One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -AyTCCACTCCActc ; Alignment reference a 0 73 15 0 4 2 93 9 5 4 1 87 8 12 9 c 0 9 43 3 85 90 2 72 5 87 93 4 66 17 62 g 0 10 9 2 7 2 0 3 1 2 0 3 13 5 14 t 0 6 31 93 2 4 3 14 87 5 4 4 11 64 13

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -AyTCCACTCCActc ; cor=; Ncor= a 0 73 15 0 4 2 93 9 5 4 1 87 8 12 9 c 0 9 43 3 85 90 2 72 5 87 93 4 66 17 62 g 0 10 9 2 7 2 0 3 1 2 0 3 13 5 14 t 0 6 31 93 2 4 3 14 87 5 4 4 11 64 13

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.920964; -ayTCCACTCCAct- ; cor=; Ncor= a 0 76 15 5 7 2 110 6 5 3 1 105 15 9 0 c 0 9 51 9 90 98 1 86 5 103 107 2 56 19 0 g 0 12 11 5 10 9 1 3 2 2 2 3 18 11 0 t 0 16 36 94 6 4 1 18 101 5 3 3 24 74 0

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=3/4; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.804687; caTTCCATTCCAtTc ; cor=; Ncor= a 9 43 6 1 0 8 60 6 1 1 3 59 5 4 6 c 41 3 8 2 59 52 3 10 1 61 57 1 15 8 44 g 10 9 0 1 1 7 3 2 1 1 7 2 3 5 5 t 7 12 53 63 7 0 1 49 64 4 0 5 44 50 12

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=4/4; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.605352; ---tccATTCCAyt- ; cor=; Ncor= a 0 0 0 9 15 15 66 1 1 1 0 66 14 10 0 c 0 0 0 13 34 29 0 0 0 66 58 0 17 11 0 g 0 0 0 8 7 14 2 0 0 0 7 2 10 7 0 t 0 0 0 38 12 10 0 67 67 1 3 0 27 40 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ryCTAGGCArv ; Alignment reference a 20 15 2 2 62 4 1 2 59 19 21 c 16 21 65 1 3 0 3 61 6 18 20 g 20 17 2 1 4 67 68 4 4 20 21 t 17 20 4 69 4 2 1 6 4 16 11

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ryCTAGGCArv ; cor=; Ncor= a 20 15 2 2 62 4 1 2 59 19 21 c 16 21 65 1 3 0 3 61 6 18 20 g 20 17 2 1 4 67 68 4 4 20 21 t 17 20 4 69 4 2 1 6 4 16 11

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.855729; msCTAGGCra- ; cor=; Ncor= a 16 10 0 0 46 1 2 1 16 18 0 c 18 14 46 0 2 3 1 45 10 11 0 g 8 14 2 0 0 42 41 0 12 10 0 t 6 10 0 48 0 2 4 2 10 9 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -ayTCCACTCCAct ; Alignment reference a 0 76 15 5 7 2 110 6 5 3 1 105 15 9 c 0 9 51 9 90 98 1 86 5 103 107 2 56 19 g 0 12 11 5 10 9 1 3 2 2 2 3 18 11 t 0 16 36 94 6 4 1 18 101 5 3 3 24 74

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -ayTCCACTCCAct ; cor=; Ncor= a 0 76 15 5 7 2 110 6 5 3 1 105 15 9 c 0 9 51 9 90 98 1 86 5 103 107 2 56 19 g 0 12 11 5 10 9 1 3 2 2 2 3 18 11 t 0 16 36 94 6 4 1 18 101 5 3 3 24 74

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.920964; -AyTCCACTCCAct ; cor=; Ncor= a 0 73 15 0 4 2 93 9 5 4 1 87 8 12 c 0 9 43 3 85 90 2 72 5 87 93 4 66 17 g 0 10 9 2 7 2 0 3 1 2 0 3 13 5 t 0 6 31 93 2 4 3 14 87 5 4 4 11 64

