One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; wwCGAwyACAha ; Alignment reference a 21 18 1 0 52 24 12 48 4 54 19 22 c 10 13 58 0 3 13 15 3 49 2 15 14 g 13 11 1 57 2 8 12 1 2 2 8 10 t 16 18 0 3 3 15 21 8 5 2 18 14

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwCGAwyACAha ; cor=; Ncor= a 21 18 1 0 52 24 12 48 4 54 19 22 c 10 13 58 0 3 13 15 3 49 2 15 14 g 13 11 1 57 2 8 12 1 2 2 8 10 t 16 18 0 3 3 15 21 8 5 2 18 14

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; adGGAGAGAAGGrd ; Alignment reference a 24 19 10 10 46 4 48 3 49 51 2 9 25 17 c 5 5 2 5 1 3 1 3 1 0 1 3 7 6 g 14 15 41 39 5 44 4 49 6 5 48 43 15 15 t 14 18 4 3 5 6 4 2 1 1 6 2 10 19

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; adGGAGAGAAGGrd ; cor=; Ncor= a 24 19 10 10 46 4 48 3 49 51 2 9 25 17 c 5 5 2 5 1 3 1 3 1 0 1 3 7 6 g 14 15 41 39 5 44 4 49 6 5 48 43 15 15 t 14 18 4 3 5 6 4 2 1 1 6 2 10 19

oligos_7nt_mkv2_m2_rc_shift3 (oligos_7nt_mkv2_m2_rc)
; dyads_m2 versus oligos_7nt_mkv2_m2_rc; m=2/2; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.596177; ---awGAAAAGGaw ; cor=; Ncor= a 0 0 0 48 49 0 86 85 84 86 7 5 39 48 c 0 0 0 13 8 0 5 4 0 2 1 1 22 12 g 0 0 0 19 13 97 5 10 15 2 93 94 15 7 t 0 0 0 21 31 4 5 2 2 11 0 1 25 34

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift7 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift7 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=7; ncol=18; -------wtCCTCTTCww ; Alignment reference a 0 0 0 0 0 0 0 32 29 6 14 6 2 8 0 7 46 36 c 0 0 0 0 0 0 0 27 28 107 101 8 105 10 1 113 26 27 g 0 0 0 0 0 0 0 12 16 1 1 0 0 3 0 1 7 15 t 0 0 0 0 0 0 0 54 52 11 9 111 18 104 124 4 46 47

oligos_7nt_mkv2_m1_shift7 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------wtCCTCTTCww ; cor=; Ncor= a 0 0 0 0 0 0 0 32 29 6 14 6 2 8 0 7 46 36 c 0 0 0 0 0 0 0 27 28 107 101 8 105 10 1 113 26 27 g 0 0 0 0 0 0 0 12 16 1 1 0 0 3 0 1 7 15 t 0 0 0 0 0 0 0 54 52 11 9 111 18 104 124 4 46 47

oligos_7nt_mkv2_m2_shift7 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 0.8614; -------wtCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 0 34 25 1 0 11 2 2 5 4 31 21 c 0 0 0 0 0 0 0 7 15 94 93 2 15 10 5 97 13 19 g 0 0 0 0 0 0 0 12 22 1 1 2 0 4 5 0 8 13 t 0 0 0 0 0 0 0 48 39 5 7 86 84 85 86 0 49 48

oligos_8nt_mkv2_m2_rc_shift6 (oligos_8nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m2_rc; m=3/4; ncol2=12; w=-1; offset=-1; strand=R; shift=6; score=0.712513; ------wwGCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 16 15 3 2 1 5 2 0 2 3 21 11 c 0 0 0 0 0 0 5 3 3 45 43 0 2 2 1 43 9 9 g 0 0 0 0 0 0 6 5 38 1 1 0 0 3 0 1 5 9 t 0 0 0 0 0 0 22 26 5 1 4 44 45 44 46 2 14 20

dyads_m3_shift0 (dyads_m3)
; oligos_7nt_mkv2_m1 versus dyads_m3; m=4/4; ncol2=18; w=-7; offset=-7; strand=D; shift=0; score=0.431384; mmCTThtwthhwwTTCwt ; cor=; Ncor= a 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14 c 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13 g 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11 t 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift7 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift7 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=7; ncol=18; -------wtCCTTTTCwt ; Alignment reference a 0 0 0 0 0 0 0 34 25 1 0 11 2 2 5 4 31 21 c 0 0 0 0 0 0 0 7 15 94 93 2 15 10 5 97 13 19 g 0 0 0 0 0 0 0 12 22 1 1 2 0 4 5 0 8 13 t 0 0 0 0 0 0 0 48 39 5 7 86 84 85 86 0 49 48

