One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.164711_2026-03-30.164711_1nojY4/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/2026/03/30/peak-motifs.2026-03-30.164711_2026-03-30.164711_1nojY4/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; awTTAGSCTAAAtcs ; Alignment reference a 29 25 8 2 60 2 1 1 3 64 63 54 10 15 16 c 17 8 3 11 5 0 18 63 1 1 0 2 7 20 18 g 11 4 5 4 2 64 50 4 0 4 2 3 6 17 22 t 12 32 53 52 2 3 0 1 65 0 4 10 46 17 13

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; awTTAGSCTAAAtcs ; cor=; Ncor= a 29 25 8 2 60 2 1 1 3 64 63 54 10 15 16 c 17 8 3 11 5 0 18 63 1 1 0 2 7 20 18 g 11 4 5 4 2 64 50 4 0 4 2 3 6 17 22 t 12 32 53 52 2 3 0 1 65 0 4 10 46 17 13

oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=2/3; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.878597; wwTTAGGCTAAwwb- ; cor=; Ncor= a 22 23 8 3 73 2 4 5 2 77 67 27 24 15 0 c 20 13 5 12 2 1 14 73 1 0 3 3 14 22 0 g 18 10 3 4 3 72 60 0 0 3 4 7 17 23 0 t 21 35 65 62 3 6 3 3 78 1 7 44 26 21 0

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.76344; --tyAGGCTAAAwk- ; cor=; Ncor= a 0 0 24 17 76 3 0 3 4 98 105 82 30 24 0 c 0 0 16 29 11 0 11 101 3 5 0 2 16 23 0 g 0 0 22 13 4 104 98 5 0 6 2 11 15 32 0 t 0 0 47 50 18 2 0 0 102 0 2 14 48 30 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -vwwTTAGCCTAAww ; Alignment reference a 0 21 26 44 7 1 78 3 3 6 3 62 65 35 21 c 0 23 17 7 4 3 0 0 60 72 3 4 3 10 18 g 0 22 14 3 3 0 1 73 14 1 2 12 5 13 20 t 0 15 24 27 67 77 2 5 4 2 73 3 8 23 22

oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -vwwTTAGCCTAAww ; cor=; Ncor= a 0 21 26 44 7 1 78 3 3 6 3 62 65 35 21 c 0 23 17 7 4 3 0 0 60 72 3 4 3 10 18 g 0 22 14 3 3 0 1 73 14 1 2 12 5 13 20 t 0 15 24 27 67 77 2 5 4 2 73 3 8 23 22

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=2/3; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.878597; sgaTTTAGSCTAAwt ; cor=; Ncor= a 13 17 46 10 4 0 65 1 0 3 2 52 53 32 12 c 22 17 6 3 2 4 0 4 50 64 2 4 5 4 11 g 18 20 7 2 0 1 1 63 18 0 5 11 3 8 17 t 16 15 10 54 63 64 3 1 1 2 60 2 8 25 29

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=3/3; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.780501; -mwTTTAGCCTra-- ; cor=; Ncor= a 0 30 48 14 2 0 102 0 0 2 18 50 47 0 0 c 0 32 15 11 2 6 0 5 98 104 4 13 22 0 0 g 0 23 16 2 0 5 3 101 11 0 11 29 16 0 0 t 0 24 30 82 105 98 4 3 0 3 76 17 24 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; mcCTCCACwy ; Alignment reference a 9 7 0 0 2 0 35 0 9 8 c 11 14 35 0 33 35 0 35 7 15 g 7 6 0 0 0 0 0 0 8 3 t 8 8 0 35 0 0 0 0 11 9

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; mcCTCCACwy ; cor=; Ncor= a 9 7 0 0 2 0 35 0 9 8 c 11 14 35 0 33 35 0 35 7 15 g 7 6 0 0 0 0 0 0 8 3 t 8 8 0 35 0 0 0 0 11 9

