One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/09/peak-motifs.2026-04-09.085746_2026-04-09.085746_eHLTRu/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/2026/04/09/peak-motifs.2026-04-09.085746_2026-04-09.085746_eHLTRu/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m7_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=10; shift=2; ncol=12; --gsCGGTGGcg ; Alignment reference a 0 0 16 27 0 0 0 0 0 0 28 11 c 0 0 19 34 116 0 0 0 0 0 45 26 g 0 0 63 46 0 116 116 0 116 116 18 58 t 0 0 18 9 0 0 0 116 0 0 25 21

oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --gsCGGTGGcg ; cor=; Ncor= a 0 0 16 27 0 0 0 0 0 0 28 11 c 0 0 19 34 116 0 0 0 0 0 45 26 g 0 0 63 46 0 116 116 0 116 116 18 58 t 0 0 18 9 0 0 0 116 0 0 25 21

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m2_rc; m=2/6; ncol2=11; w=-1; offset=-1; strand=R; shift=1; score=0.687419; -cgGCGGCGGcg ; cor=; Ncor= a 0 126 90 34 43 20 39 26 19 57 126 109 c 0 459 235 56 866 39 54 864 33 92 483 217 g 0 229 526 815 13 876 829 18 888 759 186 522 t 0 138 101 47 30 17 30 44 12 44 157 104

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m1; m=3/6; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.681045; -csGCGGCGGcg ; cor=; Ncor= a 0 100 64 34 15 6 35 12 12 57 96 87 c 0 408 209 52 768 30 53 756 33 92 410 186 g 0 188 456 676 9 765 691 13 757 614 166 463 t 0 111 78 45 15 6 28 26 5 44 135 71

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m7 versus positions_6nt_m1_rc; m=4/6; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.625133; gcGGCGGCGGcg ; cor=; Ncor= a 113 92 15 17 29 16 25 18 18 34 87 70 c 125 314 38 28 561 7 31 562 12 56 307 130 g 284 103 536 548 4 585 541 7 576 497 121 361 t 93 106 26 22 21 7 18 28 9 28 100 54

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_6nt_mkv3_m7 versus positions_6nt_m2; m=5/6; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.552591; -cgsCGGCGGCG ; cor=; Ncor= a 0 57 72 102 21 2 33 10 6 42 3 25 c 0 328 142 172 520 20 44 580 12 57 575 23 g 0 151 337 225 34 579 501 4 589 481 11 553 t 0 72 57 109 33 7 30 14 1 28 19 7

positions_6nt_m4_shift1 (positions_6nt_m4)
; oligos_6nt_mkv3_m7 versus positions_6nt_m4; m=6/6; ncol2=14; w=-1; offset=-1; strand=D; shift=1; score=0.528087; -cgGCGGCGGCg ; cor=; Ncor= a 0 48 48 11 11 14 8 10 9 7 15 39 c 0 178 83 19 329 12 16 335 6 19 309 52 g 0 84 181 313 6 325 330 2 337 324 23 185 t 0 50 48 17 14 9 6 13 8 10 13 84

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift3 ; 8 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; ---cgCCGCCGCcg ; Alignment reference a 0 0 0 104 157 44 12 44 30 17 30 47 101 138 c 0 0 0 522 186 759 888 18 829 876 13 815 526 229 g 0 0 0 217 483 92 33 864 54 39 866 56 235 459 t 0 0 0 109 126 57 19 26 39 20 43 34 90 126

oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---cgCCGCCGCcg ; cor=; Ncor= a 0 0 0 104 157 44 12 44 30 17 30 47 101 138 c 0 0 0 522 186 759 888 18 829 876 13 815 526 229 g 0 0 0 217 483 92 33 864 54 39 866 56 235 459 t 0 0 0 109 126 57 19 26 39 20 43 34 90 126

oligos_6nt_mkv3_m1_rc_shift3 (oligos_6nt_mkv3_m1_rc)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m1_rc; m=2/7; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.99892; ---cgCCGCCGCsg ; cor=; Ncor= a 0 0 0 71 135 44 5 26 28 6 15 45 78 111 c 0 0 0 463 166 614 757 13 691 765 9 676 456 188 g 0 0 0 186 410 92 33 756 53 30 768 52 209 408 t 0 0 0 87 96 57 12 12 35 6 15 34 64 100

oligos_6nt_mkv3_m10_rc_shift3 (oligos_6nt_mkv3_m10_rc)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m10_rc; m=3/7; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.941385; ---sgyCGCCGCsg ; cor=; Ncor= a 0 0 0 52 95 44 5 11 23 1 6 20 64 91 c 0 0 0 373 154 185 641 13 573 635 4 548 368 130 g 0 0 0 167 327 92 11 630 25 20 646 54 166 351 t 0 0 0 67 83 338 2 5 38 3 3 37 61 87

positions_6nt_m1_shift3 (positions_6nt_m1)
; oligos_6nt_mkv3_m2 versus positions_6nt_m1; m=4/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.902416; ---cgCCGCCGCCg ; cor=; Ncor= a 0 0 0 54 100 28 9 28 18 7 21 22 26 106 c 0 0 0 361 121 497 576 7 541 585 4 548 536 103 g 0 0 0 130 307 56 12 562 31 7 561 28 38 314 t 0 0 0 70 87 34 18 18 25 16 29 17 15 92

positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)
; oligos_6nt_mkv3_m2 versus positions_6nt_m2_rc; m=5/7; ncol2=13; w=-2; offset=-2; strand=R; shift=1; score=0.77504; -ssCGCCGCCGscg ; cor=; Ncor= a 0 92 88 7 19 28 1 14 30 7 33 109 57 72 c 0 154 241 553 11 481 589 4 501 579 34 225 337 151 g 0 301 154 23 575 57 12 580 44 20 520 172 142 328 t 0 61 125 25 3 42 6 10 33 2 21 102 72 57

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; oligos_6nt_mkv3_m2 versus positions_6nt_m4_rc; m=6/7; ncol2=14; w=-3; offset=-3; strand=R; shift=0; score=0.769003; csCcGCCGCCGCcg ; cor=; Ncor= a 49 51 19 84 13 10 8 13 6 9 14 17 48 50 c 173 96 271 185 23 324 337 2 330 325 6 313 181 84 g 87 171 39 52 309 19 6 335 16 12 329 19 83 178 t 51 42 31 39 15 7 9 10 8 14 11 11 48 48

oligos_6nt_mkv3_m7_rc_shift3 (oligos_6nt_mkv3_m7_rc)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m7_rc; m=7/7; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.687419; ---cgCCACCGsc- ; cor=; Ncor= a 0 0 0 21 25 0 0 116 0 0 0 9 18 0 c 0 0 0 58 18 116 116 0 116 116 0 46 63 0 g 0 0 0 26 45 0 0 0 0 0 116 34 19 0 t 0 0 0 11 28 0 0 0 0 0 0 27 16 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; sgTGTACAcs ; Alignment reference a 34 37 3 18 0 188 2 158 41 41 c 54 38 18 7 0 0 166 10 73 60 g 59 73 10 159 0 0 7 17 39 55 t 41 40 157 4 188 0 13 3 35 32

positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; sgTGTACAcs ; cor=; Ncor= a 34 37 3 18 0 188 2 158 41 41 c 54 38 18 7 0 0 166 10 73 60 g 59 73 10 159 0 0 7 17 39 55 t 41 40 157 4 188 0 13 3 35 32

positions_6nt_m7_rc_shift0 (positions_6nt_m7_rc)
; positions_6nt_m3 versus positions_6nt_m7_rc; m=2/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.748315; ssTGCACAvm ; cor=; Ncor= a 19 16 0 1 0 94 0 94 32 25 c 27 35 0 0 90 0 94 0 24 32 g 26 25 0 93 0 0 0 0 25 22 t 22 18 94 0 4 0 0 0 13 15

