One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/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/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; htTCACCAACCmCmhm ; Alignment reference a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 13 11 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 10 16 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 4 2 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2 9 7

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; htTCACCAACCmCmhm ; cor=; Ncor= a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 13 11 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 10 16 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 4 2 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2 9 7

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; dyads_m1 versus oligos_8nt_mkv2_m1; m=2/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.932232; mtTCACCAACCmCmm- ; cor=; Ncor= a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 9 0 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 9 0 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 4 0 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2 7 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; dyads_m1 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.846547; mtTcACCAACCCmm-- ; cor=; Ncor= a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 0 0 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 0 0 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 0 0 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8 0 0

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; dyads_m1 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.778017; -ytcACCAACCCmm-- ; cor=; Ncor= a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 0 0 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 0 0 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 0 0 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift1 ; 5 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=14; shift=1; ncol=15; -aatgCATGCATgww ; Alignment reference a 0 19 26 7 10 3 44 3 2 2 47 5 6 14 21 c 0 10 6 9 4 41 0 3 1 49 0 3 7 12 6 g 0 11 10 1 29 1 5 0 47 1 1 0 35 8 10 t 0 12 10 35 9 7 3 46 2 0 4 44 4 18 15

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -aatgCATGCATgww ; cor=; Ncor= a 0 19 26 7 10 3 44 3 2 2 47 5 6 14 21 c 0 10 6 9 4 41 0 3 1 49 0 3 7 12 6 g 0 11 10 1 29 1 5 0 47 1 1 0 35 8 10 t 0 12 10 35 9 7 3 46 2 0 4 44 4 18 15

oligos_8nt_mkv2_m4_rc_shift0 (oligos_8nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m4_rc; m=2/4; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.77123; wrrTGCATGCAyyw- ; cor=; Ncor= a 9 8 11 2 2 0 27 2 1 1 24 6 7 14 0 c 4 6 1 2 2 28 0 0 0 25 1 11 8 3 0 g 3 9 11 1 24 0 0 0 28 1 2 1 6 4 0 t 13 6 6 24 1 1 2 27 0 2 2 11 8 8 0

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=3/4; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.659079; ---wrCATGCAtr-- ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 0 0 c 0 0 0 12 8 49 0 3 0 50 3 8 6 0 0 g 0 0 0 5 17 0 2 0 50 0 2 4 14 0 0 t 0 0 0 20 10 1 2 47 0 0 4 26 12 0 0

dyads_m3_shift3 (dyads_m3)
; oligos_7nt_mkv2_m3 versus dyads_m3; m=4/4; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.659079; ---wrCATGCAtr-- ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 0 0 c 0 0 0 12 8 49 0 3 0 50 3 8 6 0 0 g 0 0 0 5 17 0 2 0 50 0 2 4 14 0 0 t 0 0 0 20 10 1 2 47 0 0 4 26 12 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m1_shift0 ; 5 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=15; shift=0; ncol=15; mtTCACCAACCmCmm ; Alignment reference a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 9 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 9 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 4 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2 7

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; mtTCACCAACCmCmm ; cor=; Ncor= a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 9 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 9 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 4 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2 7

dyads_m1_shift0 (dyads_m1)
; oligos_8nt_mkv2_m1 versus dyads_m1; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.932232; htTCACCAACCmCmh ; cor=; Ncor= a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 13 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 10 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 4 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2 9

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.904395; mtTcACCAACCCmm- ; cor=; Ncor= a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 0 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 0 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 0 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8 0

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.832751; -ytcACCAACCCmm- ; cor=; Ncor= a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 0 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 0 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 0 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8 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=12; shift=0; ncol=12; waACGsCGTtwa ; Alignment reference a 11 12 23 0 1 2 1 1 1 2 11 10 c 3 5 1 25 0 14 23 0 1 5 0 4 g 1 5 0 0 24 7 1 23 0 3 1 6 t 10 3 1 0 0 2 0 1 23 15 13 5