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=3/4; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.756515; caTTCCATTCCAtT ; cor=; Ncor= a 9 43 6 1 0 8 60 6 1 1 3 59 5 4 c 41 3 8 2 59 52 3 10 1 61 57 1 15 8 g 10 9 0 1 1 7 3 2 1 1 7 2 3 5 t 7 12 53 63 7 0 1 49 64 4 0 5 44 50

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=4/4; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.679969; ---tccATTCCAyt ; cor=; Ncor= a 0 0 0 9 15 15 66 1 1 1 0 66 14 10 c 0 0 0 13 34 29 0 0 0 66 58 0 17 11 g 0 0 0 8 7 14 2 0 0 0 7 2 10 7 t 0 0 0 38 12 10 0 67 67 1 3 0 27 40

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; vkCCCCGCsc ; Alignment reference a 13 8 1 0 1 0 1 2 7 9 c 15 9 48 47 49 50 0 45 23 19 g 15 19 1 3 0 0 49 0 13 12 t 7 14 0 0 0 0 0 3 7 10

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; vkCCCCGCsc ; cor=; Ncor= a 13 8 1 0 1 0 1 2 7 9 c 15 9 48 47 49 50 0 45 23 19 g 15 19 1 3 0 0 49 0 13 12 t 7 14 0 0 0 0 0 3 7 10

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 5 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=15; shift=0; ncol=15; gAaTGGAATGGAAtg ; Alignment reference a 12 50 44 5 0 4 64 49 1 0 7 63 53 12 7 c 5 5 3 2 7 1 1 2 3 7 1 1 0 9 10 g 44 8 15 1 57 61 1 10 3 52 59 2 8 3 41 t 6 4 5 59 3 1 1 6 60 8 0 1 6 43 9

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gAaTGGAATGGAAtg ; cor=; Ncor= a 12 50 44 5 0 4 64 49 1 0 7 63 53 12 7 c 5 5 3 2 7 1 1 2 3 7 1 1 0 9 10 g 44 8 15 1 57 61 1 10 3 52 59 2 8 3 41 t 6 4 5 59 3 1 1 6 60 8 0 1 6 43 9

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=2/4; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.804687; gagTGGAGTGGArT- ; cor=; Ncor= a 13 64 11 4 4 5 87 14 3 4 2 93 31 6 0 c 14 5 13 3 0 2 1 3 0 2 7 2 9 10 0 g 62 17 66 4 93 87 5 72 2 90 85 3 43 9 0 t 9 12 8 87 1 4 5 9 93 2 4 0 15 73 0

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=3/4; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.756515; -agTGGAGTGGArt- ; cor=; Ncor= a 0 74 24 3 3 5 101 18 1 4 6 94 36 16 0 c 0 11 18 3 2 2 2 3 1 9 10 5 11 12 0 g 0 19 56 2 107 103 5 86 1 98 90 9 51 9 0 t 0 9 15 105 1 3 5 6 110 2 7 5 15 76 0

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=4/4; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.673394; -arTGGAATgga--- ; cor=; Ncor= a 0 40 27 0 3 1 67 67 0 10 12 38 0 0 0 c 0 7 10 2 7 0 0 0 2 14 7 8 0 0 0 g 0 11 17 0 58 66 0 0 0 29 34 13 0 0 0 t 0 10 14 66 0 1 1 1 66 15 15 9 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=13; shift=3; ncol=16; ---AwATATAATATAT ; Alignment reference a 0 0 0 38 14 49 2 46 5 41 41 3 44 5 36 8 c 0 0 0 1 3 0 1 0 1 1 1 1 1 6 1 6 g 0 0 0 2 1 1 0 3 0 1 0 1 3 2 7 2 t 0 0 0 9 32 0 47 1 44 7 8 45 2 37 6 34

oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---AwATATAATATAT ; cor=; Ncor= a 0 0 0 38 14 49 2 46 5 41 41 3 44 5 36 8 c 0 0 0 1 3 0 1 0 1 1 1 1 1 6 1 6 g 0 0 0 2 1 1 0 3 0 1 0 1 3 2 7 2 t 0 0 0 9 32 0 47 1 44 7 8 45 2 37 6 34

