One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.171534_2025-12-18.171534_bJonYL/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.2025-12-18.171534_2025-12-18.171534_bJonYL/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 4 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=13; shift=0; ncol=13; kAtAGATAGATAk ; Alignment reference a 127 551 142 699 8 731 11 732 19 735 9 574 136 c 53 57 58 1 47 7 15 0 74 7 15 42 76 g 273 56 74 8 627 11 14 13 598 8 41 85 288 t 300 89 479 45 71 4 713 8 62 3 688 52 253

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; kAtAGATAGATAk ; cor=; Ncor= a 127 551 142 699 8 731 11 732 19 735 9 574 136 c 53 57 58 1 47 7 15 0 74 7 15 42 76 g 273 56 74 8 627 11 14 13 598 8 41 85 288 t 300 89 479 45 71 4 713 8 62 3 688 52 253

oligos_7nt_mkv4_m3_rc_shift2 (oligos_7nt_mkv4_m3_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.833093; --wAGATAGATAk ; cor=; Ncor= a 0 0 148 405 0 492 12 510 1 489 15 399 117 c 0 0 32 10 0 14 20 0 0 14 15 11 48 g 0 0 49 15 529 12 14 10 523 16 43 74 193 t 0 0 300 99 0 11 483 9 5 10 456 45 171

oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.519059; ---awATACATAt ; cor=; Ncor= a 0 0 0 441 213 579 0 841 0 716 0 814 186 c 0 0 0 140 73 59 0 0 841 0 0 27 108 g 0 0 0 65 110 134 0 0 0 113 0 0 111 t 0 0 0 195 445 69 841 0 0 12 841 0 436

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; aaAAGAAAww ; Alignment reference a 147 157 326 326 0 326 326 326 125 143 c 34 26 0 0 0 0 0 0 33 48 g 66 72 0 0 326 0 0 0 76 52 t 79 71 0 0 0 0 0 0 92 83

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; aaAAGAAAww ; cor=; Ncor= a 147 157 326 326 0 326 326 326 125 143 c 34 26 0 0 0 0 0 0 33 48 g 66 72 0 0 326 0 0 0 76 52 t 79 71 0 0 0 0 0 0 92 83

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 3 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; mTATCTATCTw ; Alignment reference a 171 45 456 10 5 9 483 11 0 99 300 c 193 74 43 16 523 10 14 12 529 15 49 g 48 11 15 14 0 0 20 14 0 10 32 t 117 399 15 489 1 510 12 492 0 405 148

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; mTATCTATCTw ; cor=; Ncor= a 171 45 456 10 5 9 483 11 0 99 300 c 193 74 43 16 523 10 14 12 529 15 49 g 48 11 15 14 0 0 20 14 0 10 32 t 117 399 15 489 1 510 12 492 0 405 148

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m3_rc; m=2/2; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.833093; mTATCTATCTa ; cor=; Ncor= a 253 52 688 3 62 8 713 4 71 45 479 c 288 85 41 8 598 13 14 11 627 8 74 g 76 42 15 7 74 0 15 7 47 1 58 t 136 574 9 735 19 732 11 731 8 699 142

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 4 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=13; shift=0; ncol=13; wwTTAAAAATTww ; Alignment reference a 74 65 8 7 186 179 186 173 174 17 22 87 78 c 26 15 3 2 0 4 1 3 4 3 1 22 13 g 26 31 8 1 0 4 3 3 9 12 9 15 22 t 72 87 179 188 12 11 8 19 11 166 166 74 85

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAATTww ; cor=; Ncor= a 74 65 8 7 186 179 186 173 174 17 22 87 78 c 26 15 3 2 0 4 1 3 4 3 1 22 13 g 26 31 8 1 0 4 3 3 9 12 9 15 22 t 72 87 179 188 12 11 8 19 11 166 166 74 85

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m3 versus positions_6nt_m1; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 0.7539; wwTTAAAAATAAw ; cor=; Ncor= a 42 40 8 5 106 104 102 106 98 5 102 85 60 c 15 16 4 2 0 1 2 0 1 2 1 6 9 g 17 14 2 3 1 1 1 0 7 5 3 1 9 t 38 42 98 102 5 6 7 6 6 100 6 20 34

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m3 versus positions_6nt_m2; m=3/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.691136; wwTTAAAAAATAa ; cor=; Ncor= a 35 31 7 3 81 81 83 86 84 83 7 79 58 c 11 12 2 3 2 2 1 0 2 1 1 3 6 g 13 12 1 4 1 1 3 1 1 2 1 1 8 t 32 36 81 81 7 7 4 4 4 5 82 8 19

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift3 ; 5 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=18; shift=3; ncol=21; ---kmATCGAATGGAATCrwm ; Alignment reference a 0 0 0 109 1123 1649 80 79 285 1928 1951 44 92 65 1951 1744 72 76 1074 1039 984 c 0 0 0 71 752 276 58 1402 45 40 7 56 19 75 11 201 57 1538 69 65 809 g 0 0 0 1002 34 38 12 259 1620 33 50 33 1881 1846 16 23 7 238 832 23 68 t 0 0 0 840 113 59 1872 282 72 21 14 1889 30 36 44 54 1886 170 47 895 161

oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/4; ncol2=18; w=0; offset=0; strand=D; shift=3; score= 1; ---kmATCGAATGGAATCrwm ; cor=; Ncor= a 0 0 0 109 1123 1649 80 79 285 1928 1951 44 92 65 1951 1744 72 76 1074 1039 984 c 0 0 0 71 752 276 58 1402 45 40 7 56 19 75 11 201 57 1538 69 65 809 g 0 0 0 1002 34 38 12 259 1620 33 50 33 1881 1846 16 23 7 238 832 23 68 t 0 0 0 840 113 59 1872 282 72 21 14 1889 30 36 44 54 1886 170 47 895 161

oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1_rc; m=2/4; ncol2=19; w=0; offset=0; strand=R; shift=3; score=0.938528; ---kmATcGAATGGAATcrwm ; cor=; Ncor= a 0 0 0 161 1430 1996 84 114 296 2335 2304 48 120 57 2355 2101 92 99 959 1490 1400 c 0 0 0 100 836 253 82 1425 40 41 14 73 214 112 11 227 74 1537 65 64 764 g 0 0 0 1232 39 71 15 572 2011 28 62 30 2039 2212 13 24 7 577 1356 18 72 t 0 0 0 932 120 105 2244 314 78 21 45 2274 52 44 46 73 2252 212 45 853 189

