One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/07/28/peak-motifs.2026-07-28.153924_2026-07-28.153924_P9lKwt/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/07/28/peak-motifs.2026-07-28.153924_2026-07-28.153924_P9lKwt/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssGcGGcGsGGGCGGGGCGGrGss ; Alignment reference a 0 0 10 15 7 12 7 8 13 4 9 3 2 9 9 3 2 4 4 7 2 2 35 6 15 12 c 0 0 27 30 8 63 12 16 56 3 53 12 6 5 70 7 4 13 4 68 15 12 14 12 34 27 g 0 0 50 42 76 14 72 65 22 86 29 73 86 77 14 81 85 72 83 14 73 78 34 69 39 42 t 0 0 7 7 3 5 3 5 3 1 3 6 0 3 1 3 3 5 3 5 4 2 11 7 6 13

oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssGcGGcGsGGGCGGGGCGGrGss ; cor=; Ncor= a 0 0 10 15 7 12 7 8 13 4 9 3 2 9 9 3 2 4 4 7 2 2 35 6 15 12 c 0 0 27 30 8 63 12 16 56 3 53 12 6 5 70 7 4 13 4 68 15 12 14 12 34 27 g 0 0 50 42 76 14 72 65 22 86 29 73 86 77 14 81 85 72 83 14 73 78 34 69 39 42 t 0 0 7 7 3 5 3 5 3 1 3 6 0 3 1 3 3 5 3 5 4 2 11 7 6 13

oligos_6nt_test_vs_ctrl_m5_rc_shift2 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/8; ncol2=24; w=0; offset=0; strand=R; shift=2; score=0.735076; --sgssCGGCGsGGCGGGGCGGmGss ; cor=; Ncor= a 0 0 6 5 2 2 0 1 3 1 1 0 1 0 2 3 1 2 1 2 2 0 10 2 4 3 c 0 0 9 5 16 15 20 2 0 20 1 13 4 2 20 0 2 0 1 20 0 2 8 1 9 7 g 0 0 9 13 8 7 5 22 21 5 21 10 21 23 4 21 21 23 24 3 21 24 6 23 12 10 t 0 0 2 3 0 2 1 1 2 0 3 3 0 1 0 2 2 1 0 1 3 0 2 0 1 6

oligos_7nt_test_vs_ctrl_m4_shift5 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/8; ncol2=24; w=0; offset=3; strand=D; shift=5; score=0.661665; -----sggcGGGGGCGGGGCcgsGss ; cor=; Ncor= a 0 0 0 0 0 12 13 12 23 8 2 6 1 5 2 3 5 9 6 5 7 18 10 3 11 10 c 0 0 0 0 0 37 28 24 60 18 9 8 8 9 106 6 5 7 4 93 80 12 64 9 70 60 g 0 0 0 0 0 57 58 77 24 92 105 104 110 104 9 111 102 104 110 20 23 71 37 103 31 39 t 0 0 0 0 0 15 22 8 14 3 5 3 2 3 4 1 9 1 1 3 11 20 10 6 9 12

oligos_7nt_test_vs_ctrl_m1_rc_shift5 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/8; ncol2=24; w=0; offset=3; strand=R; shift=5; score=0.658641; -----gsGcGGGGGCGGGGCGcGGcs ; cor=; Ncor= a 0 0 0 0 0 13 12 4 10 10 3 2 5 8 6 3 0 7 2 5 2 11 7 5 14 5 c 0 0 0 0 0 24 26 15 60 15 7 17 12 7 86 3 7 6 4 82 21 57 8 16 59 58 g 0 0 0 0 0 49 47 73 19 70 86 77 83 83 5 93 90 86 93 10 76 24 83 72 22 28 t 0 0 0 0 0 15 16 9 12 6 5 5 1 3 4 2 4 2 2 4 2 9 3 8 6 10

oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=5/8; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.656911; ssccGCGGCGCGGGGCGGGcGcss-- ; cor=; Ncor= a 3 7 9 6 2 6 3 3 3 3 6 3 2 2 2 5 4 3 1 7 3 5 5 3 0 0 c 21 23 37 41 6 50 3 4 46 7 52 6 3 6 6 51 7 16 4 43 11 45 20 17 0 0 g 36 28 16 15 55 10 56 56 14 56 6 58 61 55 59 6 52 48 61 14 49 15 32 35 0 0 t 7 9 5 5 4 1 5 4 4 1 3 0 1 4 0 5 4 0 1 3 4 2 10 12 0 0

oligos_6nt_test_vs_ctrl_m4_rc_shift6 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/8; ncol2=24; w=0; offset=4; strand=R; shift=6; score=0.562263; ------sssSsGGGCGGGGCGCGGCs ; cor=; Ncor= a 0 0 0 0 0 0 2 2 0 1 4 0 0 2 2 0 0 2 0 0 0 1 1 0 0 0 c 0 0 0 0 0 0 7 7 9 16 9 2 4 2 17 0 3 1 1 21 1 18 0 4 18 14 g 0 0 0 0 0 0 12 13 13 6 7 20 19 19 2 22 18 20 22 1 21 3 20 17 3 6 t 0 0 0 0 0 0 2 1 1 0 3 1 0 0 2 1 2 0 0 1 1 1 2 2 2 3

oligos_6nt_test_vs_ctrl_m1_rc_shift7 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=7/8; ncol2=24; w=0; offset=5; strand=R; shift=7; score=0.533977; -------scGGGGGCGGGGCcGCGCs ; cor=; Ncor= a 0 0 0 0 0 0 0 7 9 2 0 3 2 1 0 1 2 3 2 1 5 3 1 1 4 1 c 0 0 0 0 0 0 0 16 15 5 5 6 2 4 39 5 3 6 2 34 29 4 34 1 32 26 g 0 0 0 0 0 0 0 16 10 35 36 32 38 37 2 36 35 33 38 6 6 30 6 37 6 15 t 0 0 0 0 0 0 0 4 9 1 2 2 1 1 2 1 3 1 1 2 3 6 2 4 1 1

oligos_6nt_test_vs_ctrl_m2_rc_shift9 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/8; ncol2=24; w=0; offset=7; strand=R; shift=9; score=0.411075; ---------sgCGGCGsGGCGGGGCs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 3 1 0 1 0 0 0 3 1 3 2 1 0 1 2 1 c 0 0 0 0 0 0 0 0 0 6 3 19 5 1 21 1 15 2 2 17 0 2 3 1 18 6 g 0 0 0 0 0 0 0 0 0 10 13 2 18 20 2 20 7 17 20 3 20 18 20 21 3 15 t 0 0 0 0 0 0 0 0 0 4 4 1 0 1 0 2 1 1 0 0 1 2 0 0 0 1

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssgCgCCCGCCCCGCGCCGCggss ; Alignment reference a 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 c 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 g 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 t 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssgCgCCCGCCCCGCGCCGCggss ; cor=; Ncor= a 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 c 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 g 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 t 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=2/7; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.799299; --cssssGCsGCCCCGCCsCGCCGcs ; cor=; Ncor= a 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 c 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 g 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 t 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3

oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=3/7; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.759556; --scGmGCGCGCkCCGCGgCCCcGsc ; cor=; Ncor= a 0 0 1 5 1 6 1 0 3 0 0 1 1 1 1 2 2 0 1 1 1 0 0 1 4 5 c 0 0 6 9 0 13 3 18 2 16 2 18 4 18 16 2 18 3 4 18 16 16 14 1 6 10 g 0 0 12 4 19 2 15 2 16 5 18 1 7 2 1 15 1 18 14 2 4 5 5 18 9 4 t 0 0 2 3 1 0 2 1 0 0 1 1 9 0 3 2 0 0 2 0 0 0 2 1 2 2

oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=4/7; ncol2=24; w=-1; offset=-1; strand=D; shift=1; score=0.667561; -ssgsgCCgCGCCCCGCCCCCgCsc- ; cor=; Ncor= a 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 15 0 c 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 49 0 g 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 24 0 t 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12 13 0

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=5/7; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.656911; ssCyCCGCCCCGCCCsCgCCgCss-- ; cor=; Ncor= a 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 3 5 3 7 7 0 0 c 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 72 14 76 42 50 0 0 g 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 12 63 8 30 27 0 0 t 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8 7 12 7 15 10 0 0

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=6/7; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.632697; cvsGsGCCGCGCCCCGCCCsSsss-- ; cor=; Ncor= a 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 0 0 c 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 0 0 g 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 0 0 t 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2 0 0

oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=7/7; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.630863; ----ssCkCCGCCCCGCCsCGCCGss ; cor=; Ncor= a 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 0 c 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 8 g 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 16 t 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2 2