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --tyAGGCTAAAwk ; Alignment reference a 0 0 24 17 76 3 0 3 4 98 105 82 30 24 c 0 0 16 29 11 0 11 101 3 5 0 2 16 23 g 0 0 22 13 4 104 98 5 0 6 2 11 15 32 t 0 0 47 50 18 2 0 0 102 0 2 14 48 30

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --tyAGGCTAAAwk ; cor=; Ncor= a 0 0 24 17 76 3 0 3 4 98 105 82 30 24 c 0 0 16 29 11 0 11 101 3 5 0 2 16 23 g 0 0 22 13 4 104 98 5 0 6 2 11 15 32 t 0 0 47 50 18 2 0 0 102 0 2 14 48 30

oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=2/5; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.780501; wwTTAGGCTAAwwb ; cor=; Ncor= a 22 23 8 3 73 2 4 5 2 77 67 27 24 15 c 20 13 5 12 2 1 14 73 1 0 3 3 14 22 g 18 10 3 4 3 72 60 0 0 3 4 7 17 23 t 21 35 65 62 3 6 3 3 78 1 7 44 26 21

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/5; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.76344; awTTAGSCTAAAtc ; cor=; Ncor= a 29 25 8 2 60 2 1 1 3 64 63 54 10 15 c 17 8 3 11 5 0 18 63 1 1 0 2 7 20 g 11 4 5 4 2 64 50 4 0 4 2 3 6 17 t 12 32 53 52 2 3 0 1 65 0 4 10 46 17

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=4/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.740658; --kbCGGGTAAAww ; cor=; Ncor= a 0 0 8 9 5 1 0 3 3 62 60 58 20 21 c 0 0 13 21 51 1 0 7 2 0 0 2 13 10 g 0 0 24 16 4 62 64 49 10 1 1 1 11 15 t 0 0 19 18 4 0 0 5 49 1 3 3 20 18

oligos_6nt_mkv2_m4_shift2 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=5/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.726572; --kbsGGGTAAAdt ; cor=; Ncor= a 0 0 19 12 9 5 1 4 2 75 70 75 25 19 c 0 0 20 25 21 3 0 3 3 3 7 1 14 17 g 0 0 24 21 45 71 83 74 3 3 3 4 21 19 t 0 0 21 26 9 5 0 3 76 3 4 4 24 29

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --kbCGGGTAAAww ; Alignment reference a 0 0 8 9 5 1 0 3 3 62 60 58 20 21 c 0 0 13 21 51 1 0 7 2 0 0 2 13 10 g 0 0 24 16 4 62 64 49 10 1 1 1 11 15 t 0 0 19 18 4 0 0 5 49 1 3 3 20 18

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --kbCGGGTAAAww ; cor=; Ncor= a 0 0 8 9 5 1 0 3 3 62 60 58 20 21 c 0 0 13 21 51 1 0 7 2 0 0 2 13 10 g 0 0 24 16 4 62 64 49 10 1 1 1 11 15 t 0 0 19 18 4 0 0 5 49 1 3 3 20 18

oligos_6nt_mkv2_m4_shift2 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.922479; --kbsGGGTAAAdt ; cor=; Ncor= a 0 0 19 12 9 5 1 4 2 75 70 75 25 19 c 0 0 20 25 21 3 0 3 3 3 7 1 14 17 g 0 0 24 21 45 71 83 74 3 3 3 4 21 19 t 0 0 21 26 9 5 0 3 76 3 4 4 24 29

