8 7 3 1 3 1 4 35 1 c 0 0 0 0 19 28 2 5 13 38 3 1 1 2 7 1 g 0 0 0 0 11 21 6 40 28 6 10 46 51 48 2 51 t 0 0 0 0 17 3 2 1 6 7 40 4 1 0 10 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; krGGATTACak ; Alignment reference a 23 35 0 4 98 10 2 97 3 58 20 c 8 8 1 2 1 11 8 1 93 9 8 g 26 40 96 97 1 4 2 2 1 13 49 t 47 21 7 1 4 79 92 4 7 24 27

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; krGGATTACak ; cor=; Ncor= a 23 35 0 4 98 10 2 97 3 58 20 c 8 8 1 2 1 11 8 1 93 9 8 g 26 40 96 97 1 4 2 2 1 13 49 t 47 21 7 1 4 79 92 4 7 24 27

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=4; ncol=14; ----rgAGGCAGrr ; Alignment reference a 0 0 0 0 44 34 148 0 1 0 132 0 57 55 c 0 0 0 0 41 35 12 3 0 165 16 2 37 31 g 0 0 0 0 46 81 5 164 165 1 17 165 57 48 t 0 0 0 0 36 17 2 0 1 1 2 0 16 33

oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----rgAGGCAGrr ; cor=; Ncor= a 0 0 0 0 44 34 148 0 1 0 132 0 57 55 c 0 0 0 0 41 35 12 3 0 165 16 2 37 31 g 0 0 0 0 46 81 5 164 165 1 17 165 57 48 t 0 0 0 0 36 17 2 0 1 1 2 0 16 33

oligos_6nt_mkv2_m3_shift4 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=4; score=0.649296; ----csAGGCTGGA ; cor=; Ncor= a 0 0 0 0 34 22 161 2 7 8 17 2 15 135 c 0 0 0 0 61 65 4 3 10 156 7 1 11 6 g 0 0 0 0 39 67 3 163 154 3 6 167 144 13 t 0 0 0 0 39 19 5 5 2 6 143 3 3 19

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1_rc; m=3/4; ncol2=17; w=-4; offset=-4; strand=R; shift=0; score=0.470341; yttGGGAGGCtGrr ; cor=; Ncor= a 13 7 8 1 3 3 62 2 2 3 8 1 32 34 c 21 17 8 4 5 4 6 1 1 62 10 0 5 3 g 17 11 10 60 60 63 1 66 67 1 5 67 29 30 t 20 36 45 6 3 1 2 2 1 5 48 3 5 4

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.440464; -ygcCCAGGCTGGA ; cor=; Ncor= a 0 18 16 10 10 6 98 2 2 5 5 3 14 76 c 0 28 20 54 76 81 1 3 11 94 3 6 7 4 g 0 24 47 16 10 12 3 97 89 2 12 90 82 8 t 0 34 21 24 8 5 2 2 2 3 84 5 1 16

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; srCTCCAGCCTGGgcr ; Alignment reference a 11 44 5 16 1 5 84 3 2 2 2 5 8 24 21 34 c 37 20 74 8 82 90 12 2 89 97 3 12 10 16 47 24 g 31 27 16 4 7 6 3 94 11 3 1 81 76 54 20 28 t 25 13 9 76 14 3 5 5 2 2 98 6 10 10 16 18

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; srCTCCAGCCTGGgcr ; cor=; Ncor= a 11 44 5 16 1 5 84 3 2 2 2 5 8 24 21 34 c 37 20 74 8 82 90 12 2 89 97 3 12 10 16 47 24 g 31 27 16 4 7 6 3 94 11 3 1 81 76 54 20 28 t 25 13 9 76 14 3 5 5 2 2 98 6 10 10 16 18