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift4 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift4 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=4; ncol=28; ----ssgsgCCgCGCCCCGCCCCCgCsc ; Alignment reference a 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 15 c 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 49 g 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 24 t 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12 13

oligos_7nt_test_vs_ctrl_m1_shift4 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----ssgsgCCgCGCCCCGCCCCCgCsc ; cor=; Ncor= a 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 15 c 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 49 g 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 24 t 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12 13

oligos_7nt_test_vs_ctrl_m4_rc_shift4 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=2/8; ncol2=24; w=0; offset=0; strand=R; shift=4; score=0.872169; ----ssCssCscgGCCCCGCCCCCgccs ; cor=; Ncor= a 0 0 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 22 15 c 0 0 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 58 57 g 0 0 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 28 37 t 0 0 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12 13 12

oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=3/8; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.828866; ---cvsGsGCCGCGCCCCGCCCsSsss- ; cor=; Ncor= a 0 0 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 0 c 0 0 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 0 g 0 0 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 0 t 0 0 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2 0

oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/8; ncol2=24; w=0; offset=1; strand=D; shift=5; score=0.667561; -----ssgCgCCCGCCCCGCGCCGCggs ; cor=; Ncor= a 0 0 0 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 c 0 0 0 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 g 0 0 0 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 t 0 0 0 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7

oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=5/8; ncol2=24; w=-2; offset=-2; strand=D; shift=2; score=0.662782; --scsGCsGCGCgGCCCCGCCCCCgs-- ; cor=; Ncor= a 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 0 0 c 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 0 0 g 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 0 0 t 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7 0 0

oligos_7nt_test_vs_ctrl_m2_rc_shift7 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2_rc; m=6/8; ncol2=24; w=0; offset=3; strand=R; shift=7; score=0.658641; -------ssCyCCGCCCCGCCCsCgCCg ; cor=; Ncor= a 0 0 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 3 5 c 0 0 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 72 14 g 0 0 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 12 63 t 0 0 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8 7 12

oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=7/8; ncol2=24; w=0; offset=3; strand=D; shift=7; score=0.580127; -------ssCkCCGCCCCGCCsCGCCGs ; cor=; Ncor= a 0 0 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 c 0 0 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 g 0 0 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 t 0 0 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=8/8; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.527422; cssssGCsGCCCCGCCsCGCCGcs---- ; cor=; Ncor= a 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 0 0 0 0 c 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 0 0 0 0 g 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 0 0 0 0 t 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---cvsGsGCCGCGCCCCGCCCsSsss ; Alignment reference a 0 0 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 c 0 0 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 g 0 0 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 t 0 0 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2

oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---cvsGsGCCGCGCCCCGCCCsSsss ; cor=; Ncor= a 0 0 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 c 0 0 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 g 0 0 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 t 0 0 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2

oligos_7nt_test_vs_ctrl_m1_shift4 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1; m=2/7; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.828866; ----ssgsgCCgCGCCCCGCCCCCgCs ; cor=; Ncor= a 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 c 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 g 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 t 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12

oligos_7nt_test_vs_ctrl_m4_rc_shift4 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/7; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.662447; ----ssCssCscgGCCCCGCCCCCgcc ; cor=; Ncor= a 0 0 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 22 c 0 0 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 58 g 0 0 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 28 t 0 0 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12 13

oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=4/7; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.632697; -----ssgCgCCCGCCCCGCGCCGCgg ; cor=; Ncor= a 0 0 0 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 c 0 0 0 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 g 0 0 0 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 t 0 0 0 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9

oligos_7nt_test_vs_ctrl_m2_rc_shift7 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=5/7; ncol2=24; w=0; offset=4; strand=R; shift=7; score=0.562263; -------ssCyCCGCCCCGCCCsCgCC ; cor=; Ncor= a 0 0 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 3 c 0 0 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 72 g 0 0 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 12 t 0 0 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8 7

oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=6/7; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.544727; cssssGCsGCCCCGCCsCGCCGcs--- ; cor=; Ncor= a 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 0 0 0 c 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 0 0 0 g 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 0 0 0 t 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3 0 0 0

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=7/7; ncol2=24; w=0; offset=4; strand=D; shift=7; score=0.533896; -------ssCkCCGCCCCGCCsCGCCG ; cor=; Ncor= a 0 0 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 c 0 0 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 g 0 0 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 t 0 0 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift5 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift5 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=5; ncol=29; -----scsGCsGCGCgGCCCCGCCCCCgs ; Alignment reference a 0 0 0 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 c 0 0 0 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 g 0 0 0 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 t 0 0 0 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7

oligos_6nt_test_vs_ctrl_m1_shift5 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----scsGCsGCGCgGCCCCGCCCCCgs ; cor=; Ncor= a 0 0 0 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 c 0 0 0 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 g 0 0 0 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 t 0 0 0 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7

oligos_7nt_test_vs_ctrl_m4_rc_shift7 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=2/8; ncol2=24; w=0; offset=2; strand=R; shift=7; score=0.803037; -------ssCssCscgGCCCCGCCCCCgc ; cor=; Ncor= a 0 0 0 0 0 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 c 0 0 0 0 0 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 g 0 0 0 0 0 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 t 0 0 0 0 0 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12

oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=3/8; ncol2=24; w=0; offset=2; strand=D; shift=7; score=0.662782; -------ssgsgCCgCGCCCCGCCCCCgC ; cor=; Ncor= a 0 0 0 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 c 0 0 0 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 g 0 0 0 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 t 0 0 0 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4

oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=4/8; ncol2=24; w=-2; offset=-2; strand=D; shift=3; score=0.620869; ---cssssGCsGCCCCGCCsCGCCGcs-- ; cor=; Ncor= a 0 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 0 0 c 0 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 0 0 g 0 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 0 0 t 0 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3 0 0

oligos_7nt_test_vs_ctrl_m2_rc_shift10 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=24; w=0; offset=5; strand=R; shift=10; score=0.533977; ----------ssCyCCGCCCCGCCCsCgC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 c 0 0 0 0 0 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 g 0 0 0 0 0 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 t 0 0 0 0 0 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8

oligos_7nt_test_vs_ctrl_m3_shift9 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=6/8; ncol2=24; w=0; offset=4; strand=D; shift=9; score=0.512085; ---------ssgrGCGGCGsCGsCGCCGC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4 2 2 15 0 1 1 0 0 1 1 0 0 0 1 2 2 2 0 1 c 0 0 0 0 0 0 0 0 0 11 13 4 6 2 22 0 5 23 6 8 23 5 19 20 3 21 25 5 25 g 0 0 0 0 0 0 0 0 0 11 8 19 7 25 5 25 21 3 20 19 5 23 8 6 23 5 0 22 2 t 0 0 0 0 0 0 0 0 0 2 5 3 0 1 0 2 2 2 1 0 0 0 1 1 0 0 1 1 0

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=7/8; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.497653; scGmGCGCGCkCCGCGgCCCcGsc----- ; cor=; Ncor= a 1 5 1 6 1 0 3 0 0 1 1 1 1 2 2 0 1 1 1 0 0 1 4 5 0 0 0 0 0 c 6 9 0 13 3 18 2 16 2 18 4 18 16 2 18 3 4 18 16 16 14 1 6 10 0 0 0 0 0 g 12 4 19 2 15 2 16 5 18 1 7 2 1 15 1 18 14 2 4 5 5 18 9 4 0 0 0 0 0 t 2 3 1 0 2 1 0 0 1 1 9 0 3 2 0 0 2 0 0 0 2 1 2 2 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_shift10 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=8/8; ncol2=24; w=0; offset=5; strand=D; shift=10; score=0.481037; ----------ssCkCCGCCCCGCCsCGCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 c 0 0 0 0 0 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 g 0 0 0 0 0 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 t 0 0 0 0 0 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift3 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift3 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---sggcGGGGGCGGGGCcgsGssGss ; Alignment reference a 0 0 0 12 13 12 23 8 2 6 1 5 2 3 5 9 6 5 7 18 10 3 11 10 6 23 22 c 0 0 0 37 28 24 60 18 9 8 8 9 106 6 5 7 4 93 80 12 64 9 70 60 22 38 35 g 0 0 0 57 58 77 24 92 105 104 110 104 9 111 102 104 110 20 23 71 37 103 31 39 83 55 55 t 0 0 0 15 22 8 14 3 5 3 2 3 4 1 9 1 1 3 11 20 10 6 9 12 10 5 9

oligos_7nt_test_vs_ctrl_m4_shift3 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---sggcGGGGGCGGGGCcgsGssGss ; cor=; Ncor= a 0 0 0 12 13 12 23 8 2 6 1 5 2 3 5 9 6 5 7 18 10 3 11 10 6 23 22 c 0 0 0 37 28 24 60 18 9 8 8 9 106 6 5 7 4 93 80 12 64 9 70 60 22 38 35 g 0 0 0 57 58 77 24 92 105 104 110 104 9 111 102 104 110 20 23 71 37 103 31 39 83 55 55 t 0 0 0 15 22 8 14 3 5 3 2 3 4 1 9 1 1 3 11 20 10 6 9 12 10 5 9

