One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/07/28/peak-motifs.2026-07-28.142026_2026-07-28.142026_EMa4ET/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/2026/07/28/peak-motifs.2026-07-28.142026_2026-07-28.142026_EMa4ET/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --smGGCCmCGCCcc ; Alignment reference a 0 0 31 67 17 5 6 0 115 1 4 3 3 12 33 c 0 0 102 58 6 4 208 214 85 209 5 212 193 139 127 g 0 0 56 40 190 207 3 4 7 8 206 0 16 34 19 t 0 0 29 53 5 2 1 0 11 0 3 3 6 33 39

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --smGGCCmCGCCcc ; cor=; Ncor= a 0 0 31 67 17 5 6 0 115 1 4 3 3 12 33 c 0 0 102 58 6 4 208 214 85 209 5 212 193 139 127 g 0 0 56 40 190 207 3 4 7 8 206 0 16 34 19 t 0 0 29 53 5 2 1 0 11 0 3 3 6 33 39

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.760024; --cmgGCCCCGCCCC ; cor=; Ncor= a 0 0 49 123 72 23 5 7 32 5 13 4 4 7 38 c 0 0 236 132 83 40 419 405 397 423 3 423 422 387 367 g 0 0 91 99 277 364 11 10 14 19 423 12 13 24 16 t 0 0 74 96 18 23 15 28 7 3 11 11 11 32 29

oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.659284; --ssgGCCCGGCss- ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 0 c 0 0 94 107 36 7 223 206 230 15 5 227 79 90 0 g 0 0 88 86 160 214 9 23 7 220 228 6 91 92 0 t 0 0 27 18 17 7 3 4 1 2 3 2 39 27 0

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=4/6; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.588152; scCCCGCCCCGCsc- ; cor=; Ncor= a 30 15 1 5 15 5 3 4 1 3 8 12 25 27 0 c 90 149 235 225 220 2 240 234 246 240 10 224 126 137 0 g 105 49 13 18 14 235 7 15 6 6 206 11 70 57 0 t 30 42 6 7 6 13 5 2 2 6 31 8 34 34 0

oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4_rc; m=5/6; ncol2=10; w=0; offset=1; strand=R; shift=3; score=0.569304; ---ssGCCTCGss-- ; cor=; Ncor= a 0 0 0 19 31 0 0 0 0 0 0 23 20 0 0 c 0 0 0 64 57 0 168 164 0 168 0 65 74 0 0 g 0 0 0 62 63 168 0 4 0 0 168 68 58 0 0 t 0 0 0 23 17 0 0 0 168 0 0 12 16 0 0

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=6/6; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.447493; ssCAGGCCCcg---- ; cor=; Ncor= a 11 28 0 143 0 2 0 3 1 22 22 0 0 0 0 c 76 51 141 0 17 1 143 124 137 61 27 0 0 0 0 g 38 44 0 0 126 139 0 16 5 34 73 0 0 0 0 t 18 20 2 0 0 1 0 0 0 26 21 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ssCCCCTCcs ; Alignment reference a 0 0 0 0 38 34 0 0 0 0 0 0 42 35 c 0 0 0 0 142 102 326 326 326 326 0 326 175 160 g 0 0 0 0 102 120 0 0 0 0 0 0 48 86 t 0 0 0 0 44 70 0 0 0 0 326 0 61 45

oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCCCCTCcs ; cor=; Ncor= a 0 0 0 0 38 34 0 0 0 0 0 0 42 35 c 0 0 0 0 142 102 326 326 326 326 0 326 175 160 g 0 0 0 0 102 120 0 0 0 0 0 0 48 86 t 0 0 0 0 44 70 0 0 0 0 326 0 61 45

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m1; m=2/3; ncol2=14; w=-4; offset=-4; strand=D; shift=0; score=0.55165; scCCCGCCCCGCsc ; cor=; Ncor= a 30 15 1 5 15 5 3 4 1 3 8 12 25 27 c 90 149 235 225 220 2 240 234 246 240 10 224 126 137 g 105 49 13 18 14 235 7 15 6 6 206 11 70 57 t 30 42 6 7 6 13 5 2 2 6 31 8 34 34