One-to-n matrix alignment; reference matrix: positions_6nt_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m6_shift0 (positions_6nt_m6)
; positions_6nt_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; wrTTcTATrt ; Alignment reference a 35 30 2 23 22 0 98 1 32 20 c 14 17 1 2 63 0 0 4 18 21 g 18 36 2 0 7 0 0 0 30 17 t 31 15 93 73 6 98 0 93 18 40

positions_6nt_m6_shift0 (positions_6nt_m6)
; positions_6nt_m6 versus positions_6nt_m6; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wrTTcTATrt ; cor=; Ncor= a 35 30 2 23 22 0 98 1 32 20 c 14 17 1 2 63 0 0 4 18 21 g 18 36 2 0 7 0 0 0 30 17 t 31 15 93 73 6 98 0 93 18 40

One-to-n matrix alignment; reference matrix: positions_6nt_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m8_shift0 (positions_6nt_m8)
; positions_6nt_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; ddTTTATTwt ; Alignment reference a 34 41 9 30 5 133 3 19 49 31 c 15 22 8 2 0 0 4 3 20 25 g 36 37 3 7 0 1 2 4 25 27 t 49 34 114 95 129 0 125 108 40 51

positions_6nt_m8_shift0 (positions_6nt_m8)
; positions_6nt_m8 versus positions_6nt_m8; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; ddTTTATTwt ; cor=; Ncor= a 34 41 9 30 5 133 3 19 49 31 c 15 22 8 2 0 0 4 3 20 25 g 36 37 3 7 0 1 2 4 25 27 t 49 34 114 95 129 0 125 108 40 51

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; cgCCGCCGCCgc ; Alignment reference a 54 100 28 9 28 18 7 21 22 26 106 93 c 361 121 497 576 7 541 585 4 548 536 103 284 g 130 307 56 12 562 31 7 561 28 38 314 125 t 70 87 34 18 18 25 16 29 17 15 92 113

positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; cgCCGCCGCCgc ; cor=; Ncor= a 54 100 28 9 28 18 7 21 22 26 106 93 c 361 121 497 576 7 541 585 4 548 536 103 284 g 130 307 56 12 562 31 7 561 28 38 314 125 t 70 87 34 18 18 25 16 29 17 15 92 113

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; positions_6nt_m1 versus oligos_6nt_mkv3_m2; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.902416; cgCCGCCGCcg- ; cor=; Ncor= a 104 157 44 12 44 30 17 30 47 101 138 0 c 522 186 759 888 18 829 876 13 815 526 229 0 g 217 483 92 33 864 54 39 866 56 235 459 0 t 109 126 57 19 26 39 20 43 34 90 126 0

oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m1_rc; m=3/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.901784; cgCCGCCGCsg- ; cor=; Ncor= a 71 135 44 5 26 28 6 15 45 78 111 0 c 463 166 614 757 13 691 765 9 676 456 188 0 g 186 410 92 33 756 53 30 768 52 209 408 0 t 87 96 57 12 12 35 6 15 34 64 100 0

oligos_6nt_mkv3_m10_rc_shift0 (oligos_6nt_mkv3_m10_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m10_rc; m=4/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.851635; sgyCGCCGCsg- ; cor=; Ncor= a 52 95 44 5 11 23 1 6 20 64 91 0 c 373 154 185 641 13 573 635 4 548 368 130 0 g 167 327 92 11 630 25 20 646 54 166 351 0 t 67 83 338 2 5 38 3 3 37 61 87 0

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)
; positions_6nt_m1 versus positions_6nt_m4_rc; m=5/7; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.795389; csCcGCCGCCGC ; cor=; Ncor= a 49 51 19 84 13 10 8 13 6 9 14 17 c 173 96 271 185 23 324 337 2 330 325 6 313 g 87 171 39 52 309 19 6 335 16 12 329 19 t 51 42 31 39 15 7 9 10 8 14 11 11

positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)
; positions_6nt_m1 versus positions_6nt_m2_rc; m=6/7; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.748995; -ssCGCCGCCGs ; cor=; Ncor= a 0 92 88 7 19 28 1 14 30 7 33 109 c 0 154 241 553 11 481 589 4 501 579 34 225 g 0 301 154 23 575 57 12 580 44 20 520 172 t 0 61 125 25 3 42 6 10 33 2 21 102

oligos_6nt_mkv3_m7_rc_shift0 (oligos_6nt_mkv3_m7_rc)
; positions_6nt_m1 versus oligos_6nt_mkv3_m7_rc; m=7/7; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.625133; cgCCACCGsc-- ; cor=; Ncor= a 21 25 0 0 116 0 0 0 9 18 0 0 c 58 18 116 116 0 116 116 0 46 63 0 0 g 26 45 0 0 0 0 0 116 34 19 0 0 t 11 28 0 0 0 0 0 0 27 16 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 8 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=11; shift=1; ncol=12; -csGCGGCGGcg ; Alignment reference a 0 100 64 34 15 6 35 12 12 57 96 87 c 0 408 209 52 768 30 53 756 33 92 410 186 g 0 188 456 676 9 765 691 13 757 614 166 463 t 0 111 78 45 15 6 28 26 5 44 135 71

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -csGCGGCGGcg ; cor=; Ncor= a 0 100 64 34 15 6 35 12 12 57 96 87 c 0 408 209 52 768 30 53 756 33 92 410 186 g 0 188 456 676 9 765 691 13 757 614 166 463 t 0 111 78 45 15 6 28 26 5 44 135 71

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m2_rc; m=2/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.99892; -cgGCGGCGGcg ; cor=; Ncor= a 0 126 90 34 43 20 39 26 19 57 126 109 c 0 459 235 56 866 39 54 864 33 92 483 217 g 0 229 526 815 13 876 829 18 888 759 186 522 t 0 138 101 47 30 17 30 44 12 44 157 104

oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m10; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.949573; -csGCGGCGrcs ; cor=; Ncor= a 0 87 61 37 3 3 38 5 2 338 83 67 c 0 351 166 54 646 20 25 630 11 92 327 167 g 0 130 368 548 4 635 573 13 641 185 154 373 t 0 91 64 20 6 1 23 11 5 44 95 52

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=4/7; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.901784; gcGGCGGCGGcg ; cor=; Ncor= a 113 92 15 17 29 16 25 18 18 34 87 70 c 125 314 38 28 561 7 31 562 12 56 307 130 g 284 103 536 548 4 585 541 7 576 497 121 361 t 93 106 26 22 21 7 18 28 9 28 100 54

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=5/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.779313; -cgsCGGCGGCG ; cor=; Ncor= a 0 57 72 102 21 2 33 10 6 42 3 25 c 0 328 142 172 520 20 44 580 12 57 575 23 g 0 151 337 225 34 579 501 4 589 481 11 553 t 0 72 57 109 33 7 30 14 1 28 19 7

positions_6nt_m4_shift1 (positions_6nt_m4)
; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=6/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.765721; -cgGCGGCGGCg ; cor=; Ncor= a 0 48 48 11 11 14 8 10 9 7 15 39 c 0 178 83 19 329 12 16 335 6 19 309 52 g 0 84 181 313 6 325 330 2 337 324 23 185 t 0 50 48 17 14 9 6 13 8 10 13 84

oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m7; m=7/7; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.681045; --gsCGGTGGcg ; cor=; Ncor= a 0 0 16 27 0 0 0 0 0 0 28 11 c 0 0 19 34 116 0 0 0 0 0 45 26 g 0 0 63 46 0 116 116 0 116 116 18 58 t 0 0 18 9 0 0 0 116 0 0 25 21

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m6_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; twTTTCAGsw ; Alignment reference a 14 24 0 0 1 0 87 0 13 28 c 21 19 0 0 0 86 0 0 26 15 g 18 15 0 0 0 0 0 87 30 17 t 34 29 87 87 86 1 0 0 18 27

oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; twTTTCAGsw ; cor=; Ncor= a 14 24 0 0 1 0 87 0 13 28 c 21 19 0 0 0 86 0 0 26 15 g 18 15 0 0 0 0 0 87 30 17 t 34 29 87 87 86 1 0 0 18 27

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m5; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.752635; wkTTACAGra ; cor=; Ncor= a 26 18 5 2 93 0 86 2 24 25 c 17 20 2 0 0 85 5 4 19 23 g 19 25 3 0 0 0 2 83 27 23 t 31 30 83 91 0 8 0 4 23 22

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m3; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.708359; wkTTGCAGGk ; cor=; Ncor= a 75 62 10 7 19 7 279 3 34 68 c 60 54 7 5 11 251 8 7 25 48 g 64 74 15 3 244 8 0 278 202 75 t 89 98 256 273 14 22 1 0 27 97