oligos_7nt_test_vs_ctrl_m1_rc_shift3 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/8; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.872169; ---gsGcGGGGGCGGGGCGcGGcscss ; cor=; Ncor= a 0 0 0 13 12 4 10 10 3 2 5 8 6 3 0 7 2 5 2 11 7 5 14 5 10 10 15 c 0 0 0 24 26 15 60 15 7 17 12 7 86 3 7 6 4 82 21 57 8 16 59 58 60 35 31 g 0 0 0 49 47 73 19 70 86 77 83 83 5 93 90 86 93 10 76 24 83 72 22 28 17 44 42 t 0 0 0 15 16 9 12 6 5 5 1 3 4 2 4 2 2 4 2 9 3 8 6 10 14 12 13

oligos_6nt_test_vs_ctrl_m1_rc_shift5 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/8; ncol2=24; w=0; offset=2; strand=R; shift=5; score=0.803037; -----scGGGGGCGGGGCcGCGCsGCs ; cor=; Ncor= a 0 0 0 0 0 7 9 2 0 3 2 1 0 1 2 3 2 1 5 3 1 1 4 1 3 5 5 c 0 0 0 0 0 16 15 5 5 6 2 4 39 5 3 6 2 34 29 4 34 1 32 26 7 30 26 g 0 0 0 0 0 16 10 35 36 32 38 37 2 36 35 33 38 6 6 30 6 37 6 15 32 7 11 t 0 0 0 0 0 4 9 1 2 2 1 1 2 1 3 1 1 2 3 6 2 4 1 1 1 1 1

oligos_6nt_test_vs_ctrl_m4_rc_shift4 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/8; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.662447; ----sssSsGGGCGGGGCGCGGCsCsb ; cor=; Ncor= a 0 0 0 0 2 2 0 1 4 0 0 2 2 0 0 2 0 0 0 1 1 0 0 0 3 0 0 c 0 0 0 0 7 7 9 16 9 2 4 2 17 0 3 1 1 21 1 18 0 4 18 14 16 11 10 g 0 0 0 0 12 13 13 6 7 20 19 19 2 22 18 20 22 1 21 3 20 17 3 6 2 9 7 t 0 0 0 0 2 1 1 0 3 1 0 0 2 1 2 0 0 1 1 1 2 2 2 3 2 3 6

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=5/8; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.661665; ssGcGGcGsGGGCGGGGCGGrGss--- ; cor=; Ncor= a 10 15 7 12 7 8 13 4 9 3 2 9 9 3 2 4 4 7 2 2 35 6 15 12 0 0 0 c 27 30 8 63 12 16 56 3 53 12 6 5 70 7 4 13 4 68 15 12 14 12 34 27 0 0 0 g 50 42 76 14 72 65 22 86 29 73 86 77 14 81 85 72 83 14 73 78 34 69 39 42 0 0 0 t 7 7 3 5 3 5 3 1 3 6 0 3 1 3 3 5 3 5 4 2 11 7 6 13 0 0 0

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/8; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.660987; --sgCGGCGsGGCGGGGCsGCssssg- ; cor=; Ncor= a 0 0 3 3 1 0 1 0 0 0 3 1 3 2 1 0 1 2 1 0 1 1 2 1 1 0 0 c 0 0 6 3 19 5 1 21 1 15 2 2 17 0 2 3 1 18 6 3 16 15 11 13 6 5 0 g 0 0 10 13 2 18 20 2 20 7 17 20 3 20 18 20 21 3 15 20 5 6 9 8 12 13 0 t 0 0 4 4 1 0 1 0 2 1 1 0 0 1 2 0 0 0 1 0 1 1 1 1 4 5 0

oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=7/8; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.585044; sgssCGGCGsGGCGGGGCGGmGss--- ; cor=; Ncor= a 6 5 2 2 0 1 3 1 1 0 1 0 2 3 1 2 1 2 2 0 10 2 4 3 0 0 0 c 9 5 16 15 20 2 0 20 1 13 4 2 20 0 2 0 1 20 0 2 8 1 9 7 0 0 0 g 9 13 8 7 5 22 21 5 21 10 21 23 4 21 21 23 24 3 21 24 6 23 12 10 0 0 0 t 2 3 0 2 1 1 2 0 3 3 0 1 0 2 2 1 0 1 3 0 2 0 1 6 0 0 0

oligos_7nt_test_vs_ctrl_m5_rc_shift10 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=8/8; ncol2=24; w=0; offset=7; strand=R; shift=10; score=0.426944; ----------gsCgGGGcCGCGGmGCG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2 2 1 2 0 0 0 2 0 0 2 3 0 9 1 1 0 c 0 0 0 0 0 0 0 0 0 0 4 9 18 5 5 4 2 14 18 1 15 1 2 7 1 18 5 g 0 0 0 0 0 0 0 0 0 0 10 6 1 14 16 16 18 4 3 18 2 16 18 4 18 2 16 t 0 0 0 0 0 0 0 0 0 0 5 4 1 0 0 1 1 1 0 2 2 1 1 1 1 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift5 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift5 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=24; shift=5; ncol=29; -----ssCkCCGCCCCGCCsCGCCGsscs ; Alignment reference a 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 0 3 2 c 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 8 13 9 g 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 16 5 9 t 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2 2 5 6

oligos_6nt_test_vs_ctrl_m5_shift5 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCkCCGCCCCGCCsCGCCGsscs ; cor=; Ncor= a 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 0 3 2 c 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 8 13 9 g 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 16 5 9 t 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2 2 5 6

oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=2/8; ncol2=24; w=-2; offset=-2; strand=D; shift=3; score=0.743783; ---cssssGCsGCCCCGCCsCGCCGcs-- ; cor=; Ncor= a 0 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 0 0 c 0 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 0 0 g 0 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 0 0 t 0 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3 0 0

oligos_7nt_test_vs_ctrl_m2_rc_shift5 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/8; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.735076; -----ssCyCCGCCCCGCCCsCgCCgCss ; cor=; Ncor= a 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 3 5 3 7 7 c 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 72 14 76 42 50 g 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 12 63 8 30 27 t 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8 7 12 7 15 10

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=4/8; ncol2=24; w=-2; offset=-2; strand=D; shift=3; score=0.630863; ---ssgCgCCCGCCCCGCGCCGCggss-- ; cor=; Ncor= a 0 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 0 0 c 0 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 0 0 g 0 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 0 0 t 0 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3 0 0

oligos_7nt_test_vs_ctrl_m4_rc_shift2 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=5/8; ncol2=24; w=-3; offset=-3; strand=R; shift=2; score=0.585044; --ssCssCscgGCCCCGCCCCCgccs--- ; cor=; Ncor= a 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 22 15 0 0 0 c 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 58 57 0 0 0 g 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 28 37 0 0 0 t 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12 13 12 0 0 0

oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=6/8; ncol2=24; w=-3; offset=-3; strand=D; shift=2; score=0.580127; --ssgsgCCgCGCCCCGCCCCCgCsc--- ; cor=; Ncor= a 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 15 0 0 0 c 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 49 0 0 0 g 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 24 0 0 0 t 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12 13 0 0 0

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=7/8; ncol2=24; w=-4; offset=-4; strand=D; shift=1; score=0.533896; -cvsGsGCCGCGCCCCGCCCsSsss---- ; cor=; Ncor= a 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 0 0 0 0 c 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 0 0 0 0 g 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 0 0 0 0 t 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2 0 0 0 0

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=8/8; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.481037; scsGCsGCGCgGCCCCGCCCCCgs----- ; cor=; Ncor= a 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 0 0 0 0 0 c 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 0 0 0 0 0 g 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 0 0 0 0 0 t 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift4 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=4; ncol=28; ----ssgrGCGGCGsCGsCGCCGCycss ; Alignment reference a 0 0 0 0 4 2 2 15 0 1 1 0 0 1 1 0 0 0 1 2 2 2 0 1 0 3 5 2 c 0 0 0 0 11 13 4 6 2 22 0 5 23 6 8 23 5 19 20 3 21 25 5 25 7 19 8 11 g 0 0 0 0 11 8 19 7 25 5 25 21 3 20 19 5 23 8 6 23 5 0 22 2 6 4 13 11 t 0 0 0 0 2 5 3 0 1 0 2 2 2 1 0 0 0 1 1 0 0 1 1 0 15 2 2 4

oligos_7nt_test_vs_ctrl_m3_shift4 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----ssgrGCGGCGsCGsCGCCGCycss ; cor=; Ncor= a 0 0 0 0 4 2 2 15 0 1 1 0 0 1 1 0 0 0 1 2 2 2 0 1 0 3 5 2 c 0 0 0 0 11 13 4 6 2 22 0 5 23 6 8 23 5 19 20 3 21 25 5 25 7 19 8 11 g 0 0 0 0 11 8 19 7 25 5 25 21 3 20 19 5 23 8 6 23 5 0 22 2 6 4 13 11 t 0 0 0 0 2 5 3 0 1 0 2 2 2 1 0 0 0 1 1 0 0 1 1 0 15 2 2 4