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m1; m=3/3; ncol2=16; w=-2; offset=-2; strand=D; shift=2; score=0.457505; --cmgGCCCCGCCC ; cor=; Ncor= a 0 0 49 123 72 23 5 7 32 5 13 4 4 7 c 0 0 236 132 83 40 419 405 397 423 3 423 422 387 g 0 0 91 99 277 364 11 10 14 19 423 12 13 24 t 0 0 74 96 18 23 15 28 7 3 11 11 11 32

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift5 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift5 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=5; ncol=16; -----ssCGGAGCCss ; Alignment reference a 0 0 0 0 0 17 26 0 0 1 153 5 10 4 17 30 c 0 0 0 0 0 49 41 156 4 7 3 5 136 133 48 40 g 0 0 0 0 0 62 73 0 152 139 0 143 2 19 68 64 t 0 0 0 0 0 28 16 0 0 9 0 3 8 0 23 22

oligos_7nt_mkv4_m4_shift5 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCGGAGCCss ; cor=; Ncor= a 0 0 0 0 0 17 26 0 0 1 153 5 10 4 17 30 c 0 0 0 0 0 49 41 156 4 7 3 5 136 133 48 40 g 0 0 0 0 0 62 73 0 152 139 0 143 2 19 68 64 t 0 0 0 0 0 28 16 0 0 9 0 3 8 0 23 22

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1_rc; m=2/2; ncol2=16; w=-5; offset=-5; strand=R; shift=0; score=0.504083; ssGGGGGCGGGGCckg ; cor=; Ncor= a 59 104 55 29 32 11 11 11 3 7 28 15 23 18 96 74 c 160 117 60 16 24 13 12 423 19 14 10 11 364 277 99 91 g 167 151 312 367 387 422 423 3 423 397 405 419 40 83 132 236 t 64 78 23 38 7 4 4 13 5 32 7 5 23 72 123 49

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; cmgGCCCCGCCCCCss ; Alignment reference a 49 123 72 23 5 7 32 5 13 4 4 7 38 23 78 64 c 236 132 83 40 419 405 397 423 3 423 422 387 367 312 151 167 g 91 99 277 364 11 10 14 19 423 12 13 24 16 60 117 160 t 74 96 18 23 15 28 7 3 11 11 11 32 29 55 104 59

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cmgGCCCCGCCCCCss ; cor=; Ncor= a 49 123 72 23 5 7 32 5 13 4 4 7 38 23 78 64 c 236 132 83 40 419 405 397 423 3 423 422 387 367 312 151 167 g 91 99 277 364 11 10 14 19 423 12 13 24 16 60 117 160 t 74 96 18 23 15 28 7 3 11 11 11 32 29 55 104 59

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=2/7; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.760024; smGGCCmCGCCcc--- ; cor=; Ncor= a 31 67 17 5 6 0 115 1 4 3 3 12 33 0 0 0 c 102 58 6 4 208 214 85 209 5 212 193 139 127 0 0 0 g 56 40 190 207 3 4 7 8 206 0 16 34 19 0 0 0 t 29 53 5 2 1 0 11 0 3 3 6 33 39 0 0 0

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/7; ncol2=14; w=0; offset=3; strand=D; shift=3; score=0.652143; ---scCCCGCCCCGCs ; cor=; Ncor= a 0 0 0 30 15 1 5 15 5 3 4 1 3 8 12 25 c 0 0 0 90 149 235 225 220 2 240 234 246 240 10 224 126 g 0 0 0 105 49 13 18 14 235 7 15 6 6 206 11 70 t 0 0 0 30 42 6 7 6 13 5 2 2 6 31 8 34

