One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.150634_2026-01-05.150634_YIpuAE/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.150634_2026-01-05.150634_YIpuAE/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift5 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=18; shift=5; ncol=23; -----wwyTTATTTTAAAgAcww ; Alignment reference a 0 0 0 0 0 25 31 18 8 5 59 6 3 4 6 66 54 63 15 59 16 30 26 c 0 0 0 0 0 10 9 30 3 6 6 5 4 1 1 3 9 4 6 6 35 10 13 g 0 0 0 0 0 14 9 8 6 3 3 3 2 2 2 5 7 4 49 4 9 12 19 t 0 0 0 0 0 29 29 22 61 64 10 64 69 71 69 4 8 7 8 9 18 26 20

oligos_6nt_test_vs_ctrl_m2_shift5 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=5; score= 1; -----wwyTTATTTTAAAgAcww ; cor=; Ncor= a 0 0 0 0 0 25 31 18 8 5 59 6 3 4 6 66 54 63 15 59 16 30 26 c 0 0 0 0 0 10 9 30 3 6 6 5 4 1 1 3 9 4 6 6 35 10 13 g 0 0 0 0 0 14 9 8 6 3 3 3 2 2 2 5 7 4 49 4 9 12 19 t 0 0 0 0 0 29 29 22 61 64 10 64 69 71 69 4 8 7 8 9 18 26 20

oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/3; ncol2=22; w=-4; offset=-4; strand=R; shift=1; score=0.701688; -wwktmTTTwATTTwAAAgaywd ; cor=; Ncor= a 0 9 9 6 3 8 6 4 2 18 23 0 0 2 8 23 24 25 5 19 5 10 7 c 0 2 5 2 5 12 1 2 3 2 1 1 2 0 2 0 0 0 3 3 11 5 4 g 0 5 2 10 3 2 1 2 1 1 0 2 1 0 2 3 1 0 16 4 2 5 8 t 0 12 12 10 17 6 20 20 22 7 4 25 25 26 16 2 3 3 4 2 10 8 9

oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/3; ncol2=23; w=-5; offset=-5; strand=R; shift=0; score=0.599832; yttTTwTTTTTTyTTwrAgAcag ; cor=; Ncor= a 12 5 7 3 4 23 4 2 3 0 1 3 9 2 5 33 34 51 6 43 8 26 13 c 15 8 12 4 2 2 3 1 2 1 4 2 17 1 2 1 2 1 8 3 32 10 9 g 6 12 6 2 5 4 0 2 0 3 1 1 2 3 3 2 16 1 36 4 4 14 24 t 24 32 32 48 46 28 50 52 52 53 51 51 29 51 47 21 5 4 7 7 13 7 11

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; awgTAAGCTAwr ; Alignment reference a 37 30 14 8 81 93 4 3 1 92 27 33 c 20 19 13 1 6 1 3 92 4 2 24 19 g 21 20 64 7 12 3 89 4 4 1 18 30 t 23 32 10 85 2 4 5 2 92 6 32 19

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; awgTAAGCTAwr ; cor=; Ncor= a 37 30 14 8 81 93 4 3 1 92 27 33 c 20 19 13 1 6 1 3 92 4 2 24 19 g 21 20 64 7 12 3 89 4 4 1 18 30 t 23 32 10 85 2 4 5 2 92 6 32 19

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=23; shift=0; ncol=23; ctgTcTywAArAAAAAAwAAaar ; Alignment reference a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 24 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 6 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 15 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5 12

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; ctgTcTywAArAAAAAAwAAaar ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 24 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 6 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 15 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5 12

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.694325; hwrtcTTTwAAATwAAAkamww- ; cor=; Ncor= a 9 8 10 2 4 3 3 2 16 26 25 25 4 7 22 20 20 6 17 10 12 12 0 c 8 5 2 4 16 0 1 3 2 0 1 2 0 1 1 2 1 2 3 10 2 5 0 g 4 5 11 3 3 0 0 0 2 0 2 1 1 2 3 2 1 12 5 2 5 2 0 t 7 10 5 19 5 25 24 23 8 2 0 0 23 18 2 4 6 8 3 6 9 9 0