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3_rc; m=2/3; ncol2=13; w=-2; offset=-2; strand=R; shift=1; score=0.601895; -wwwTATATATwww-- ; cor=; Ncor= a 0 29 37 39 5 84 1 76 2 86 12 23 38 24 0 0 c 0 6 13 3 1 0 4 0 3 1 2 4 5 8 0 0 g 0 7 10 7 1 2 3 5 0 1 3 6 9 7 0 0 t 0 49 31 42 84 5 83 10 86 3 74 58 39 52 0 0

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=3/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.515514; wwTATATATAww---- ; cor=; Ncor= a 36 33 9 64 4 65 0 58 1 52 22 19 0 0 0 0 c 6 4 3 0 1 1 0 3 1 2 7 5 0 0 0 0 g 5 7 2 1 3 0 1 1 0 3 4 6 0 0 0 0 t 19 22 52 1 58 0 65 4 64 9 33 36 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTATATATAww ; Alignment reference a 0 36 33 9 64 4 65 0 58 1 52 22 19 c 0 6 4 3 0 1 1 0 3 1 2 7 5 g 0 5 7 2 1 3 0 1 1 0 3 4 6 t 0 19 22 52 1 58 0 65 4 64 9 33 36

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -wwTATATATAww ; cor=; Ncor= a 0 36 33 9 64 4 65 0 58 1 52 22 19 c 0 6 4 3 0 1 1 0 3 1 2 7 5 g 0 5 7 2 1 3 0 1 1 0 3 4 6 t 0 19 22 52 1 58 0 65 4 64 9 33 36

oligos_6nt_mkv2_m3_rc_shift0 (oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=2/3; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.85648; wwwTATATATwww ; cor=; Ncor= a 29 37 39 5 84 1 76 2 86 12 23 38 24 c 6 13 3 1 0 4 0 3 1 2 4 5 8 g 7 10 7 1 2 3 5 0 1 3 6 9 7 t 49 31 42 84 5 83 10 86 3 74 58 39 52

oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=13; w=0; offset=3; strand=D; shift=4; score=0.515514; ----AwATATAAT ; cor=; Ncor= a 0 0 0 0 38 14 49 2 46 5 41 41 3 c 0 0 0 0 1 3 0 1 0 1 1 1 1 g 0 0 0 0 2 1 1 0 3 0 1 0 1 t 0 0 0 0 9 32 0 47 1 44 7 8 45

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---tccATTCCAyt ; Alignment reference a 0 0 0 9 15 15 66 1 1 1 0 66 14 10 c 0 0 0 13 34 29 0 0 0 66 58 0 17 11 g 0 0 0 8 7 14 2 0 0 0 7 2 10 7 t 0 0 0 38 12 10 0 67 67 1 3 0 27 40

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---tccATTCCAyt ; cor=; Ncor= a 0 0 0 9 15 15 66 1 1 1 0 66 14 10 c 0 0 0 13 34 29 0 0 0 66 58 0 17 11 g 0 0 0 8 7 14 2 0 0 0 7 2 10 7 t 0 0 0 38 12 10 0 67 67 1 3 0 27 40

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=13; w=-2; offset=-2; strand=D; shift=1; score=0.679969; -ayTCCACTCCAct ; cor=; Ncor= a 0 76 15 5 7 2 110 6 5 3 1 105 15 9 c 0 9 51 9 90 98 1 86 5 103 107 2 56 19 g 0 12 11 5 10 9 1 3 2 2 2 3 18 11 t 0 16 36 94 6 4 1 18 101 5 3 3 24 74

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=3/4; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.673394; caTTCCATTCCAtT ; cor=; Ncor= a 9 43 6 1 0 8 60 6 1 1 3 59 5 4 c 41 3 8 2 59 52 3 10 1 61 57 1 15 8 g 10 9 0 1 1 7 3 2 1 1 7 2 3 5 t 7 12 53 63 7 0 1 49 64 4 0 5 44 50