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=4/7; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.561512; ssgGCCCGGCss---- ; cor=; Ncor= a 29 27 25 10 3 5 0 1 2 3 29 29 0 0 0 0 c 94 107 36 7 223 206 230 15 5 227 79 90 0 0 0 0 g 88 86 160 214 9 23 7 220 228 6 91 92 0 0 0 0 t 27 18 17 7 3 4 1 2 3 2 39 27 0 0 0 0

oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=5/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.504083; ssGGCTCCGss----- ; cor=; Ncor= a 22 23 0 8 3 0 9 0 0 16 28 0 0 0 0 0 c 64 68 19 2 143 0 139 152 0 73 62 0 0 0 0 0 g 40 48 133 136 5 3 7 4 156 41 49 0 0 0 0 0 t 30 17 4 10 5 153 1 0 0 26 17 0 0 0 0 0

oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m5; m=6/7; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.457505; --ssCCCCTCcs---- ; cor=; Ncor= a 0 0 38 34 0 0 0 0 0 0 42 35 0 0 0 0 c 0 0 142 102 326 326 326 326 0 326 175 160 0 0 0 0 g 0 0 102 120 0 0 0 0 0 0 48 86 0 0 0 0 t 0 0 44 70 0 0 0 0 326 0 61 45 0 0 0 0

oligos_6nt_mkv3_m4_rc_shift1 (oligos_6nt_mkv3_m4_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=7/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.442239; -ssGCCTCGss----- ; cor=; Ncor= a 0 19 31 0 0 0 0 0 0 23 20 0 0 0 0 0 c 0 64 57 0 168 164 0 168 0 65 74 0 0 0 0 0 g 0 62 63 168 0 4 0 0 168 68 58 0 0 0 0 0 t 0 23 17 0 0 0 168 0 0 12 16 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; vsCGAGCGAGss ; Alignment reference a 61 26 7 5 177 4 6 2 138 18 34 29 c 57 57 164 11 16 5 182 5 27 28 69 67 g 63 99 23 182 5 190 9 194 25 140 79 84 t 20 19 7 3 3 2 4 0 11 15 19 21

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; vsCGAGCGAGss ; cor=; Ncor= a 61 26 7 5 177 4 6 2 138 18 34 29 c 57 57 164 11 16 5 182 5 27 28 69 67 g 63 99 23 182 5 190 9 194 25 140 79 84 t 20 19 7 3 3 2 4 0 11 15 19 21

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=5; ncol=15; -----ssCGAGGCss ; Alignment reference a 0 0 0 0 0 16 12 0 0 168 0 0 0 17 23 c 0 0 0 0 0 58 68 168 0 0 4 0 168 63 62 g 0 0 0 0 0 74 65 0 168 0 164 168 0 57 64 t 0 0 0 0 0 20 23 0 0 0 0 0 0 31 19

oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCGAGGCss ; cor=; Ncor= a 0 0 0 0 0 16 12 0 0 168 0 0 0 17 23 c 0 0 0 0 0 58 68 168 0 0 4 0 168 63 62 g 0 0 0 0 0 74 65 0 168 0 164 168 0 57 64 t 0 0 0 0 0 20 23 0 0 0 0 0 0 31 19

oligos_7nt_mkv4_m2_rc_shift3 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=13; w=-2; offset=-2; strand=R; shift=3; score=0.569304; ---ggGGCGkGGCCk ; cor=; Ncor= a 0 0 0 39 33 6 3 3 0 11 0 1 2 5 53 c 0 0 0 19 34 16 0 206 8 7 4 3 207 190 40 g 0 0 0 127 139 193 212 5 209 85 214 208 4 6 58 t 0 0 0 33 12 3 3 4 1 115 0 6 5 17 67

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=3/3; ncol2=16; w=-5; offset=-5; strand=R; shift=0; score=0.442239; ssGGGGGCGGGGCck ; cor=; Ncor= a 59 104 55 29 32 11 11 11 3 7 28 15 23 18 96 c 160 117 60 16 24 13 12 423 19 14 10 11 364 277 99 g 167 151 312 367 387 422 423 3 423 397 405 419 40 83 132 t 64 78 23 38 7 4 4 13 5 32 7 5 23 72 123

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --ssgGCCCGGCss ; Alignment reference a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 c 0 0 94 107 36 7 223 206 230 15 5 227 79 90 g 0 0 88 86 160 214 9 23 7 220 228 6 91 92 t 0 0 27 18 17 7 3 4 1 2 3 2 39 27

oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ssgGCCCGGCss ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 c 0 0 94 107 36 7 223 206 230 15 5 227 79 90 g 0 0 88 86 160 214 9 23 7 220 228 6 91 92 t 0 0 27 18 17 7 3 4 1 2 3 2 39 27