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1_rc; m=3/4; ncol2=21; w=-3; offset=-3; strand=R; shift=0; score=0.849484; whrkmATCGAATGGAATCrwm ; cor=; Ncor= a 800 489 979 70 788 1553 54 86 265 1754 1764 21 82 68 1770 1523 88 52 743 1156 1092 c 52 520 77 63 904 188 54 1285 20 25 7 70 17 54 9 236 49 1311 63 47 555 g 440 8 737 715 30 30 12 194 1476 31 33 8 1694 1675 5 21 7 246 976 17 55 t 535 810 34 979 105 56 1707 262 66 17 23 1728 34 30 43 47 1683 218 45 607 125

oligos_7nt_mkv4_m5_shift10 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=4/4; ncol2=13; w=0; offset=7; strand=D; shift=10; score=0.475577; ----------ATGGAmTCGAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 574 19 34 17 593 315 35 1 22 608 588 c 0 0 0 0 0 0 0 0 0 0 12 48 5 12 7 291 32 604 13 13 4 g 0 0 0 0 0 0 0 0 0 0 24 21 584 584 4 3 2 12 586 5 17 t 0 0 0 0 0 0 0 0 0 0 18 540 5 15 24 19 559 11 7 2 19

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---awATACATAtw ; Alignment reference a 0 0 0 441 213 579 0 841 0 716 0 814 186 487 c 0 0 0 140 73 59 0 0 841 0 0 27 108 49 g 0 0 0 65 110 134 0 0 0 113 0 0 111 73 t 0 0 0 195 445 69 841 0 0 12 841 0 436 232

oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---awATACATAtw ; cor=; Ncor= a 0 0 0 441 213 579 0 841 0 716 0 814 186 487 c 0 0 0 140 73 59 0 0 841 0 0 27 108 49 g 0 0 0 65 110 134 0 0 0 113 0 0 111 73 t 0 0 0 195 445 69 841 0 0 12 841 0 436 232

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3; m=2/2; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.519059; kAtAGATAGATAk- ; cor=; Ncor= a 127 551 142 699 8 731 11 732 19 735 9 574 136 0 c 53 57 58 1 47 7 15 0 74 7 15 42 76 0 g 273 56 74 8 627 11 14 13 598 8 41 85 288 0 t 300 89 479 45 71 4 713 8 62 3 688 52 253 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; awgTAGAATAta ; Alignment reference a 93 91 57 6 217 8 217 227 17 214 53 120 c 47 17 4 4 0 1 5 3 2 7 46 23 g 40 24 161 0 6 205 1 5 3 7 29 40 t 57 105 15 227 14 23 14 2 215 9 109 54

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; awgTAGAATAta ; cor=; Ncor= a 93 91 57 6 217 8 217 227 17 214 53 120 c 47 17 4 4 0 1 5 3 2 7 46 23 g 40 24 161 0 6 205 1 5 3 7 29 40 t 57 105 15 227 14 23 14 2 215 9 109 54

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; -----wwAAATAAww ; Alignment reference a 0 0 0 0 0 188 179 411 411 411 0 411 411 163 163 c 0 0 0 0 0 50 49 0 0 0 0 0 0 60 61 g 0 0 0 0 0 47 77 0 0 0 0 0 0 45 54 t 0 0 0 0 0 126 106 0 0 0 411 0 0 143 133

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; -----wwAAATAAww ; cor=; Ncor= a 0 0 0 0 0 188 179 411 411 411 0 411 411 163 163 c 0 0 0 0 0 50 49 0 0 0 0 0 0 60 61 g 0 0 0 0 0 47 77 0 0 0 0 0 0 45 54 t 0 0 0 0 0 126 106 0 0 0 411 0 0 143 133

positions_6nt_m1_shift1 (positions_6nt_m1)
; oligos_6nt_mkv3_m4 versus positions_6nt_m1; m=2/3; ncol2=15; w=-4; offset=-4; strand=D; shift=1; score=0.606468; -wwTTAAAAATAAww ; cor=; Ncor= a 0 42 40 8 5 106 104 102 106 98 5 102 85 60 47 c 0 15 16 4 2 0 1 2 0 1 2 1 6 9 13 g 0 17 14 2 3 1 1 1 0 7 5 3 1 9 9 t 0 38 42 98 102 5 6 7 6 6 100 6 20 34 43

positions_6nt_m2_shift0 (positions_6nt_m2)
; oligos_6nt_mkv3_m4 versus positions_6nt_m2; m=3/3; ncol2=16; w=-5; offset=-5; strand=D; shift=0; score=0.560875; wwTTAAAAAATAaAw ; cor=; Ncor= a 35 31 7 3 81 81 83 86 84 83 7 79 58 62 40 c 11 12 2 3 2 2 1 0 2 1 1 3 6 6 7 g 13 12 1 4 1 1 3 1 1 2 1 1 8 10 12 t 32 36 81 81 7 7 4 4 4 5 82 8 19 13 32

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 5 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=16; shift=0; ncol=16; wwTTAAAAAATAaAww ; Alignment reference a 35 31 7 3 81 81 83 86 84 83 7 79 58 62 40 43 c 11 12 2 3 2 2 1 0 2 1 1 3 6 6 7 11 g 13 12 1 4 1 1 3 1 1 2 1 1 8 10 12 8 t 32 36 81 81 7 7 4 4 4 5 82 8 19 13 32 29

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAAATAaAww ; cor=; Ncor= a 35 31 7 3 81 81 83 86 84 83 7 79 58 62 40 43 c 11 12 2 3 2 2 1 0 2 1 1 3 6 6 7 11 g 13 12 1 4 1 1 3 1 1 2 1 1 8 10 12 8 t 32 36 81 81 7 7 4 4 4 5 82 8 19 13 32 29