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=3/6; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.599832; wwgTcTTTAAAATAArww----- ; cor=; Ncor= a 20 26 18 9 8 7 8 4 69 71 69 64 10 64 61 22 29 29 0 0 0 0 0 c 19 12 9 4 49 4 7 5 2 2 2 3 3 3 6 8 9 14 0 0 0 0 0 g 13 10 35 6 6 4 9 3 1 1 4 5 6 6 3 30 9 10 0 0 0 0 0 t 26 30 16 59 15 63 54 66 6 4 3 6 59 5 8 18 31 25 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=4/6; ncol2=16; w=0; offset=7; strand=D; shift=7; score=0.593102; -------wwdmAAAAAAtAAraa ; cor=; Ncor= a 0 0 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 c 0 0 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 g 0 0 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 t 0 0 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36

oligos_7nt_test_vs_ctrl_m4_shift7 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=5/6; ncol2=14; w=0; offset=7; strand=D; shift=7; score=0.527954; -------waArAAAAAAAcaa-- ; cor=; Ncor= a 0 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 0 0 c 0 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 0 0 g 0 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 0 0 t 0 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70 0 0

oligos_6nt_test_vs_ctrl_m4_shift6 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=6/6; ncol2=24; w=0; offset=6; strand=D; shift=6; score=0.514428; ------aaAArAAAAAAmAAAww ; cor=; Ncor= a 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 114 78 59 c 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 5 2 9 g 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 4 5 15 t 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5 3 41 43

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; wwAAAACATGTTTTww ; Alignment reference a 58 55 110 110 124 136 19 137 10 19 7 15 17 21 43 40 c 22 24 7 16 12 5 109 4 3 7 6 3 11 16 32 34 g 34 32 16 11 3 6 7 3 4 109 5 12 16 7 24 22 t 40 43 21 17 15 7 19 10 137 19 136 124 110 110 55 58

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/1; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; wwAAAACATGTTTTww ; cor=; Ncor= a 58 55 110 110 124 136 19 137 10 19 7 15 17 21 43 40 c 22 24 7 16 12 5 109 4 3 7 6 3 11 16 32 34 g 34 32 16 11 3 6 7 3 4 109 5 12 16 7 24 22 t 40 43 21 17 15 7 19 10 137 19 136 124 110 110 55 58

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift7 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift7 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=14; shift=7; ncol=21; -------waArAAAAAAAcaa ; Alignment reference a 0 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 c 0 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 g 0 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 t 0 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70

oligos_7nt_test_vs_ctrl_m4_shift7 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=7; score= 1; -------waArAAAAAAAcaa ; cor=; Ncor= a 0 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 c 0 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 g 0 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 t 0 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70

oligos_6nt_test_vs_ctrl_m5_shift5 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=2/4; ncol2=16; w=-2; offset=-2; strand=D; shift=5; score=0.697407; -----wwdmAAAAAAtAAraa ; cor=; Ncor= a 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 c 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 g 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 t 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=23; w=-7; offset=-7; strand=D; shift=0; score=0.527954; ctgTcTywAArAAAAAAwAAa ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7

oligos_6nt_test_vs_ctrl_m4_shift7 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=4/4; ncol2=24; w=0; offset=0; strand=D; shift=7; score=0.50682; -------aaAArAAAAAAmAA ; cor=; Ncor= a 0 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 c 0 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 g 0 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 t 0 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift6 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift6 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=6; ncol=30; ------aaAArAAAAAAmAAAwwAAArAaa ; Alignment reference a 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 114 78 59 112 103 108 55 99 66 75 c 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 5 2 9 6 8 5 18 6 15 20 g 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 4 5 15 2 4 10 43 9 21 11 t 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5 3 41 43 6 11 3 10 12 24 20

oligos_6nt_test_vs_ctrl_m4_shift6 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------aaAArAAAAAAmAAAwwAAArAaa ; cor=; Ncor= a 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 114 78 59 112 103 108 55 99 66 75 c 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 5 2 9 6 8 5 18 6 15 20 g 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 4 5 15 2 4 10 43 9 21 11 t 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5 3 41 43 6 11 3 10 12 24 20

oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=2/4; ncol2=16; w=0; offset=1; strand=D; shift=7; score=0.543161; -------wwdmAAAAAAtAAraa------- ; cor=; Ncor= a 0 0 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=23; w=-6; offset=-6; strand=D; shift=0; score=0.514428; ctgTcTywAArAAAAAAwAAaar------- ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 24 0 0 0 0 0 0 0 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 6 0 0 0 0 0 0 0 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 15 0 0 0 0 0 0 0 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5 12 0 0 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m4_shift6 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=4/4; ncol2=14; w=0; offset=0; strand=D; shift=6; score=0.50682; ------waArAAAAAAAcaa---------- ; cor=; Ncor= a 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift7 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=16; shift=7; ncol=23; -------wwdmAAAAAAtAAraa ; Alignment reference a 0 0 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 c 0 0 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 g 0 0 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 t 0 0 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36

oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=7; score= 1; -------wwdmAAAAAAtAAraa ; cor=; Ncor= a 0 0 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 c 0 0 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 g 0 0 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 t 0 0 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36

oligos_7nt_test_vs_ctrl_m4_shift9 (oligos_7nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4; m=2/4; ncol2=14; w=0; offset=2; strand=D; shift=9; score=0.697407; ---------waArAAAAAAAcaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 c 0 0 0 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 g 0 0 0 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 t 0 0 0 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=23; w=-7; offset=-7; strand=D; shift=0; score=0.593102; ctgTcTywAArAAAAAAwAAaar ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 24 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 6 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 15 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5 12

oligos_6nt_test_vs_ctrl_m4_shift6 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=4/4; ncol2=24; w=-1; offset=-1; strand=D; shift=6; score=0.543161; ------aaAArAAAAAAmAAAww ; cor=; Ncor= a 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 114 78 59 c 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 5 2 9 g 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 4 5 15 t 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5 3 41 43

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=22; shift=0; ncol=22; hwrtcTTTwAAATwAAAkamww ; Alignment reference a 9 8 10 2 4 3 3 2 16 26 25 25 4 7 22 20 20 6 17 10 12 12 c 8 5 2 4 16 0 1 3 2 0 1 2 0 1 1 2 1 2 3 10 2 5 g 4 5 11 3 3 0 0 0 2 0 2 1 1 2 3 2 1 12 5 2 5 2 t 7 10 5 19 5 25 24 23 8 2 0 0 23 18 2 4 6 8 3 6 9 9

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/3; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; hwrtcTTTwAAATwAAAkamww ; cor=; Ncor= a 9 8 10 2 4 3 3 2 16 26 25 25 4 7 22 20 20 6 17 10 12 12 c 8 5 2 4 16 0 1 3 2 0 1 2 0 1 1 2 1 2 3 10 2 5 g 4 5 11 3 3 0 0 0 2 0 2 1 1 2 3 2 1 12 5 2 5 2 t 7 10 5 19 5 25 24 23 8 2 0 0 23 18 2 4 6 8 3 6 9 9

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/3; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.701688; wwgTcTTTAAAATAArww---- ; cor=; Ncor= a 20 26 18 9 8 7 8 4 69 71 69 64 10 64 61 22 29 29 0 0 0 0 c 19 12 9 4 49 4 7 5 2 2 2 3 3 3 6 8 9 14 0 0 0 0 g 13 10 35 6 6 4 9 3 1 1 4 5 6 6 3 30 9 10 0 0 0 0 t 26 30 16 59 15 63 54 66 6 4 3 6 59 5 8 18 31 25 0 0 0 0

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.694325; ctgTcTywAArAAAAAAwAAaa ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; dhCAACATACyy ; Alignment reference a 35 33 8 95 99 9 107 3 91 8 23 21 c 14 31 92 7 10 93 1 4 1 91 34 33 g 29 20 2 4 1 8 2 0 7 9 18 25 t 34 28 10 6 2 2 2 105 13 4 37 33

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; dhCAACATACyy ; cor=; Ncor= a 35 33 8 95 99 9 107 3 91 8 23 21 c 14 31 92 7 10 93 1 4 1 91 34 33 g 29 20 2 4 1 8 2 0 7 9 18 25 t 34 28 10 6 2 2 2 105 13 4 37 33

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAAGTTAGwh ; Alignment reference a 60 67 179 185 18 13 14 195 12 56 52 c 38 32 11 1 7 4 3 3 12 34 60 g 37 40 3 5 158 13 6 1 162 45 37 t 66 62 8 10 18 171 178 2 15 66 52