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.700136; -hcTCCAGCCTsg--- ; cor=; Ncor= a 0 57 27 19 3 3 143 6 2 5 5 19 39 0 0 0 c 0 51 75 13 144 167 6 3 154 163 3 67 39 0 0 0 g 0 19 35 6 11 1 7 156 10 3 4 65 61 0 0 0 t 0 46 36 135 15 2 17 8 7 2 161 22 34 0 0 0

oligos_6nt_mkv2_m4_rc_shift3 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=3/4; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.440464; ---yyCTGCCTcy--- ; cor=; Ncor= a 0 0 0 33 16 0 2 1 1 0 2 17 36 0 0 0 c 0 0 0 48 57 165 17 1 165 164 5 81 46 0 0 0 g 0 0 0 31 37 2 16 165 0 3 12 35 41 0 0 0 t 0 0 0 55 57 0 132 0 1 0 148 34 44 0 0 0

oligos_6nt_mkv2_m1_rc_shift4 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=4/4; ncol2=16; w=0; offset=4; strand=R; shift=4; score=0.430418; ----ysAGgCTGGGaG ; cor=; Ncor= a 0 0 0 0 7 2 44 8 7 3 1 3 1 4 35 1 c 0 0 0 0 19 28 2 5 13 38 3 1 1 2 7 1 g 0 0 0 0 11 21 6 40 28 6 10 46 51 48 2 51 t 0 0 0 0 17 3 2 1 6 7 40 4 1 0 10 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; yrCyyCaGCCTCCCaar ; Alignment reference a 12 19 0 4 5 3 48 5 1 2 2 1 3 6 45 36 20 c 26 13 64 30 29 67 5 1 67 66 1 63 60 60 10 11 17 g 8 31 4 3 5 0 10 62 1 1 6 4 5 4 8 17 21 t 25 8 3 34 32 1 8 3 2 2 62 3 3 1 8 7 13

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; yrCyyCaGCCTCCCaar ; cor=; Ncor= a 12 19 0 4 5 3 48 5 1 2 2 1 3 6 45 36 20 c 26 13 64 30 29 67 5 1 67 66 1 63 60 60 10 11 17 g 8 31 4 3 5 0 10 62 1 1 6 4 5 4 8 17 21 t 25 8 3 34 32 1 8 3 2 2 62 3 3 1 8 7 13

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.566971; -hcTCCAGCCTsg---- ; cor=; Ncor= a 0 57 27 19 3 3 143 6 2 5 5 19 39 0 0 0 0 c 0 51 75 13 144 167 6 3 154 163 3 67 39 0 0 0 0 g 0 19 35 6 11 1 7 156 10 3 4 65 61 0 0 0 0 t 0 46 36 135 15 2 17 8 7 2 161 22 34 0 0 0 0

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/4; ncol2=16; w=0; offset=5; strand=D; shift=5; score= 0.5105; -----cyGCCtCCCAGc ; cor=; Ncor= a 0 0 0 0 0 3 13 2 1 1 10 0 1 4 40 7 6 c 0 0 0 0 0 34 15 6 48 51 2 48 51 46 10 6 28 g 0 0 0 0 0 9 12 45 2 1 7 2 1 1 3 38 13 t 0 0 0 0 0 8 14 1 3 1 35 4 1 3 1 3 7

oligos_6nt_mkv2_m4_rc_shift3 (oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=4/4; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.470341; ---yyCTGCCTcy---- ; cor=; Ncor= a 0 0 0 33 16 0 2 1 1 0 2 17 36 0 0 0 0 c 0 0 0 48 57 165 17 1 165 164 5 81 46 0 0 0 0 g 0 0 0 31 37 2 16 165 0 3 12 35 41 0 0 0 0 t 0 0 0 55 57 0 132 0 1 0 148 34 44 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; wwAAAATAAAww ; Alignment reference a 115 123 254 269 274 271 5 262 256 261 133 113 c 34 41 8 4 5 6 6 7 19 8 48 38 g 53 37 14 10 8 3 7 3 10 8 37 44 t 96 97 22 15 11 18 280 26 13 21 80 103