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.740658; --tyAGGCTAAAwk ; cor=; Ncor= a 0 0 24 17 76 3 0 3 4 98 105 82 30 24 c 0 0 16 29 11 0 11 101 3 5 0 2 16 23 g 0 0 22 13 4 104 98 5 0 6 2 11 15 32 t 0 0 47 50 18 2 0 0 102 0 2 14 48 30

oligos_6nt_mkv2_m2_rc_shift0 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=4/4; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.551296; watGCGGGGaAam- ; cor=; Ncor= a 35 31 15 3 2 2 0 11 4 62 66 29 35 0 c 11 20 9 6 90 8 2 1 0 5 5 19 24 0 g 14 21 14 83 0 84 90 82 87 9 10 23 17 0 t 34 22 56 2 2 0 2 0 3 18 13 23 18 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; yyCAGGGTCtwk ; Alignment reference a 12 14 1 59 2 3 3 1 1 6 19 12 c 18 17 54 1 3 3 2 0 58 6 14 14 g 14 11 4 1 52 50 53 1 1 15 12 18 t 17 19 2 0 4 5 3 59 1 34 16 17

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; yyCAGGGTCtwk ; cor=; Ncor= a 12 14 1 59 2 3 3 1 1 6 19 12 c 18 17 54 1 3 3 2 0 58 6 14 14 g 14 11 4 1 52 50 53 1 1 15 12 18 t 17 19 2 0 4 5 3 59 1 34 16 17

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -ktTtCCCCGCatw ; Alignment reference a 0 18 23 13 18 3 0 2 0 2 2 56 22 34 c 0 17 23 10 9 87 82 90 84 0 83 14 21 14 g 0 24 19 5 5 0 1 2 8 90 6 9 20 11 t 0 35 29 66 62 4 11 0 2 2 3 15 31 35

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -ktTtCCCCGCatw ; cor=; Ncor= a 0 18 23 13 18 3 0 2 0 2 2 56 22 34 c 0 17 23 10 9 87 82 90 84 0 83 14 21 14 g 0 24 19 5 5 0 1 2 8 90 6 9 20 11 t 0 35 29 66 62 4 11 0 2 2 3 15 31 35

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.988595; -ktttCCCCGCAyw ; cor=; Ncor= a 0 15 17 13 15 2 0 3 0 1 0 56 17 26 c 0 9 17 10 6 66 56 65 63 0 66 6 18 10 g 0 20 16 5 2 0 1 1 5 67 2 2 13 7 t 0 25 19 41 46 1 12 0 1 1 1 5 21 26

oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=3/3; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.551296; wwTTTACCCGvm-- ; cor=; Ncor= a 18 20 3 3 1 49 5 0 0 4 18 19 0 0 c 15 11 1 1 1 10 49 64 62 4 16 24 0 0 g 10 13 2 0 0 2 7 0 1 51 21 13 0 0 t 21 20 58 60 62 3 3 0 1 5 9 8 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; ktttCCCCGCAyw ; Alignment reference a 15 17 13 15 2 0 3 0 1 0 56 17 26 c 9 17 10 6 66 56 65 63 0 66 6 18 10 g 20 16 5 2 0 1 1 5 67 2 2 13 7 t 25 19 41 46 1 12 0 1 1 1 5 21 26

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ktttCCCCGCAyw ; cor=; Ncor= a 15 17 13 15 2 0 3 0 1 0 56 17 26 c 9 17 10 6 66 56 65 63 0 66 6 18 10 g 20 16 5 2 0 1 1 5 67 2 2 13 7 t 25 19 41 46 1 12 0 1 1 1 5 21 26

oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=2/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.988595; ktTtCCCCGCatw ; cor=; Ncor= a 18 23 13 18 3 0 2 0 2 2 56 22 34 c 17 23 10 9 87 82 90 84 0 83 14 21 14 g 24 19 5 5 0 1 2 8 90 6 9 20 11 t 35 29 66 62 4 11 0 2 2 3 15 31 35

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; kkCTTGGCma ; Alignment reference a 11 8 0 0 0 0 0 0 22 18 c 11 11 49 0 0 0 0 49 17 10 g 13 15 0 0 0 49 49 0 6 12 t 14 15 0 49 49 0 0 0 4 9

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; kkCTTGGCma ; cor=; Ncor= a 11 8 0 0 0 0 0 0 22 18 c 11 11 49 0 0 0 0 49 17 10 g 13 15 0 0 0 49 49 0 6 12 t 14 15 0 49 49 0 0 0 4 9