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.659284; --smGGCCmCGCCc ; cor=; Ncor= a 0 0 31 67 17 5 6 0 115 1 4 3 3 12 c 0 0 102 58 6 4 208 214 85 209 5 212 193 139 g 0 0 56 40 190 207 3 4 7 8 206 0 16 34 t 0 0 29 53 5 2 1 0 11 0 3 3 6 33

oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=3/4; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.561512; --cmgGCCCCGCCC ; cor=; Ncor= a 0 0 49 123 72 23 5 7 32 5 13 4 4 7 c 0 0 236 132 83 40 419 405 397 423 3 423 422 387 g 0 0 91 99 277 364 11 10 14 19 423 12 13 24 t 0 0 74 96 18 23 15 28 7 3 11 11 11 32

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5; m=4/4; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.453107; ssCAGGCCCcg--- ; cor=; Ncor= a 11 28 0 143 0 2 0 3 1 22 22 0 0 0 c 76 51 141 0 17 1 143 124 137 61 27 0 0 0 g 38 44 0 0 126 139 0 16 5 34 73 0 0 0 t 18 20 2 0 0 1 0 0 0 26 21 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=14; shift=3; ncol=17; ---scCCCGCCCCGCsc ; Alignment reference a 0 0 0 30 15 1 5 15 5 3 4 1 3 8 12 25 27 c 0 0 0 90 149 235 225 220 2 240 234 246 240 10 224 126 137 g 0 0 0 105 49 13 18 14 235 7 15 6 6 206 11 70 57 t 0 0 0 30 42 6 7 6 13 5 2 2 6 31 8 34 34

oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---scCCCGCCCCGCsc ; cor=; Ncor= a 0 0 0 30 15 1 5 15 5 3 4 1 3 8 12 25 27 c 0 0 0 90 149 235 225 220 2 240 234 246 240 10 224 126 137 g 0 0 0 105 49 13 18 14 235 7 15 6 6 206 11 70 57 t 0 0 0 30 42 6 7 6 13 5 2 2 6 31 8 34 34

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/4; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.652143; cmgGCCCCGCCCCCss- ; cor=; Ncor= a 49 123 72 23 5 7 32 5 13 4 4 7 38 23 78 64 0 c 236 132 83 40 419 405 397 423 3 423 422 387 367 312 151 167 0 g 91 99 277 364 11 10 14 19 423 12 13 24 16 60 117 160 0 t 74 96 18 23 15 28 7 3 11 11 11 32 29 55 104 59 0

oligos_7nt_mkv4_m2_shift5 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/4; ncol2=13; w=0; offset=2; strand=D; shift=5; score=0.588152; -----smGGCCmCGCCc ; cor=; Ncor= a 0 0 0 0 0 31 67 17 5 6 0 115 1 4 3 3 12 c 0 0 0 0 0 102 58 6 4 208 214 85 209 5 212 193 139 g 0 0 0 0 0 56 40 190 207 3 4 7 8 206 0 16 34 t 0 0 0 0 0 29 53 5 2 1 0 11 0 3 3 6 33

oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=10; w=0; offset=4; strand=D; shift=7; score=0.55165; -------ssCCCCTCcs ; cor=; Ncor= a 0 0 0 0 0 0 0 38 34 0 0 0 0 0 0 42 35 c 0 0 0 0 0 0 0 142 102 326 326 326 326 0 326 175 160 g 0 0 0 0 0 0 0 102 120 0 0 0 0 0 0 48 86 t 0 0 0 0 0 0 0 44 70 0 0 0 0 326 0 61 45

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; srGCCAATCass ; Alignment reference a 23 41 20 4 6 150 145 4 6 79 30 30 c 57 36 14 152 151 7 9 10 137 25 47 56 g 42 61 116 4 1 2 4 3 13 36 59 47 t 39 23 11 1 3 2 3 144 5 21 25 28

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; srGCCAATCass ; cor=; Ncor= a 23 41 20 4 6 150 145 4 6 79 30 30 c 57 36 14 152 151 7 9 10 137 25 47 56 g 42 61 116 4 1 2 4 3 13 36 59 47 t 39 23 11 1 3 2 3 144 5 21 25 28