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=2/4; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.795568; -wwTTAAAAATAAwww ; cor=; Ncor= a 0 42 40 8 5 106 104 102 106 98 5 102 85 60 47 48 c 0 15 16 4 2 0 1 2 0 1 2 1 6 9 13 10 g 0 17 14 2 3 1 1 1 0 7 5 3 1 9 9 12 t 0 38 42 98 102 5 6 7 6 6 100 6 20 34 43 42

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m2 versus positions_6nt_m3; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.691136; wwTTAAAAATTww--- ; cor=; Ncor= a 74 65 8 7 186 179 186 173 174 17 22 87 78 0 0 0 c 26 15 3 2 0 4 1 3 4 3 1 22 13 0 0 0 g 26 31 8 1 0 4 3 3 9 12 9 15 22 0 0 0 t 72 87 179 188 12 11 8 19 11 166 166 74 85 0 0 0

oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)
; positions_6nt_m2 versus oligos_6nt_mkv3_m4; m=4/4; ncol2=10; w=0; offset=5; strand=D; shift=5; score=0.560875; -----wwAAATAAww- ; cor=; Ncor= a 0 0 0 0 0 188 179 411 411 411 0 411 411 163 163 0 c 0 0 0 0 0 50 49 0 0 0 0 0 0 60 61 0 g 0 0 0 0 0 47 77 0 0 0 0 0 0 45 54 0 t 0 0 0 0 0 126 106 0 0 0 411 0 0 143 133 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -wwTTAAAAATAAwww ; Alignment reference a 0 42 40 8 5 106 104 102 106 98 5 102 85 60 47 48 c 0 15 16 4 2 0 1 2 0 1 2 1 6 9 13 10 g 0 17 14 2 3 1 1 1 0 7 5 3 1 9 9 12 t 0 38 42 98 102 5 6 7 6 6 100 6 20 34 43 42

positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -wwTTAAAAATAAwww ; cor=; Ncor= a 0 42 40 8 5 106 104 102 106 98 5 102 85 60 47 48 c 0 15 16 4 2 0 1 2 0 1 2 1 6 9 13 10 g 0 17 14 2 3 1 1 1 0 7 5 3 1 9 9 12 t 0 38 42 98 102 5 6 7 6 6 100 6 20 34 43 42

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=2/4; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.795568; wwTTAAAAAATAaAww ; cor=; Ncor= a 35 31 7 3 81 81 83 86 84 83 7 79 58 62 40 43 c 11 12 2 3 2 2 1 0 2 1 1 3 6 6 7 11 g 13 12 1 4 1 1 3 1 1 2 1 1 8 10 12 8 t 32 36 81 81 7 7 4 4 4 5 82 8 19 13 32 29

positions_6nt_m3_shift1 (positions_6nt_m3)
; positions_6nt_m1 versus positions_6nt_m3; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 0.7539; -wwTTAAAAATTww-- ; cor=; Ncor= a 0 74 65 8 7 186 179 186 173 174 17 22 87 78 0 0 c 0 26 15 3 2 0 4 1 3 4 3 1 22 13 0 0 g 0 26 31 8 1 0 4 3 3 9 12 9 15 22 0 0 t 0 72 87 179 188 12 11 8 19 11 166 166 74 85 0 0

oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)
; positions_6nt_m1 versus oligos_6nt_mkv3_m4; m=4/4; ncol2=10; w=0; offset=4; strand=D; shift=5; score=0.606468; -----wwAAATAAww- ; cor=; Ncor= a 0 0 0 0 0 188 179 411 411 411 0 411 411 163 163 0 c 0 0 0 0 0 50 49 0 0 0 0 0 0 60 61 0 g 0 0 0 0 0 47 77 0 0 0 0 0 0 45 54 0 t 0 0 0 0 0 126 106 0 0 0 411 0 0 143 133 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 5 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=21; shift=1; ncol=22; -kwyGATTCCATTCGATkmydw ; Alignment reference a 0 125 607 45 218 1683 47 43 30 34 1728 23 17 66 262 1707 56 105 979 34 810 535 c 0 55 17 976 246 7 21 5 1675 1694 8 33 31 1476 194 12 30 30 715 737 8 440 g 0 555 47 63 1311 49 236 9 54 17 70 7 25 20 1285 54 188 904 63 77 520 52 t 0 1092 1156 743 52 88 1523 1770 68 82 21 1764 1754 265 86 54 1553 788 70 979 489 800

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=21; w=0; offset=0; strand=D; shift=1; score= 1; -kwyGATTCCATTCGATkmydw ; cor=; Ncor= a 0 125 607 45 218 1683 47 43 30 34 1728 23 17 66 262 1707 56 105 979 34 810 535 c 0 55 17 976 246 7 21 5 1675 1694 8 33 31 1476 194 12 30 30 715 737 8 440 g 0 555 47 63 1311 49 236 9 54 17 70 7 25 20 1285 54 188 904 63 77 520 52 t 0 1092 1156 743 52 88 1523 1770 68 82 21 1764 1754 265 86 54 1553 788 70 979 489 800

oligos_7nt_mkv4_m2_rc_shift1 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2_rc; m=2/4; ncol2=18; w=0; offset=0; strand=R; shift=1; score=0.849484; -kwyGATTCCATTCGATkm--- ; cor=; Ncor= a 0 161 895 47 170 1886 54 44 36 30 1889 14 21 72 282 1872 59 113 840 0 0 0 c 0 68 23 832 238 7 23 16 1846 1881 33 50 33 1620 259 12 38 34 1002 0 0 0 g 0 809 65 69 1538 57 201 11 75 19 56 7 40 45 1402 58 276 752 71 0 0 0 t 0 984 1039 1074 76 72 1744 1951 65 92 44 1951 1928 285 79 80 1649 1123 109 0 0 0