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 8 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=13; shift=0; ncol=13; cgsCGGCGGCGss ; Alignment reference a 57 72 102 21 2 33 10 6 42 3 25 125 61 c 328 142 172 520 20 44 580 12 57 575 23 154 301 g 151 337 225 34 579 501 4 589 481 11 553 241 154 t 72 57 109 33 7 30 14 1 28 19 7 88 92

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; cgsCGGCGGCGss ; cor=; Ncor= a 57 72 102 21 2 33 10 6 42 3 25 125 61 c 328 142 172 520 20 44 580 12 57 575 23 154 301 g 151 337 225 34 579 501 4 589 481 11 553 241 154 t 72 57 109 33 7 30 14 1 28 19 7 88 92

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m2 versus positions_6nt_m4; m=2/7; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.857109; cgGCGGCGGCgGs ; cor=; Ncor= a 48 48 11 11 14 8 10 9 7 15 39 31 42 c 178 83 19 329 12 16 335 6 19 309 52 39 171 g 84 181 313 6 325 330 2 337 324 23 185 271 96 t 50 48 17 14 9 6 13 8 10 13 84 19 51

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; positions_6nt_m2 versus oligos_6nt_mkv3_m1; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.779313; csGCGGCGGcg-- ; cor=; Ncor= a 100 64 34 15 6 35 12 12 57 96 87 0 0 c 408 209 52 768 30 53 756 33 92 410 186 0 0 g 188 456 676 9 765 691 13 757 614 166 463 0 0 t 111 78 45 15 6 28 26 5 44 135 71 0 0

oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)
; positions_6nt_m2 versus oligos_6nt_mkv3_m2_rc; m=4/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.77504; cgGCGGCGGcg-- ; cor=; Ncor= a 126 90 34 43 20 39 26 19 57 126 109 0 0 c 459 235 56 866 39 54 864 33 92 483 217 0 0 g 229 526 815 13 876 829 18 888 759 186 522 0 0 t 138 101 47 30 17 30 44 12 44 157 104 0 0

positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)
; positions_6nt_m2 versus positions_6nt_m1_rc; m=5/7; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.748995; --gcGGCGGCGGc ; cor=; Ncor= a 0 0 113 92 15 17 29 16 25 18 18 34 87 c 0 0 125 314 38 28 561 7 31 562 12 56 307 g 0 0 284 103 536 548 4 585 541 7 576 497 121 t 0 0 93 106 26 22 21 7 18 28 9 28 100

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; positions_6nt_m2 versus oligos_6nt_mkv3_m10; m=6/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.734006; csGCGGCGrcs-- ; cor=; Ncor= a 87 61 37 3 3 38 5 2 338 83 67 0 0 c 351 166 54 646 20 25 630 11 92 327 167 0 0 g 130 368 548 4 635 573 13 641 185 154 373 0 0 t 91 64 20 6 1 23 11 5 44 95 52 0 0

oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)
; positions_6nt_m2 versus oligos_6nt_mkv3_m7; m=7/7; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.552591; -gsCGGTGGcg-- ; cor=; Ncor= a 0 16 27 0 0 0 0 0 0 28 11 0 0 c 0 19 34 116 0 0 0 0 0 45 26 0 0 g 0 63 46 0 116 116 0 116 116 18 58 0 0 t 0 18 9 0 0 0 116 0 0 25 21 0 0

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=11; shift=0; ncol=11; wkTTGCAGGkk ; Alignment reference a 75 62 10 7 19 7 279 3 34 68 69 c 60 54 7 5 11 251 8 7 25 48 65 g 64 74 15 3 244 8 0 278 202 75 72 t 89 98 256 273 14 22 1 0 27 97 82

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wkTTGCAGGkk ; cor=; Ncor= a 75 62 10 7 19 7 279 3 34 68 69 c 60 54 7 5 11 251 8 7 25 48 65 g 64 74 15 3 244 8 0 278 202 75 72 t 89 98 256 273 14 22 1 0 27 97 82

oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m6; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.708359; twTTTCAGsw- ; cor=; Ncor= a 14 24 0 0 1 0 87 0 13 28 0 c 21 19 0 0 0 86 0 0 26 15 0 g 18 15 0 0 0 0 0 87 30 17 0 t 34 29 87 87 86 1 0 0 18 27 0

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m5; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.68852; wkTTACAGra- ; cor=; Ncor= a 26 18 5 2 93 0 86 2 24 25 0 c 17 20 2 0 0 85 5 4 19 23 0 g 19 25 3 0 0 0 2 83 27 23 0 t 31 30 83 91 0 8 0 4 23 22 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 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=12; shift=0; ncol=12; ysGCCATGGCsr ; Alignment reference a 39 46 9 6 7 206 10 3 5 18 37 77 c 77 78 12 220 212 8 12 14 5 197 75 43 g 43 75 197 5 14 12 8 212 220 12 78 77 t 77 37 18 5 3 10 206 7 6 9 46 39

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ysGCCATGGCsr ; cor=; Ncor= a 39 46 9 6 7 206 10 3 5 18 37 77 c 77 78 12 220 212 8 12 14 5 197 75 43 g 43 75 197 5 14 12 8 212 220 12 78 77 t 77 37 18 5 3 10 206 7 6 9 46 39

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m9_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; csTCGTCGkc ; Alignment reference a 19 24 4 3 0 0 7 0 35 27 c 98 58 4 181 0 1 177 2 40 98 g 36 86 0 0 184 0 0 182 47 29 t 31 16 176 0 0 183 0 0 62 30

oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; csTCGTCGkc ; cor=; Ncor= a 19 24 4 3 0 0 7 0 35 27 c 98 58 4 181 0 1 177 2 40 98 g 36 86 0 0 184 0 0 182 47 29 t 31 16 176 0 0 183 0 0 62 30

oligos_6nt_mkv3_m8_rc_shift0 (oligos_6nt_mkv3_m8_rc)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m8_rc; m=2/3; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.999752; csTCGTCGtc ; cor=; Ncor= a 19 23 4 5 0 0 9 0 38 27 c 101 56 2 180 0 1 176 1 40 98 g 37 90 0 0 185 0 0 184 46 28 t 28 16 179 0 0 184 0 0 61 32

oligos_6nt_mkv3_m10_rc_shift0 (oligos_6nt_mkv3_m10_rc)
; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m10_rc; m=3/3; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.655435; sgyCGCCGCs ; cor=; Ncor= a 52 95 44 5 11 23 1 6 20 64 c 373 154 185 641 13 573 635 4 548 368 g 167 327 92 11 630 25 20 646 54 166 t 67 83 338 2 5 38 3 3 37 61

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 8 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=14; shift=0; ncol=14; cgGCGGCGGCgGsg ; Alignment reference a 48 48 11 11 14 8 10 9 7 15 39 31 42 51 c 178 83 19 329 12 16 335 6 19 309 52 39 171 87 g 84 181 313 6 325 330 2 337 324 23 185 271 96 173 t 50 48 17 14 9 6 13 8 10 13 84 19 51 49

positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/7; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; cgGCGGCGGCgGsg ; cor=; Ncor= a 48 48 11 11 14 8 10 9 7 15 39 31 42 51 c 178 83 19 329 12 16 335 6 19 309 52 39 171 87 g 84 181 313 6 325 330 2 337 324 23 185 271 96 173 t 50 48 17 14 9 6 13 8 10 13 84 19 51 49

positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m4 versus positions_6nt_m2; m=2/7; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.857109; cgsCGGCGGCGss- ; cor=; Ncor= a 57 72 102 21 2 33 10 6 42 3 25 125 61 0 c 328 142 172 520 20 44 580 12 57 575 23 154 301 0 g 151 337 225 34 579 501 4 589 481 11 553 241 154 0 t 72 57 109 33 7 30 14 1 28 19 7 88 92 0

positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)
; positions_6nt_m4 versus positions_6nt_m1_rc; m=3/7; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.795389; --gcGGCGGCGGcg ; cor=; Ncor= a 0 0 113 92 15 17 29 16 25 18 18 34 87 70 c 0 0 125 314 38 28 561 7 31 562 12 56 307 130 g 0 0 284 103 536 548 4 585 541 7 576 497 121 361 t 0 0 93 106 26 22 21 7 18 28 9 28 100 54

oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)
; positions_6nt_m4 versus oligos_6nt_mkv3_m2_rc; m=4/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.769003; cgGCGGCGGcg--- ; cor=; Ncor= a 126 90 34 43 20 39 26 19 57 126 109 0 0 0 c 459 235 56 866 39 54 864 33 92 483 217 0 0 0 g 229 526 815 13 876 829 18 888 759 186 522 0 0 0 t 138 101 47 30 17 30 44 12 44 157 104 0 0 0

oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; positions_6nt_m4 versus oligos_6nt_mkv3_m1; m=5/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.765721; csGCGGCGGcg--- ; cor=; Ncor= a 100 64 34 15 6 35 12 12 57 96 87 0 0 0 c 408 209 52 768 30 53 756 33 92 410 186 0 0 0 g 188 456 676 9 765 691 13 757 614 166 463 0 0 0 t 111 78 45 15 6 28 26 5 44 135 71 0 0 0