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAATAAAww ; cor=; Ncor= a 115 123 254 269 274 271 5 262 256 261 133 113 c 34 41 8 4 5 6 6 7 19 8 48 38 g 53 37 14 10 8 3 7 3 10 8 37 44 t 96 97 22 15 11 18 280 26 13 21 80 103

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=16; shift=5; ncol=21; -----cyGCCtCCCAGcCTsr ; Alignment reference a 0 0 0 0 0 3 13 2 1 1 10 0 1 4 40 7 6 1 2 3 17 c 0 0 0 0 0 34 15 6 48 51 2 48 51 46 10 6 28 40 6 21 11 g 0 0 0 0 0 9 12 45 2 1 7 2 1 1 3 38 13 5 2 28 19 t 0 0 0 0 0 8 14 1 3 1 35 4 1 3 1 3 7 8 44 2 7

oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=5; score= 1; -----cyGCCtCCCAGcCTsr ; cor=; Ncor= a 0 0 0 0 0 3 13 2 1 1 10 0 1 4 40 7 6 1 2 3 17 c 0 0 0 0 0 34 15 6 48 51 2 48 51 46 10 6 28 40 6 21 11 g 0 0 0 0 0 9 12 45 2 1 7 2 1 1 3 38 13 5 2 28 19 t 0 0 0 0 0 8 14 1 3 1 35 4 1 3 1 3 7 8 44 2 7

oligos_6nt_mkv2_m3_rc_shift9 (oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=2/4; ncol2=12; w=0; offset=4; strand=R; shift=9; score=0.528999; ---------hcTCCAGCCTsg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 57 27 19 3 3 143 6 2 5 5 19 39 c 0 0 0 0 0 0 0 0 0 51 75 13 144 167 6 3 154 163 3 67 39 g 0 0 0 0 0 0 0 0 0 19 35 6 11 1 7 156 10 3 4 65 61 t 0 0 0 0 0 0 0 0 0 46 36 135 15 2 17 8 7 2 161 22 34

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score= 0.5105; yrCyyCaGCCTCCCaar---- ; cor=; Ncor= a 12 19 0 4 5 3 48 5 1 2 2 1 3 6 45 36 20 0 0 0 0 c 26 13 64 30 29 67 5 1 67 66 1 63 60 60 10 11 17 0 0 0 0 g 8 31 4 3 5 0 10 62 1 1 6 4 5 4 8 17 21 0 0 0 0 t 25 8 3 34 32 1 8 3 2 2 62 3 3 1 8 7 13 0 0 0 0

