One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/10/peak-motifs.2026-01-10.155300_2026-01-10.155300_GuwVfF/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/10/peak-motifs.2026-01-10.155300_2026-01-10.155300_GuwVfF/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssCCGGGCCss ; Alignment reference a 0 0 0 44 22 2 0 0 6 7 7 2 26 29 c 0 0 0 102 97 257 272 4 50 5 262 255 88 99 g 0 0 0 92 109 15 2 270 209 257 3 17 128 112 t 0 0 0 36 46 0 0 0 9 5 2 0 32 34

oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCCGGGCCss ; cor=; Ncor= a 0 0 0 44 22 2 0 0 6 7 7 2 26 29 c 0 0 0 102 97 257 272 4 50 5 262 255 88 99 g 0 0 0 92 109 15 2 270 209 257 3 17 128 112 t 0 0 0 36 46 0 0 0 9 5 2 0 32 34

oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=2; score=0.598458; --sssCCAGGCss- ; cor=; Ncor= a 0 0 76 52 31 0 0 336 1 3 2 71 42 0 c 0 0 93 131 124 339 326 4 13 2 338 105 117 0 g 0 0 112 90 135 0 14 4 329 338 0 92 137 0 t 0 0 63 71 54 5 4 0 1 1 4 76 48 0

oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5_rc; m=3/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.40393; ssGCTCCGGss--- ; cor=; Ncor= a 44 49 8 12 6 7 2 1 9 50 53 0 0 0 c 113 115 4 245 3 250 277 8 18 98 80 0 0 0 g 101 88 265 20 34 29 8 279 255 100 102 0 0 0 t 30 36 11 11 245 2 1 0 6 40 53 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 3 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=11; shift=0; ncol=11; bscAGGACCys ; Alignment reference a 71 75 41 338 6 1 367 6 6 61 52 c 94 122 241 13 13 11 0 352 337 107 108 g 103 105 57 15 346 348 0 3 14 78 125 t 101 67 30 3 4 9 2 8 12 123 84

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; bscAGGACCys ; cor=; Ncor= a 71 75 41 338 6 1 367 6 6 61 52 c 94 122 241 13 13 11 0 352 337 107 108 g 103 105 57 15 346 348 0 3 14 78 125 t 101 67 30 3 4 9 2 8 12 123 84

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.867083; ssCAGGACCTs ; cor=; Ncor= a 70 50 20 336 9 7 288 7 2 13 38 c 96 155 312 6 3 15 22 335 353 36 117 g 114 97 21 15 352 341 15 18 2 13 147 t 87 65 14 10 3 4 42 7 10 305 65

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; sssCCAGGCss ; Alignment reference a 76 52 31 0 0 336 1 3 2 71 42 c 93 131 124 339 326 4 13 2 338 105 117 g 112 90 135 0 14 4 329 338 0 92 137 t 63 71 54 5 4 0 1 1 4 76 48

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; sssCCAGGCss ; cor=; Ncor= a 76 52 31 0 0 336 1 3 2 71 42 c 93 131 124 339 326 4 13 2 338 105 117 g 112 90 135 0 14 4 329 338 0 92 137 t 63 71 54 5 4 0 1 1 4 76 48

oligos_7nt_mkv4_m2_shift1 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.598458; -ssCCGGGCCs ; cor=; Ncor= a 0 44 22 2 0 0 6 7 7 2 26 c 0 102 97 257 272 4 50 5 262 255 88 g 0 92 109 15 2 270 209 257 3 17 128 t 0 36 46 0 0 0 9 5 2 0 32

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; rwAAGAAAwa ; Alignment reference a 102 90 297 286 3 294 283 297 98 118 c 47 63 1 10 12 0 8 3 65 65 g 91 70 2 0 245 0 0 0 55 59 t 65 82 5 9 45 11 14 5 87 63

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; rwAAGAAAwa ; cor=; Ncor= a 102 90 297 286 3 294 283 297 98 118 c 47 63 1 10 12 0 8 3 65 65 g 91 70 2 0 245 0 0 0 55 59 t 65 82 5 9 45 11 14 5 87 63