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ssCAGGCCCcg ; Alignment reference a 11 28 0 143 0 2 0 3 1 22 22 c 76 51 141 0 17 1 143 124 137 61 27 g 38 44 0 0 126 139 0 16 5 34 73 t 18 20 2 0 0 1 0 0 0 26 21

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCAGGCCCcg ; cor=; Ncor= a 11 28 0 143 0 2 0 3 1 22 22 c 76 51 141 0 17 1 143 124 137 61 27 g 38 44 0 0 126 139 0 16 5 34 73 t 18 20 2 0 0 1 0 0 0 26 21

oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.453107; --ssgGCCCGG ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 c 0 0 94 107 36 7 223 206 230 15 5 g 0 0 88 86 160 214 9 23 7 220 228 t 0 0 27 18 17 7 3 4 1 2 3

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.447493; --smGGCCmCG ; cor=; Ncor= a 0 0 31 67 17 5 6 0 115 1 4 c 0 0 102 58 6 4 208 214 85 209 5 g 0 0 56 40 190 207 3 4 7 8 206 t 0 0 29 53 5 2 1 0 11 0 3

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --smGGCCmCGCCcc ; Alignment reference a 0 0 31 67 17 5 6 0 115 1 4 3 3 12 33 c 0 0 102 58 6 4 208 214 85 209 5 212 193 139 127 g 0 0 56 40 190 207 3 4 7 8 206 0 16 34 19 t 0 0 29 53 5 2 1 0 11 0 3 3 6 33 39
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/6; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --smGGCCmCGCCcc ; cor=; Ncor= a 0 0 31 67 17 5 6 0 115 1 4 3 3 12 33 c 0 0 102 58 6 4 208 214 85 209 5 212 193 139 127 g 0 0 56 40 190 207 3 4 7 8 206 0 16 34 19 t 0 0 29 53 5 2 1 0 11 0 3 3 6 33 39
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1; m=2/6; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.760024; --cmgGCCCCGCCCC ; cor=; Ncor= a 0 0 49 123 72 23 5 7 32 5 13 4 4 7 38 c 0 0 236 132 83 40 419 405 397 423 3 423 422 387 367 g 0 0 91 99 277 364 11 10 14 19 423 12 13 24 16 t 0 0 74 96 18 23 15 28 7 3 11 11 11 32 29
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=3/6; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.659284; --ssgGCCCGGCss- ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 0 c 0 0 94 107 36 7 223 206 230 15 5 227 79 90 0 g 0 0 88 86 160 214 9 23 7 220 228 6 91 92 0 t 0 0 27 18 17 7 3 4 1 2 3 2 39 27 0