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; positions_6nt_m4 versus oligos_6nt_mkv3_m10; m=6/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.711013; csGCGGCGrcs--- ; cor=; Ncor= a 87 61 37 3 3 38 5 2 338 83 67 0 0 0 c 351 166 54 646 20 25 630 11 92 327 167 0 0 0 g 130 368 548 4 635 573 13 641 185 154 373 0 0 0 t 91 64 20 6 1 23 11 5 44 95 52 0 0 0

oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)
; positions_6nt_m4 versus oligos_6nt_mkv3_m7; m=7/7; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.528087; -gsCGGTGGcg--- ; cor=; Ncor= a 0 16 27 0 0 0 0 0 0 28 11 0 0 0 c 0 19 34 116 0 0 0 0 0 45 26 0 0 0 g 0 63 46 0 116 116 0 116 116 18 58 0 0 0 t 0 18 9 0 0 0 116 0 0 25 21 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m10_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=11; shift=1; ncol=12; -csGCGGCGrcs ; Alignment reference a 0 87 61 37 3 3 38 5 2 338 83 67 c 0 351 166 54 646 20 25 630 11 92 327 167 g 0 130 368 548 4 635 573 13 641 185 154 373 t 0 91 64 20 6 1 23 11 5 44 95 52

oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -csGCGGCGrcs ; cor=; Ncor= a 0 87 61 37 3 3 38 5 2 338 83 67 c 0 351 166 54 646 20 25 630 11 92 327 167 g 0 130 368 548 4 635 573 13 641 185 154 373 t 0 91 64 20 6 1 23 11 5 44 95 52

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m1; m=2/8; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.949573; -csGCGGCGGcg ; cor=; Ncor= a 0 100 64 34 15 6 35 12 12 57 96 87 c 0 408 209 52 768 30 53 756 33 92 410 186 g 0 188 456 676 9 765 691 13 757 614 166 463 t 0 111 78 45 15 6 28 26 5 44 135 71

oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m2_rc; m=3/8; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.941385; -cgGCGGCGGcg ; cor=; Ncor= a 0 126 90 34 43 20 39 26 19 57 126 109 c 0 459 235 56 866 39 54 864 33 92 483 217 g 0 229 526 815 13 876 829 18 888 759 186 522 t 0 138 101 47 30 17 30 44 12 44 157 104

positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)
; oligos_6nt_mkv3_m10 versus positions_6nt_m1_rc; m=4/8; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.851635; gcGGCGGCGGcg ; cor=; Ncor= a 113 92 15 17 29 16 25 18 18 34 87 70 c 125 314 38 28 561 7 31 562 12 56 307 130 g 284 103 536 548 4 585 541 7 576 497 121 361 t 93 106 26 22 21 7 18 28 9 28 100 54

positions_6nt_m2_shift1 (positions_6nt_m2)
; oligos_6nt_mkv3_m10 versus positions_6nt_m2; m=5/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.734006; -cgsCGGCGGCG ; cor=; Ncor= a 0 57 72 102 21 2 33 10 6 42 3 25 c 0 328 142 172 520 20 44 580 12 57 575 23 g 0 151 337 225 34 579 501 4 589 481 11 553 t 0 72 57 109 33 7 30 14 1 28 19 7

positions_6nt_m4_shift1 (positions_6nt_m4)
; oligos_6nt_mkv3_m10 versus positions_6nt_m4; m=6/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.711013; -cgGCGGCGGCg ; cor=; Ncor= a 0 48 48 11 11 14 8 10 9 7 15 39 c 0 178 83 19 329 12 16 335 6 19 309 52 g 0 84 181 313 6 325 330 2 337 324 23 185 t 0 50 48 17 14 9 6 13 8 10 13 84

oligos_6nt_mkv3_m9_rc_shift2 (oligos_6nt_mkv3_m9_rc)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m9_rc; m=7/8; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.655435; --gmCGACGAsg ; cor=; Ncor= a 0 0 30 62 0 0 183 0 0 176 16 31 c 0 0 29 47 182 0 0 184 0 0 86 36 g 0 0 98 40 2 177 1 0 181 4 58 98 t 0 0 27 35 0 7 0 0 3 4 24 19

oligos_6nt_mkv3_m8_shift2 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m8; m=8/8; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.654143; --gaCGACGAsg ; cor=; Ncor= a 0 0 32 61 0 0 184 0 0 179 16 28 c 0 0 28 46 184 0 0 185 0 0 90 37 g 0 0 98 40 1 176 1 0 180 2 56 101 t 0 0 27 38 0 9 0 0 5 4 23 19

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; rwTAATCTwh ; Alignment reference a 23 27 2 85 73 3 17 1 41 26 c 14 14 0 0 7 6 61 1 11 24 g 31 19 0 0 5 2 5 2 13 9 t 20 28 86 3 3 77 5 84 23 29

positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; rwTAATCTwh ; cor=; Ncor= a 23 27 2 85 73 3 17 1 41 26 c 14 14 0 0 7 6 61 1 11 24 g 31 19 0 0 5 2 5 2 13 9 t 20 28 86 3 3 77 5 84 23 29

One-to-n matrix alignment; reference matrix: positions_6nt_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m7_shift0 (positions_6nt_m7)
; positions_6nt_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; kbTGTGCAss ; Alignment reference a 15 13 0 0 0 4 0 94 18 22 c 22 25 0 0 0 0 93 0 25 26 g 32 24 0 94 0 90 0 0 35 27 t 25 32 94 0 94 0 1 0 16 19

positions_6nt_m7_shift0 (positions_6nt_m7)
; positions_6nt_m7 versus positions_6nt_m7; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; kbTGTGCAss ; cor=; Ncor= a 15 13 0 0 0 4 0 94 18 22 c 22 25 0 0 0 0 93 0 25 26 g 32 24 0 94 0 90 0 0 35 27 t 25 32 94 0 94 0 1 0 16 19

positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc)
; positions_6nt_m7 versus positions_6nt_m3_rc; m=2/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.748315; sgTGTACAcs ; cor=; Ncor= a 32 35 3 13 0 188 4 157 40 41 c 55 39 17 7 0 0 159 10 73 59 g 60 73 10 166 0 0 7 18 38 54 t 41 41 158 2 188 0 18 3 37 34

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m8_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m8_shift1 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=1; ncol=11; -gaCGACGAsg ; Alignment reference a 0 32 61 0 0 184 0 0 179 16 28 c 0 28 46 184 0 0 185 0 0 90 37 g 0 98 40 1 176 1 0 180 2 56 101 t 0 27 38 0 9 0 0 5 4 23 19

oligos_6nt_mkv3_m8_shift1 (oligos_6nt_mkv3_m8)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -gaCGACGAsg ; cor=; Ncor= a 0 32 61 0 0 184 0 0 179 16 28 c 0 28 46 184 0 0 185 0 0 90 37 g 0 98 40 1 176 1 0 180 2 56 101 t 0 27 38 0 9 0 0 5 4 23 19

oligos_6nt_mkv3_m9_rc_shift1 (oligos_6nt_mkv3_m9_rc)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m9_rc; m=2/3; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.999752; -gmCGACGAsg ; cor=; Ncor= a 0 30 62 0 0 183 0 0 176 16 31 c 0 29 47 182 0 0 184 0 0 86 36 g 0 98 40 2 177 1 0 181 4 58 98 t 0 27 35 0 7 0 0 3 4 24 19

oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)
; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m10; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.654143; csGCGGCGrcs ; cor=; Ncor= a 87 61 37 3 3 38 5 2 338 83 67 c 351 166 54 646 20 25 630 11 92 327 167 g 130 368 548 4 635 573 13 641 185 154 373 t 91 64 20 6 1 23 11 5 44 95 52