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAAGTTAGwh ; cor=; Ncor= a 60 67 179 185 18 13 14 195 12 56 52 c 38 32 11 1 7 4 3 3 12 34 60 g 37 40 3 5 158 13 6 1 162 45 37 t 66 62 8 10 18 171 178 2 15 66 52

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift5 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=18; shift=5; ncol=23; -----wwyTTATTTTAAAgAcww ; Alignment reference a 0 0 0 0 0 25 31 18 8 5 59 6 3 4 6 66 54 63 15 59 16 30 26 c 0 0 0 0 0 10 9 30 3 6 6 5 4 1 1 3 9 4 6 6 35 10 13 g 0 0 0 0 0 14 9 8 6 3 3 3 2 2 2 5 7 4 49 4 9 12 19 t 0 0 0 0 0 29 29 22 61 64 10 64 69 71 69 4 8 7 8 9 18 26 20
oligos_6nt_test_vs_ctrl_m2_shift5 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=5; score= 1; -----wwyTTATTTTAAAgAcww ; cor=; Ncor= a 0 0 0 0 0 25 31 18 8 5 59 6 3 4 6 66 54 63 15 59 16 30 26 c 0 0 0 0 0 10 9 30 3 6 6 5 4 1 1 3 9 4 6 6 35 10 13 g 0 0 0 0 0 14 9 8 6 3 3 3 2 2 2 5 7 4 49 4 9 12 19 t 0 0 0 0 0 29 29 22 61 64 10 64 69 71 69 4 8 7 8 9 18 26 20
oligos_6nt_test_vs_ctrl_m3_rc_shift1 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/3; ncol2=22; w=-4; offset=-4; strand=R; shift=1; score=0.701688; -wwktmTTTwATTTwAAAgaywd ; cor=; Ncor= a 0 9 9 6 3 8 6 4 2 18 23 0 0 2 8 23 24 25 5 19 5 10 7 c 0 2 5 2 5 12 1 2 3 2 1 1 2 0 2 0 0 0 3 3 11 5 4 g 0 5 2 10 3 2 1 2 1 1 0 2 1 0 2 3 1 0 16 4 2 5 8 t 0 12 12 10 17 6 20 20 22 7 4 25 25 26 16 2 3 3 4 2 10 8 9
oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/3; ncol2=23; w=-5; offset=-5; strand=R; shift=0; score=0.599832; yttTTwTTTTTTyTTwrAgAcag ; cor=; Ncor= a 12 5 7 3 4 23 4 2 3 0 1 3 9 2 5 33 34 51 6 43 8 26 13 c 15 8 12 4 2 2 3 1 2 1 4 2 17 1 2 1 2 1 8 3 32 10 9 g 6 12 6 2 5 4 0 2 0 3 1 1 2 3 3 2 16 1 36 4 4 14 24 t 24 32 32 48 46 28 50 52 52 53 51 51 29 51 47 21 5 4 7 7 13 7 11

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=23; shift=0; ncol=23; ctgTcTywAArAAAAAAwAAaar ; Alignment reference a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 24 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 6 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 15 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5 12
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/6; ncol2=23; w=0; offset=0; strand=D; shift=0; score= 1; ctgTcTywAArAAAAAAwAAaar ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 24 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 6 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 15 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5 12
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=2/6; ncol2=22; w=0; offset=0; strand=D; shift=0; score=0.694325; hwrtcTTTwAAATwAAAkamww- ; cor=; Ncor= a 9 8 10 2 4 3 3 2 16 26 25 25 4 7 22 20 20 6 17 10 12 12 0 c 8 5 2 4 16 0 1 3 2 0 1 2 0 1 1 2 1 2 3 10 2 5 0 g 4 5 11 3 3 0 0 0 2 0 2 1 1 2 3 2 1 12 5 2 5 2 0 t 7 10 5 19 5 25 24 23 8 2 0 0 23 18 2 4 6 8 3 6 9 9 0
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=3/6; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.599832; wwgTcTTTAAAATAArww----- ; cor=; Ncor= a 20 26 18 9 8 7 8 4 69 71 69 64 10 64 61 22 29 29 0 0 0 0 0 c 19 12 9 4 49 4 7 5 2 2 2 3 3 3 6 8 9 14 0 0 0 0 0 g 13 10 35 6 6 4 9 3 1 1 4 5 6 6 3 30 9 10 0 0 0 0 0 t 26 30 16 59 15 63 54 66 6 4 3 6 59 5 8 18 31 25 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=4/6; ncol2=16; w=0; offset=7; strand=D; shift=7; score=0.593102; -------wwdmAAAAAAtAAraa ; cor=; Ncor= a 0 0 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 c 0 0 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 g 0 0 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 t 0 0 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36
oligos_7nt_test_vs_ctrl_m4_shift7 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=5/6; ncol2=14; w=0; offset=7; strand=D; shift=7; score=0.527954; -------waArAAAAAAAcaa-- ; cor=; Ncor= a 0 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 0 0 c 0 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 0 0 g 0 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 0 0 t 0 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70 0 0
oligos_6nt_test_vs_ctrl_m4_shift6 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=6/6; ncol2=24; w=0; offset=6; strand=D; shift=6; score=0.514428; ------aaAArAAAAAAmAAAww ; cor=; Ncor= a 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 114 78 59 c 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 5 2 9 g 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 4 5 15 t 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5 3 41 43