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1; m=4/6; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.588152; scCCCGCCCCGCsc- ; cor=; Ncor= a 30 15 1 5 15 5 3 4 1 3 8 12 25 27 0 c 90 149 235 225 220 2 240 234 246 240 10 224 126 137 0 g 105 49 13 18 14 235 7 15 6 6 206 11 70 57 0 t 30 42 6 7 6 13 5 2 2 6 31 8 34 34 0
oligos_6nt_mkv3_m4_rc_shift3 (oligos_6nt_mkv3_m4_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4_rc; m=5/6; ncol2=10; w=0; offset=1; strand=R; shift=3; score=0.569304; ---ssGCCTCGss-- ; cor=; Ncor= a 0 0 0 19 31 0 0 0 0 0 0 23 20 0 0 c 0 0 0 64 57 0 168 164 0 168 0 65 74 0 0 g 0 0 0 62 63 168 0 4 0 0 168 68 58 0 0 t 0 0 0 23 17 0 0 0 168 0 0 12 16 0 0
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=6/6; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.447493; ssCAGGCCCcg---- ; cor=; Ncor= a 11 28 0 143 0 2 0 3 1 22 22 0 0 0 0 c 76 51 141 0 17 1 143 124 137 61 27 0 0 0 0 g 38 44 0 0 126 139 0 16 5 34 73 0 0 0 0 t 18 20 2 0 0 1 0 0 0 26 21 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=4; ncol=14; ----ssCCCCTCcs ; Alignment reference a 0 0 0 0 38 34 0 0 0 0 0 0 42 35 c 0 0 0 0 142 102 326 326 326 326 0 326 175 160 g 0 0 0 0 102 120 0 0 0 0 0 0 48 86 t 0 0 0 0 44 70 0 0 0 0 326 0 61 45
oligos_6nt_mkv3_m5_shift4 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----ssCCCCTCcs ; cor=; Ncor= a 0 0 0 0 38 34 0 0 0 0 0 0 42 35 c 0 0 0 0 142 102 326 326 326 326 0 326 175 160 g 0 0 0 0 102 120 0 0 0 0 0 0 48 86 t 0 0 0 0 44 70 0 0 0 0 326 0 61 45
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m1; m=2/3; ncol2=14; w=-4; offset=-4; strand=D; shift=0; score=0.55165; scCCCGCCCCGCsc ; cor=; Ncor= a 30 15 1 5 15 5 3 4 1 3 8 12 25 27 c 90 149 235 225 220 2 240 234 246 240 10 224 126 137 g 105 49 13 18 14 235 7 15 6 6 206 11 70 57 t 30 42 6 7 6 13 5 2 2 6 31 8 34 34
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m1; m=3/3; ncol2=16; w=-2; offset=-2; strand=D; shift=2; score=0.457505; --cmgGCCCCGCCC ; cor=; Ncor= a 0 0 49 123 72 23 5 7 32 5 13 4 4 7 c 0 0 236 132 83 40 419 405 397 423 3 423 422 387 g 0 0 91 99 277 364 11 10 14 19 423 12 13 24 t 0 0 74 96 18 23 15 28 7 3 11 11 11 32