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=3/4; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.810334; akwygATTCCATTCgATkm--- ; cor=; Ncor= a 1345 189 853 45 212 2252 73 46 44 52 2274 45 21 78 314 2244 105 120 932 0 0 0 c 400 72 18 1356 577 7 24 13 2212 2039 30 62 28 2011 572 15 71 39 1232 0 0 0 g 99 764 64 65 1537 74 227 11 112 214 73 14 41 40 1425 82 253 836 100 0 0 0 t 581 1400 1490 959 99 92 2101 2355 57 120 48 2304 2335 296 114 84 1996 1430 161 0 0 0

oligos_7nt_mkv4_m5_rc_shift9 (oligos_7nt_mkv4_m5_rc)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5_rc; m=4/4; ncol2=13; w=0; offset=8; strand=R; shift=9; score=0.499388; ---------CATTCGAkTCCAT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 21 542 19 2 7 11 559 19 24 15 5 540 18 c 0 0 0 0 0 0 0 0 0 534 26 17 5 586 12 2 3 4 584 584 21 24 g 0 0 0 0 0 0 0 0 0 16 26 4 13 13 604 32 291 7 12 5 48 12 t 0 0 0 0 0 0 0 0 0 57 34 588 608 22 1 35 315 593 17 34 19 574

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift7 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift7 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=13; shift=7; ncol=20; -------ATGGAmTCGAATG ; Alignment reference a 0 0 0 0 0 0 0 574 19 34 17 593 315 35 1 22 608 588 34 57 c 0 0 0 0 0 0 0 12 48 5 12 7 291 32 604 13 13 4 26 16 g 0 0 0 0 0 0 0 24 21 584 584 4 3 2 12 586 5 17 26 534 t 0 0 0 0 0 0 0 18 540 5 15 24 19 559 11 7 2 19 542 21

oligos_7nt_mkv4_m5_shift7 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=7; score= 1; -------ATGGAmTCGAATG ; cor=; Ncor= a 0 0 0 0 0 0 0 574 19 34 17 593 315 35 1 22 608 588 34 57 c 0 0 0 0 0 0 0 12 48 5 12 7 291 32 604 13 13 4 26 16 g 0 0 0 0 0 0 0 24 21 584 584 4 3 2 12 586 5 17 26 534 t 0 0 0 0 0 0 0 18 540 5 15 24 19 559 11 7 2 19 542 21

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m1_rc; m=2/4; ncol2=19; w=-7; offset=-7; strand=R; shift=0; score=0.537861; kmATcGAATGGAATcrwmt- ; cor=; Ncor= a 161 1430 1996 84 114 296 2335 2304 48 120 57 2355 2101 92 99 959 1490 1400 581 0 c 100 836 253 82 1425 40 41 14 73 214 112 11 227 74 1537 65 64 764 99 0 g 1232 39 71 15 572 2011 28 62 30 2039 2212 13 24 7 577 1356 18 72 400 0 t 932 120 105 2244 314 78 21 45 2274 52 44 46 73 2252 212 45 853 189 1345 0

oligos_6nt_mkv3_m1_rc_shift7 (oligos_6nt_mkv3_m1_rc)
; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1_rc; m=3/4; ncol2=21; w=0; offset=0; strand=R; shift=7; score=0.499388; -------whrkmATCGAATG ; cor=; Ncor= a 0 0 0 0 0 0 0 800 489 979 70 788 1553 54 86 265 1754 1764 21 82 c 0 0 0 0 0 0 0 52 520 77 63 904 188 54 1285 20 25 7 70 17 g 0 0 0 0 0 0 0 440 8 737 715 30 30 12 194 1476 31 33 8 1694 t 0 0 0 0 0 0 0 535 810 34 979 105 56 1707 262 66 17 23 1728 34

oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=4/4; ncol2=18; w=-7; offset=-7; strand=D; shift=0; score=0.475577; kmATCGAATGGAATCrwm-- ; cor=; Ncor= a 109 1123 1649 80 79 285 1928 1951 44 92 65 1951 1744 72 76 1074 1039 984 0 0 c 71 752 276 58 1402 45 40 7 56 19 75 11 201 57 1538 69 65 809 0 0 g 1002 34 38 12 259 1620 33 50 33 1881 1846 16 23 7 238 832 23 68 0 0 t 840 113 59 1872 282 72 21 14 1889 30 36 44 54 1886 170 47 895 161 0 0

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=11; shift=0; ncol=11; kwyGATGATkm ; Alignment reference a 123 332 182 0 949 4 0 947 1 114 285 c 38 41 347 0 0 4 0 1 5 20 503 g 254 36 15 957 1 1 957 6 15 244 98 t 542 548 413 0 7 948 0 3 936 579 71

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; kwyGATGATkm ; cor=; Ncor= a 123 332 182 0 949 4 0 947 1 114 285 c 38 41 347 0 0 4 0 1 5 20 503 g 254 36 15 957 1 1 957 6 15 244 98 t 542 548 413 0 7 948 0 3 936 579 71

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=19; shift=1; ncol=20; -akwygATTCCATTCgATkm ; Alignment reference a 0 1345 189 853 45 212 2252 73 46 44 52 2274 45 21 78 314 2244 105 120 932 c 0 400 72 18 1356 577 7 24 13 2212 2039 30 62 28 2011 572 15 71 39 1232 g 0 99 764 64 65 1537 74 227 11 112 214 73 14 41 40 1425 82 253 836 100 t 0 581 1400 1490 959 99 92 2101 2355 57 120 48 2304 2335 296 114 84 1996 1430 161

oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -akwygATTCCATTCgATkm ; cor=; Ncor= a 0 1345 189 853 45 212 2252 73 46 44 52 2274 45 21 78 314 2244 105 120 932 c 0 400 72 18 1356 577 7 24 13 2212 2039 30 62 28 2011 572 15 71 39 1232 g 0 99 764 64 65 1537 74 227 11 112 214 73 14 41 40 1425 82 253 836 100 t 0 581 1400 1490 959 99 92 2101 2355 57 120 48 2304 2335 296 114 84 1996 1430 161

oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2_rc; m=2/4; ncol2=18; w=0; offset=1; strand=R; shift=2; score=0.938528; --kwyGATTCCATTCGATkm ; cor=; Ncor= a 0 0 161 895 47 170 1886 54 44 36 30 1889 14 21 72 282 1872 59 113 840 c 0 0 68 23 832 238 7 23 16 1846 1881 33 50 33 1620 259 12 38 34 1002 g 0 0 809 65 69 1538 57 201 11 75 19 56 7 40 45 1402 58 276 752 71 t 0 0 984 1039 1074 76 72 1744 1951 65 92 44 1951 1928 285 79 80 1649 1123 109