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=4/4; ncol2=14; w=-2; offset=-2; strand=D; shift=1; score=0.605352; -AyTCCACTCCAct ; cor=; Ncor= a 0 73 15 0 4 2 93 9 5 4 1 87 8 12 c 0 9 43 3 85 90 2 72 5 87 93 4 66 17 g 0 10 9 2 7 2 0 3 1 2 0 3 13 5 t 0 6 31 93 2 4 3 14 87 5 4 4 11 64

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --wwwATATATAwww ; Alignment reference a 0 0 52 39 58 74 3 86 10 83 5 84 42 31 49 c 0 0 7 9 6 3 1 0 5 3 2 1 7 10 7 g 0 0 8 5 4 2 1 3 0 4 0 1 3 13 6 t 0 0 24 38 23 12 86 2 76 1 84 5 39 37 29

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --wwwATATATAwww ; cor=; Ncor= a 0 0 52 39 58 74 3 86 10 83 5 84 42 31 49 c 0 0 7 9 6 3 1 0 5 3 2 1 7 10 7 g 0 0 8 5 4 2 1 3 0 4 0 1 3 13 6 t 0 0 24 38 23 12 86 2 76 1 84 5 39 37 29

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.85648; --wwTATATATAww- ; cor=; Ncor= a 0 0 36 33 9 64 4 65 0 58 1 52 22 19 0 c 0 0 6 4 3 0 1 1 0 3 1 2 7 5 0 g 0 0 5 7 2 1 3 0 1 1 0 3 4 6 0 t 0 0 19 22 52 1 58 0 65 4 64 9 33 36 0

oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=3/3; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.601895; ATATATTATATwT-- ; cor=; Ncor= a 34 6 37 2 45 8 7 44 1 47 0 32 9 0 0 c 2 7 2 3 1 0 1 0 3 0 1 1 2 0 0 g 6 1 6 1 1 1 1 1 0 1 0 3 1 0 0 t 8 36 5 44 3 41 41 5 46 2 49 14 38 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 3 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=10; shift=0; ncol=10; msCTAGGCra ; Alignment reference a 16 10 0 0 46 1 2 1 16 18 c 18 14 46 0 2 3 1 45 10 11 g 8 14 2 0 0 42 41 0 12 10 t 6 10 0 48 0 2 4 2 10 9

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; msCTAGGCra ; cor=; Ncor= a 16 10 0 0 46 1 2 1 16 18 c 18 14 46 0 2 3 1 45 10 11 g 8 14 2 0 0 42 41 0 12 10 t 6 10 0 48 0 2 4 2 10 9

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.855729; ryCTAGGCAr ; cor=; Ncor= a 20 15 2 2 62 4 1 2 59 19 c 16 21 65 1 3 0 3 61 6 18 g 20 17 2 1 4 67 68 4 4 20 t 17 20 4 69 4 2 1 6 4 16