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; cmgGCCCCGCCCCCss ; Alignment reference a 49 123 72 23 5 7 32 5 13 4 4 7 38 23 78 64 c 236 132 83 40 419 405 397 423 3 423 422 387 367 312 151 167 g 91 99 277 364 11 10 14 19 423 12 13 24 16 60 117 160 t 74 96 18 23 15 28 7 3 11 11 11 32 29 55 104 59
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/7; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; cmgGCCCCGCCCCCss ; cor=; Ncor= a 49 123 72 23 5 7 32 5 13 4 4 7 38 23 78 64 c 236 132 83 40 419 405 397 423 3 423 422 387 367 312 151 167 g 91 99 277 364 11 10 14 19 423 12 13 24 16 60 117 160 t 74 96 18 23 15 28 7 3 11 11 11 32 29 55 104 59
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=2/7; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.760024; smGGCCmCGCCcc--- ; cor=; Ncor= a 31 67 17 5 6 0 115 1 4 3 3 12 33 0 0 0 c 102 58 6 4 208 214 85 209 5 212 193 139 127 0 0 0 g 56 40 190 207 3 4 7 8 206 0 16 34 19 0 0 0 t 29 53 5 2 1 0 11 0 3 3 6 33 39 0 0 0
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/7; ncol2=14; w=0; offset=3; strand=D; shift=3; score=0.652143; ---scCCCGCCCCGCs ; cor=; Ncor= a 0 0 0 30 15 1 5 15 5 3 4 1 3 8 12 25 c 0 0 0 90 149 235 225 220 2 240 234 246 240 10 224 126 g 0 0 0 105 49 13 18 14 235 7 15 6 6 206 11 70 t 0 0 0 30 42 6 7 6 13 5 2 2 6 31 8 34
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=4/7; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.561512; ssgGCCCGGCss---- ; cor=; Ncor= a 29 27 25 10 3 5 0 1 2 3 29 29 0 0 0 0 c 94 107 36 7 223 206 230 15 5 227 79 90 0 0 0 0 g 88 86 160 214 9 23 7 220 228 6 91 92 0 0 0 0 t 27 18 17 7 3 4 1 2 3 2 39 27 0 0 0 0
oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4_rc; m=5/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.504083; ssGGCTCCGss----- ; cor=; Ncor= a 22 23 0 8 3 0 9 0 0 16 28 0 0 0 0 0 c 64 68 19 2 143 0 139 152 0 73 62 0 0 0 0 0 g 40 48 133 136 5 3 7 4 156 41 49 0 0 0 0 0 t 30 17 4 10 5 153 1 0 0 26 17 0 0 0 0 0
oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m5; m=6/7; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.457505; --ssCCCCTCcs---- ; cor=; Ncor= a 0 0 38 34 0 0 0 0 0 0 42 35 0 0 0 0 c 0 0 142 102 326 326 326 326 0 326 175 160 0 0 0 0 g 0 0 102 120 0 0 0 0 0 0 48 86 0 0 0 0 t 0 0 44 70 0 0 0 0 326 0 61 45 0 0 0 0
oligos_6nt_mkv3_m4_rc_shift1 (oligos_6nt_mkv3_m4_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m4_rc; m=7/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.442239; -ssGCCTCGss----- ; cor=; Ncor= a 0 19 31 0 0 0 0 0 0 23 20 0 0 0 0 0 c 0 64 57 0 168 164 0 168 0 65 74 0 0 0 0 0 g 0 62 63 168 0 4 0 0 168 68 58 0 0 0 0 0 t 0 23 17 0 0 0 168 0 0 12 16 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=10; shift=5; ncol=15; -----ssCGAGGCss ; Alignment reference a 0 0 0 0 0 16 12 0 0 168 0 0 0 17 23 c 0 0 0 0 0 58 68 168 0 0 4 0 168 63 62 g 0 0 0 0 0 74 65 0 168 0 164 168 0 57 64 t 0 0 0 0 0 20 23 0 0 0 0 0 0 31 19
oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCGAGGCss ; cor=; Ncor= a 0 0 0 0 0 16 12 0 0 168 0 0 0 17 23 c 0 0 0 0 0 58 68 168 0 0 4 0 168 63 62 g 0 0 0 0 0 74 65 0 168 0 164 168 0 57 64 t 0 0 0 0 0 20 23 0 0 0 0 0 0 31 19
oligos_7nt_mkv4_m2_rc_shift3 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=13; w=-2; offset=-2; strand=R; shift=3; score=0.569304; ---ggGGCGkGGCCk ; cor=; Ncor= a 0 0 0 39 33 6 3 3 0 11 0 1 2 5 53 c 0 0 0 19 34 16 0 206 8 7 4 3 207 190 40 g 0 0 0 127 139 193 212 5 209 85 214 208 4 6 58 t 0 0 0 33 12 3 3 4 1 115 0 6 5 17 67
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m1_rc; m=3/3; ncol2=16; w=-5; offset=-5; strand=R; shift=0; score=0.442239; ssGGGGGCGGGGCck ; cor=; Ncor= a 59 104 55 29 32 11 11 11 3 7 28 15 23 18 96 c 160 117 60 16 24 13 12 423 19 14 10 11 364 277 99 g 167 151 312 367 387 422 423 3 423 397 405 419 40 83 132 t 64 78 23 38 7 4 4 13 5 32 7 5 23 72 123