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=21; w=0; offset=1; strand=D; shift=2; score=0.810334; --kwyGATTCCATTCGATkm ; cor=; Ncor= a 0 0 125 607 45 218 1683 47 43 30 34 1728 23 17 66 262 1707 56 105 979 c 0 0 55 17 976 246 7 21 5 1675 1694 8 33 31 1476 194 12 30 30 715 g 0 0 555 47 63 1311 49 236 9 54 17 70 7 25 20 1285 54 188 904 63 t 0 0 1092 1156 743 52 88 1523 1770 68 82 21 1764 1754 265 86 54 1553 788 70

oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5_rc; m=4/4; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.537861; CATTCGAkTCCAT------- ; cor=; Ncor= a 21 542 19 2 7 11 559 19 24 15 5 540 18 0 0 0 0 0 0 0 c 534 26 17 5 586 12 2 3 4 584 584 21 24 0 0 0 0 0 0 0 g 16 26 4 13 13 604 32 291 7 12 5 48 12 0 0 0 0 0 0 0 t 57 34 588 608 22 1 35 315 593 17 34 19 574 0 0 0 0 0 0 0

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=13; shift=0; ncol=13; kAtAGATAGATAk ; Alignment reference a 127 551 142 699 8 731 11 732 19 735 9 574 136 c 53 57 58 1 47 7 15 0 74 7 15 42 76 g 273 56 74 8 627 11 14 13 598 8 41 85 288 t 300 89 479 45 71 4 713 8 62 3 688 52 253
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; kAtAGATAGATAk ; cor=; Ncor= a 127 551 142 699 8 731 11 732 19 735 9 574 136 c 53 57 58 1 47 7 15 0 74 7 15 42 76 g 273 56 74 8 627 11 14 13 598 8 41 85 288 t 300 89 479 45 71 4 713 8 62 3 688 52 253
oligos_7nt_mkv4_m3_rc_shift2 (oligos_7nt_mkv4_m3_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m3_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.833093; --wAGATAGATAk ; cor=; Ncor= a 0 0 148 405 0 492 12 510 1 489 15 399 117 c 0 0 32 10 0 14 20 0 0 14 15 11 48 g 0 0 49 15 529 12 14 10 523 16 43 74 193 t 0 0 300 99 0 11 483 9 5 10 456 45 171
oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2; m=3/3; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.519059; ---awATACATAt ; cor=; Ncor= a 0 0 0 441 213 579 0 841 0 716 0 814 186 c 0 0 0 140 73 59 0 0 841 0 0 27 108 g 0 0 0 65 110 134 0 0 0 113 0 0 111 t 0 0 0 195 445 69 841 0 0 12 841 0 436

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; wwTTAAAAATTww ; Alignment reference a 74 65 8 7 186 179 186 173 174 17 22 87 78 c 26 15 3 2 0 4 1 3 4 3 1 22 13 g 26 31 8 1 0 4 3 3 9 12 9 15 22 t 72 87 179 188 12 11 8 19 11 166 166 74 85
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAATTww ; cor=; Ncor= a 74 65 8 7 186 179 186 173 174 17 22 87 78 c 26 15 3 2 0 4 1 3 4 3 1 22 13 g 26 31 8 1 0 4 3 3 9 12 9 15 22 t 72 87 179 188 12 11 8 19 11 166 166 74 85
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m3 versus positions_6nt_m1; m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 0.7539; wwTTAAAAATAAw ; cor=; Ncor= a 42 40 8 5 106 104 102 106 98 5 102 85 60 c 15 16 4 2 0 1 2 0 1 2 1 6 9 g 17 14 2 3 1 1 1 0 7 5 3 1 9 t 38 42 98 102 5 6 7 6 6 100 6 20 34
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m3 versus positions_6nt_m2; m=3/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.691136; wwTTAAAAAATAa ; cor=; Ncor= a 35 31 7 3 81 81 83 86 84 83 7 79 58 c 11 12 2 3 2 2 1 0 2 1 1 3 6 g 13 12 1 4 1 1 3 1 1 2 1 1 8 t 32 36 81 81 7 7 4 4 4 5 82 8 19