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift7 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=14; shift=7; ncol=21; -------waArAAAAAAAcaa ; Alignment reference a 0 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 c 0 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 g 0 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 t 0 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70
oligos_7nt_test_vs_ctrl_m4_shift7 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=7; score= 1; -------waArAAAAAAAcaa ; cor=; Ncor= a 0 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 c 0 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 g 0 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 t 0 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70
oligos_6nt_test_vs_ctrl_m5_shift5 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=2/4; ncol2=16; w=-2; offset=-2; strand=D; shift=5; score=0.697407; -----wwdmAAAAAAtAAraa ; cor=; Ncor= a 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 c 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 g 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 t 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=23; w=-7; offset=-7; strand=D; shift=0; score=0.527954; ctgTcTywAArAAAAAAwAAa ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7
oligos_6nt_test_vs_ctrl_m4_shift7 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=4/4; ncol2=24; w=0; offset=0; strand=D; shift=7; score=0.50682; -------aaAArAAAAAAmAA ; cor=; Ncor= a 0 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 c 0 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 g 0 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 t 0 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift6 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=6; ncol=30; ------aaAArAAAAAAmAAAwwAAArAaa ; Alignment reference a 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 114 78 59 112 103 108 55 99 66 75 c 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 5 2 9 6 8 5 18 6 15 20 g 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 4 5 15 2 4 10 43 9 21 11 t 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5 3 41 43 6 11 3 10 12 24 20
oligos_6nt_test_vs_ctrl_m4_shift6 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=6; score= 1; ------aaAArAAAAAAmAAAwwAAArAaa ; cor=; Ncor= a 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 114 78 59 112 103 108 55 99 66 75 c 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 5 2 9 6 8 5 18 6 15 20 g 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 4 5 15 2 4 10 43 9 21 11 t 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5 3 41 43 6 11 3 10 12 24 20
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=2/4; ncol2=16; w=0; offset=1; strand=D; shift=7; score=0.543161; -------wwdmAAAAAAtAAraa------- ; cor=; Ncor= a 0 0 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=23; w=-6; offset=-6; strand=D; shift=0; score=0.514428; ctgTcTywAArAAAAAAwAAaar------- ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 24 0 0 0 0 0 0 0 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 6 0 0 0 0 0 0 0 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 15 0 0 0 0 0 0 0 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5 12 0 0 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m4_shift6 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=4/4; ncol2=14; w=0; offset=0; strand=D; shift=6; score=0.50682; ------waArAAAAAAAcaa---------- ; cor=; Ncor= a 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=16; shift=7; ncol=23; -------wwdmAAAAAAtAAraa ; Alignment reference a 0 0 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 c 0 0 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 g 0 0 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 t 0 0 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=7; score= 1; -------wwdmAAAAAAtAAraa ; cor=; Ncor= a 0 0 0 0 0 0 0 62 51 49 44 155 148 161 169 160 155 38 148 148 69 85 85 c 0 0 0 0 0 0 0 22 32 16 101 7 7 6 1 4 5 15 4 8 12 30 28 g 0 0 0 0 0 0 0 23 32 64 9 3 9 3 0 3 3 5 6 8 71 17 25 t 0 0 0 0 0 0 0 67 59 45 20 9 10 4 4 7 11 116 16 10 22 42 36
oligos_7nt_test_vs_ctrl_m4_shift9 (oligos_7nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4; m=2/4; ncol2=14; w=0; offset=2; strand=D; shift=9; score=0.697407; ---------waArAAAAAAAcaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 130 142 273 97 310 298 291 280 300 284 299 79 160 146 c 0 0 0 0 0 0 0 0 0 44 58 6 33 6 8 14 18 11 12 10 159 51 75 g 0 0 0 0 0 0 0 0 0 55 49 16 176 4 10 9 8 2 7 3 29 44 35 t 0 0 0 0 0 0 0 0 0 97 77 31 20 6 10 12 20 13 23 14 59 71 70
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=23; w=-7; offset=-7; strand=D; shift=0; score=0.593102; ctgTcTywAArAAAAAAwAAaar ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 24 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 6 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 15 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5 12
oligos_6nt_test_vs_ctrl_m4_shift6 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=4/4; ncol2=24; w=-1; offset=-1; strand=D; shift=6; score=0.543161; ------aaAArAAAAAAmAAAww ; cor=; Ncor= a 0 0 0 0 0 0 72 77 99 100 74 117 118 115 112 114 117 70 114 115 114 78 59 c 0 0 0 0 0 0 17 11 8 2 8 5 3 1 4 4 0 37 5 3 5 2 9 g 0 0 0 0 0 0 14 16 7 6 40 1 3 1 4 2 3 13 2 3 4 5 15 t 0 0 0 0 0 0 23 22 12 18 4 3 2 9 6 6 6 6 5 5 3 41 43