oligos_7nt_mkv2_m2_rc_shift9 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=16; w=0; offset=4; strand=R; shift=9; score=0.430418; ---------ygcCCAGGCTGG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 18 16 10 10 6 98 2 2 5 5 3 14 c 0 0 0 0 0 0 0 0 0 28 20 54 76 81 1 3 11 94 3 6 7 g 0 0 0 0 0 0 0 0 0 24 47 16 10 12 3 97 89 2 12 90 82 t 0 0 0 0 0 0 0 0 0 34 21 24 8 5 2 2 2 3 84 5 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift4 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=12; shift=4; ncol=16; ----csAGGCTGGAgd ; Alignment reference a 0 0 0 0 34 22 161 2 7 8 17 2 15 135 36 46 c 0 0 0 0 61 65 4 3 10 156 7 1 11 6 35 19 g 0 0 0 0 39 67 3 163 154 3 6 167 144 13 75 51 t 0 0 0 0 39 19 5 5 2 6 143 3 3 19 27 57
oligos_6nt_mkv2_m3_shift4 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=4; score= 1; ----csAGGCTGGAgd ; cor=; Ncor= a 0 0 0 0 34 22 161 2 7 8 17 2 15 135 36 46 c 0 0 0 0 61 65 4 3 10 156 7 1 11 6 35 19 g 0 0 0 0 39 67 3 163 154 3 6 167 144 13 75 51 t 0 0 0 0 39 19 5 5 2 6 143 3 3 19 27 57
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc; m=2/5; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.700136; -ygcCCAGGCTGGAGy ; cor=; Ncor= a 0 18 16 10 10 6 98 2 2 5 5 3 14 76 9 13 c 0 28 20 54 76 81 1 3 11 94 3 6 7 4 16 27 g 0 24 47 16 10 12 3 97 89 2 12 90 82 8 74 20 t 0 34 21 24 8 5 2 2 2 3 84 5 1 16 5 44
oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m4; m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.649296; ----rgAGGCAGrr-- ; cor=; Ncor= a 0 0 0 0 44 34 148 0 1 0 132 0 57 55 0 0 c 0 0 0 0 41 35 12 3 0 165 16 2 37 31 0 0 g 0 0 0 0 46 81 5 164 165 1 17 165 57 48 0 0 t 0 0 0 0 36 17 2 0 1 1 2 0 16 33 0 0
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=4/5; ncol2=17; w=-4; offset=-4; strand=R; shift=0; score=0.566971; yttGGGAGGCtGrrGy ; cor=; Ncor= a 13 7 8 1 3 3 62 2 2 3 8 1 32 34 3 8 c 21 17 8 4 5 4 6 1 1 62 10 0 5 3 4 31 g 17 11 10 60 60 63 1 66 67 1 5 67 29 30 64 13 t 20 36 45 6 3 1 2 2 1 5 48 3 5 4 0 19
oligos_6nt_mkv2_m1_rc_shift4 (oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=5/5; ncol2=16; w=0; offset=0; strand=R; shift=4; score=0.528999; ----ysAGgCTGGGaG ; cor=; Ncor= a 0 0 0 0 7 2 44 8 7 3 1 3 1 4 35 1 c 0 0 0 0 19 28 2 5 13 38 3 1 1 2 7 1 g 0 0 0 0 11 21 6 40 28 6 10 46 51 48 2 51 t 0 0 0 0 17 3 2 1 6 7 40 4 1 0 10 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=4; ncol=14; ----rgAGGCAGrr ; Alignment reference a 0 0 0 0 44 34 148 0 1 0 132 0 57 55 c 0 0 0 0 41 35 12 3 0 165 16 2 37 31 g 0 0 0 0 46 81 5 164 165 1 17 165 57 48 t 0 0 0 0 36 17 2 0 1 1 2 0 16 33
oligos_6nt_mkv2_m4_shift4 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----rgAGGCAGrr ; cor=; Ncor= a 0 0 0 0 44 34 148 0 1 0 132 0 57 55 c 0 0 0 0 41 35 12 3 0 165 16 2 37 31 g 0 0 0 0 46 81 5 164 165 1 17 165 57 48 t 0 0 0 0 36 17 2 0 1 1 2 0 16 33
oligos_6nt_mkv2_m3_shift4 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m3; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=4; score=0.649296; ----csAGGCTGGA ; cor=; Ncor= a 0 0 0 0 34 22 161 2 7 8 17 2 15 135 c 0 0 0 0 61 65 4 3 10 156 7 1 11 6 g 0 0 0 0 39 67 3 163 154 3 6 167 144 13 t 0 0 0 0 39 19 5 5 2 6 143 3 3 19
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1_rc; m=3/4; ncol2=17; w=-4; offset=-4; strand=R; shift=0; score=0.470341; yttGGGAGGCtGrr ; cor=; Ncor= a 13 7 8 1 3 3 62 2 2 3 8 1 32 34 c 21 17 8 4 5 4 6 1 1 62 10 0 5 3 g 17 11 10 60 60 63 1 66 67 1 5 67 29 30 t 20 36 45 6 3 1 2 2 1 5 48 3 5 4
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=16; w=-3; offset=-3; strand=R; shift=1; score=0.440464; -ygcCCAGGCTGGA ; cor=; Ncor= a 0 18 16 10 10 6 98 2 2 5 5 3 14 76 c 0 28 20 54 76 81 1 3 11 94 3 6 7 4 g 0 24 47 16 10 12 3 97 89 2 12 90 82 8 t 0 34 21 24 8 5 2 2 2 3 84 5 1 16