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/3; ncol2=24; w=-2; offset=-2; strand=R; shift=2; score=0.611368; --sgCGGCGsGGCGGGGCsGCssssg-- ; cor=; Ncor= a 0 0 3 3 1 0 1 0 0 0 3 1 3 2 1 0 1 2 1 0 1 1 2 1 1 0 0 0 c 0 0 6 3 19 5 1 21 1 15 2 2 17 0 2 3 1 18 6 3 16 15 11 13 6 5 0 0 g 0 0 10 13 2 18 20 2 20 7 17 20 3 20 18 20 21 3 15 20 5 6 9 8 12 13 0 0 t 0 0 4 4 1 0 1 0 2 1 1 0 0 1 2 0 0 0 1 0 1 1 1 1 4 5 0 0

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.512085; scsGCsGCGCgGCCCCGCCCCCgs---- ; cor=; Ncor= a 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 0 0 0 0 c 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 0 0 0 0 g 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 0 0 0 0 t 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift2 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=2; ncol=26; --cssssGCsGCCCCGCCsCGCCGcs ; Alignment reference a 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 c 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 g 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 t 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --cssssGCsGCCCCGCCsCGCCGcs ; cor=; Ncor= a 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 c 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 g 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 t 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3

oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/9; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.799299; --ssgCgCCCGCCCCGCGCCGCggss ; cor=; Ncor= a 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 c 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 g 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 t 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3

oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=3/9; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.743783; ----ssCkCCGCCCCGCCsCGCCGss ; cor=; Ncor= a 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 0 c 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 8 g 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 16 t 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2 2

oligos_7nt_test_vs_ctrl_m4_rc_shift1 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/9; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.660987; -ssCssCscgGCCCCGCCCCCgccs- ; cor=; Ncor= a 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 22 15 0 c 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 58 57 0 g 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 28 37 0 t 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12 13 12 0

oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=5/9; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.620869; ----scsGCsGCGCgGCCCCGCCCCC ; cor=; Ncor= a 0 0 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 c 0 0 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 g 0 0 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 t 0 0 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=6/9; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.611368; ssgrGCGGCGsCGsCGCCGCycss-- ; cor=; Ncor= a 4 2 2 15 0 1 1 0 0 1 1 0 0 0 1 2 2 2 0 1 0 3 5 2 0 0 c 11 13 4 6 2 22 0 5 23 6 8 23 5 19 20 3 21 25 5 25 7 19 8 11 0 0 g 11 8 19 7 25 5 25 21 3 20 19 5 23 8 6 23 5 0 22 2 6 4 13 11 0 0 t 2 5 3 0 1 0 2 2 2 1 0 0 0 1 1 0 0 1 1 0 15 2 2 4 0 0

oligos_6nt_test_vs_ctrl_m4_shift5 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=7/9; ncol2=24; w=0; offset=3; strand=D; shift=5; score=0.544727; -----cvsGsGCCGCGCCCCGCCCsS ; cor=; Ncor= a 0 0 0 0 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 c 0 0 0 0 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 g 0 0 0 0 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 t 0 0 0 0 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1

oligos_7nt_test_vs_ctrl_m1_shift6 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=8/9; ncol2=24; w=0; offset=4; strand=D; shift=6; score=0.527422; ------ssgsgCCgCGCCCCGCCCCC ; cor=; Ncor= a 0 0 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 c 0 0 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 g 0 0 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 t 0 0 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10

oligos_7nt_test_vs_ctrl_m2_rc_shift9 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2_rc; m=9/9; ncol2=24; w=0; offset=7; strand=R; shift=9; score=0.411075; ---------ssCyCCGCCCCGCCCsC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 c 0 0 0 0 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 g 0 0 0 0 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 t 0 0 0 0 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 5 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=24; shift=0; ncol=24; scGmGCGCGCkCCGCGgCCCcGsc ; Alignment reference a 1 5 1 6 1 0 3 0 0 1 1 1 1 2 2 0 1 1 1 0 0 1 4 5 c 6 9 0 13 3 18 2 16 2 18 4 18 16 2 18 3 4 18 16 16 14 1 6 10 g 12 4 19 2 15 2 16 5 18 1 7 2 1 15 1 18 14 2 4 5 5 18 9 4 t 2 3 1 0 2 1 0 0 1 1 9 0 3 2 0 0 2 0 0 0 2 1 2 2

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=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; scGmGCGCGCkCCGCGgCCCcGsc ; cor=; Ncor= a 1 5 1 6 1 0 3 0 0 1 1 1 1 2 2 0 1 1 1 0 0 1 4 5 c 6 9 0 13 3 18 2 16 2 18 4 18 16 2 18 3 4 18 16 16 14 1 6 10 g 12 4 19 2 15 2 16 5 18 1 7 2 1 15 1 18 14 2 4 5 5 18 9 4 t 2 3 1 0 2 1 0 0 1 1 9 0 3 2 0 0 2 0 0 0 2 1 2 2

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.759556; ssgCgCCCGCCCCGCGCCGCggss ; cor=; Ncor= a 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 c 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 g 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 t 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3

oligos_6nt_test_vs_ctrl_m1_shift5 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.497653; -----scsGCsGCGCgGCCCCGCC ; cor=; Ncor= a 0 0 0 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 c 0 0 0 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 g 0 0 0 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 t 0 0 0 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2