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 3 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=12; shift=0; ncol=12; ssCAGGACCTss ; Alignment reference a 70 50 20 336 9 7 288 7 2 13 38 57 c 96 155 312 6 3 15 22 335 353 36 117 116 g 114 97 21 15 352 341 15 18 2 13 147 141 t 87 65 14 10 3 4 42 7 10 305 65 53

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ssCAGGACCTss ; cor=; Ncor= a 70 50 20 336 9 7 288 7 2 13 38 57 c 96 155 312 6 3 15 22 335 353 36 117 116 g 114 97 21 15 352 341 15 18 2 13 147 141 t 87 65 14 10 3 4 42 7 10 305 65 53

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m3; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.867083; bscAGGACCys- ; cor=; Ncor= a 71 75 41 338 6 1 367 6 6 61 52 0 c 94 122 241 13 13 11 0 352 337 107 108 0 g 103 105 57 15 346 348 0 3 14 78 125 0 t 101 67 30 3 4 9 2 8 12 123 84 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --ssCGGAGCsss ; Alignment reference a 0 0 26 17 0 0 0 208 1 0 27 27 30 c 0 0 88 88 215 0 5 4 2 215 69 62 69 g 0 0 66 75 0 215 208 0 209 0 68 87 84 t 0 0 35 35 0 0 2 3 3 0 51 39 32

oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --ssCGGAGCsss ; cor=; Ncor= a 0 0 26 17 0 0 0 208 1 0 27 27 30 c 0 0 88 88 215 0 5 4 2 215 69 62 69 g 0 0 66 75 0 215 208 0 209 0 68 87 84 t 0 0 35 35 0 0 2 3 3 0 51 39 32

oligos_7nt_mkv4_m5_shift1 (oligos_7nt_mkv4_m5)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5; m=2/4; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.793178; -ssCCGGAGCss- ; cor=; Ncor= a 0 53 40 6 0 1 2 245 11 11 36 30 0 c 0 102 100 255 279 8 29 34 20 265 88 101 0 g 0 80 98 18 8 277 250 3 245 4 115 113 0 t 0 53 50 9 1 2 7 6 12 8 49 44 0

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.669104; -ssGCGGGGCGss ; cor=; Ncor= a 0 70 62 8 11 12 18 19 15 23 25 74 65 c 0 155 172 38 493 35 19 32 23 482 56 152 150 g 0 243 224 470 9 456 486 472 487 10 409 235 253 t 0 61 71 13 16 26 6 6 4 14 39 68 61

oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m4_rc; m=4/4; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.545206; ssGGCGGGGCsg- ; cor=; Ncor= a 79 94 23 10 9 14 18 25 20 49 71 101 0 c 188 173 45 35 573 40 42 34 13 483 204 145 0 g 261 268 516 540 4 530 535 526 558 47 211 283 0 t 68 61 12 11 10 12 1 11 5 17 110 67 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; csCCCTCCCss ; Alignment reference a 32 43 2 6 9 1 7 9 1 37 45 c 107 97 260 245 227 0 257 248 260 97 106 g 65 67 2 13 29 2 1 7 4 86 76 t 61 58 1 1 0 262 0 1 0 45 38

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; csCCCTCCCss ; cor=; Ncor= a 32 43 2 6 9 1 7 9 1 37 45 c 107 97 260 245 227 0 257 248 260 97 106 g 65 67 2 13 29 2 1 7 4 86 76 t 61 58 1 1 0 262 0 1 0 45 38

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=1; ncol=13; -csGCCCCGCCss ; Alignment reference a 0 67 110 17 5 11 1 12 10 11 12 61 68 c 0 283 211 47 558 526 535 530 4 540 516 268 261 g 0 145 204 483 13 34 42 40 573 35 45 173 188 t 0 101 71 49 20 25 18 14 9 10 23 94 79

oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -csGCCCCGCCss ; cor=; Ncor= a 0 67 110 17 5 11 1 12 10 11 12 61 68 c 0 283 211 47 558 526 535 530 4 540 516 268 261 g 0 145 204 483 13 34 42 40 573 35 45 173 188 t 0 101 71 49 20 25 18 14 9 10 23 94 79