oligos_7nt_mkv2_m2_shift7 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------wtCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 0 34 25 1 0 11 2 2 5 4 31 21 c 0 0 0 0 0 0 0 7 15 94 93 2 15 10 5 97 13 19 g 0 0 0 0 0 0 0 12 22 1 1 2 0 4 5 0 8 13 t 0 0 0 0 0 0 0 48 39 5 7 86 84 85 86 0 49 48

oligos_7nt_mkv2_m1_shift7 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 0.8614; -------wtCCTCTTCww ; cor=; Ncor= a 0 0 0 0 0 0 0 32 29 6 14 6 2 8 0 7 46 36 c 0 0 0 0 0 0 0 27 28 107 101 8 105 10 1 113 26 27 g 0 0 0 0 0 0 0 12 16 1 1 0 0 3 0 1 7 15 t 0 0 0 0 0 0 0 54 52 11 9 111 18 104 124 4 46 47

oligos_8nt_mkv2_m2_rc_shift6 (oligos_8nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m2_rc; m=3/5; ncol2=12; w=-1; offset=-1; strand=R; shift=6; score=0.859293; ------wwGCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 16 15 3 2 1 5 2 0 2 3 21 11 c 0 0 0 0 0 0 5 3 3 45 43 0 2 2 1 43 9 9 g 0 0 0 0 0 0 6 5 38 1 1 0 0 3 0 1 5 9 t 0 0 0 0 0 0 22 26 5 1 4 44 45 44 46 2 14 20

dyads_m2_rc_shift7 (dyads_m2_rc)
; oligos_7nt_mkv2_m2 versus dyads_m2_rc; m=4/5; ncol2=14; w=0; offset=0; strand=R; shift=7; score=0.596177; -------hyCCTTCTCTC ; cor=; Ncor= a 0 0 0 0 0 0 0 19 10 2 6 1 1 2 4 6 5 3 c 0 0 0 0 0 0 0 15 15 43 48 5 6 49 4 44 5 39 g 0 0 0 0 0 0 0 6 7 3 1 0 1 3 1 3 1 5 t 0 0 0 0 0 0 0 17 25 9 2 51 49 3 48 4 46 10

dyads_m3_shift0 (dyads_m3)
; oligos_7nt_mkv2_m2 versus dyads_m3; m=5/5; ncol2=18; w=-7; offset=-7; strand=D; shift=0; score=0.433324; mmCTThtwthhwwTTCwt ; cor=; Ncor= a 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14 c 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13 g 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11 t 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAATGATtrw ; Alignment reference a 28 20 80 80 0 0 80 0 17 29 24 c 15 18 0 0 3 0 0 0 8 13 16 g 12 14 0 0 0 80 0 0 19 20 12 t 25 28 0 0 77 0 0 80 36 18 28

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwAATGATtrw ; cor=; Ncor= a 28 20 80 80 0 0 80 0 17 29 24 c 15 18 0 0 3 0 0 0 8 13 16 g 12 14 0 0 0 80 0 0 19 20 12 t 25 28 0 0 77 0 0 80 36 18 28

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; mmCTThtwthhwwTTCwt ; Alignment reference a 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14 c 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13 g 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11 t 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; mmCTThtwthhwwTTCwt ; cor=; Ncor= a 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14 c 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13 g 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11 t 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28

oligos_7nt_mkv2_m2_shift7 (oligos_7nt_mkv2_m2)
; dyads_m3 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=11; w=0; offset=7; strand=D; shift=7; score=0.433324; -------wtCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 0 34 25 1 0 11 2 2 5 4 31 21 c 0 0 0 0 0 0 0 7 15 94 93 2 15 10 5 97 13 19 g 0 0 0 0 0 0 0 12 22 1 1 2 0 4 5 0 8 13 t 0 0 0 0 0 0 0 48 39 5 7 86 84 85 86 0 49 48

oligos_7nt_mkv2_m1_shift7 (oligos_7nt_mkv2_m1)
; dyads_m3 versus oligos_7nt_mkv2_m1; m=3/3; ncol2=11; w=0; offset=7; strand=D; shift=7; score=0.431384; -------wtCCTCTTCww ; cor=; Ncor= a 0 0 0 0 0 0 0 32 29 6 14 6 2 8 0 7 46 36 c 0 0 0 0 0 0 0 27 28 107 101 8 105 10 1 113 26 27 g 0 0 0 0 0 0 0 12 16 1 1 0 0 3 0 1 7 15 t 0 0 0 0 0 0 0 54 52 11 9 111 18 104 124 4 46 47