oligos_7nt_test_vs_ctrl_m4_rc_shift7 (oligos_7nt_test_vs_ctrl_m4_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/4; ncol2=24; w=0; offset=7; strand=R; shift=7; score=0.426944; -------ssCssCscgGCCCCGCC ; cor=; Ncor= a 0 0 0 0 0 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 c 0 0 0 0 0 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 g 0 0 0 0 0 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 t 0 0 0 0 0 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssGcGGcGsGGGCGGGGCGGrGss ; Alignment reference a 0 0 10 15 7 12 7 8 13 4 9 3 2 9 9 3 2 4 4 7 2 2 35 6 15 12 c 0 0 27 30 8 63 12 16 56 3 53 12 6 5 70 7 4 13 4 68 15 12 14 12 34 27 g 0 0 50 42 76 14 72 65 22 86 29 73 86 77 14 81 85 72 83 14 73 78 34 69 39 42 t 0 0 7 7 3 5 3 5 3 1 3 6 0 3 1 3 3 5 3 5 4 2 11 7 6 13
oligos_7nt_test_vs_ctrl_m2_shift2 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssGcGGcGsGGGCGGGGCGGrGss ; cor=; Ncor= a 0 0 10 15 7 12 7 8 13 4 9 3 2 9 9 3 2 4 4 7 2 2 35 6 15 12 c 0 0 27 30 8 63 12 16 56 3 53 12 6 5 70 7 4 13 4 68 15 12 14 12 34 27 g 0 0 50 42 76 14 72 65 22 86 29 73 86 77 14 81 85 72 83 14 73 78 34 69 39 42 t 0 0 7 7 3 5 3 5 3 1 3 6 0 3 1 3 3 5 3 5 4 2 11 7 6 13
oligos_6nt_test_vs_ctrl_m5_rc_shift2 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/8; ncol2=24; w=0; offset=0; strand=R; shift=2; score=0.735076; --sgssCGGCGsGGCGGGGCGGmGss ; cor=; Ncor= a 0 0 6 5 2 2 0 1 3 1 1 0 1 0 2 3 1 2 1 2 2 0 10 2 4 3 c 0 0 9 5 16 15 20 2 0 20 1 13 4 2 20 0 2 0 1 20 0 2 8 1 9 7 g 0 0 9 13 8 7 5 22 21 5 21 10 21 23 4 21 21 23 24 3 21 24 6 23 12 10 t 0 0 2 3 0 2 1 1 2 0 3 3 0 1 0 2 2 1 0 1 3 0 2 0 1 6
oligos_7nt_test_vs_ctrl_m4_shift5 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/8; ncol2=24; w=0; offset=3; strand=D; shift=5; score=0.661665; -----sggcGGGGGCGGGGCcgsGss ; cor=; Ncor= a 0 0 0 0 0 12 13 12 23 8 2 6 1 5 2 3 5 9 6 5 7 18 10 3 11 10 c 0 0 0 0 0 37 28 24 60 18 9 8 8 9 106 6 5 7 4 93 80 12 64 9 70 60 g 0 0 0 0 0 57 58 77 24 92 105 104 110 104 9 111 102 104 110 20 23 71 37 103 31 39 t 0 0 0 0 0 15 22 8 14 3 5 3 2 3 4 1 9 1 1 3 11 20 10 6 9 12
oligos_7nt_test_vs_ctrl_m1_rc_shift5 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/8; ncol2=24; w=0; offset=3; strand=R; shift=5; score=0.658641; -----gsGcGGGGGCGGGGCGcGGcs ; cor=; Ncor= a 0 0 0 0 0 13 12 4 10 10 3 2 5 8 6 3 0 7 2 5 2 11 7 5 14 5 c 0 0 0 0 0 24 26 15 60 15 7 17 12 7 86 3 7 6 4 82 21 57 8 16 59 58 g 0 0 0 0 0 49 47 73 19 70 86 77 83 83 5 93 90 86 93 10 76 24 83 72 22 28 t 0 0 0 0 0 15 16 9 12 6 5 5 1 3 4 2 4 2 2 4 2 9 3 8 6 10
oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=5/8; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.656911; ssccGCGGCGCGGGGCGGGcGcss-- ; cor=; Ncor= a 3 7 9 6 2 6 3 3 3 3 6 3 2 2 2 5 4 3 1 7 3 5 5 3 0 0 c 21 23 37 41 6 50 3 4 46 7 52 6 3 6 6 51 7 16 4 43 11 45 20 17 0 0 g 36 28 16 15 55 10 56 56 14 56 6 58 61 55 59 6 52 48 61 14 49 15 32 35 0 0 t 7 9 5 5 4 1 5 4 4 1 3 0 1 4 0 5 4 0 1 3 4 2 10 12 0 0
oligos_6nt_test_vs_ctrl_m4_rc_shift6 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=6/8; ncol2=24; w=0; offset=4; strand=R; shift=6; score=0.562263; ------sssSsGGGCGGGGCGCGGCs ; cor=; Ncor= a 0 0 0 0 0 0 2 2 0 1 4 0 0 2 2 0 0 2 0 0 0 1 1 0 0 0 c 0 0 0 0 0 0 7 7 9 16 9 2 4 2 17 0 3 1 1 21 1 18 0 4 18 14 g 0 0 0 0 0 0 12 13 13 6 7 20 19 19 2 22 18 20 22 1 21 3 20 17 3 6 t 0 0 0 0 0 0 2 1 1 0 3 1 0 0 2 1 2 0 0 1 1 1 2 2 2 3
oligos_6nt_test_vs_ctrl_m1_rc_shift7 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=7/8; ncol2=24; w=0; offset=5; strand=R; shift=7; score=0.533977; -------scGGGGGCGGGGCcGCGCs ; cor=; Ncor= a 0 0 0 0 0 0 0 7 9 2 0 3 2 1 0 1 2 3 2 1 5 3 1 1 4 1 c 0 0 0 0 0 0 0 16 15 5 5 6 2 4 39 5 3 6 2 34 29 4 34 1 32 26 g 0 0 0 0 0 0 0 16 10 35 36 32 38 37 2 36 35 33 38 6 6 30 6 37 6 15 t 0 0 0 0 0 0 0 4 9 1 2 2 1 1 2 1 3 1 1 2 3 6 2 4 1 1
oligos_6nt_test_vs_ctrl_m2_rc_shift9 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2_rc; m=8/8; ncol2=24; w=0; offset=7; strand=R; shift=9; score=0.411075; ---------sgCGGCGsGGCGGGGCs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 3 1 0 1 0 0 0 3 1 3 2 1 0 1 2 1 c 0 0 0 0 0 0 0 0 0 6 3 19 5 1 21 1 15 2 2 17 0 2 3 1 18 6 g 0 0 0 0 0 0 0 0 0 10 13 2 18 20 2 20 7 17 20 3 20 18 20 21 3 15 t 0 0 0 0 0 0 0 0 0 4 4 1 0 1 0 2 1 1 0 0 1 2 0 0 0 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=2; ncol=26; --ssgCgCCCGCCCCGCGCCGCggss ; Alignment reference a 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 c 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 g 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 t 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --ssgCgCCCGCCCCGCGCCGCggss ; cor=; Ncor= a 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 c 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 g 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 t 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=2/7; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.799299; --cssssGCsGCCCCGCCsCGCCGcs ; cor=; Ncor= a 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 c 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 g 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 t 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3
oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=3/7; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.759556; --scGmGCGCGCkCCGCGgCCCcGsc ; cor=; Ncor= a 0 0 1 5 1 6 1 0 3 0 0 1 1 1 1 2 2 0 1 1 1 0 0 1 4 5 c 0 0 6 9 0 13 3 18 2 16 2 18 4 18 16 2 18 3 4 18 16 16 14 1 6 10 g 0 0 12 4 19 2 15 2 16 5 18 1 7 2 1 15 1 18 14 2 4 5 5 18 9 4 t 0 0 2 3 1 0 2 1 0 0 1 1 9 0 3 2 0 0 2 0 0 0 2 1 2 2
oligos_7nt_test_vs_ctrl_m1_shift1 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=4/7; ncol2=24; w=-1; offset=-1; strand=D; shift=1; score=0.667561; -ssgsgCCgCGCCCCGCCCCCgCsc- ; cor=; Ncor= a 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 15 0 c 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 49 0 g 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 24 0 t 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12 13 0
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=5/7; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.656911; ssCyCCGCCCCGCCCsCgCCgCss-- ; cor=; Ncor= a 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 3 5 3 7 7 0 0 c 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 72 14 76 42 50 0 0 g 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 12 63 8 30 27 0 0 t 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8 7 12 7 15 10 0 0
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4; m=6/7; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.632697; cvsGsGCCGCGCCCCGCCCsSsss-- ; cor=; Ncor= a 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 0 0 c 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 0 0 g 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 0 0 t 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2 0 0
oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=7/7; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.630863; ----ssCkCCGCCCCGCCsCGCCGss ; cor=; Ncor= a 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 0 c 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 8 g 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 16 t 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift4 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=4; ncol=28; ----ssgsgCCgCGCCCCGCCCCCgCsc ; Alignment reference a 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 15 c 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 49 g 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 24 t 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12 13
oligos_7nt_test_vs_ctrl_m1_shift4 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----ssgsgCCgCGCCCCGCCCCCgCsc ; cor=; Ncor= a 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 15 c 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 49 g 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 24 t 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12 13
oligos_7nt_test_vs_ctrl_m4_rc_shift4 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=2/8; ncol2=24; w=0; offset=0; strand=R; shift=4; score=0.872169; ----ssCssCscgGCCCCGCCCCCgccs ; cor=; Ncor= a 0 0 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 22 15 c 0 0 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 58 57 g 0 0 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 28 37 t 0 0 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12 13 12
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=3/8; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.828866; ---cvsGsGCCGCGCCCCGCCCsSsss- ; cor=; Ncor= a 0 0 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 0 c 0 0 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 0 g 0 0 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 0 t 0 0 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2 0
oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=4/8; ncol2=24; w=0; offset=1; strand=D; shift=5; score=0.667561; -----ssgCgCCCGCCCCGCGCCGCggs ; cor=; Ncor= a 0 0 0 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 c 0 0 0 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 g 0 0 0 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 t 0 0 0 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7
oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=5/8; ncol2=24; w=-2; offset=-2; strand=D; shift=2; score=0.662782; --scsGCsGCGCgGCCCCGCCCCCgs-- ; cor=; Ncor= a 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 0 0 c 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 0 0 g 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 0 0 t 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7 0 0
oligos_7nt_test_vs_ctrl_m2_rc_shift7 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2_rc; m=6/8; ncol2=24; w=0; offset=3; strand=R; shift=7; score=0.658641; -------ssCyCCGCCCCGCCCsCgCCg ; cor=; Ncor= a 0 0 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 3 5 c 0 0 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 72 14 g 0 0 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 12 63 t 0 0 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8 7 12