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; kbsGGGTAAAdt ; Alignment reference a 19 12 9 5 1 4 2 75 70 75 25 19 c 20 25 21 3 0 3 3 3 7 1 14 17 g 24 21 45 71 83 74 3 3 3 4 21 19 t 21 26 9 5 0 3 76 3 4 4 24 29

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; kbsGGGTAAAdt ; cor=; Ncor= a 19 12 9 5 1 4 2 75 70 75 25 19 c 20 25 21 3 0 3 3 3 7 1 14 17 g 24 21 45 71 83 74 3 3 3 4 21 19 t 21 26 9 5 0 3 76 3 4 4 24 29

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.922479; kbCGGGTAAAww ; cor=; Ncor= a 8 9 5 1 0 3 3 62 60 58 20 21 c 13 21 51 1 0 7 2 0 0 2 13 10 g 24 16 4 62 64 49 10 1 1 1 11 15 t 19 18 4 0 0 5 49 1 3 3 20 18

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=3/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.726572; tyAGGCTAAAwk ; cor=; Ncor= a 24 17 76 3 0 3 4 98 105 82 30 24 c 16 29 11 0 11 101 3 5 0 2 16 23 g 22 13 4 104 98 5 0 6 2 11 15 32 t 47 50 18 2 0 0 102 0 2 14 48 30