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; awGAAAAGGCww ; Alignment reference a 20 14 2 46 44 45 44 4 1 5 26 22 c 9 5 1 0 3 0 0 1 1 38 5 6 g 9 9 43 1 2 2 0 43 45 3 3 5 t 11 21 3 2 0 2 5 1 2 3 15 16

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; awGAAAAGGCww ; cor=; Ncor= a 20 14 2 46 44 45 44 4 1 5 26 22 c 9 5 1 0 3 0 0 1 1 38 5 6 g 9 9 43 1 2 2 0 43 45 3 3 5 t 11 21 3 2 0 2 5 1 2 3 15 16

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=2/3; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.859293; awGAAAAGGaw- ; cor=; Ncor= a 48 49 0 86 85 84 86 7 5 39 48 0 c 13 8 0 5 4 0 2 1 1 22 12 0 g 19 13 97 5 10 15 2 93 94 15 7 0 t 21 31 4 5 2 2 11 0 1 25 34 0

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=3/3; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.712513; wwGAAGAGGaw- ; cor=; Ncor= a 47 46 4 124 104 18 111 9 11 52 54 0 c 15 7 1 0 3 0 0 1 1 16 12 0 g 27 26 113 1 10 105 8 101 107 28 27 0 t 36 46 7 0 8 2 6 14 6 29 32 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m3_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m3_shift2 (oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --rwGGAGGAGAwr ; Alignment reference a 0 0 12 16 3 3 36 0 5 35 3 35 16 18 c 0 0 1 4 0 0 4 0 2 2 1 0 4 2 g 0 0 21 6 36 38 0 41 35 3 36 6 10 13 t 0 0 8 16 3 1 2 1 0 2 2 1 12 9

oligos_8nt_mkv2_m3_shift2 (oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --rwGGAGGAGAwr ; cor=; Ncor= a 0 0 12 16 3 3 36 0 5 35 3 35 16 18 c 0 0 1 4 0 0 4 0 2 2 1 0 4 2 g 0 0 21 6 36 38 0 41 35 3 36 6 10 13 t 0 0 8 16 3 1 2 1 0 2 2 1 12 9

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m5; m=2/2; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.620502; wrGTGGAGGArr-- ; cor=; Ncor= a 15 15 1 9 0 3 35 8 2 40 15 21 0 0 c 2 8 0 1 3 0 1 0 0 1 3 4 0 0 g 8 15 42 1 37 39 1 34 40 0 16 12 0 0 t 18 5 0 32 3 1 6 1 1 2 9 6 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; wrGTGGAGGArr ; Alignment reference a 15 15 1 9 0 3 35 8 2 40 15 21 c 2 8 0 1 3 0 1 0 0 1 3 4 g 8 15 42 1 37 39 1 34 40 0 16 12 t 18 5 0 32 3 1 6 1 1 2 9 6

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wrGTGGAGGArr ; cor=; Ncor= a 15 15 1 9 0 3 35 8 2 40 15 21 c 2 8 0 1 3 0 1 0 0 1 3 4 g 8 15 42 1 37 39 1 34 40 0 16 12 t 18 5 0 32 3 1 6 1 1 2 9 6

oligos_8nt_mkv2_m3_shift2 (oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m3; m=2/2; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.620502; --rwGGAGGAGA ; cor=; Ncor= a 0 0 12 16 3 3 36 0 5 35 3 35 c 0 0 1 4 0 0 4 0 2 2 1 0 g 0 0 21 6 36 38 0 41 35 3 36 6 t 0 0 8 16 3 1 2 1 0 2 2 1

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wyCTTACTACww ; Alignment reference a 17 9 1 3 1 40 2 2 43 2 17 20 c 6 12 43 1 3 1 38 1 1 40 8 4 g 4 5 1 0 0 1 2 1 1 2 2 2 t 19 20 1 42 42 4 4 42 1 2 19 20