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --ssgGCCCGGCss ; Alignment reference a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 c 0 0 94 107 36 7 223 206 230 15 5 227 79 90 g 0 0 88 86 160 214 9 23 7 220 228 6 91 92 t 0 0 27 18 17 7 3 4 1 2 3 2 39 27
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --ssgGCCCGGCss ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 3 29 29 c 0 0 94 107 36 7 223 206 230 15 5 227 79 90 g 0 0 88 86 160 214 9 23 7 220 228 6 91 92 t 0 0 27 18 17 7 3 4 1 2 3 2 39 27
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m2; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=2; score=0.659284; --smGGCCmCGCCc ; cor=; Ncor= a 0 0 31 67 17 5 6 0 115 1 4 3 3 12 c 0 0 102 58 6 4 208 214 85 209 5 212 193 139 g 0 0 56 40 190 207 3 4 7 8 206 0 16 34 t 0 0 29 53 5 2 1 0 11 0 3 3 6 33
oligos_7nt_mkv4_m1_shift2 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m1; m=3/4; ncol2=16; w=0; offset=0; strand=D; shift=2; score=0.561512; --cmgGCCCCGCCC ; cor=; Ncor= a 0 0 49 123 72 23 5 7 32 5 13 4 4 7 c 0 0 236 132 83 40 419 405 397 423 3 423 422 387 g 0 0 91 99 277 364 11 10 14 19 423 12 13 24 t 0 0 74 96 18 23 15 28 7 3 11 11 11 32
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5; m=4/4; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.453107; ssCAGGCCCcg--- ; cor=; Ncor= a 11 28 0 143 0 2 0 3 1 22 22 0 0 0 c 76 51 141 0 17 1 143 124 137 61 27 0 0 0 g 38 44 0 0 126 139 0 16 5 34 73 0 0 0 t 18 20 2 0 0 1 0 0 0 26 21 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=14; shift=3; ncol=17; ---scCCCGCCCCGCsc ; Alignment reference a 0 0 0 30 15 1 5 15 5 3 4 1 3 8 12 25 27 c 0 0 0 90 149 235 225 220 2 240 234 246 240 10 224 126 137 g 0 0 0 105 49 13 18 14 235 7 15 6 6 206 11 70 57 t 0 0 0 30 42 6 7 6 13 5 2 2 6 31 8 34 34
oligos_6nt_mkv3_m1_shift3 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---scCCCGCCCCGCsc ; cor=; Ncor= a 0 0 0 30 15 1 5 15 5 3 4 1 3 8 12 25 27 c 0 0 0 90 149 235 225 220 2 240 234 246 240 10 224 126 137 g 0 0 0 105 49 13 18 14 235 7 15 6 6 206 11 70 57 t 0 0 0 30 42 6 7 6 13 5 2 2 6 31 8 34 34
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/4; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.652143; cmgGCCCCGCCCCCss- ; cor=; Ncor= a 49 123 72 23 5 7 32 5 13 4 4 7 38 23 78 64 0 c 236 132 83 40 419 405 397 423 3 423 422 387 367 312 151 167 0 g 91 99 277 364 11 10 14 19 423 12 13 24 16 60 117 160 0 t 74 96 18 23 15 28 7 3 11 11 11 32 29 55 104 59 0
oligos_7nt_mkv4_m2_shift5 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/4; ncol2=13; w=0; offset=2; strand=D; shift=5; score=0.588152; -----smGGCCmCGCCc ; cor=; Ncor= a 0 0 0 0 0 31 67 17 5 6 0 115 1 4 3 3 12 c 0 0 0 0 0 102 58 6 4 208 214 85 209 5 212 193 139 g 0 0 0 0 0 56 40 190 207 3 4 7 8 206 0 16 34 t 0 0 0 0 0 29 53 5 2 1 0 11 0 3 3 6 33
oligos_6nt_mkv3_m5_shift7 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m5; m=4/4; ncol2=10; w=0; offset=4; strand=D; shift=7; score=0.55165; -------ssCCCCTCcs ; cor=; Ncor= a 0 0 0 0 0 0 0 38 34 0 0 0 0 0 0 42 35 c 0 0 0 0 0 0 0 142 102 326 326 326 326 0 326 175 160 g 0 0 0 0 0 0 0 102 120 0 0 0 0 0 0 48 86 t 0 0 0 0 0 0 0 44 70 0 0 0 0 326 0 61 45

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ssCAGGCCCcg ; Alignment reference a 11 28 0 143 0 2 0 3 1 22 22 c 76 51 141 0 17 1 143 124 137 61 27 g 38 44 0 0 126 139 0 16 5 34 73 t 18 20 2 0 0 1 0 0 0 26 21
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ssCAGGCCCcg ; cor=; Ncor= a 11 28 0 143 0 2 0 3 1 22 22 c 76 51 141 0 17 1 143 124 137 61 27 g 38 44 0 0 126 139 0 16 5 34 73 t 18 20 2 0 0 1 0 0 0 26 21
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.453107; --ssgGCCCGG ; cor=; Ncor= a 0 0 29 27 25 10 3 5 0 1 2 c 0 0 94 107 36 7 223 206 230 15 5 g 0 0 88 86 160 214 9 23 7 220 228 t 0 0 27 18 17 7 3 4 1 2 3
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.447493; --smGGCCmCG ; cor=; Ncor= a 0 0 31 67 17 5 6 0 115 1 4 c 0 0 102 58 6 4 208 214 85 209 5 g 0 0 56 40 190 207 3 4 7 8 206 t 0 0 29 53 5 2 1 0 11 0 3