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 4 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; wkTTACAGra ; Alignment reference a 26 18 5 2 93 0 86 2 24 25 c 17 20 2 0 0 85 5 4 19 23 g 19 25 3 0 0 0 2 83 27 23 t 31 30 83 91 0 8 0 4 23 22

oligos_6nt_mkv3_m5_shift0 (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=0; score= 1; wkTTACAGra ; cor=; Ncor= a 26 18 5 2 93 0 86 2 24 25 c 17 20 2 0 0 85 5 4 19 23 g 19 25 3 0 0 0 2 83 27 23 t 31 30 83 91 0 8 0 4 23 22

oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m6; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.752635; twTTTCAGsw ; cor=; Ncor= a 14 24 0 0 1 0 87 0 13 28 c 21 19 0 0 0 86 0 0 26 15 g 18 15 0 0 0 0 0 87 30 17 t 34 29 87 87 86 1 0 0 18 27

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m3; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.68852; wkTTGCAGGk ; cor=; Ncor= a 75 62 10 7 19 7 279 3 34 68 c 60 54 7 5 11 251 8 7 25 48 g 64 74 15 3 244 8 0 278 202 75 t 89 98 256 273 14 22 1 0 27 97

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7; m=0 (reference); ncol1=10; shift=2; ncol=12; --gsCGGTGGcg ; Alignment reference a 0 0 16 27 0 0 0 0 0 0 28 11 c 0 0 19 34 116 0 0 0 0 0 45 26 g 0 0 63 46 0 116 116 0 116 116 18 58 t 0 0 18 9 0 0 0 116 0 0 25 21
oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m7; m=1/6; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --gsCGGTGGcg ; cor=; Ncor= a 0 0 16 27 0 0 0 0 0 0 28 11 c 0 0 19 34 116 0 0 0 0 0 45 26 g 0 0 63 46 0 116 116 0 116 116 18 58 t 0 0 18 9 0 0 0 116 0 0 25 21
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m2_rc; m=2/6; ncol2=11; w=-1; offset=-1; strand=R; shift=1; score=0.687419; -cgGCGGCGGcg ; cor=; Ncor= a 0 126 90 34 43 20 39 26 19 57 126 109 c 0 459 235 56 866 39 54 864 33 92 483 217 g 0 229 526 815 13 876 829 18 888 759 186 522 t 0 138 101 47 30 17 30 44 12 44 157 104
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m7 versus oligos_6nt_mkv3_m1; m=3/6; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.681045; -csGCGGCGGcg ; cor=; Ncor= a 0 100 64 34 15 6 35 12 12 57 96 87 c 0 408 209 52 768 30 53 756 33 92 410 186 g 0 188 456 676 9 765 691 13 757 614 166 463 t 0 111 78 45 15 6 28 26 5 44 135 71
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m7 versus positions_6nt_m1_rc; m=4/6; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.625133; gcGGCGGCGGcg ; cor=; Ncor= a 113 92 15 17 29 16 25 18 18 34 87 70 c 125 314 38 28 561 7 31 562 12 56 307 130 g 284 103 536 548 4 585 541 7 576 497 121 361 t 93 106 26 22 21 7 18 28 9 28 100 54
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_6nt_mkv3_m7 versus positions_6nt_m2; m=5/6; ncol2=13; w=-1; offset=-1; strand=D; shift=1; score=0.552591; -cgsCGGCGGCG ; cor=; Ncor= a 0 57 72 102 21 2 33 10 6 42 3 25 c 0 328 142 172 520 20 44 580 12 57 575 23 g 0 151 337 225 34 579 501 4 589 481 11 553 t 0 72 57 109 33 7 30 14 1 28 19 7
positions_6nt_m4_shift1 (positions_6nt_m4)				; oligos_6nt_mkv3_m7 versus positions_6nt_m4; m=6/6; ncol2=14; w=-1; offset=-1; strand=D; shift=1; score=0.528087; -cgGCGGCGGCg ; cor=; Ncor= a 0 48 48 11 11 14 8 10 9 7 15 39 c 0 178 83 19 329 12 16 335 6 19 309 52 g 0 84 181 313 6 325 330 2 337 324 23 185 t 0 50 48 17 14 9 6 13 8 10 13 84