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m1_rc; m=2/3; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.795431; ssCGCCCCGCss- ; cor=; Ncor= a 61 68 39 14 4 6 6 26 16 13 71 61 0 c 253 235 409 10 487 472 486 456 9 470 224 243 0 g 150 152 56 482 23 32 19 35 493 38 172 155 0 t 65 74 25 23 15 19 18 12 11 8 62 70 0

oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m2_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.545206; sssGCTCCGss-- ; cor=; Ncor= a 32 39 51 0 3 3 2 0 0 35 35 0 0 c 84 87 68 0 209 0 208 215 0 75 66 0 0 g 69 62 69 215 2 4 5 0 215 88 88 0 0 t 30 27 27 0 1 208 0 0 0 17 26 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssCCGGAGCss ; Alignment reference a 0 0 0 53 40 6 0 1 2 245 11 11 36 30 c 0 0 0 102 100 255 279 8 29 34 20 265 88 101 g 0 0 0 80 98 18 8 277 250 3 245 4 115 113 t 0 0 0 53 50 9 1 2 7 6 12 8 49 44

oligos_7nt_mkv4_m5_shift3 (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=3; score= 1; ---ssCCGGAGCss ; cor=; Ncor= a 0 0 0 53 40 6 0 1 2 245 11 11 36 30 c 0 0 0 102 100 255 279 8 29 34 20 265 88 101 g 0 0 0 80 98 18 8 277 250 3 245 4 115 113 t 0 0 0 53 50 9 1 2 7 6 12 8 49 44

oligos_6nt_mkv3_m2_shift4 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.793178; ----ssCGGAGCss ; cor=; Ncor= a 0 0 0 0 26 17 0 0 0 208 1 0 27 27 c 0 0 0 0 88 88 215 0 5 4 2 215 69 62 g 0 0 0 0 66 75 0 215 208 0 209 0 68 87 t 0 0 0 0 35 35 0 0 2 3 3 0 51 39

oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2_rc; m=3/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.40393; ssGGCCCGGss--- ; cor=; Ncor= a 34 32 0 2 5 9 0 0 0 46 36 0 0 0 c 112 128 17 3 257 209 270 2 15 109 92 0 0 0 g 99 88 255 262 5 50 4 272 257 97 102 0 0 0 t 29 26 2 7 7 6 0 0 2 22 44 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -ssGCGGGGCGss ; Alignment reference a 0 70 62 8 11 12 18 19 15 23 25 74 65 c 0 155 172 38 493 35 19 32 23 482 56 152 150 g 0 243 224 470 9 456 486 472 487 10 409 235 253 t 0 61 71 13 16 26 6 6 4 14 39 68 61

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCGGGGCGss ; cor=; Ncor= a 0 70 62 8 11 12 18 19 15 23 25 74 65 c 0 155 172 38 493 35 19 32 23 482 56 152 150 g 0 243 224 470 9 456 486 472 487 10 409 235 253 t 0 61 71 13 16 26 6 6 4 14 39 68 61

oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4_rc; m=2/3; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.795431; ssGGCGGGGCsg- ; cor=; Ncor= a 79 94 23 10 9 14 18 25 20 49 71 101 0 c 188 173 45 35 573 40 42 34 13 483 204 145 0 g 261 268 516 540 4 530 535 526 558 47 211 283 0 t 68 61 12 11 10 12 1 11 5 17 110 67 0

oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.669104; --ssCGGAGCsss ; cor=; Ncor= a 0 0 26 17 0 0 0 208 1 0 27 27 30 c 0 0 88 88 215 0 5 4 2 215 69 62 69 g 0 0 66 75 0 215 208 0 209 0 68 87 84 t 0 0 35 35 0 0 2 3 3 0 51 39 32