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -AyTCCACTCCActc ; Alignment reference a 0 73 15 0 4 2 93 9 5 4 1 87 8 12 9 c 0 9 43 3 85 90 2 72 5 87 93 4 66 17 62 g 0 10 9 2 7 2 0 3 1 2 0 3 13 5 14 t 0 6 31 93 2 4 3 14 87 5 4 4 11 64 13
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -AyTCCACTCCActc ; cor=; Ncor= a 0 73 15 0 4 2 93 9 5 4 1 87 8 12 9 c 0 9 43 3 85 90 2 72 5 87 93 4 66 17 62 g 0 10 9 2 7 2 0 3 1 2 0 3 13 5 14 t 0 6 31 93 2 4 3 14 87 5 4 4 11 64 13
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score=0.920964; -ayTCCACTCCAct- ; cor=; Ncor= a 0 76 15 5 7 2 110 6 5 3 1 105 15 9 0 c 0 9 51 9 90 98 1 86 5 103 107 2 56 19 0 g 0 12 11 5 10 9 1 3 2 2 2 3 18 11 0 t 0 16 36 94 6 4 1 18 101 5 3 3 24 74 0
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=3/4; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.804687; caTTCCATTCCAtTc ; cor=; Ncor= a 9 43 6 1 0 8 60 6 1 1 3 59 5 4 6 c 41 3 8 2 59 52 3 10 1 61 57 1 15 8 44 g 10 9 0 1 1 7 3 2 1 1 7 2 3 5 5 t 7 12 53 63 7 0 1 49 64 4 0 5 44 50 12
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=4/4; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.605352; ---tccATTCCAyt- ; cor=; Ncor= a 0 0 0 9 15 15 66 1 1 1 0 66 14 10 0 c 0 0 0 13 34 29 0 0 0 66 58 0 17 11 0 g 0 0 0 8 7 14 2 0 0 0 7 2 10 7 0 t 0 0 0 38 12 10 0 67 67 1 3 0 27 40 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -ayTCCACTCCAct ; Alignment reference a 0 76 15 5 7 2 110 6 5 3 1 105 15 9 c 0 9 51 9 90 98 1 86 5 103 107 2 56 19 g 0 12 11 5 10 9 1 3 2 2 2 3 18 11 t 0 16 36 94 6 4 1 18 101 5 3 3 24 74
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=1; score= 1; -ayTCCACTCCAct ; cor=; Ncor= a 0 76 15 5 7 2 110 6 5 3 1 105 15 9 c 0 9 51 9 90 98 1 86 5 103 107 2 56 19 g 0 12 11 5 10 9 1 3 2 2 2 3 18 11 t 0 16 36 94 6 4 1 18 101 5 3 3 24 74
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.920964; -AyTCCACTCCAct ; cor=; Ncor= a 0 73 15 0 4 2 93 9 5 4 1 87 8 12 c 0 9 43 3 85 90 2 72 5 87 93 4 66 17 g 0 10 9 2 7 2 0 3 1 2 0 3 13 5 t 0 6 31 93 2 4 3 14 87 5 4 4 11 64
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=3/4; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.756515; caTTCCATTCCAtT ; cor=; Ncor= a 9 43 6 1 0 8 60 6 1 1 3 59 5 4 c 41 3 8 2 59 52 3 10 1 61 57 1 15 8 g 10 9 0 1 1 7 3 2 1 1 7 2 3 5 t 7 12 53 63 7 0 1 49 64 4 0 5 44 50
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=4/4; ncol2=11; w=0; offset=2; strand=D; shift=3; score=0.679969; ---tccATTCCAyt ; cor=; Ncor= a 0 0 0 9 15 15 66 1 1 1 0 66 14 10 c 0 0 0 13 34 29 0 0 0 66 58 0 17 11 g 0 0 0 8 7 14 2 0 0 0 7 2 10 7 t 0 0 0 38 12 10 0 67 67 1 3 0 27 40