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; srCTCCAGCCTGGgcr ; Alignment reference a 11 44 5 16 1 5 84 3 2 2 2 5 8 24 21 34 c 37 20 74 8 82 90 12 2 89 97 3 12 10 16 47 24 g 31 27 16 4 7 6 3 94 11 3 1 81 76 54 20 28 t 25 13 9 76 14 3 5 5 2 2 98 6 10 10 16 18
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; srCTCCAGCCTGGgcr ; cor=; Ncor= a 11 44 5 16 1 5 84 3 2 2 2 5 8 24 21 34 c 37 20 74 8 82 90 12 2 89 97 3 12 10 16 47 24 g 31 27 16 4 7 6 3 94 11 3 1 81 76 54 20 28 t 25 13 9 76 14 3 5 5 2 2 98 6 10 10 16 18
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.700136; -hcTCCAGCCTsg--- ; cor=; Ncor= a 0 57 27 19 3 3 143 6 2 5 5 19 39 0 0 0 c 0 51 75 13 144 167 6 3 154 163 3 67 39 0 0 0 g 0 19 35 6 11 1 7 156 10 3 4 65 61 0 0 0 t 0 46 36 135 15 2 17 8 7 2 161 22 34 0 0 0
oligos_6nt_mkv2_m4_rc_shift3 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m4_rc; m=3/4; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.440464; ---yyCTGCCTcy--- ; cor=; Ncor= a 0 0 0 33 16 0 2 1 1 0 2 17 36 0 0 0 c 0 0 0 48 57 165 17 1 165 164 5 81 46 0 0 0 g 0 0 0 31 37 2 16 165 0 3 12 35 41 0 0 0 t 0 0 0 55 57 0 132 0 1 0 148 34 44 0 0 0
oligos_6nt_mkv2_m1_rc_shift4 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=4/4; ncol2=16; w=0; offset=4; strand=R; shift=4; score=0.430418; ----ysAGgCTGGGaG ; cor=; Ncor= a 0 0 0 0 7 2 44 8 7 3 1 3 1 4 35 1 c 0 0 0 0 19 28 2 5 13 38 3 1 1 2 7 1 g 0 0 0 0 11 21 6 40 28 6 10 46 51 48 2 51 t 0 0 0 0 17 3 2 1 6 7 40 4 1 0 10 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; yrCyyCaGCCTCCCaar ; Alignment reference a 12 19 0 4 5 3 48 5 1 2 2 1 3 6 45 36 20 c 26 13 64 30 29 67 5 1 67 66 1 63 60 60 10 11 17 g 8 31 4 3 5 0 10 62 1 1 6 4 5 4 8 17 21 t 25 8 3 34 32 1 8 3 2 2 62 3 3 1 8 7 13
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; yrCyyCaGCCTCCCaar ; cor=; Ncor= a 12 19 0 4 5 3 48 5 1 2 2 1 3 6 45 36 20 c 26 13 64 30 29 67 5 1 67 66 1 63 60 60 10 11 17 g 8 31 4 3 5 0 10 62 1 1 6 4 5 4 8 17 21 t 25 8 3 34 32 1 8 3 2 2 62 3 3 1 8 7 13
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=2/4; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.566971; -hcTCCAGCCTsg---- ; cor=; Ncor= a 0 57 27 19 3 3 143 6 2 5 5 19 39 0 0 0 0 c 0 51 75 13 144 167 6 3 154 163 3 67 39 0 0 0 0 g 0 19 35 6 11 1 7 156 10 3 4 65 61 0 0 0 0 t 0 46 36 135 15 2 17 8 7 2 161 22 34 0 0 0 0