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wyCTTACTACww ; cor=; Ncor= a 17 9 1 3 1 40 2 2 43 2 17 20 c 6 12 43 1 3 1 38 1 1 40 8 4 g 4 5 1 0 0 1 2 1 1 2 2 2 t 19 20 1 42 42 4 4 42 1 2 19 20

oligos_6nt_mkv2_m2_rc_shift1 (oligos_6nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=2/2; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.721532; -whTTACTAhw- ; cor=; Ncor= a 0 19 14 0 0 55 0 0 55 17 16 0 c 0 12 16 0 0 0 55 0 0 14 9 0 g 0 4 8 0 0 0 0 0 0 8 8 0 t 0 20 17 55 55 0 0 55 0 16 22 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift1 ; 3 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=10; shift=1; ncol=11; -wdTAGTAAdw ; Alignment reference a 0 22 16 0 55 0 0 55 55 17 20 c 0 8 8 0 0 0 0 0 0 8 4 g 0 9 14 0 0 55 0 0 0 16 12 t 0 16 17 55 0 0 55 0 0 14 19

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wdTAGTAAdw ; cor=; Ncor= a 0 22 16 0 55 0 0 55 55 17 20 c 0 8 8 0 0 0 0 0 0 8 4 g 0 9 14 0 0 55 0 0 0 16 12 t 0 16 17 55 0 0 55 0 0 14 19

oligos_8nt_mkv2_m1_rc_shift0 (oligos_8nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m1_rc; m=2/2; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.721532; wwGTAGTAAGr ; cor=; Ncor= a 20 19 2 1 42 4 4 42 42 1 20 c 2 2 2 1 1 2 1 0 0 1 5 g 4 8 40 1 1 38 1 3 1 43 12 t 20 17 2 43 2 2 40 1 3 1 9

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; wrAGATAGwd ; Alignment reference a 16 19 48 0 52 0 46 0 21 15 c 5 3 2 0 0 0 5 0 5 7 g 12 18 2 52 0 1 0 52 10 15 t 19 12 0 0 0 51 1 0 16 15

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; wrAGATAGwd ; cor=; Ncor= a 16 19 48 0 52 0 46 0 21 15 c 5 3 2 0 0 0 5 0 5 7 g 12 18 2 52 0 1 0 52 10 15 t 19 12 0 0 0 51 1 0 16 15

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wdGGGACAgaaw ; Alignment reference a 21 21 3 3 1 54 4 50 10 32 24 22 c 7 4 2 2 0 1 53 1 9 7 10 10 g 9 15 52 49 57 2 1 7 34 6 11 9 t 22 19 2 5 1 2 1 1 6 14 14 18

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wdGGGACAgaaw ; cor=; Ncor= a 21 21 3 3 1 54 4 50 10 32 24 22 c 7 4 2 2 0 1 53 1 9 7 10 10 g 9 15 52 49 57 2 1 7 34 6 11 9 t 22 19 2 5 1 2 1 1 6 14 14 18

oligos_8nt_mkv2_m4_shift0 (oligos_8nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m4; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.795083; wwGTGACAGAkw ; cor=; Ncor= a 18 13 3 1 1 34 4 35 3 36 9 13 c 4 3 0 2 0 0 30 1 2 1 1 5 g 5 6 35 2 37 2 3 2 34 0 15 9 t 12 17 1 34 1 3 2 1 0 2 14 12

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; whACCAAAww ; Alignment reference a 18 19 63 0 0 61 63 63 25 25 c 12 16 0 63 62 0 0 0 9 12 g 13 10 0 0 1 2 0 0 11 4 t 20 18 0 0 0 0 0 0 18 22

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; whACCAAAww ; cor=; Ncor= a 18 19 63 0 0 61 63 63 25 25 c 12 16 0 63 62 0 0 0 9 12 g 13 10 0 0 1 2 0 0 11 4 t 20 18 0 0 0 0 0 0 18 22

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m4_shift0 (oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwGTGACAGAkw ; Alignment reference a 18 13 3 1 1 34 4 35 3 36 9 13 c 4 3 0 2 0 0 30 1 2 1 1 5 g 5 6 35 2 37 2 3 2 34 0 15 9 t 12 17 1 34 1 3 2 1 0 2 14 12

oligos_8nt_mkv2_m4_shift0 (oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwGTGACAGAkw ; cor=; Ncor= a 18 13 3 1 1 34 4 35 3 36 9 13 c 4 3 0 2 0 0 30 1 2 1 1 5 g 5 6 35 2 37 2 3 2 34 0 15 9 t 12 17 1 34 1 3 2 1 0 2 14 12