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=22; shift=0; ncol=22; hwrtcTTTwAAATwAAAkamww ; Alignment reference a 9 8 10 2 4 3 3 2 16 26 25 25 4 7 22 20 20 6 17 10 12 12 c 8 5 2 4 16 0 1 3 2 0 1 2 0 1 1 2 1 2 3 10 2 5 g 4 5 11 3 3 0 0 0 2 0 2 1 1 2 3 2 1 12 5 2 5 2 t 7 10 5 19 5 25 24 23 8 2 0 0 23 18 2 4 6 8 3 6 9 9
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/3; ncol2=22; w=0; offset=0; strand=D; shift=0; score= 1; hwrtcTTTwAAATwAAAkamww ; cor=; Ncor= a 9 8 10 2 4 3 3 2 16 26 25 25 4 7 22 20 20 6 17 10 12 12 c 8 5 2 4 16 0 1 3 2 0 1 2 0 1 1 2 1 2 3 10 2 5 g 4 5 11 3 3 0 0 0 2 0 2 1 1 2 3 2 1 12 5 2 5 2 t 7 10 5 19 5 25 24 23 8 2 0 0 23 18 2 4 6 8 3 6 9 9
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/3; ncol2=18; w=0; offset=0; strand=R; shift=0; score=0.701688; wwgTcTTTAAAATAArww---- ; cor=; Ncor= a 20 26 18 9 8 7 8 4 69 71 69 64 10 64 61 22 29 29 0 0 0 0 c 19 12 9 4 49 4 7 5 2 2 2 3 3 3 6 8 9 14 0 0 0 0 g 13 10 35 6 6 4 9 3 1 1 4 5 6 6 3 30 9 10 0 0 0 0 t 26 30 16 59 15 63 54 66 6 4 3 6 59 5 8 18 31 25 0 0 0 0
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=23; w=0; offset=0; strand=D; shift=0; score=0.694325; ctgTcTywAArAAAAAAwAAaa ; cor=; Ncor= a 11 7 13 7 7 4 5 21 47 51 29 51 51 53 52 52 50 28 46 48 32 32 c 24 14 4 4 36 1 16 2 3 3 2 1 1 3 0 2 0 4 5 2 6 12 g 9 10 32 3 8 1 2 1 2 1 17 2 4 1 2 1 3 2 2 4 12 8 t 13 26 8 43 6 51 34 33 5 2 9 3 1 0 3 2 4 23 4 3 7 5