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; awTTAGSCTAAAtcs ; Alignment reference a 29 25 8 2 60 2 1 1 3 64 63 54 10 15 16 c 17 8 3 11 5 0 18 63 1 1 0 2 7 20 18 g 11 4 5 4 2 64 50 4 0 4 2 3 6 17 22 t 12 32 53 52 2 3 0 1 65 0 4 10 46 17 13
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; awTTAGSCTAAAtcs ; cor=; Ncor= a 29 25 8 2 60 2 1 1 3 64 63 54 10 15 16 c 17 8 3 11 5 0 18 63 1 1 0 2 7 20 18 g 11 4 5 4 2 64 50 4 0 4 2 3 6 17 22 t 12 32 53 52 2 3 0 1 65 0 4 10 46 17 13
oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=2/3; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.878597; wwTTAGGCTAAwwb- ; cor=; Ncor= a 22 23 8 3 73 2 4 5 2 77 67 27 24 15 0 c 20 13 5 12 2 1 14 73 1 0 3 3 14 22 0 g 18 10 3 4 3 72 60 0 0 3 4 7 17 23 0 t 21 35 65 62 3 6 3 3 78 1 7 44 26 21 0
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.76344; --tyAGGCTAAAwk- ; cor=; Ncor= a 0 0 24 17 76 3 0 3 4 98 105 82 30 24 0 c 0 0 16 29 11 0 11 101 3 5 0 2 16 23 0 g 0 0 22 13 4 104 98 5 0 6 2 11 15 32 0 t 0 0 47 50 18 2 0 0 102 0 2 14 48 30 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=14; shift=1; ncol=15; -vwwTTAGCCTAAww ; Alignment reference a 0 21 26 44 7 1 78 3 3 6 3 62 65 35 21 c 0 23 17 7 4 3 0 0 60 72 3 4 3 10 18 g 0 22 14 3 3 0 1 73 14 1 2 12 5 13 20 t 0 15 24 27 67 77 2 5 4 2 73 3 8 23 22
oligos_7nt_mkv2_m5_shift1 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -vwwTTAGCCTAAww ; cor=; Ncor= a 0 21 26 44 7 1 78 3 3 6 3 62 65 35 21 c 0 23 17 7 4 3 0 0 60 72 3 4 3 10 18 g 0 22 14 3 3 0 1 73 14 1 2 12 5 13 20 t 0 15 24 27 67 77 2 5 4 2 73 3 8 23 22
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1_rc; m=2/3; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.878597; sgaTTTAGSCTAAwt ; cor=; Ncor= a 13 17 46 10 4 0 65 1 0 3 2 52 53 32 12 c 22 17 6 3 2 4 0 4 50 64 2 4 5 4 11 g 18 20 7 2 0 1 1 63 18 0 5 11 3 8 17 t 16 15 10 54 63 64 3 1 1 2 60 2 8 25 29
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1_rc; m=3/3; ncol2=12; w=0; offset=0; strand=R; shift=1; score=0.780501; -mwTTTAGCCTra-- ; cor=; Ncor= a 0 30 48 14 2 0 102 0 0 2 18 50 47 0 0 c 0 32 15 11 2 6 0 5 98 104 4 13 22 0 0 g 0 23 16 2 0 5 3 101 11 0 11 29 16 0 0 t 0 24 30 82 105 98 4 3 0 3 76 17 24 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --tyAGGCTAAAwk ; Alignment reference a 0 0 24 17 76 3 0 3 4 98 105 82 30 24 c 0 0 16 29 11 0 11 101 3 5 0 2 16 23 g 0 0 22 13 4 104 98 5 0 6 2 11 15 32 t 0 0 47 50 18 2 0 0 102 0 2 14 48 30
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --tyAGGCTAAAwk ; cor=; Ncor= a 0 0 24 17 76 3 0 3 4 98 105 82 30 24 c 0 0 16 29 11 0 11 101 3 5 0 2 16 23 g 0 0 22 13 4 104 98 5 0 6 2 11 15 32 t 0 0 47 50 18 2 0 0 102 0 2 14 48 30
oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=2/5; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.780501; wwTTAGGCTAAwwb ; cor=; Ncor= a 22 23 8 3 73 2 4 5 2 77 67 27 24 15 c 20 13 5 12 2 1 14 73 1 0 3 3 14 22 g 18 10 3 4 3 72 60 0 0 3 4 7 17 23 t 21 35 65 62 3 6 3 3 78 1 7 44 26 21
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/5; ncol2=15; w=-2; offset=-2; strand=D; shift=0; score=0.76344; awTTAGSCTAAAtc ; cor=; Ncor= a 29 25 8 2 60 2 1 1 3 64 63 54 10 15 c 17 8 3 11 5 0 18 63 1 1 0 2 7 20 g 11 4 5 4 2 64 50 4 0 4 2 3 6 17 t 12 32 53 52 2 3 0 1 65 0 4 10 46 17
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=4/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.740658; --kbCGGGTAAAww ; cor=; Ncor= a 0 0 8 9 5 1 0 3 3 62 60 58 20 21 c 0 0 13 21 51 1 0 7 2 0 0 2 13 10 g 0 0 24 16 4 62 64 49 10 1 1 1 11 15 t 0 0 19 18 4 0 0 5 49 1 3 3 20 18
oligos_6nt_mkv2_m4_shift2 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=5/5; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.726572; --kbsGGGTAAAdt ; cor=; Ncor= a 0 0 19 12 9 5 1 4 2 75 70 75 25 19 c 0 0 20 25 21 3 0 3 3 3 7 1 14 17 g 0 0 24 21 45 71 83 74 3 3 3 4 21 19 t 0 0 21 26 9 5 0 3 76 3 4 4 24 29