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_8nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.795083; wdGGGACAgaaw ; cor=; Ncor= a 21 21 3 3 1 54 4 50 10 32 24 22 c 7 4 2 2 0 1 53 1 9 7 10 10 g 9 15 52 49 57 2 1 7 34 6 11 9 t 22 19 2 5 1 2 1 1 6 14 14 18

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift7 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=7; ncol=18; -------wtCCTCTTCww ; Alignment reference a 0 0 0 0 0 0 0 32 29 6 14 6 2 8 0 7 46 36 c 0 0 0 0 0 0 0 27 28 107 101 8 105 10 1 113 26 27 g 0 0 0 0 0 0 0 12 16 1 1 0 0 3 0 1 7 15 t 0 0 0 0 0 0 0 54 52 11 9 111 18 104 124 4 46 47
oligos_7nt_mkv2_m1_shift7 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------wtCCTCTTCww ; cor=; Ncor= a 0 0 0 0 0 0 0 32 29 6 14 6 2 8 0 7 46 36 c 0 0 0 0 0 0 0 27 28 107 101 8 105 10 1 113 26 27 g 0 0 0 0 0 0 0 12 16 1 1 0 0 3 0 1 7 15 t 0 0 0 0 0 0 0 54 52 11 9 111 18 104 124 4 46 47
oligos_7nt_mkv2_m2_shift7 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 0.8614; -------wtCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 0 34 25 1 0 11 2 2 5 4 31 21 c 0 0 0 0 0 0 0 7 15 94 93 2 15 10 5 97 13 19 g 0 0 0 0 0 0 0 12 22 1 1 2 0 4 5 0 8 13 t 0 0 0 0 0 0 0 48 39 5 7 86 84 85 86 0 49 48
oligos_8nt_mkv2_m2_rc_shift6 (oligos_8nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m2_rc; m=3/4; ncol2=12; w=-1; offset=-1; strand=R; shift=6; score=0.712513; ------wwGCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 16 15 3 2 1 5 2 0 2 3 21 11 c 0 0 0 0 0 0 5 3 3 45 43 0 2 2 1 43 9 9 g 0 0 0 0 0 0 6 5 38 1 1 0 0 3 0 1 5 9 t 0 0 0 0 0 0 22 26 5 1 4 44 45 44 46 2 14 20
dyads_m3_shift0 (dyads_m3)				; oligos_7nt_mkv2_m1 versus dyads_m3; m=4/4; ncol2=18; w=-7; offset=-7; strand=D; shift=0; score=0.431384; mmCTThtwthhwwTTCwt ; cor=; Ncor= a 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14 c 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13 g 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11 t 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift7 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=7; ncol=18; -------wtCCTTTTCwt ; Alignment reference a 0 0 0 0 0 0 0 34 25 1 0 11 2 2 5 4 31 21 c 0 0 0 0 0 0 0 7 15 94 93 2 15 10 5 97 13 19 g 0 0 0 0 0 0 0 12 22 1 1 2 0 4 5 0 8 13 t 0 0 0 0 0 0 0 48 39 5 7 86 84 85 86 0 49 48
oligos_7nt_mkv2_m2_shift7 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 1; -------wtCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 0 34 25 1 0 11 2 2 5 4 31 21 c 0 0 0 0 0 0 0 7 15 94 93 2 15 10 5 97 13 19 g 0 0 0 0 0 0 0 12 22 1 1 2 0 4 5 0 8 13 t 0 0 0 0 0 0 0 48 39 5 7 86 84 85 86 0 49 48
oligos_7nt_mkv2_m1_shift7 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=11; w=0; offset=0; strand=D; shift=7; score= 0.8614; -------wtCCTCTTCww ; cor=; Ncor= a 0 0 0 0 0 0 0 32 29 6 14 6 2 8 0 7 46 36 c 0 0 0 0 0 0 0 27 28 107 101 8 105 10 1 113 26 27 g 0 0 0 0 0 0 0 12 16 1 1 0 0 3 0 1 7 15 t 0 0 0 0 0 0 0 54 52 11 9 111 18 104 124 4 46 47
oligos_8nt_mkv2_m2_rc_shift6 (oligos_8nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m2_rc; m=3/5; ncol2=12; w=-1; offset=-1; strand=R; shift=6; score=0.859293; ------wwGCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 16 15 3 2 1 5 2 0 2 3 21 11 c 0 0 0 0 0 0 5 3 3 45 43 0 2 2 1 43 9 9 g 0 0 0 0 0 0 6 5 38 1 1 0 0 3 0 1 5 9 t 0 0 0 0 0 0 22 26 5 1 4 44 45 44 46 2 14 20
dyads_m2_rc_shift7 (dyads_m2_rc)				; oligos_7nt_mkv2_m2 versus dyads_m2_rc; m=4/5; ncol2=14; w=0; offset=0; strand=R; shift=7; score=0.596177; -------hyCCTTCTCTC ; cor=; Ncor= a 0 0 0 0 0 0 0 19 10 2 6 1 1 2 4 6 5 3 c 0 0 0 0 0 0 0 15 15 43 48 5 6 49 4 44 5 39 g 0 0 0 0 0 0 0 6 7 3 1 0 1 3 1 3 1 5 t 0 0 0 0 0 0 0 17 25 9 2 51 49 3 48 4 46 10
dyads_m3_shift0 (dyads_m3)				; oligos_7nt_mkv2_m2 versus dyads_m3; m=5/5; ncol2=18; w=-7; offset=-7; strand=D; shift=0; score=0.433324; mmCTThtwthhwwTTCwt ; cor=; Ncor= a 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14 c 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13 g 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11 t 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift0 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; mmCTThtwthhwwTTCwt ; Alignment reference a 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14 c 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13 g 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11 t 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28
dyads_m3_shift0 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/3; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; mmCTThtwthhwwTTCwt ; cor=; Ncor= a 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14 c 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13 g 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11 t 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28
oligos_7nt_mkv2_m2_shift7 (oligos_7nt_mkv2_m2)				; dyads_m3 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=11; w=0; offset=7; strand=D; shift=7; score=0.433324; -------wtCCTTTTCwt ; cor=; Ncor= a 0 0 0 0 0 0 0 34 25 1 0 11 2 2 5 4 31 21 c 0 0 0 0 0 0 0 7 15 94 93 2 15 10 5 97 13 19 g 0 0 0 0 0 0 0 12 22 1 1 2 0 4 5 0 8 13 t 0 0 0 0 0 0 0 48 39 5 7 86 84 85 86 0 49 48
oligos_7nt_mkv2_m1_shift7 (oligos_7nt_mkv2_m1)				; dyads_m3 versus oligos_7nt_mkv2_m1; m=3/3; ncol2=11; w=0; offset=7; strand=D; shift=7; score=0.431384; -------wtCCTCTTCww ; cor=; Ncor= a 0 0 0 0 0 0 0 32 29 6 14 6 2 8 0 7 46 36 c 0 0 0 0 0 0 0 27 28 107 101 8 105 10 1 113 26 27 g 0 0 0 0 0 0 0 12 16 1 1 0 0 3 0 1 7 15 t 0 0 0 0 0 0 0 54 52 11 9 111 18 104 124 4 46 47