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=15; shift=0; ncol=15; gAaTGGAATGGAAtg ; Alignment reference a 12 50 44 5 0 4 64 49 1 0 7 63 53 12 7 c 5 5 3 2 7 1 1 2 3 7 1 1 0 9 10 g 44 8 15 1 57 61 1 10 3 52 59 2 8 3 41 t 6 4 5 59 3 1 1 6 60 8 0 1 6 43 9
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; gAaTGGAATGGAAtg ; cor=; Ncor= a 12 50 44 5 0 4 64 49 1 0 7 63 53 12 7 c 5 5 3 2 7 1 1 2 3 7 1 1 0 9 10 g 44 8 15 1 57 61 1 10 3 52 59 2 8 3 41 t 6 4 5 59 3 1 1 6 60 8 0 1 6 43 9
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=2/4; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.804687; gagTGGAGTGGArT- ; cor=; Ncor= a 13 64 11 4 4 5 87 14 3 4 2 93 31 6 0 c 14 5 13 3 0 2 1 3 0 2 7 2 9 10 0 g 62 17 66 4 93 87 5 72 2 90 85 3 43 9 0 t 9 12 8 87 1 4 5 9 93 2 4 0 15 73 0
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=3/4; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.756515; -agTGGAGTGGArt- ; cor=; Ncor= a 0 74 24 3 3 5 101 18 1 4 6 94 36 16 0 c 0 11 18 3 2 2 2 3 1 9 10 5 11 12 0 g 0 19 56 2 107 103 5 86 1 98 90 9 51 9 0 t 0 9 15 105 1 3 5 6 110 2 7 5 15 76 0
oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2_rc; m=4/4; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.673394; -arTGGAATgga--- ; cor=; Ncor= a 0 40 27 0 3 1 67 67 0 10 12 38 0 0 0 c 0 7 10 2 7 0 0 0 2 14 7 8 0 0 0 g 0 11 17 0 58 66 0 0 0 29 34 13 0 0 0 t 0 10 14 66 0 1 1 1 66 15 15 9 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=13; shift=3; ncol=16; ---AwATATAATATAT ; Alignment reference a 0 0 0 38 14 49 2 46 5 41 41 3 44 5 36 8 c 0 0 0 1 3 0 1 0 1 1 1 1 1 6 1 6 g 0 0 0 2 1 1 0 3 0 1 0 1 3 2 7 2 t 0 0 0 9 32 0 47 1 44 7 8 45 2 37 6 34
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---AwATATAATATAT ; cor=; Ncor= a 0 0 0 38 14 49 2 46 5 41 41 3 44 5 36 8 c 0 0 0 1 3 0 1 0 1 1 1 1 1 6 1 6 g 0 0 0 2 1 1 0 3 0 1 0 1 3 2 7 2 t 0 0 0 9 32 0 47 1 44 7 8 45 2 37 6 34
oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3_rc; m=2/3; ncol2=13; w=-2; offset=-2; strand=R; shift=1; score=0.601895; -wwwTATATATwww-- ; cor=; Ncor= a 0 29 37 39 5 84 1 76 2 86 12 23 38 24 0 0 c 0 6 13 3 1 0 4 0 3 1 2 4 5 8 0 0 g 0 7 10 7 1 2 3 5 0 1 3 6 9 7 0 0 t 0 49 31 42 84 5 83 10 86 3 74 58 39 52 0 0
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3; m=3/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.515514; wwTATATATAww---- ; cor=; Ncor= a 36 33 9 64 4 65 0 58 1 52 22 19 0 0 0 0 c 6 4 3 0 1 1 0 3 1 2 7 5 0 0 0 0 g 5 7 2 1 3 0 1 1 0 3 4 6 0 0 0 0 t 19 22 52 1 58 0 65 4 64 9 33 36 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTATATATAww ; Alignment reference a 0 36 33 9 64 4 65 0 58 1 52 22 19 c 0 6 4 3 0 1 1 0 3 1 2 7 5 g 0 5 7 2 1 3 0 1 1 0 3 4 6 t 0 19 22 52 1 58 0 65 4 64 9 33 36
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -wwTATATATAww ; cor=; Ncor= a 0 36 33 9 64 4 65 0 58 1 52 22 19 c 0 6 4 3 0 1 1 0 3 1 2 7 5 g 0 5 7 2 1 3 0 1 1 0 3 4 6 t 0 19 22 52 1 58 0 65 4 64 9 33 36
oligos_6nt_mkv2_m3_rc_shift0 (oligos_6nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc; m=2/3; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.85648; wwwTATATATwww ; cor=; Ncor= a 29 37 39 5 84 1 76 2 86 12 23 38 24 c 6 13 3 1 0 4 0 3 1 2 4 5 8 g 7 10 7 1 2 3 5 0 1 3 6 9 7 t 49 31 42 84 5 83 10 86 3 74 58 39 52
oligos_7nt_mkv2_m4_shift4 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4; m=3/3; ncol2=13; w=0; offset=3; strand=D; shift=4; score=0.515514; ----AwATATAAT ; cor=; Ncor= a 0 0 0 0 38 14 49 2 46 5 41 41 3 c 0 0 0 0 1 3 0 1 0 1 1 1 1 g 0 0 0 0 2 1 1 0 3 0 1 0 1 t 0 0 0 0 9 32 0 47 1 44 7 8 45