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssCCGGGCCss ; Alignment reference a 0 0 0 44 22 2 0 0 6 7 7 2 26 29 c 0 0 0 102 97 257 272 4 50 5 262 255 88 99 g 0 0 0 92 109 15 2 270 209 257 3 17 128 112 t 0 0 0 36 46 0 0 0 9 5 2 0 32 34
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ssCCGGGCCss ; cor=; Ncor= a 0 0 0 44 22 2 0 0 6 7 7 2 26 29 c 0 0 0 102 97 257 272 4 50 5 262 255 88 99 g 0 0 0 92 109 15 2 270 209 257 3 17 128 112 t 0 0 0 36 46 0 0 0 9 5 2 0 32 34
oligos_6nt_mkv3_m4_shift2 (oligos_6nt_mkv3_m4)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=2; score=0.598458; --sssCCAGGCss- ; cor=; Ncor= a 0 0 76 52 31 0 0 336 1 3 2 71 42 0 c 0 0 93 131 124 339 326 4 13 2 338 105 117 0 g 0 0 112 90 135 0 14 4 329 338 0 92 137 0 t 0 0 63 71 54 5 4 0 1 1 4 76 48 0
oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5_rc; m=3/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.40393; ssGCTCCGGss--- ; cor=; Ncor= a 44 49 8 12 6 7 2 1 9 50 53 0 0 0 c 113 115 4 245 3 250 277 8 18 98 80 0 0 0 g 101 88 265 20 34 29 8 279 255 100 102 0 0 0 t 30 36 11 11 245 2 1 0 6 40 53 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --ssCGGAGCsss ; Alignment reference a 0 0 26 17 0 0 0 208 1 0 27 27 30 c 0 0 88 88 215 0 5 4 2 215 69 62 69 g 0 0 66 75 0 215 208 0 209 0 68 87 84 t 0 0 35 35 0 0 2 3 3 0 51 39 32
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --ssCGGAGCsss ; cor=; Ncor= a 0 0 26 17 0 0 0 208 1 0 27 27 30 c 0 0 88 88 215 0 5 4 2 215 69 62 69 g 0 0 66 75 0 215 208 0 209 0 68 87 84 t 0 0 35 35 0 0 2 3 3 0 51 39 32
oligos_7nt_mkv4_m5_shift1 (oligos_7nt_mkv4_m5)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m5; m=2/4; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.793178; -ssCCGGAGCss- ; cor=; Ncor= a 0 53 40 6 0 1 2 245 11 11 36 30 0 c 0 102 100 255 279 8 29 34 20 265 88 101 0 g 0 80 98 18 8 277 250 3 245 4 115 113 0 t 0 53 50 9 1 2 7 6 12 8 49 44 0
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.669104; -ssGCGGGGCGss ; cor=; Ncor= a 0 70 62 8 11 12 18 19 15 23 25 74 65 c 0 155 172 38 493 35 19 32 23 482 56 152 150 g 0 243 224 470 9 456 486 472 487 10 409 235 253 t 0 61 71 13 16 26 6 6 4 14 39 68 61
oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m4_rc; m=4/4; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.545206; ssGGCGGGGCsg- ; cor=; Ncor= a 79 94 23 10 9 14 18 25 20 49 71 101 0 c 188 173 45 35 573 40 42 34 13 483 204 145 0 g 261 268 516 540 4 530 535 526 558 47 211 283 0 t 68 61 12 11 10 12 1 11 5 17 110 67 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=1; ncol=13; -csGCCCCGCCss ; Alignment reference a 0 67 110 17 5 11 1 12 10 11 12 61 68 c 0 283 211 47 558 526 535 530 4 540 516 268 261 g 0 145 204 483 13 34 42 40 573 35 45 173 188 t 0 101 71 49 20 25 18 14 9 10 23 94 79
oligos_7nt_mkv4_m4_shift1 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -csGCCCCGCCss ; cor=; Ncor= a 0 67 110 17 5 11 1 12 10 11 12 61 68 c 0 283 211 47 558 526 535 530 4 540 516 268 261 g 0 145 204 483 13 34 42 40 573 35 45 173 188 t 0 101 71 49 20 25 18 14 9 10 23 94 79