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; ---cgCCGCCGCcg ; Alignment reference a 0 0 0 104 157 44 12 44 30 17 30 47 101 138 c 0 0 0 522 186 759 888 18 829 876 13 815 526 229 g 0 0 0 217 483 92 33 864 54 39 866 56 235 459 t 0 0 0 109 126 57 19 26 39 20 43 34 90 126
oligos_6nt_mkv3_m2_shift3 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---cgCCGCCGCcg ; cor=; Ncor= a 0 0 0 104 157 44 12 44 30 17 30 47 101 138 c 0 0 0 522 186 759 888 18 829 876 13 815 526 229 g 0 0 0 217 483 92 33 864 54 39 866 56 235 459 t 0 0 0 109 126 57 19 26 39 20 43 34 90 126
oligos_6nt_mkv3_m1_rc_shift3 (oligos_6nt_mkv3_m1_rc)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m1_rc; m=2/7; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.99892; ---cgCCGCCGCsg ; cor=; Ncor= a 0 0 0 71 135 44 5 26 28 6 15 45 78 111 c 0 0 0 463 166 614 757 13 691 765 9 676 456 188 g 0 0 0 186 410 92 33 756 53 30 768 52 209 408 t 0 0 0 87 96 57 12 12 35 6 15 34 64 100
oligos_6nt_mkv3_m10_rc_shift3 (oligos_6nt_mkv3_m10_rc)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m10_rc; m=3/7; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.941385; ---sgyCGCCGCsg ; cor=; Ncor= a 0 0 0 52 95 44 5 11 23 1 6 20 64 91 c 0 0 0 373 154 185 641 13 573 635 4 548 368 130 g 0 0 0 167 327 92 11 630 25 20 646 54 166 351 t 0 0 0 67 83 338 2 5 38 3 3 37 61 87
positions_6nt_m1_shift3 (positions_6nt_m1)				; oligos_6nt_mkv3_m2 versus positions_6nt_m1; m=4/7; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.902416; ---cgCCGCCGCCg ; cor=; Ncor= a 0 0 0 54 100 28 9 28 18 7 21 22 26 106 c 0 0 0 361 121 497 576 7 541 585 4 548 536 103 g 0 0 0 130 307 56 12 562 31 7 561 28 38 314 t 0 0 0 70 87 34 18 18 25 16 29 17 15 92
positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)				; oligos_6nt_mkv3_m2 versus positions_6nt_m2_rc; m=5/7; ncol2=13; w=-2; offset=-2; strand=R; shift=1; score=0.77504; -ssCGCCGCCGscg ; cor=; Ncor= a 0 92 88 7 19 28 1 14 30 7 33 109 57 72 c 0 154 241 553 11 481 589 4 501 579 34 225 337 151 g 0 301 154 23 575 57 12 580 44 20 520 172 142 328 t 0 61 125 25 3 42 6 10 33 2 21 102 72 57
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; oligos_6nt_mkv3_m2 versus positions_6nt_m4_rc; m=6/7; ncol2=14; w=-3; offset=-3; strand=R; shift=0; score=0.769003; csCcGCCGCCGCcg ; cor=; Ncor= a 49 51 19 84 13 10 8 13 6 9 14 17 48 50 c 173 96 271 185 23 324 337 2 330 325 6 313 181 84 g 87 171 39 52 309 19 6 335 16 12 329 19 83 178 t 51 42 31 39 15 7 9 10 8 14 11 11 48 48
oligos_6nt_mkv3_m7_rc_shift3 (oligos_6nt_mkv3_m7_rc)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m7_rc; m=7/7; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.687419; ---cgCCACCGsc- ; cor=; Ncor= a 0 0 0 21 25 0 0 116 0 0 0 9 18 0 c 0 0 0 58 18 116 116 0 116 116 0 46 63 0 g 0 0 0 26 45 0 0 0 0 0 116 34 19 0 t 0 0 0 11 28 0 0 0 0 0 0 27 16 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; cgCCGCCGCCgc ; Alignment reference a 54 100 28 9 28 18 7 21 22 26 106 93 c 361 121 497 576 7 541 585 4 548 536 103 284 g 130 307 56 12 562 31 7 561 28 38 314 125 t 70 87 34 18 18 25 16 29 17 15 92 113
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/7; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; cgCCGCCGCCgc ; cor=; Ncor= a 54 100 28 9 28 18 7 21 22 26 106 93 c 361 121 497 576 7 541 585 4 548 536 103 284 g 130 307 56 12 562 31 7 561 28 38 314 125 t 70 87 34 18 18 25 16 29 17 15 92 113
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; positions_6nt_m1 versus oligos_6nt_mkv3_m2; m=2/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.902416; cgCCGCCGCcg- ; cor=; Ncor= a 104 157 44 12 44 30 17 30 47 101 138 0 c 522 186 759 888 18 829 876 13 815 526 229 0 g 217 483 92 33 864 54 39 866 56 235 459 0 t 109 126 57 19 26 39 20 43 34 90 126 0
oligos_6nt_mkv3_m1_rc_shift0 (oligos_6nt_mkv3_m1_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m1_rc; m=3/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.901784; cgCCGCCGCsg- ; cor=; Ncor= a 71 135 44 5 26 28 6 15 45 78 111 0 c 463 166 614 757 13 691 765 9 676 456 188 0 g 186 410 92 33 756 53 30 768 52 209 408 0 t 87 96 57 12 12 35 6 15 34 64 100 0
oligos_6nt_mkv3_m10_rc_shift0 (oligos_6nt_mkv3_m10_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m10_rc; m=4/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.851635; sgyCGCCGCsg- ; cor=; Ncor= a 52 95 44 5 11 23 1 6 20 64 91 0 c 373 154 185 641 13 573 635 4 548 368 130 0 g 167 327 92 11 630 25 20 646 54 166 351 0 t 67 83 338 2 5 38 3 3 37 61 87 0
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)				; positions_6nt_m1 versus positions_6nt_m4_rc; m=5/7; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.795389; csCcGCCGCCGC ; cor=; Ncor= a 49 51 19 84 13 10 8 13 6 9 14 17 c 173 96 271 185 23 324 337 2 330 325 6 313 g 87 171 39 52 309 19 6 335 16 12 329 19 t 51 42 31 39 15 7 9 10 8 14 11 11
positions_6nt_m2_rc_shift1 (positions_6nt_m2_rc)				; positions_6nt_m1 versus positions_6nt_m2_rc; m=6/7; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.748995; -ssCGCCGCCGs ; cor=; Ncor= a 0 92 88 7 19 28 1 14 30 7 33 109 c 0 154 241 553 11 481 589 4 501 579 34 225 g 0 301 154 23 575 57 12 580 44 20 520 172 t 0 61 125 25 3 42 6 10 33 2 21 102
oligos_6nt_mkv3_m7_rc_shift0 (oligos_6nt_mkv3_m7_rc)				; positions_6nt_m1 versus oligos_6nt_mkv3_m7_rc; m=7/7; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.625133; cgCCACCGsc-- ; cor=; Ncor= a 21 25 0 0 116 0 0 0 9 18 0 0 c 58 18 116 116 0 116 116 0 46 63 0 0 g 26 45 0 0 0 0 0 116 34 19 0 0 t 11 28 0 0 0 0 0 0 27 16 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=11; shift=1; ncol=12; -csGCGGCGGcg ; Alignment reference a 0 100 64 34 15 6 35 12 12 57 96 87 c 0 408 209 52 768 30 53 756 33 92 410 186 g 0 188 456 676 9 765 691 13 757 614 166 463 t 0 111 78 45 15 6 28 26 5 44 135 71
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -csGCGGCGGcg ; cor=; Ncor= a 0 100 64 34 15 6 35 12 12 57 96 87 c 0 408 209 52 768 30 53 756 33 92 410 186 g 0 188 456 676 9 765 691 13 757 614 166 463 t 0 111 78 45 15 6 28 26 5 44 135 71
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m2_rc; m=2/7; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.99892; -cgGCGGCGGcg ; cor=; Ncor= a 0 126 90 34 43 20 39 26 19 57 126 109 c 0 459 235 56 866 39 54 864 33 92 483 217 g 0 229 526 815 13 876 829 18 888 759 186 522 t 0 138 101 47 30 17 30 44 12 44 157 104
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m10; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.949573; -csGCGGCGrcs ; cor=; Ncor= a 0 87 61 37 3 3 38 5 2 338 83 67 c 0 351 166 54 646 20 25 630 11 92 327 167 g 0 130 368 548 4 635 573 13 641 185 154 373 t 0 91 64 20 6 1 23 11 5 44 95 52
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=4/7; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.901784; gcGGCGGCGGcg ; cor=; Ncor= a 113 92 15 17 29 16 25 18 18 34 87 70 c 125 314 38 28 561 7 31 562 12 56 307 130 g 284 103 536 548 4 585 541 7 576 497 121 361 t 93 106 26 22 21 7 18 28 9 28 100 54
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=5/7; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.779313; -cgsCGGCGGCG ; cor=; Ncor= a 0 57 72 102 21 2 33 10 6 42 3 25 c 0 328 142 172 520 20 44 580 12 57 575 23 g 0 151 337 225 34 579 501 4 589 481 11 553 t 0 72 57 109 33 7 30 14 1 28 19 7
positions_6nt_m4_shift1 (positions_6nt_m4)				; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=6/7; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.765721; -cgGCGGCGGCg ; cor=; Ncor= a 0 48 48 11 11 14 8 10 9 7 15 39 c 0 178 83 19 329 12 16 335 6 19 309 52 g 0 84 181 313 6 325 330 2 337 324 23 185 t 0 50 48 17 14 9 6 13 8 10 13 84
oligos_6nt_mkv3_m7_shift2 (oligos_6nt_mkv3_m7)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m7; m=7/7; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.681045; --gsCGGTGGcg ; cor=; Ncor= a 0 0 16 27 0 0 0 0 0 0 28 11 c 0 0 19 34 116 0 0 0 0 0 45 26 g 0 0 63 46 0 116 116 0 116 116 18 58 t 0 0 18 9 0 0 0 116 0 0 25 21

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6; m=0 (reference); ncol1=10; shift=0; ncol=10; twTTTCAGsw ; Alignment reference a 14 24 0 0 1 0 87 0 13 28 c 21 19 0 0 0 86 0 0 26 15 g 18 15 0 0 0 0 0 87 30 17 t 34 29 87 87 86 1 0 0 18 27
oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m6; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; twTTTCAGsw ; cor=; Ncor= a 14 24 0 0 1 0 87 0 13 28 c 21 19 0 0 0 86 0 0 26 15 g 18 15 0 0 0 0 0 87 30 17 t 34 29 87 87 86 1 0 0 18 27
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m5; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.752635; wkTTACAGra ; cor=; Ncor= a 26 18 5 2 93 0 86 2 24 25 c 17 20 2 0 0 85 5 4 19 23 g 19 25 3 0 0 0 2 83 27 23 t 31 30 83 91 0 8 0 4 23 22
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m6 versus oligos_6nt_mkv3_m3; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.708359; wkTTGCAGGk ; cor=; Ncor= a 75 62 10 7 19 7 279 3 34 68 c 60 54 7 5 11 251 8 7 25 48 g 64 74 15 3 244 8 0 278 202 75 t 89 98 256 273 14 22 1 0 27 97