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---tccATTCCAyt ; Alignment reference a 0 0 0 9 15 15 66 1 1 1 0 66 14 10 c 0 0 0 13 34 29 0 0 0 66 58 0 17 11 g 0 0 0 8 7 14 2 0 0 0 7 2 10 7 t 0 0 0 38 12 10 0 67 67 1 3 0 27 40
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---tccATTCCAyt ; cor=; Ncor= a 0 0 0 9 15 15 66 1 1 1 0 66 14 10 c 0 0 0 13 34 29 0 0 0 66 58 0 17 11 g 0 0 0 8 7 14 2 0 0 0 7 2 10 7 t 0 0 0 38 12 10 0 67 67 1 3 0 27 40
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=2/4; ncol2=13; w=-2; offset=-2; strand=D; shift=1; score=0.679969; -ayTCCACTCCAct ; cor=; Ncor= a 0 76 15 5 7 2 110 6 5 3 1 105 15 9 c 0 9 51 9 90 98 1 86 5 103 107 2 56 19 g 0 12 11 5 10 9 1 3 2 2 2 3 18 11 t 0 16 36 94 6 4 1 18 101 5 3 3 24 74
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=3/4; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.673394; caTTCCATTCCAtT ; cor=; Ncor= a 9 43 6 1 0 8 60 6 1 1 3 59 5 4 c 41 3 8 2 59 52 3 10 1 61 57 1 15 8 g 10 9 0 1 1 7 3 2 1 1 7 2 3 5 t 7 12 53 63 7 0 1 49 64 4 0 5 44 50
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=4/4; ncol2=14; w=-2; offset=-2; strand=D; shift=1; score=0.605352; -AyTCCACTCCAct ; cor=; Ncor= a 0 73 15 0 4 2 93 9 5 4 1 87 8 12 c 0 9 43 3 85 90 2 72 5 87 93 4 66 17 g 0 10 9 2 7 2 0 3 1 2 0 3 13 5 t 0 6 31 93 2 4 3 14 87 5 4 4 11 64

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --wwwATATATAwww ; Alignment reference a 0 0 52 39 58 74 3 86 10 83 5 84 42 31 49 c 0 0 7 9 6 3 1 0 5 3 2 1 7 10 7 g 0 0 8 5 4 2 1 3 0 4 0 1 3 13 6 t 0 0 24 38 23 12 86 2 76 1 84 5 39 37 29
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --wwwATATATAwww ; cor=; Ncor= a 0 0 52 39 58 74 3 86 10 83 5 84 42 31 49 c 0 0 7 9 6 3 1 0 5 3 2 1 7 10 7 g 0 0 8 5 4 2 1 3 0 4 0 1 3 13 6 t 0 0 24 38 23 12 86 2 76 1 84 5 39 37 29
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.85648; --wwTATATATAww- ; cor=; Ncor= a 0 0 36 33 9 64 4 65 0 58 1 52 22 19 0 c 0 0 6 4 3 0 1 1 0 3 1 2 7 5 0 g 0 0 5 7 2 1 3 0 1 1 0 3 4 6 0 t 0 0 19 22 52 1 58 0 65 4 64 9 33 36 0
oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=3/3; ncol2=13; w=-2; offset=-2; strand=R; shift=0; score=0.601895; ATATATTATATwT-- ; cor=; Ncor= a 34 6 37 2 45 8 7 44 1 47 0 32 9 0 0 c 2 7 2 3 1 0 1 0 3 0 1 1 2 0 0 g 6 1 6 1 1 1 1 1 0 1 0 3 1 0 0 t 8 36 5 44 3 41 41 5 46 2 49 14 38 0 0