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=18; shift=3; ncol=21; ---kmATCGAATGGAATCrwm ; Alignment reference a 0 0 0 109 1123 1649 80 79 285 1928 1951 44 92 65 1951 1744 72 76 1074 1039 984 c 0 0 0 71 752 276 58 1402 45 40 7 56 19 75 11 201 57 1538 69 65 809 g 0 0 0 1002 34 38 12 259 1620 33 50 33 1881 1846 16 23 7 238 832 23 68 t 0 0 0 840 113 59 1872 282 72 21 14 1889 30 36 44 54 1886 170 47 895 161
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/4; ncol2=18; w=0; offset=0; strand=D; shift=3; score= 1; ---kmATCGAATGGAATCrwm ; cor=; Ncor= a 0 0 0 109 1123 1649 80 79 285 1928 1951 44 92 65 1951 1744 72 76 1074 1039 984 c 0 0 0 71 752 276 58 1402 45 40 7 56 19 75 11 201 57 1538 69 65 809 g 0 0 0 1002 34 38 12 259 1620 33 50 33 1881 1846 16 23 7 238 832 23 68 t 0 0 0 840 113 59 1872 282 72 21 14 1889 30 36 44 54 1886 170 47 895 161
oligos_7nt_mkv4_m1_rc_shift3 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m1_rc; m=2/4; ncol2=19; w=0; offset=0; strand=R; shift=3; score=0.938528; ---kmATcGAATGGAATcrwm ; cor=; Ncor= a 0 0 0 161 1430 1996 84 114 296 2335 2304 48 120 57 2355 2101 92 99 959 1490 1400 c 0 0 0 100 836 253 82 1425 40 41 14 73 214 112 11 227 74 1537 65 64 764 g 0 0 0 1232 39 71 15 572 2011 28 62 30 2039 2212 13 24 7 577 1356 18 72 t 0 0 0 932 120 105 2244 314 78 21 45 2274 52 44 46 73 2252 212 45 853 189
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m1_rc; m=3/4; ncol2=21; w=-3; offset=-3; strand=R; shift=0; score=0.849484; whrkmATCGAATGGAATCrwm ; cor=; Ncor= a 800 489 979 70 788 1553 54 86 265 1754 1764 21 82 68 1770 1523 88 52 743 1156 1092 c 52 520 77 63 904 188 54 1285 20 25 7 70 17 54 9 236 49 1311 63 47 555 g 440 8 737 715 30 30 12 194 1476 31 33 8 1694 1675 5 21 7 246 976 17 55 t 535 810 34 979 105 56 1707 262 66 17 23 1728 34 30 43 47 1683 218 45 607 125
oligos_7nt_mkv4_m5_shift10 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5; m=4/4; ncol2=13; w=0; offset=7; strand=D; shift=10; score=0.475577; ----------ATGGAmTCGAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 574 19 34 17 593 315 35 1 22 608 588 c 0 0 0 0 0 0 0 0 0 0 12 48 5 12 7 291 32 604 13 13 4 g 0 0 0 0 0 0 0 0 0 0 24 21 584 584 4 3 2 12 586 5 17 t 0 0 0 0 0 0 0 0 0 0 18 540 5 15 24 19 559 11 7 2 19

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; -----wwAAATAAww ; Alignment reference a 0 0 0 0 0 188 179 411 411 411 0 411 411 163 163 c 0 0 0 0 0 50 49 0 0 0 0 0 0 60 61 g 0 0 0 0 0 47 77 0 0 0 0 0 0 45 54 t 0 0 0 0 0 126 106 0 0 0 411 0 0 143 133
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; -----wwAAATAAww ; cor=; Ncor= a 0 0 0 0 0 188 179 411 411 411 0 411 411 163 163 c 0 0 0 0 0 50 49 0 0 0 0 0 0 60 61 g 0 0 0 0 0 47 77 0 0 0 0 0 0 45 54 t 0 0 0 0 0 126 106 0 0 0 411 0 0 143 133
positions_6nt_m1_shift1 (positions_6nt_m1)				; oligos_6nt_mkv3_m4 versus positions_6nt_m1; m=2/3; ncol2=15; w=-4; offset=-4; strand=D; shift=1; score=0.606468; -wwTTAAAAATAAww ; cor=; Ncor= a 0 42 40 8 5 106 104 102 106 98 5 102 85 60 47 c 0 15 16 4 2 0 1 2 0 1 2 1 6 9 13 g 0 17 14 2 3 1 1 1 0 7 5 3 1 9 9 t 0 38 42 98 102 5 6 7 6 6 100 6 20 34 43
positions_6nt_m2_shift0 (positions_6nt_m2)				; oligos_6nt_mkv3_m4 versus positions_6nt_m2; m=3/3; ncol2=16; w=-5; offset=-5; strand=D; shift=0; score=0.560875; wwTTAAAAAATAaAw ; cor=; Ncor= a 35 31 7 3 81 81 83 86 84 83 7 79 58 62 40 c 11 12 2 3 2 2 1 0 2 1 1 3 6 6 7 g 13 12 1 4 1 1 3 1 1 2 1 1 8 10 12 t 32 36 81 81 7 7 4 4 4 5 82 8 19 13 32