oligos_6nt_test_vs_ctrl_m5_shift7 (oligos_6nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=7/8; ncol2=24; w=0; offset=3; strand=D; shift=7; score=0.580127; -------ssCkCCGCCCCGCCsCGCCGs ; cor=; Ncor= a 0 0 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 c 0 0 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 g 0 0 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 t 0 0 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=8/8; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.527422; cssssGCsGCCCCGCCsCGCCGcs---- ; cor=; Ncor= a 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 0 0 0 0 c 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 0 0 0 0 g 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 0 0 0 0 t 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---cvsGsGCCGCGCCCCGCCCsSsss ; Alignment reference a 0 0 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 c 0 0 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 g 0 0 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 t 0 0 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2
oligos_6nt_test_vs_ctrl_m4_shift3 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/7; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---cvsGsGCCGCGCCCCGCCCsSsss ; cor=; Ncor= a 0 0 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 c 0 0 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 g 0 0 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 t 0 0 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2
oligos_7nt_test_vs_ctrl_m1_shift4 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1; m=2/7; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.828866; ----ssgsgCCgCGCCCCGCCCCCgCs ; cor=; Ncor= a 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 c 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 g 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 t 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12
oligos_7nt_test_vs_ctrl_m4_rc_shift4 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4_rc; m=3/7; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.662447; ----ssCssCscgGCCCCGCCCCCgcc ; cor=; Ncor= a 0 0 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 22 c 0 0 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 58 g 0 0 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 28 t 0 0 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12 13
oligos_6nt_test_vs_ctrl_m3_shift5 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3; m=4/7; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.632697; -----ssgCgCCCGCCCCGCGCCGCgg ; cor=; Ncor= a 0 0 0 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 c 0 0 0 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 g 0 0 0 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 t 0 0 0 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9
oligos_7nt_test_vs_ctrl_m2_rc_shift7 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2_rc; m=5/7; ncol2=24; w=0; offset=4; strand=R; shift=7; score=0.562263; -------ssCyCCGCCCCGCCCsCgCC ; cor=; Ncor= a 0 0 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 3 c 0 0 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 72 g 0 0 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 12 t 0 0 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8 7
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=6/7; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.544727; cssssGCsGCCCCGCCsCGCCGcs--- ; cor=; Ncor= a 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 0 0 0 c 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 0 0 0 g 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 0 0 0 t 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3 0 0 0
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=7/7; ncol2=24; w=0; offset=4; strand=D; shift=7; score=0.533896; -------ssCkCCGCCCCGCCsCGCCG ; cor=; Ncor= a 0 0 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 c 0 0 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 g 0 0 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 t 0 0 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift5 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=5; ncol=29; -----scsGCsGCGCgGCCCCGCCCCCgs ; Alignment reference a 0 0 0 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 c 0 0 0 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 g 0 0 0 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 t 0 0 0 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7
oligos_6nt_test_vs_ctrl_m1_shift5 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----scsGCsGCGCgGCCCCGCCCCCgs ; cor=; Ncor= a 0 0 0 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 c 0 0 0 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 g 0 0 0 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 t 0 0 0 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7
oligos_7nt_test_vs_ctrl_m4_rc_shift7 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4_rc; m=2/8; ncol2=24; w=0; offset=2; strand=R; shift=7; score=0.803037; -------ssCssCscgGCCCCGCCCCCgc ; cor=; Ncor= a 0 0 0 0 0 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 c 0 0 0 0 0 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 g 0 0 0 0 0 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 t 0 0 0 0 0 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=3/8; ncol2=24; w=0; offset=2; strand=D; shift=7; score=0.662782; -------ssgsgCCgCGCCCCGCCCCCgC ; cor=; Ncor= a 0 0 0 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 c 0 0 0 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 g 0 0 0 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 t 0 0 0 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=4/8; ncol2=24; w=-2; offset=-2; strand=D; shift=3; score=0.620869; ---cssssGCsGCCCCGCCsCGCCGcs-- ; cor=; Ncor= a 0 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 0 0 c 0 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 0 0 g 0 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 0 0 t 0 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3 0 0
oligos_7nt_test_vs_ctrl_m2_rc_shift10 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2_rc; m=5/8; ncol2=24; w=0; offset=5; strand=R; shift=10; score=0.533977; ----------ssCyCCGCCCCGCCCsCgC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 c 0 0 0 0 0 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 g 0 0 0 0 0 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 t 0 0 0 0 0 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8
oligos_7nt_test_vs_ctrl_m3_shift9 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=6/8; ncol2=24; w=0; offset=4; strand=D; shift=9; score=0.512085; ---------ssgrGCGGCGsCGsCGCCGC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4 2 2 15 0 1 1 0 0 1 1 0 0 0 1 2 2 2 0 1 c 0 0 0 0 0 0 0 0 0 11 13 4 6 2 22 0 5 23 6 8 23 5 19 20 3 21 25 5 25 g 0 0 0 0 0 0 0 0 0 11 8 19 7 25 5 25 21 3 20 19 5 23 8 6 23 5 0 22 2 t 0 0 0 0 0 0 0 0 0 2 5 3 0 1 0 2 2 2 1 0 0 0 1 1 0 0 1 1 0
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=7/8; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.497653; scGmGCGCGCkCCGCGgCCCcGsc----- ; cor=; Ncor= a 1 5 1 6 1 0 3 0 0 1 1 1 1 2 2 0 1 1 1 0 0 1 4 5 0 0 0 0 0 c 6 9 0 13 3 18 2 16 2 18 4 18 16 2 18 3 4 18 16 16 14 1 6 10 0 0 0 0 0 g 12 4 19 2 15 2 16 5 18 1 7 2 1 15 1 18 14 2 4 5 5 18 9 4 0 0 0 0 0 t 2 3 1 0 2 1 0 0 1 1 9 0 3 2 0 0 2 0 0 0 2 1 2 2 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_shift10 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=8/8; ncol2=24; w=0; offset=5; strand=D; shift=10; score=0.481037; ----------ssCkCCGCCCCGCCsCGCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 c 0 0 0 0 0 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 g 0 0 0 0 0 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 t 0 0 0 0 0 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift3 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=3; ncol=27; ---sggcGGGGGCGGGGCcgsGssGss ; Alignment reference a 0 0 0 12 13 12 23 8 2 6 1 5 2 3 5 9 6 5 7 18 10 3 11 10 6 23 22 c 0 0 0 37 28 24 60 18 9 8 8 9 106 6 5 7 4 93 80 12 64 9 70 60 22 38 35 g 0 0 0 57 58 77 24 92 105 104 110 104 9 111 102 104 110 20 23 71 37 103 31 39 83 55 55 t 0 0 0 15 22 8 14 3 5 3 2 3 4 1 9 1 1 3 11 20 10 6 9 12 10 5 9
oligos_7nt_test_vs_ctrl_m4_shift3 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---sggcGGGGGCGGGGCcgsGssGss ; cor=; Ncor= a 0 0 0 12 13 12 23 8 2 6 1 5 2 3 5 9 6 5 7 18 10 3 11 10 6 23 22 c 0 0 0 37 28 24 60 18 9 8 8 9 106 6 5 7 4 93 80 12 64 9 70 60 22 38 35 g 0 0 0 57 58 77 24 92 105 104 110 104 9 111 102 104 110 20 23 71 37 103 31 39 83 55 55 t 0 0 0 15 22 8 14 3 5 3 2 3 4 1 9 1 1 3 11 20 10 6 9 12 10 5 9
oligos_7nt_test_vs_ctrl_m1_rc_shift3 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/8; ncol2=24; w=0; offset=0; strand=R; shift=3; score=0.872169; ---gsGcGGGGGCGGGGCGcGGcscss ; cor=; Ncor= a 0 0 0 13 12 4 10 10 3 2 5 8 6 3 0 7 2 5 2 11 7 5 14 5 10 10 15 c 0 0 0 24 26 15 60 15 7 17 12 7 86 3 7 6 4 82 21 57 8 16 59 58 60 35 31 g 0 0 0 49 47 73 19 70 86 77 83 83 5 93 90 86 93 10 76 24 83 72 22 28 17 44 42 t 0 0 0 15 16 9 12 6 5 5 1 3 4 2 4 2 2 4 2 9 3 8 6 10 14 12 13
oligos_6nt_test_vs_ctrl_m1_rc_shift5 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/8; ncol2=24; w=0; offset=2; strand=R; shift=5; score=0.803037; -----scGGGGGCGGGGCcGCGCsGCs ; cor=; Ncor= a 0 0 0 0 0 7 9 2 0 3 2 1 0 1 2 3 2 1 5 3 1 1 4 1 3 5 5 c 0 0 0 0 0 16 15 5 5 6 2 4 39 5 3 6 2 34 29 4 34 1 32 26 7 30 26 g 0 0 0 0 0 16 10 35 36 32 38 37 2 36 35 33 38 6 6 30 6 37 6 15 32 7 11 t 0 0 0 0 0 4 9 1 2 2 1 1 2 1 3 1 1 2 3 6 2 4 1 1 1 1 1
oligos_6nt_test_vs_ctrl_m4_rc_shift4 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/8; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.662447; ----sssSsGGGCGGGGCGCGGCsCsb ; cor=; Ncor= a 0 0 0 0 2 2 0 1 4 0 0 2 2 0 0 2 0 0 0 1 1 0 0 0 3 0 0 c 0 0 0 0 7 7 9 16 9 2 4 2 17 0 3 1 1 21 1 18 0 4 18 14 16 11 10 g 0 0 0 0 12 13 13 6 7 20 19 19 2 22 18 20 22 1 21 3 20 17 3 6 2 9 7 t 0 0 0 0 2 1 1 0 3 1 0 0 2 1 2 0 0 1 1 1 2 2 2 3 2 3 6
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=5/8; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.661665; ssGcGGcGsGGGCGGGGCGGrGss--- ; cor=; Ncor= a 10 15 7 12 7 8 13 4 9 3 2 9 9 3 2 4 4 7 2 2 35 6 15 12 0 0 0 c 27 30 8 63 12 16 56 3 53 12 6 5 70 7 4 13 4 68 15 12 14 12 34 27 0 0 0 g 50 42 76 14 72 65 22 86 29 73 86 77 14 81 85 72 83 14 73 78 34 69 39 42 0 0 0 t 7 7 3 5 3 5 3 1 3 6 0 3 1 3 3 5 3 5 4 2 11 7 6 13 0 0 0
oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2_rc; m=6/8; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.660987; --sgCGGCGsGGCGGGGCsGCssssg- ; cor=; Ncor= a 0 0 3 3 1 0 1 0 0 0 3 1 3 2 1 0 1 2 1 0 1 1 2 1 1 0 0 c 0 0 6 3 19 5 1 21 1 15 2 2 17 0 2 3 1 18 6 3 16 15 11 13 6 5 0 g 0 0 10 13 2 18 20 2 20 7 17 20 3 20 18 20 21 3 15 20 5 6 9 8 12 13 0 t 0 0 4 4 1 0 1 0 2 1 1 0 0 1 2 0 0 0 1 0 1 1 1 1 4 5 0
oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5_rc; m=7/8; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.585044; sgssCGGCGsGGCGGGGCGGmGss--- ; cor=; Ncor= a 6 5 2 2 0 1 3 1 1 0 1 0 2 3 1 2 1 2 2 0 10 2 4 3 0 0 0 c 9 5 16 15 20 2 0 20 1 13 4 2 20 0 2 0 1 20 0 2 8 1 9 7 0 0 0 g 9 13 8 7 5 22 21 5 21 10 21 23 4 21 21 23 24 3 21 24 6 23 12 10 0 0 0 t 2 3 0 2 1 1 2 0 3 3 0 1 0 2 2 1 0 1 3 0 2 0 1 6 0 0 0
oligos_7nt_test_vs_ctrl_m5_rc_shift10 (oligos_7nt_test_vs_ctrl_m5_rc)				; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5_rc; m=8/8; ncol2=24; w=0; offset=7; strand=R; shift=10; score=0.426944; ----------gsCgGGGcCGCGGmGCG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 2 2 1 2 0 0 0 2 0 0 2 3 0 9 1 1 0 c 0 0 0 0 0 0 0 0 0 0 4 9 18 5 5 4 2 14 18 1 15 1 2 7 1 18 5 g 0 0 0 0 0 0 0 0 0 0 10 6 1 14 16 16 18 4 3 18 2 16 18 4 18 2 16 t 0 0 0 0 0 0 0 0 0 0 5 4 1 0 0 1 1 1 0 2 2 1 1 1 1 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift5 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=24; shift=5; ncol=29; -----ssCkCCGCCCCGCCsCGCCGsscs ; Alignment reference a 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 0 3 2 c 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 8 13 9 g 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 16 5 9 t 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2 2 5 6
oligos_6nt_test_vs_ctrl_m5_shift5 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/8; ncol2=24; w=0; offset=0; strand=D; shift=5; score= 1; -----ssCkCCGCCCCGCCsCGCCGsscs ; cor=; Ncor= a 0 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 0 3 2 c 0 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 8 13 9 g 0 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 16 5 9 t 0 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2 2 5 6
oligos_6nt_test_vs_ctrl_m2_shift3 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2; m=2/8; ncol2=24; w=-2; offset=-2; strand=D; shift=3; score=0.743783; ---cssssGCsGCCCCGCCsCGCCGcs-- ; cor=; Ncor= a 0 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 0 0 c 0 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 0 0 g 0 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 0 0 t 0 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3 0 0
oligos_7nt_test_vs_ctrl_m2_rc_shift5 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/8; ncol2=24; w=0; offset=0; strand=R; shift=5; score=0.735076; -----ssCyCCGCCCCGCCCsCgCCgCss ; cor=; Ncor= a 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 3 5 3 5 3 7 7 c 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 22 65 72 14 76 42 50 g 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 56 16 12 63 8 30 27 t 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4 13 8 7 12 7 15 10
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=4/8; ncol2=24; w=-2; offset=-2; strand=D; shift=3; score=0.630863; ---ssgCgCCCGCCCCGCGCCGCggss-- ; cor=; Ncor= a 0 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 0 0 c 0 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 0 0 g 0 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 0 0 t 0 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3 0 0
oligos_7nt_test_vs_ctrl_m4_rc_shift2 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=5/8; ncol2=24; w=-3; offset=-3; strand=R; shift=2; score=0.585044; --ssCssCscgGCCCCGCCCCCgccs--- ; cor=; Ncor= a 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 22 15 0 0 0 c 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 58 57 0 0 0 g 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 28 37 0 0 0 t 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12 13 12 0 0 0
oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=6/8; ncol2=24; w=-3; offset=-3; strand=D; shift=2; score=0.580127; --ssgsgCCgCGCCCCGCCCCCgCsc--- ; cor=; Ncor= a 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 12 9 16 15 0 0 0 c 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 19 73 47 49 0 0 0 g 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 60 15 26 24 0 0 0 t 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10 10 4 12 13 0 0 0
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=7/8; ncol2=24; w=-4; offset=-4; strand=D; shift=1; score=0.533896; -cvsGsGCCGCGCCCCGCCCsSsss---- ; cor=; Ncor= a 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 1 1 2 0 0 0 0 c 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 13 13 12 0 0 0 0 g 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 9 7 7 0 0 0 0 t 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1 0 2 2 0 0 0 0
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=8/8; ncol2=24; w=-5; offset=-5; strand=D; shift=0; score=0.481037; scsGCsGCGCgGCCCCGCCCCCgs----- ; cor=; Ncor= a 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 0 0 0 0 0 c 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 0 0 0 0 0 g 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 0 0 0 0 0 t 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift4 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=4; ncol=28; ----ssgrGCGGCGsCGsCGCCGCycss ; Alignment reference a 0 0 0 0 4 2 2 15 0 1 1 0 0 1 1 0 0 0 1 2 2 2 0 1 0 3 5 2 c 0 0 0 0 11 13 4 6 2 22 0 5 23 6 8 23 5 19 20 3 21 25 5 25 7 19 8 11 g 0 0 0 0 11 8 19 7 25 5 25 21 3 20 19 5 23 8 6 23 5 0 22 2 6 4 13 11 t 0 0 0 0 2 5 3 0 1 0 2 2 2 1 0 0 0 1 1 0 0 1 1 0 15 2 2 4
oligos_7nt_test_vs_ctrl_m3_shift4 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/3; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----ssgrGCGGCGsCGsCGCCGCycss ; cor=; Ncor= a 0 0 0 0 4 2 2 15 0 1 1 0 0 1 1 0 0 0 1 2 2 2 0 1 0 3 5 2 c 0 0 0 0 11 13 4 6 2 22 0 5 23 6 8 23 5 19 20 3 21 25 5 25 7 19 8 11 g 0 0 0 0 11 8 19 7 25 5 25 21 3 20 19 5 23 8 6 23 5 0 22 2 6 4 13 11 t 0 0 0 0 2 5 3 0 1 0 2 2 2 1 0 0 0 1 1 0 0 1 1 0 15 2 2 4
oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/3; ncol2=24; w=-2; offset=-2; strand=R; shift=2; score=0.611368; --sgCGGCGsGGCGGGGCsGCssssg-- ; cor=; Ncor= a 0 0 3 3 1 0 1 0 0 0 3 1 3 2 1 0 1 2 1 0 1 1 2 1 1 0 0 0 c 0 0 6 3 19 5 1 21 1 15 2 2 17 0 2 3 1 18 6 3 16 15 11 13 6 5 0 0 g 0 0 10 13 2 18 20 2 20 7 17 20 3 20 18 20 21 3 15 20 5 6 9 8 12 13 0 0 t 0 0 4 4 1 0 1 0 2 1 1 0 0 1 2 0 0 0 1 0 1 1 1 1 4 5 0 0
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.512085; scsGCsGCGCgGCCCCGCCCCCgs---- ; cor=; Ncor= a 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 9 4 0 0 0 0 c 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 10 16 0 0 0 0 g 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 15 16 0 0 0 0 t 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2 9 7 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=2; ncol=26; --cssssGCsGCCCCGCCsCGCCGcs ; Alignment reference a 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 c 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 g 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 t 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --cssssGCsGCCCCGCCsCGCCGcs ; cor=; Ncor= a 0 0 5 4 1 1 1 1 0 1 0 0 0 2 1 0 0 1 1 2 0 1 0 1 4 4 c 0 0 13 12 8 9 6 5 20 15 3 21 20 18 20 3 20 17 7 20 2 20 18 2 13 10 g 0 0 5 6 13 11 15 16 3 6 18 1 3 2 0 17 2 2 15 1 21 1 5 19 3 6 t 0 0 0 1 1 2 1 1 0 1 2 1 0 1 2 3 1 3 0 0 0 1 0 1 3 3
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/9; ncol2=24; w=0; offset=0; strand=D; shift=2; score=0.799299; --ssgCgCCCGCCCCGCGCCGCggss ; cor=; Ncor= a 0 0 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 c 0 0 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 g 0 0 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 t 0 0 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3
oligos_6nt_test_vs_ctrl_m5_shift4 (oligos_6nt_test_vs_ctrl_m5)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=3/9; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.743783; ----ssCkCCGCCCCGCCsCGCCGss ; cor=; Ncor= a 0 0 0 0 6 1 0 2 0 3 1 0 1 2 2 0 1 0 3 3 0 2 1 1 2 0 c 0 0 0 0 10 12 23 6 24 21 3 24 23 21 21 4 23 21 10 21 5 21 22 5 7 8 g 0 0 0 0 7 9 1 8 2 0 20 1 0 2 0 20 2 4 13 1 20 0 2 20 15 16 t 0 0 0 0 3 4 2 10 0 2 2 1 2 1 3 2 0 1 0 1 1 3 1 0 2 2
oligos_7nt_test_vs_ctrl_m4_rc_shift1 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/9; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.660987; -ssCssCscgGCCCCGCCCCCgccs- ; cor=; Ncor= a 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 3 5 3 14 8 22 15 0 c 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 104 105 92 24 77 58 57 0 g 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 8 9 18 60 24 28 37 0 t 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1 6 2 8 23 12 13 12 0
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=5/9; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.620869; ----scsGCsGCGCgGCCCCGCCCCC ; cor=; Ncor= a 0 0 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 2 2 1 c 0 0 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 32 36 35 g 0 0 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 6 5 5 t 0 0 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2 3 0 2
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=6/9; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.611368; ssgrGCGGCGsCGsCGCCGCycss-- ; cor=; Ncor= a 4 2 2 15 0 1 1 0 0 1 1 0 0 0 1 2 2 2 0 1 0 3 5 2 0 0 c 11 13 4 6 2 22 0 5 23 6 8 23 5 19 20 3 21 25 5 25 7 19 8 11 0 0 g 11 8 19 7 25 5 25 21 3 20 19 5 23 8 6 23 5 0 22 2 6 4 13 11 0 0 t 2 5 3 0 1 0 2 2 2 1 0 0 0 1 1 0 0 1 1 0 15 2 2 4 0 0
oligos_6nt_test_vs_ctrl_m4_shift5 (oligos_6nt_test_vs_ctrl_m4)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=7/9; ncol2=24; w=0; offset=3; strand=D; shift=5; score=0.544727; -----cvsGsGCCGCGCCCCGCCCsS ; cor=; Ncor= a 0 0 0 0 0 2 6 3 2 3 2 2 2 1 1 1 0 0 2 1 2 0 0 1 3 0 c 0 0 0 0 0 12 7 9 2 6 3 17 20 3 21 1 22 20 18 22 2 19 19 20 7 6 g 0 0 0 0 0 5 10 11 16 14 18 4 0 18 1 21 1 1 3 0 17 2 4 2 9 16 t 0 0 0 0 0 4 0 0 3 0 0 0 1 1 0 0 0 2 0 0 2 2 0 0 4 1
oligos_7nt_test_vs_ctrl_m1_shift6 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=8/9; ncol2=24; w=0; offset=4; strand=D; shift=6; score=0.527422; ------ssgsgCCgCGCCCCGCCCCC ; cor=; Ncor= a 0 0 0 0 0 0 13 12 14 10 6 8 3 9 2 4 2 2 4 2 4 3 1 5 5 6 c 0 0 0 0 0 0 42 44 17 28 22 72 83 24 76 10 93 86 90 93 5 83 83 77 86 70 g 0 0 0 0 0 0 31 35 60 58 59 16 8 57 21 82 4 6 7 3 86 7 12 17 7 15 t 0 0 0 0 0 0 15 10 10 5 14 5 7 11 2 5 2 7 0 3 6 8 5 2 3 10
oligos_7nt_test_vs_ctrl_m2_rc_shift9 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2_rc; m=9/9; ncol2=24; w=0; offset=7; strand=R; shift=9; score=0.411075; ---------ssCyCCGCCCCGCCCsC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 13 6 7 11 2 4 5 3 5 3 3 1 3 0 6 3 1 c 0 0 0 0 0 0 0 0 0 42 39 69 34 78 73 14 83 72 85 81 14 77 86 73 29 86 g 0 0 0 0 0 0 0 0 0 27 34 12 14 12 15 68 4 13 4 7 70 5 6 12 53 3 t 0 0 0 0 0 0 0 0 0 12 15 6 35 2 2 7 4 4 2 3 9 9 2 3 9 4