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/4; ncol2=16; w=0; offset=5; strand=D; shift=5; score= 0.5105; -----cyGCCtCCCAGc ; cor=; Ncor= a 0 0 0 0 0 3 13 2 1 1 10 0 1 4 40 7 6 c 0 0 0 0 0 34 15 6 48 51 2 48 51 46 10 6 28 g 0 0 0 0 0 9 12 45 2 1 7 2 1 1 3 38 13 t 0 0 0 0 0 8 14 1 3 1 35 4 1 3 1 3 7
oligos_6nt_mkv2_m4_rc_shift3 (oligos_6nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4_rc; m=4/4; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.470341; ---yyCTGCCTcy---- ; cor=; Ncor= a 0 0 0 33 16 0 2 1 1 0 2 17 36 0 0 0 0 c 0 0 0 48 57 165 17 1 165 164 5 81 46 0 0 0 0 g 0 0 0 31 37 2 16 165 0 3 12 35 41 0 0 0 0 t 0 0 0 55 57 0 132 0 1 0 148 34 44 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=16; shift=5; ncol=21; -----cyGCCtCCCAGcCTsr ; Alignment reference a 0 0 0 0 0 3 13 2 1 1 10 0 1 4 40 7 6 1 2 3 17 c 0 0 0 0 0 34 15 6 48 51 2 48 51 46 10 6 28 40 6 21 11 g 0 0 0 0 0 9 12 45 2 1 7 2 1 1 3 38 13 5 2 28 19 t 0 0 0 0 0 8 14 1 3 1 35 4 1 3 1 3 7 8 44 2 7
oligos_6nt_mkv2_m1_shift5 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=5; score= 1; -----cyGCCtCCCAGcCTsr ; cor=; Ncor= a 0 0 0 0 0 3 13 2 1 1 10 0 1 4 40 7 6 1 2 3 17 c 0 0 0 0 0 34 15 6 48 51 2 48 51 46 10 6 28 40 6 21 11 g 0 0 0 0 0 9 12 45 2 1 7 2 1 1 3 38 13 5 2 28 19 t 0 0 0 0 0 8 14 1 3 1 35 4 1 3 1 3 7 8 44 2 7
oligos_6nt_mkv2_m3_rc_shift9 (oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3_rc; m=2/4; ncol2=12; w=0; offset=4; strand=R; shift=9; score=0.528999; ---------hcTCCAGCCTsg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 57 27 19 3 3 143 6 2 5 5 19 39 c 0 0 0 0 0 0 0 0 0 51 75 13 144 167 6 3 154 163 3 67 39 g 0 0 0 0 0 0 0 0 0 19 35 6 11 1 7 156 10 3 4 65 61 t 0 0 0 0 0 0 0 0 0 46 36 135 15 2 17 8 7 2 161 22 34
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=17; w=-5; offset=-5; strand=D; shift=0; score= 0.5105; yrCyyCaGCCTCCCaar---- ; cor=; Ncor= a 12 19 0 4 5 3 48 5 1 2 2 1 3 6 45 36 20 0 0 0 0 c 26 13 64 30 29 67 5 1 67 66 1 63 60 60 10 11 17 0 0 0 0 g 8 31 4 3 5 0 10 62 1 1 6 4 5 4 8 17 21 0 0 0 0 t 25 8 3 34 32 1 8 3 2 2 62 3 3 1 8 7 13 0 0 0 0
oligos_7nt_mkv2_m2_rc_shift9 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=4/4; ncol2=16; w=0; offset=4; strand=R; shift=9; score=0.430418; ---------ygcCCAGGCTGG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 18 16 10 10 6 98 2 2 5 5 3 14 c 0 0 0 0 0 0 0 0 0 28 20 54 76 81 1 3 11 94 3 6 7 g 0 0 0 0 0 0 0 0 0 24 47 16 10 12 3 97 89 2 12 90 82 t 0 0 0 0 0 0 0 0 0 34 21 24 8 5 2 2 2 3 84 5 1