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; wwTTAAAAAATAaAww ; Alignment reference a 35 31 7 3 81 81 83 86 84 83 7 79 58 62 40 43 c 11 12 2 3 2 2 1 0 2 1 1 3 6 6 7 11 g 13 12 1 4 1 1 3 1 1 2 1 1 8 10 12 8 t 32 36 81 81 7 7 4 4 4 5 82 8 19 13 32 29
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; wwTTAAAAAATAaAww ; cor=; Ncor= a 35 31 7 3 81 81 83 86 84 83 7 79 58 62 40 43 c 11 12 2 3 2 2 1 0 2 1 1 3 6 6 7 11 g 13 12 1 4 1 1 3 1 1 2 1 1 8 10 12 8 t 32 36 81 81 7 7 4 4 4 5 82 8 19 13 32 29
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=2/4; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.795568; -wwTTAAAAATAAwww ; cor=; Ncor= a 0 42 40 8 5 106 104 102 106 98 5 102 85 60 47 48 c 0 15 16 4 2 0 1 2 0 1 2 1 6 9 13 10 g 0 17 14 2 3 1 1 1 0 7 5 3 1 9 9 12 t 0 38 42 98 102 5 6 7 6 6 100 6 20 34 43 42
positions_6nt_m3_shift0 (positions_6nt_m3)				; positions_6nt_m2 versus positions_6nt_m3; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.691136; wwTTAAAAATTww--- ; cor=; Ncor= a 74 65 8 7 186 179 186 173 174 17 22 87 78 0 0 0 c 26 15 3 2 0 4 1 3 4 3 1 22 13 0 0 0 g 26 31 8 1 0 4 3 3 9 12 9 15 22 0 0 0 t 72 87 179 188 12 11 8 19 11 166 166 74 85 0 0 0
oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)				; positions_6nt_m2 versus oligos_6nt_mkv3_m4; m=4/4; ncol2=10; w=0; offset=5; strand=D; shift=5; score=0.560875; -----wwAAATAAww- ; cor=; Ncor= a 0 0 0 0 0 188 179 411 411 411 0 411 411 163 163 0 c 0 0 0 0 0 50 49 0 0 0 0 0 0 60 61 0 g 0 0 0 0 0 47 77 0 0 0 0 0 0 45 54 0 t 0 0 0 0 0 126 106 0 0 0 411 0 0 143 133 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -wwTTAAAAATAAwww ; Alignment reference a 0 42 40 8 5 106 104 102 106 98 5 102 85 60 47 48 c 0 15 16 4 2 0 1 2 0 1 2 1 6 9 13 10 g 0 17 14 2 3 1 1 1 0 7 5 3 1 9 9 12 t 0 38 42 98 102 5 6 7 6 6 100 6 20 34 43 42
positions_6nt_m1_shift1 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -wwTTAAAAATAAwww ; cor=; Ncor= a 0 42 40 8 5 106 104 102 106 98 5 102 85 60 47 48 c 0 15 16 4 2 0 1 2 0 1 2 1 6 9 13 10 g 0 17 14 2 3 1 1 1 0 7 5 3 1 9 9 12 t 0 38 42 98 102 5 6 7 6 6 100 6 20 34 43 42
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=2/4; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.795568; wwTTAAAAAATAaAww ; cor=; Ncor= a 35 31 7 3 81 81 83 86 84 83 7 79 58 62 40 43 c 11 12 2 3 2 2 1 0 2 1 1 3 6 6 7 11 g 13 12 1 4 1 1 3 1 1 2 1 1 8 10 12 8 t 32 36 81 81 7 7 4 4 4 5 82 8 19 13 32 29
positions_6nt_m3_shift1 (positions_6nt_m3)				; positions_6nt_m1 versus positions_6nt_m3; m=3/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 0.7539; -wwTTAAAAATTww-- ; cor=; Ncor= a 0 74 65 8 7 186 179 186 173 174 17 22 87 78 0 0 c 0 26 15 3 2 0 4 1 3 4 3 1 22 13 0 0 g 0 26 31 8 1 0 4 3 3 9 12 9 15 22 0 0 t 0 72 87 179 188 12 11 8 19 11 166 166 74 85 0 0
oligos_6nt_mkv3_m4_shift5 (oligos_6nt_mkv3_m4)				; positions_6nt_m1 versus oligos_6nt_mkv3_m4; m=4/4; ncol2=10; w=0; offset=4; strand=D; shift=5; score=0.606468; -----wwAAATAAww- ; cor=; Ncor= a 0 0 0 0 0 188 179 411 411 411 0 411 411 163 163 0 c 0 0 0 0 0 50 49 0 0 0 0 0 0 60 61 0 g 0 0 0 0 0 47 77 0 0 0 0 0 0 45 54 0 t 0 0 0 0 0 126 106 0 0 0 411 0 0 143 133 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=21; shift=1; ncol=22; -kwyGATTCCATTCGATkmydw ; Alignment reference a 0 125 607 45 218 1683 47 43 30 34 1728 23 17 66 262 1707 56 105 979 34 810 535 c 0 55 17 976 246 7 21 5 1675 1694 8 33 31 1476 194 12 30 30 715 737 8 440 g 0 555 47 63 1311 49 236 9 54 17 70 7 25 20 1285 54 188 904 63 77 520 52 t 0 1092 1156 743 52 88 1523 1770 68 82 21 1764 1754 265 86 54 1553 788 70 979 489 800
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=21; w=0; offset=0; strand=D; shift=1; score= 1; -kwyGATTCCATTCGATkmydw ; cor=; Ncor= a 0 125 607 45 218 1683 47 43 30 34 1728 23 17 66 262 1707 56 105 979 34 810 535 c 0 55 17 976 246 7 21 5 1675 1694 8 33 31 1476 194 12 30 30 715 737 8 440 g 0 555 47 63 1311 49 236 9 54 17 70 7 25 20 1285 54 188 904 63 77 520 52 t 0 1092 1156 743 52 88 1523 1770 68 82 21 1764 1754 265 86 54 1553 788 70 979 489 800
oligos_7nt_mkv4_m2_rc_shift1 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2_rc; m=2/4; ncol2=18; w=0; offset=0; strand=R; shift=1; score=0.849484; -kwyGATTCCATTCGATkm--- ; cor=; Ncor= a 0 161 895 47 170 1886 54 44 36 30 1889 14 21 72 282 1872 59 113 840 0 0 0 c 0 68 23 832 238 7 23 16 1846 1881 33 50 33 1620 259 12 38 34 1002 0 0 0 g 0 809 65 69 1538 57 201 11 75 19 56 7 40 45 1402 58 276 752 71 0 0 0 t 0 984 1039 1074 76 72 1744 1951 65 92 44 1951 1928 285 79 80 1649 1123 109 0 0 0
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=3/4; ncol2=19; w=-1; offset=-1; strand=D; shift=0; score=0.810334; akwygATTCCATTCgATkm--- ; cor=; Ncor= a 1345 189 853 45 212 2252 73 46 44 52 2274 45 21 78 314 2244 105 120 932 0 0 0 c 400 72 18 1356 577 7 24 13 2212 2039 30 62 28 2011 572 15 71 39 1232 0 0 0 g 99 764 64 65 1537 74 227 11 112 214 73 14 41 40 1425 82 253 836 100 0 0 0 t 581 1400 1490 959 99 92 2101 2355 57 120 48 2304 2335 296 114 84 1996 1430 161 0 0 0
oligos_7nt_mkv4_m5_rc_shift9 (oligos_7nt_mkv4_m5_rc)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5_rc; m=4/4; ncol2=13; w=0; offset=8; strand=R; shift=9; score=0.499388; ---------CATTCGAkTCCAT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 21 542 19 2 7 11 559 19 24 15 5 540 18 c 0 0 0 0 0 0 0 0 0 534 26 17 5 586 12 2 3 4 584 584 21 24 g 0 0 0 0 0 0 0 0 0 16 26 4 13 13 604 32 291 7 12 5 48 12 t 0 0 0 0 0 0 0 0 0 57 34 588 608 22 1 35 315 593 17 34 19 574