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; waACGsCGTtwa ; cor=; Ncor= a 11 12 23 0 1 2 1 1 1 2 11 10 c 3 5 1 25 0 14 23 0 1 5 0 4 g 1 5 0 0 24 7 1 23 0 3 1 6 t 10 3 1 0 0 2 0 1 23 15 13 5

oligos_8nt_mkv2_m2_rc_shift0 (oligos_8nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m2_rc; m=2/2; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.977661; waACGCCGTTwr ; cor=; Ncor= a 9 7 16 0 1 0 1 1 1 0 8 6 c 3 4 1 18 0 14 16 0 1 2 0 2 g 1 4 0 0 17 2 1 16 0 1 1 6 t 5 3 1 0 0 2 0 1 16 15 9 4

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=11; shift=0; ncol=11; wwaAAAACAww ; Alignment reference a 45 39 43 107 107 107 107 0 107 49 50 c 16 22 23 0 0 0 0 107 0 12 11 g 11 15 23 0 0 0 0 0 0 13 12 t 35 31 18 0 0 0 0 0 0 33 34

dyads_m2_shift0 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwaAAAACAww ; cor=; Ncor= a 45 39 43 107 107 107 107 0 107 49 50 c 16 22 23 0 0 0 0 107 0 12 11 g 11 15 23 0 0 0 0 0 0 13 12 t 35 31 18 0 0 0 0 0 0 33 34

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; dyads_m2 versus oligos_6nt_mkv2_m4; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.909091; -waAAAACAww ; cor=; Ncor= a 0 39 43 107 107 107 107 0 107 49 50 c 0 22 23 0 0 0 0 107 0 12 11 g 0 15 23 0 0 0 0 0 0 13 12 t 0 31 18 0 0 0 0 0 0 33 34

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; wwTAATTAww ; Alignment reference a 36 29 0 84 84 0 0 84 29 26 c 11 14 0 0 0 0 0 0 12 11 g 11 12 0 0 0 0 0 0 14 11 t 26 29 84 0 0 84 84 0 29 36

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; wwTAATTAww ; cor=; Ncor= a 36 29 0 84 84 0 0 84 29 26 c 11 14 0 0 0 0 0 0 12 11 g 11 12 0 0 0 0 0 0 14 11 t 26 29 84 0 0 84 84 0 29 36

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m4_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m4_shift1 (oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -wrrTGCATGCAyyw ; Alignment reference a 0 8 8 11 2 2 0 27 2 1 1 24 6 6 13 c 0 4 6 1 2 1 28 0 0 0 24 1 11 9 3 g 0 3 8 11 1 25 0 0 0 28 2 2 1 6 4 t 0 14 7 6 24 1 1 2 27 0 2 2 11 8 9

oligos_8nt_mkv2_m4_shift1 (oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m4; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wrrTGCATGCAyyw ; cor=; Ncor= a 0 8 8 11 2 2 0 27 2 1 1 24 6 6 13 c 0 4 6 1 2 1 28 0 0 0 24 1 11 9 3 g 0 3 8 11 1 25 0 0 0 28 2 2 1 6 4 t 0 14 7 6 24 1 1 2 27 0 2 2 11 8 9

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=2/4; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.77123; wwcATGCATGcatt- ; cor=; Ncor= a 15 18 4 44 4 0 2 46 3 7 9 35 10 12 0 c 10 8 35 0 1 1 47 0 5 1 29 1 10 11 0 g 6 12 7 3 0 49 1 3 0 41 4 9 6 10 0 t 21 14 6 5 47 2 2 3 44 3 10 7 26 19 0

dyads_m3_rc_shift2 (dyads_m3_rc)
; oligos_8nt_mkv2_m4 versus dyads_m3_rc; m=3/4; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.654056; --yaTGCATGyw--- ; cor=; Ncor= a 0 0 12 26 4 0 0 47 2 1 10 20 0 0 0 c 0 0 14 4 2 0 50 0 2 0 17 5 0 0 0 g 0 0 6 8 3 50 0 3 0 49 8 12 0 0 0 t 0 0 18 12 41 0 0 0 46 0 15 13 0 0 0

oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=4/4; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.654056; --yaTGCATGyw--- ; cor=; Ncor= a 0 0 12 26 4 0 0 47 2 1 10 20 0 0 0 c 0 0 14 4 2 0 50 0 2 0 17 5 0 0 0 g 0 0 6 8 3 50 0 3 0 49 8 12 0 0 0 t 0 0 18 12 41 0 0 0 46 0 15 13 0 0 0