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --kbCGGGTAAAww ; Alignment reference a 0 0 8 9 5 1 0 3 3 62 60 58 20 21 c 0 0 13 21 51 1 0 7 2 0 0 2 13 10 g 0 0 24 16 4 62 64 49 10 1 1 1 11 15 t 0 0 19 18 4 0 0 5 49 1 3 3 20 18
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --kbCGGGTAAAww ; cor=; Ncor= a 0 0 8 9 5 1 0 3 3 62 60 58 20 21 c 0 0 13 21 51 1 0 7 2 0 0 2 13 10 g 0 0 24 16 4 62 64 49 10 1 1 1 11 15 t 0 0 19 18 4 0 0 5 49 1 3 3 20 18
oligos_6nt_mkv2_m4_shift2 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.922479; --kbsGGGTAAAdt ; cor=; Ncor= a 0 0 19 12 9 5 1 4 2 75 70 75 25 19 c 0 0 20 25 21 3 0 3 3 3 7 1 14 17 g 0 0 24 21 45 71 83 74 3 3 3 4 21 19 t 0 0 21 26 9 5 0 3 76 3 4 4 24 29
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=3/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.740658; --tyAGGCTAAAwk ; cor=; Ncor= a 0 0 24 17 76 3 0 3 4 98 105 82 30 24 c 0 0 16 29 11 0 11 101 3 5 0 2 16 23 g 0 0 22 13 4 104 98 5 0 6 2 11 15 32 t 0 0 47 50 18 2 0 0 102 0 2 14 48 30
oligos_6nt_mkv2_m2_rc_shift0 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=4/4; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.551296; watGCGGGGaAam- ; cor=; Ncor= a 35 31 15 3 2 2 0 11 4 62 66 29 35 0 c 11 20 9 6 90 8 2 1 0 5 5 19 24 0 g 14 21 14 83 0 84 90 82 87 9 10 23 17 0 t 34 22 56 2 2 0 2 0 3 18 13 23 18 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -ktTtCCCCGCatw ; Alignment reference a 0 18 23 13 18 3 0 2 0 2 2 56 22 34 c 0 17 23 10 9 87 82 90 84 0 83 14 21 14 g 0 24 19 5 5 0 1 2 8 90 6 9 20 11 t 0 35 29 66 62 4 11 0 2 2 3 15 31 35
oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -ktTtCCCCGCatw ; cor=; Ncor= a 0 18 23 13 18 3 0 2 0 2 2 56 22 34 c 0 17 23 10 9 87 82 90 84 0 83 14 21 14 g 0 24 19 5 5 0 1 2 8 90 6 9 20 11 t 0 35 29 66 62 4 11 0 2 2 3 15 31 35
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.988595; -ktttCCCCGCAyw ; cor=; Ncor= a 0 15 17 13 15 2 0 3 0 1 0 56 17 26 c 0 9 17 10 6 66 56 65 63 0 66 6 18 10 g 0 20 16 5 2 0 1 1 5 67 2 2 13 7 t 0 25 19 41 46 1 12 0 1 1 1 5 21 26
oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4_rc; m=3/3; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.551296; wwTTTACCCGvm-- ; cor=; Ncor= a 18 20 3 3 1 49 5 0 0 4 18 19 0 0 c 15 11 1 1 1 10 49 64 62 4 16 24 0 0 g 10 13 2 0 0 2 7 0 1 51 21 13 0 0 t 21 20 58 60 62 3 3 0 1 5 9 8 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; kbsGGGTAAAdt ; Alignment reference a 19 12 9 5 1 4 2 75 70 75 25 19 c 20 25 21 3 0 3 3 3 7 1 14 17 g 24 21 45 71 83 74 3 3 3 4 21 19 t 21 26 9 5 0 3 76 3 4 4 24 29
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; kbsGGGTAAAdt ; cor=; Ncor= a 19 12 9 5 1 4 2 75 70 75 25 19 c 20 25 21 3 0 3 3 3 7 1 14 17 g 24 21 45 71 83 74 3 3 3 4 21 19 t 21 26 9 5 0 3 76 3 4 4 24 29
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.922479; kbCGGGTAAAww ; cor=; Ncor= a 8 9 5 1 0 3 3 62 60 58 20 21 c 13 21 51 1 0 7 2 0 0 2 13 10 g 24 16 4 62 64 49 10 1 1 1 11 15 t 19 18 4 0 0 5 49 1 3 3 20 18
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=3/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.726572; tyAGGCTAAAwk ; cor=; Ncor= a 24 17 76 3 0 3 4 98 105 82 30 24 c 16 29 11 0 11 101 3 5 0 2 16 23 g 22 13 4 104 98 5 0 6 2 11 15 32 t 47 50 18 2 0 0 102 0 2 14 48 30