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; cgsCGGCGGCGss ; Alignment reference a 57 72 102 21 2 33 10 6 42 3 25 125 61 c 328 142 172 520 20 44 580 12 57 575 23 154 301 g 151 337 225 34 579 501 4 589 481 11 553 241 154 t 72 57 109 33 7 30 14 1 28 19 7 88 92
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/7; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; cgsCGGCGGCGss ; cor=; Ncor= a 57 72 102 21 2 33 10 6 42 3 25 125 61 c 328 142 172 520 20 44 580 12 57 575 23 154 301 g 151 337 225 34 579 501 4 589 481 11 553 241 154 t 72 57 109 33 7 30 14 1 28 19 7 88 92
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m2 versus positions_6nt_m4; m=2/7; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.857109; cgGCGGCGGCgGs ; cor=; Ncor= a 48 48 11 11 14 8 10 9 7 15 39 31 42 c 178 83 19 329 12 16 335 6 19 309 52 39 171 g 84 181 313 6 325 330 2 337 324 23 185 271 96 t 50 48 17 14 9 6 13 8 10 13 84 19 51
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; positions_6nt_m2 versus oligos_6nt_mkv3_m1; m=3/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.779313; csGCGGCGGcg-- ; cor=; Ncor= a 100 64 34 15 6 35 12 12 57 96 87 0 0 c 408 209 52 768 30 53 756 33 92 410 186 0 0 g 188 456 676 9 765 691 13 757 614 166 463 0 0 t 111 78 45 15 6 28 26 5 44 135 71 0 0
oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)				; positions_6nt_m2 versus oligos_6nt_mkv3_m2_rc; m=4/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.77504; cgGCGGCGGcg-- ; cor=; Ncor= a 126 90 34 43 20 39 26 19 57 126 109 0 0 c 459 235 56 866 39 54 864 33 92 483 217 0 0 g 229 526 815 13 876 829 18 888 759 186 522 0 0 t 138 101 47 30 17 30 44 12 44 157 104 0 0
positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)				; positions_6nt_m2 versus positions_6nt_m1_rc; m=5/7; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.748995; --gcGGCGGCGGc ; cor=; Ncor= a 0 0 113 92 15 17 29 16 25 18 18 34 87 c 0 0 125 314 38 28 561 7 31 562 12 56 307 g 0 0 284 103 536 548 4 585 541 7 576 497 121 t 0 0 93 106 26 22 21 7 18 28 9 28 100
oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)				; positions_6nt_m2 versus oligos_6nt_mkv3_m10; m=6/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.734006; csGCGGCGrcs-- ; cor=; Ncor= a 87 61 37 3 3 38 5 2 338 83 67 0 0 c 351 166 54 646 20 25 630 11 92 327 167 0 0 g 130 368 548 4 635 573 13 641 185 154 373 0 0 t 91 64 20 6 1 23 11 5 44 95 52 0 0
oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)				; positions_6nt_m2 versus oligos_6nt_mkv3_m7; m=7/7; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.552591; -gsCGGTGGcg-- ; cor=; Ncor= a 0 16 27 0 0 0 0 0 0 28 11 0 0 c 0 19 34 116 0 0 0 0 0 45 26 0 0 g 0 63 46 0 116 116 0 116 116 18 58 0 0 t 0 18 9 0 0 0 116 0 0 25 21 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=11; shift=0; ncol=11; wkTTGCAGGkk ; Alignment reference a 75 62 10 7 19 7 279 3 34 68 69 c 60 54 7 5 11 251 8 7 25 48 65 g 64 74 15 3 244 8 0 278 202 75 72 t 89 98 256 273 14 22 1 0 27 97 82
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wkTTGCAGGkk ; cor=; Ncor= a 75 62 10 7 19 7 279 3 34 68 69 c 60 54 7 5 11 251 8 7 25 48 65 g 64 74 15 3 244 8 0 278 202 75 72 t 89 98 256 273 14 22 1 0 27 97 82
oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m6; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.708359; twTTTCAGsw- ; cor=; Ncor= a 14 24 0 0 1 0 87 0 13 28 0 c 21 19 0 0 0 86 0 0 26 15 0 g 18 15 0 0 0 0 0 87 30 17 0 t 34 29 87 87 86 1 0 0 18 27 0
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m5; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.68852; wkTTACAGra- ; cor=; Ncor= a 26 18 5 2 93 0 86 2 24 25 0 c 17 20 2 0 0 85 5 4 19 23 0 g 19 25 3 0 0 0 2 83 27 23 0 t 31 30 83 91 0 8 0 4 23 22 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; csTCGTCGkc ; Alignment reference a 19 24 4 3 0 0 7 0 35 27 c 98 58 4 181 0 1 177 2 40 98 g 36 86 0 0 184 0 0 182 47 29 t 31 16 176 0 0 183 0 0 62 30
oligos_6nt_mkv3_m9_shift0 (oligos_6nt_mkv3_m9)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m9; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; csTCGTCGkc ; cor=; Ncor= a 19 24 4 3 0 0 7 0 35 27 c 98 58 4 181 0 1 177 2 40 98 g 36 86 0 0 184 0 0 182 47 29 t 31 16 176 0 0 183 0 0 62 30
oligos_6nt_mkv3_m8_rc_shift0 (oligos_6nt_mkv3_m8_rc)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m8_rc; m=2/3; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.999752; csTCGTCGtc ; cor=; Ncor= a 19 23 4 5 0 0 9 0 38 27 c 101 56 2 180 0 1 176 1 40 98 g 37 90 0 0 185 0 0 184 46 28 t 28 16 179 0 0 184 0 0 61 32
oligos_6nt_mkv3_m10_rc_shift0 (oligos_6nt_mkv3_m10_rc)				; oligos_6nt_mkv3_m9 versus oligos_6nt_mkv3_m10_rc; m=3/3; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.655435; sgyCGCCGCs ; cor=; Ncor= a 52 95 44 5 11 23 1 6 20 64 c 373 154 185 641 13 573 635 4 548 368 g 167 327 92 11 630 25 20 646 54 166 t 67 83 338 2 5 38 3 3 37 61