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=10; shift=3; ncol=13; ---wrCATGCAtr ; Alignment reference a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12

dyads_m3_shift3 (dyads_m3)
; oligos_6nt_mkv2_m2 versus dyads_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wrCATGCAtr ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wrCATGCAtr ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=3/4; ncol2=14; w=-2; offset=-2; strand=D; shift=1; score=0.659079; -aatgCATGCATg ; cor=; Ncor= a 0 19 26 7 10 3 44 3 2 2 47 5 6 c 0 10 6 9 4 41 0 3 1 49 0 3 7 g 0 11 10 1 29 1 5 0 47 1 1 0 35 t 0 12 10 35 9 7 3 46 2 0 4 44 4

oligos_8nt_mkv2_m4_rc_shift0 (oligos_8nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m4_rc; m=4/4; ncol2=14; w=-3; offset=-3; strand=R; shift=0; score=0.654056; wrrTGCATGCAyy ; cor=; Ncor= a 9 8 11 2 2 0 27 2 1 1 24 6 7 c 4 6 1 2 2 28 0 0 0 25 1 11 8 g 3 9 11 1 24 0 0 0 28 1 2 1 6 t 13 6 6 24 1 1 2 27 0 2 2 11 8

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m5_shift0 ; 5 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=13; shift=0; ncol=13; dagAGAGAGAGag ; Alignment reference a 26 56 14 81 6 83 9 85 7 73 10 51 22 c 13 8 6 2 4 3 2 2 1 1 4 8 12 g 29 8 60 2 77 2 79 1 80 7 70 19 38 t 24 20 12 7 5 4 2 4 4 11 8 14 20

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m5; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; dagAGAGAGAGag ; cor=; Ncor= a 26 56 14 81 6 83 9 85 7 73 10 51 22 c 13 8 6 2 4 3 2 2 1 1 4 8 12 g 29 8 60 2 77 2 79 1 80 7 70 19 38 t 24 20 12 7 5 4 2 4 4 11 8 14 20

dyads_m5_rc_shift0 (dyads_m5_rc)
; oligos_8nt_mkv2_m5 versus dyads_m5_rc; m=2/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.818578; dwGAGAGAGag-- ; cor=; Ncor= a 26 54 6 90 9 88 8 87 4 51 19 0 0 c 10 6 4 1 3 2 1 1 4 7 14 0 0 g 33 11 78 2 81 1 86 4 82 17 43 0 0 t 26 24 7 2 2 4 0 3 5 20 19 0 0

oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)
; oligos_8nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=3/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.818578; dwGAGAGAGag-- ; cor=; Ncor= a 26 54 6 90 9 88 8 87 4 51 19 0 0 c 10 6 4 1 3 2 1 1 4 7 14 0 0 g 33 11 78 2 81 1 86 4 82 17 43 0 0 t 26 24 7 2 2 4 0 3 5 20 19 0 0

dyads_m4_rc_shift4 (dyads_m4_rc)
; oligos_8nt_mkv2_m5 versus dyads_m4_rc; m=4/4; ncol2=12; w=0; offset=4; strand=R; shift=4; score=0.417683; ----daGAGwGGG ; cor=; Ncor= a 0 0 0 0 10 19 2 31 2 14 4 3 1 c 0 0 0 0 1 4 0 1 0 1 1 0 0 g 0 0 0 0 12 3 30 1 32 4 27 30 32 t 0 0 0 0 11 8 2 1 0 15 2 1 1