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift7 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=13; shift=7; ncol=20; -------ATGGAmTCGAATG ; Alignment reference a 0 0 0 0 0 0 0 574 19 34 17 593 315 35 1 22 608 588 34 57 c 0 0 0 0 0 0 0 12 48 5 12 7 291 32 604 13 13 4 26 16 g 0 0 0 0 0 0 0 24 21 584 584 4 3 2 12 586 5 17 26 534 t 0 0 0 0 0 0 0 18 540 5 15 24 19 559 11 7 2 19 542 21
oligos_7nt_mkv4_m5_shift7 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=7; score= 1; -------ATGGAmTCGAATG ; cor=; Ncor= a 0 0 0 0 0 0 0 574 19 34 17 593 315 35 1 22 608 588 34 57 c 0 0 0 0 0 0 0 12 48 5 12 7 291 32 604 13 13 4 26 16 g 0 0 0 0 0 0 0 24 21 584 584 4 3 2 12 586 5 17 26 534 t 0 0 0 0 0 0 0 18 540 5 15 24 19 559 11 7 2 19 542 21
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m1_rc; m=2/4; ncol2=19; w=-7; offset=-7; strand=R; shift=0; score=0.537861; kmATcGAATGGAATcrwmt- ; cor=; Ncor= a 161 1430 1996 84 114 296 2335 2304 48 120 57 2355 2101 92 99 959 1490 1400 581 0 c 100 836 253 82 1425 40 41 14 73 214 112 11 227 74 1537 65 64 764 99 0 g 1232 39 71 15 572 2011 28 62 30 2039 2212 13 24 7 577 1356 18 72 400 0 t 932 120 105 2244 314 78 21 45 2274 52 44 46 73 2252 212 45 853 189 1345 0
oligos_6nt_mkv3_m1_rc_shift7 (oligos_6nt_mkv3_m1_rc)				; oligos_7nt_mkv4_m5 versus oligos_6nt_mkv3_m1_rc; m=3/4; ncol2=21; w=0; offset=0; strand=R; shift=7; score=0.499388; -------whrkmATCGAATG ; cor=; Ncor= a 0 0 0 0 0 0 0 800 489 979 70 788 1553 54 86 265 1754 1764 21 82 c 0 0 0 0 0 0 0 52 520 77 63 904 188 54 1285 20 25 7 70 17 g 0 0 0 0 0 0 0 440 8 737 715 30 30 12 194 1476 31 33 8 1694 t 0 0 0 0 0 0 0 535 810 34 979 105 56 1707 262 66 17 23 1728 34
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m2; m=4/4; ncol2=18; w=-7; offset=-7; strand=D; shift=0; score=0.475577; kmATCGAATGGAATCrwm-- ; cor=; Ncor= a 109 1123 1649 80 79 285 1928 1951 44 92 65 1951 1744 72 76 1074 1039 984 0 0 c 71 752 276 58 1402 45 40 7 56 19 75 11 201 57 1538 69 65 809 0 0 g 1002 34 38 12 259 1620 33 50 33 1881 1846 16 23 7 238 832 23 68 0 0 t 840 113 59 1872 282 72 21 14 1889 30 36 44 54 1886 170 47 895 161 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=19; shift=1; ncol=20; -akwygATTCCATTCgATkm ; Alignment reference a 0 1345 189 853 45 212 2252 73 46 44 52 2274 45 21 78 314 2244 105 120 932 c 0 400 72 18 1356 577 7 24 13 2212 2039 30 62 28 2011 572 15 71 39 1232 g 0 99 764 64 65 1537 74 227 11 112 214 73 14 41 40 1425 82 253 836 100 t 0 581 1400 1490 959 99 92 2101 2355 57 120 48 2304 2335 296 114 84 1996 1430 161
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -akwygATTCCATTCgATkm ; cor=; Ncor= a 0 1345 189 853 45 212 2252 73 46 44 52 2274 45 21 78 314 2244 105 120 932 c 0 400 72 18 1356 577 7 24 13 2212 2039 30 62 28 2011 572 15 71 39 1232 g 0 99 764 64 65 1537 74 227 11 112 214 73 14 41 40 1425 82 253 836 100 t 0 581 1400 1490 959 99 92 2101 2355 57 120 48 2304 2335 296 114 84 1996 1430 161
oligos_7nt_mkv4_m2_rc_shift2 (oligos_7nt_mkv4_m2_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2_rc; m=2/4; ncol2=18; w=0; offset=1; strand=R; shift=2; score=0.938528; --kwyGATTCCATTCGATkm ; cor=; Ncor= a 0 0 161 895 47 170 1886 54 44 36 30 1889 14 21 72 282 1872 59 113 840 c 0 0 68 23 832 238 7 23 16 1846 1881 33 50 33 1620 259 12 38 34 1002 g 0 0 809 65 69 1538 57 201 11 75 19 56 7 40 45 1402 58 276 752 71 t 0 0 984 1039 1074 76 72 1744 1951 65 92 44 1951 1928 285 79 80 1649 1123 109
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=3/4; ncol2=21; w=0; offset=1; strand=D; shift=2; score=0.810334; --kwyGATTCCATTCGATkm ; cor=; Ncor= a 0 0 125 607 45 218 1683 47 43 30 34 1728 23 17 66 262 1707 56 105 979 c 0 0 55 17 976 246 7 21 5 1675 1694 8 33 31 1476 194 12 30 30 715 g 0 0 555 47 63 1311 49 236 9 54 17 70 7 25 20 1285 54 188 904 63 t 0 0 1092 1156 743 52 88 1523 1770 68 82 21 1764 1754 265 86 54 1553 788 70
oligos_7nt_mkv4_m5_rc_shift0 (oligos_7nt_mkv4_m5_rc)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5_rc; m=4/4; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.537861; CATTCGAkTCCAT------- ; cor=; Ncor= a 21 542 19 2 7 11 559 19 24 15 5 540 18 0 0 0 0 0 0 0 c 534 26 17 5 586 12 2 3 4 584 584 21 24 0 0 0 0 0 0 0 g 16 26 4 13 13 604 32 291 7 12 5 48 12 0 0 0 0 0 0 0 t 57 34 588 608 22 1 35 315 593 17 34 19 574 0 0 0 0 0 0 0