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=24; shift=0; ncol=24; scGmGCGCGCkCCGCGgCCCcGsc ; Alignment reference a 1 5 1 6 1 0 3 0 0 1 1 1 1 2 2 0 1 1 1 0 0 1 4 5 c 6 9 0 13 3 18 2 16 2 18 4 18 16 2 18 3 4 18 16 16 14 1 6 10 g 12 4 19 2 15 2 16 5 18 1 7 2 1 15 1 18 14 2 4 5 5 18 9 4 t 2 3 1 0 2 1 0 0 1 1 9 0 3 2 0 0 2 0 0 0 2 1 2 2
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=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; scGmGCGCGCkCCGCGgCCCcGsc ; cor=; Ncor= a 1 5 1 6 1 0 3 0 0 1 1 1 1 2 2 0 1 1 1 0 0 1 4 5 c 6 9 0 13 3 18 2 16 2 18 4 18 16 2 18 3 4 18 16 16 14 1 6 10 g 12 4 19 2 15 2 16 5 18 1 7 2 1 15 1 18 14 2 4 5 5 18 9 4 t 2 3 1 0 2 1 0 0 1 1 9 0 3 2 0 0 2 0 0 0 2 1 2 2
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=2/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score=0.759556; ssgCgCCCGCCCCGCGCCGCggss ; cor=; Ncor= a 12 10 2 4 3 1 0 4 5 0 4 1 0 3 1 4 4 5 1 4 5 5 9 7 c 35 32 15 49 14 61 48 52 6 59 55 61 58 6 56 14 56 56 10 55 15 16 28 36 g 17 20 45 11 43 4 16 7 51 6 6 3 6 52 7 46 4 3 50 6 41 37 23 21 t 3 5 5 3 7 1 3 4 5 2 2 2 3 6 3 3 3 3 6 2 6 9 7 3
oligos_6nt_test_vs_ctrl_m1_shift5 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m1; m=3/4; ncol2=24; w=0; offset=5; strand=D; shift=5; score=0.497653; -----scsGCsGCGCgGCCCCGCC ; cor=; Ncor= a 0 0 0 0 0 3 5 1 1 1 1 1 4 2 6 3 2 1 1 3 1 2 1 1 c 0 0 0 0 0 22 20 11 7 32 15 6 37 6 30 6 6 38 33 35 36 2 37 38 g 0 0 0 0 0 14 10 26 30 7 26 32 1 34 4 29 34 2 6 3 5 39 4 2 t 0 0 0 0 0 4 8 5 5 3 1 4 1 1 3 5 1 2 3 2 1 0 1 2
oligos_7nt_test_vs_ctrl_m4_rc_shift7 (oligos_7nt_test_vs_ctrl_m4_rc)				; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m4_rc; m=4/4; ncol2=24; w=0; offset=7; strand=R; shift=7; score=0.426944; -------ssCssCscgGCCCCGCC ; cor=; Ncor= a 0 0 0 0 0 0 0 9 5 10 12 9 6 10 20 11 3 1 1 9 1 4 3 2 c 0 0 0 0 0 0 0 55 55 83 39 31 103 37 71 23 20 110 104 102 111 9 104 110 g 0 0 0 0 0 0 0 35 38 22 60 70 9 64 12 80 93 4 7 5 6 106 9 8 t 0 0 0 0 0 0 0 22 23 6 10 11 3 10 18 7 5 6 9 5 3 2 5 1