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)				; oligos_8nt_mkv2_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; awGAAAAGGCww ; Alignment reference a 20 14 2 46 44 45 44 4 1 5 26 22 c 9 5 1 0 3 0 0 1 1 38 5 6 g 9 9 43 1 2 2 0 43 45 3 3 5 t 11 21 3 2 0 2 5 1 2 3 15 16
oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; awGAAAAGGCww ; cor=; Ncor= a 20 14 2 46 44 45 44 4 1 5 26 22 c 9 5 1 0 3 0 0 1 1 38 5 6 g 9 9 43 1 2 2 0 43 45 3 3 5 t 11 21 3 2 0 2 5 1 2 3 15 16
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=2/3; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.859293; awGAAAAGGaw- ; cor=; Ncor= a 48 49 0 86 85 84 86 7 5 39 48 0 c 13 8 0 5 4 0 2 1 1 22 12 0 g 19 13 97 5 10 15 2 93 94 15 7 0 t 21 31 4 5 2 2 11 0 1 25 34 0
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=3/3; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.712513; wwGAAGAGGaw- ; cor=; Ncor= a 47 46 4 124 104 18 111 9 11 52 54 0 c 15 7 1 0 3 0 0 1 1 16 12 0 g 27 26 113 1 10 105 8 101 107 28 27 0 t 36 46 7 0 8 2 6 14 6 29 32 0