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=14; shift=0; ncol=14; cgGCGGCGGCgGsg ; Alignment reference a 48 48 11 11 14 8 10 9 7 15 39 31 42 51 c 178 83 19 329 12 16 335 6 19 309 52 39 171 87 g 84 181 313 6 325 330 2 337 324 23 185 271 96 173 t 50 48 17 14 9 6 13 8 10 13 84 19 51 49
positions_6nt_m4_shift0 (positions_6nt_m4)				; positions_6nt_m4 versus positions_6nt_m4; m=1/7; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; cgGCGGCGGCgGsg ; cor=; Ncor= a 48 48 11 11 14 8 10 9 7 15 39 31 42 51 c 178 83 19 329 12 16 335 6 19 309 52 39 171 87 g 84 181 313 6 325 330 2 337 324 23 185 271 96 173 t 50 48 17 14 9 6 13 8 10 13 84 19 51 49
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m4 versus positions_6nt_m2; m=2/7; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.857109; cgsCGGCGGCGss- ; cor=; Ncor= a 57 72 102 21 2 33 10 6 42 3 25 125 61 0 c 328 142 172 520 20 44 580 12 57 575 23 154 301 0 g 151 337 225 34 579 501 4 589 481 11 553 241 154 0 t 72 57 109 33 7 30 14 1 28 19 7 88 92 0
positions_6nt_m1_rc_shift2 (positions_6nt_m1_rc)				; positions_6nt_m4 versus positions_6nt_m1_rc; m=3/7; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.795389; --gcGGCGGCGGcg ; cor=; Ncor= a 0 0 113 92 15 17 29 16 25 18 18 34 87 70 c 0 0 125 314 38 28 561 7 31 562 12 56 307 130 g 0 0 284 103 536 548 4 585 541 7 576 497 121 361 t 0 0 93 106 26 22 21 7 18 28 9 28 100 54
oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)				; positions_6nt_m4 versus oligos_6nt_mkv3_m2_rc; m=4/7; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.769003; cgGCGGCGGcg--- ; cor=; Ncor= a 126 90 34 43 20 39 26 19 57 126 109 0 0 0 c 459 235 56 866 39 54 864 33 92 483 217 0 0 0 g 229 526 815 13 876 829 18 888 759 186 522 0 0 0 t 138 101 47 30 17 30 44 12 44 157 104 0 0 0
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; positions_6nt_m4 versus oligos_6nt_mkv3_m1; m=5/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.765721; csGCGGCGGcg--- ; cor=; Ncor= a 100 64 34 15 6 35 12 12 57 96 87 0 0 0 c 408 209 52 768 30 53 756 33 92 410 186 0 0 0 g 188 456 676 9 765 691 13 757 614 166 463 0 0 0 t 111 78 45 15 6 28 26 5 44 135 71 0 0 0
oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)				; positions_6nt_m4 versus oligos_6nt_mkv3_m10; m=6/7; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.711013; csGCGGCGrcs--- ; cor=; Ncor= a 87 61 37 3 3 38 5 2 338 83 67 0 0 0 c 351 166 54 646 20 25 630 11 92 327 167 0 0 0 g 130 368 548 4 635 573 13 641 185 154 373 0 0 0 t 91 64 20 6 1 23 11 5 44 95 52 0 0 0
oligos_6nt_mkv3_m7_shift1 (oligos_6nt_mkv3_m7)				; positions_6nt_m4 versus oligos_6nt_mkv3_m7; m=7/7; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.528087; -gsCGGTGGcg--- ; cor=; Ncor= a 0 16 27 0 0 0 0 0 0 28 11 0 0 0 c 0 19 34 116 0 0 0 0 0 45 26 0 0 0 g 0 63 46 0 116 116 0 116 116 18 58 0 0 0 t 0 18 9 0 0 0 116 0 0 25 21 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m10; m=0 (reference); ncol1=11; shift=1; ncol=12; -csGCGGCGrcs ; Alignment reference a 0 87 61 37 3 3 38 5 2 338 83 67 c 0 351 166 54 646 20 25 630 11 92 327 167 g 0 130 368 548 4 635 573 13 641 185 154 373 t 0 91 64 20 6 1 23 11 5 44 95 52
oligos_6nt_mkv3_m10_shift1 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m10; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -csGCGGCGrcs ; cor=; Ncor= a 0 87 61 37 3 3 38 5 2 338 83 67 c 0 351 166 54 646 20 25 630 11 92 327 167 g 0 130 368 548 4 635 573 13 641 185 154 373 t 0 91 64 20 6 1 23 11 5 44 95 52
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m1; m=2/8; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.949573; -csGCGGCGGcg ; cor=; Ncor= a 0 100 64 34 15 6 35 12 12 57 96 87 c 0 408 209 52 768 30 53 756 33 92 410 186 g 0 188 456 676 9 765 691 13 757 614 166 463 t 0 111 78 45 15 6 28 26 5 44 135 71
oligos_6nt_mkv3_m2_rc_shift1 (oligos_6nt_mkv3_m2_rc)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m2_rc; m=3/8; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.941385; -cgGCGGCGGcg ; cor=; Ncor= a 0 126 90 34 43 20 39 26 19 57 126 109 c 0 459 235 56 866 39 54 864 33 92 483 217 g 0 229 526 815 13 876 829 18 888 759 186 522 t 0 138 101 47 30 17 30 44 12 44 157 104
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc)				; oligos_6nt_mkv3_m10 versus positions_6nt_m1_rc; m=4/8; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.851635; gcGGCGGCGGcg ; cor=; Ncor= a 113 92 15 17 29 16 25 18 18 34 87 70 c 125 314 38 28 561 7 31 562 12 56 307 130 g 284 103 536 548 4 585 541 7 576 497 121 361 t 93 106 26 22 21 7 18 28 9 28 100 54
positions_6nt_m2_shift1 (positions_6nt_m2)				; oligos_6nt_mkv3_m10 versus positions_6nt_m2; m=5/8; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.734006; -cgsCGGCGGCG ; cor=; Ncor= a 0 57 72 102 21 2 33 10 6 42 3 25 c 0 328 142 172 520 20 44 580 12 57 575 23 g 0 151 337 225 34 579 501 4 589 481 11 553 t 0 72 57 109 33 7 30 14 1 28 19 7
positions_6nt_m4_shift1 (positions_6nt_m4)				; oligos_6nt_mkv3_m10 versus positions_6nt_m4; m=6/8; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.711013; -cgGCGGCGGCg ; cor=; Ncor= a 0 48 48 11 11 14 8 10 9 7 15 39 c 0 178 83 19 329 12 16 335 6 19 309 52 g 0 84 181 313 6 325 330 2 337 324 23 185 t 0 50 48 17 14 9 6 13 8 10 13 84
oligos_6nt_mkv3_m9_rc_shift2 (oligos_6nt_mkv3_m9_rc)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m9_rc; m=7/8; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.655435; --gmCGACGAsg ; cor=; Ncor= a 0 0 30 62 0 0 183 0 0 176 16 31 c 0 0 29 47 182 0 0 184 0 0 86 36 g 0 0 98 40 2 177 1 0 181 4 58 98 t 0 0 27 35 0 7 0 0 3 4 24 19
oligos_6nt_mkv3_m8_shift2 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m10 versus oligos_6nt_mkv3_m8; m=8/8; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.654143; --gaCGACGAsg ; cor=; Ncor= a 0 0 32 61 0 0 184 0 0 179 16 28 c 0 0 28 46 184 0 0 185 0 0 90 37 g 0 0 98 40 1 176 1 0 180 2 56 101 t 0 0 27 38 0 9 0 0 5 4 23 19

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m8_shift1 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m8; m=0 (reference); ncol1=10; shift=1; ncol=11; -gaCGACGAsg ; Alignment reference a 0 32 61 0 0 184 0 0 179 16 28 c 0 28 46 184 0 0 185 0 0 90 37 g 0 98 40 1 176 1 0 180 2 56 101 t 0 27 38 0 9 0 0 5 4 23 19
oligos_6nt_mkv3_m8_shift1 (oligos_6nt_mkv3_m8)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m8; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -gaCGACGAsg ; cor=; Ncor= a 0 32 61 0 0 184 0 0 179 16 28 c 0 28 46 184 0 0 185 0 0 90 37 g 0 98 40 1 176 1 0 180 2 56 101 t 0 27 38 0 9 0 0 5 4 23 19
oligos_6nt_mkv3_m9_rc_shift1 (oligos_6nt_mkv3_m9_rc)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m9_rc; m=2/3; ncol2=10; w=0; offset=0; strand=R; shift=1; score=0.999752; -gmCGACGAsg ; cor=; Ncor= a 0 30 62 0 0 183 0 0 176 16 31 c 0 29 47 182 0 0 184 0 0 86 36 g 0 98 40 2 177 1 0 181 4 58 98 t 0 27 35 0 7 0 0 3 4 24 19
oligos_6nt_mkv3_m10_shift0 (oligos_6nt_mkv3_m10)				; oligos_6nt_mkv3_m8 versus oligos_6nt_mkv3_m10; m=3/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.654143; csGCGGCGrcs ; cor=; Ncor= a 87 61 37 3 3 38 5 2 338 83 67 c 351 166 54 646 20 25 630 11 92 327 167 g 130 368 548 4 635 573 13 641 185 154 373 t 91 64 20 6 1 23 11 5 44 95 52

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; wkTTACAGra ; Alignment reference a 26 18 5 2 93 0 86 2 24 25 c 17 20 2 0 0 85 5 4 19 23 g 19 25 3 0 0 0 2 83 27 23 t 31 30 83 91 0 8 0 4 23 22
oligos_6nt_mkv3_m5_shift0 (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=0; score= 1; wkTTACAGra ; cor=; Ncor= a 26 18 5 2 93 0 86 2 24 25 c 17 20 2 0 0 85 5 4 19 23 g 19 25 3 0 0 0 2 83 27 23 t 31 30 83 91 0 8 0 4 23 22
oligos_6nt_mkv3_m6_shift0 (oligos_6nt_mkv3_m6)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m6; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.752635; twTTTCAGsw ; cor=; Ncor= a 14 24 0 0 1 0 87 0 13 28 c 21 19 0 0 0 86 0 0 26 15 g 18 15 0 0 0 0 0 87 30 17 t 34 29 87 87 86 1 0 0 18 27
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m3; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.68852; wkTTGCAGGk ; cor=; Ncor= a 75 62 10 7 19 7 279 3 34 68 c 60 54 7 5 11 251 8 7 25 48 g 64 74 15 3 244 8 0 278 202 75 t 89 98 256 273 14 22 1 0 27 97