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m1_rc; m=2/3; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.795431; ssCGCCCCGCss- ; cor=; Ncor= a 61 68 39 14 4 6 6 26 16 13 71 61 0 c 253 235 409 10 487 472 486 456 9 470 224 243 0 g 150 152 56 482 23 32 19 35 493 38 172 155 0 t 65 74 25 23 15 19 18 12 11 8 62 70 0
oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m2_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.545206; sssGCTCCGss-- ; cor=; Ncor= a 32 39 51 0 3 3 2 0 0 35 35 0 0 c 84 87 68 0 209 0 208 215 0 75 66 0 0 g 69 62 69 215 2 4 5 0 215 88 88 0 0 t 30 27 27 0 1 208 0 0 0 17 26 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssCCGGAGCss ; Alignment reference a 0 0 0 53 40 6 0 1 2 245 11 11 36 30 c 0 0 0 102 100 255 279 8 29 34 20 265 88 101 g 0 0 0 80 98 18 8 277 250 3 245 4 115 113 t 0 0 0 53 50 9 1 2 7 6 12 8 49 44
oligos_7nt_mkv4_m5_shift3 (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=3; score= 1; ---ssCCGGAGCss ; cor=; Ncor= a 0 0 0 53 40 6 0 1 2 245 11 11 36 30 c 0 0 0 102 100 255 279 8 29 34 20 265 88 101 g 0 0 0 80 98 18 8 277 250 3 245 4 115 113 t 0 0 0 53 50 9 1 2 7 6 12 8 49 44
oligos_6nt_mkv3_m2_shift4 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m2; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=4; score=0.793178; ----ssCGGAGCss ; cor=; Ncor= a 0 0 0 0 26 17 0 0 0 208 1 0 27 27 c 0 0 0 0 88 88 215 0 5 4 2 215 69 62 g 0 0 0 0 66 75 0 215 208 0 209 0 68 87 t 0 0 0 0 35 35 0 0 2 3 3 0 51 39
oligos_7nt_mkv4_m2_rc_shift0 (oligos_7nt_mkv4_m2_rc)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2_rc; m=3/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.40393; ssGGCCCGGss--- ; cor=; Ncor= a 34 32 0 2 5 9 0 0 0 46 36 0 0 0 c 112 128 17 3 257 209 270 2 15 109 92 0 0 0 g 99 88 255 262 5 50 4 272 257 97 102 0 0 0 t 29 26 2 7 7 6 0 0 2 22 44 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -ssGCGGGGCGss ; Alignment reference a 0 70 62 8 11 12 18 19 15 23 25 74 65 c 0 155 172 38 493 35 19 32 23 482 56 152 150 g 0 243 224 470 9 456 486 472 487 10 409 235 253 t 0 61 71 13 16 26 6 6 4 14 39 68 61
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -ssGCGGGGCGss ; cor=; Ncor= a 0 70 62 8 11 12 18 19 15 23 25 74 65 c 0 155 172 38 493 35 19 32 23 482 56 152 150 g 0 243 224 470 9 456 486 472 487 10 409 235 253 t 0 61 71 13 16 26 6 6 4 14 39 68 61
oligos_7nt_mkv4_m4_rc_shift0 (oligos_7nt_mkv4_m4_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4_rc; m=2/3; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.795431; ssGGCGGGGCsg- ; cor=; Ncor= a 79 94 23 10 9 14 18 25 20 49 71 101 0 c 188 173 45 35 573 40 42 34 13 483 204 145 0 g 261 268 516 540 4 530 535 526 558 47 211 283 0 t 68 61 12 11 10 12 1 11 5 17 110 67 0
oligos_6nt_mkv3_m2_shift2 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.669104; --ssCGGAGCsss ; cor=; Ncor= a 0 0 26 17 0 0 0 208 1 0 27 27 30 c 0 0 88 88 215 0 5 4 2 215 69 62 69 g 0 0 66 75 0 215 208 0 209 0 68 87 84 t 0 0 35 35 0 0 2 3 3 0 51 39 32