One-to-n matrix alignment; reference matrix: dyads_m3_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift3 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=10; shift=3; ncol=13; ---wrCATGCAtr ; Alignment reference a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12

dyads_m3_shift3 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wrCATGCAtr ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; dyads_m3 versus oligos_6nt_mkv2_m2; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wrCATGCAtr ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; dyads_m3 versus oligos_7nt_mkv2_m3; m=3/4; ncol2=14; w=-2; offset=-2; strand=D; shift=1; score=0.659079; -aatgCATGCATg ; cor=; Ncor= a 0 19 26 7 10 3 44 3 2 2 47 5 6 c 0 10 6 9 4 41 0 3 1 49 0 3 7 g 0 11 10 1 29 1 5 0 47 1 1 0 35 t 0 12 10 35 9 7 3 46 2 0 4 44 4

oligos_8nt_mkv2_m4_rc_shift0 (oligos_8nt_mkv2_m4_rc)
; dyads_m3 versus oligos_8nt_mkv2_m4_rc; m=4/4; ncol2=14; w=-3; offset=-3; strand=R; shift=0; score=0.654056; wrrTGCATGCAyy ; cor=; Ncor= a 9 8 11 2 2 0 27 2 1 1 24 6 7 c 4 6 1 2 2 28 0 0 0 25 1 11 8 g 3 9 11 1 24 0 0 0 28 1 2 1 6 t 13 6 6 24 1 1 2 27 0 2 2 11 8

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=1; ncol=11; -waAAAACAww ; Alignment reference a 0 39 43 107 107 107 107 0 107 49 50 c 0 22 23 0 0 0 0 107 0 12 11 g 0 15 23 0 0 0 0 0 0 13 12 t 0 31 18 0 0 0 0 0 0 33 34

oligos_6nt_mkv2_m4_shift1 (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=1; score= 1; -waAAAACAww ; cor=; Ncor= a 0 39 43 107 107 107 107 0 107 49 50 c 0 22 23 0 0 0 0 107 0 12 11 g 0 15 23 0 0 0 0 0 0 13 12 t 0 31 18 0 0 0 0 0 0 33 34

dyads_m2_shift0 (dyads_m2)
; oligos_6nt_mkv2_m4 versus dyads_m2; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.909091; wwaAAAACAww ; cor=; Ncor= a 45 39 43 107 107 107 107 0 107 49 50 c 16 22 23 0 0 0 0 107 0 12 11 g 11 15 23 0 0 0 0 0 0 13 12 t 35 31 18 0 0 0 0 0 0 33 34

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; wtGGTGGAGAhw ; Alignment reference a 9 6 2 1 5 1 3 22 1 26 10 10 c 2 7 0 0 1 0 0 4 0 1 9 2 g 7 4 26 28 1 27 23 1 28 1 1 5 t 11 12 1 0 22 1 3 2 0 1 9 12

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wtGGTGGAGAhw ; cor=; Ncor= a 9 6 2 1 5 1 3 22 1 26 10 10 c 2 7 0 0 1 0 0 4 0 1 9 2 g 7 4 26 28 1 27 23 1 28 1 1 5 t 11 12 1 0 22 1 3 2 0 1 9 12

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 5 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=14; shift=0; ncol=14; mtTcACCAACCCmm ; Alignment reference a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8

oligos_7nt_mkv2_m1_shift0 (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=0; score= 1; mtTcACCAACCCmm ; cor=; Ncor= a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8

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=1; strand=D; shift=1; score=0.907614; -ytcACCAACCCmm ; cor=; Ncor= a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=3/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.904395; mtTCACCAACCmCm ; cor=; Ncor= a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2

dyads_m1_shift0 (dyads_m1)
; oligos_7nt_mkv2_m1 versus dyads_m1; m=4/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.846547; htTCACCAACCmCm ; cor=; Ncor= a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m2_shift0 ; 3 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; ywAACGGCGTtw ; Alignment reference a 4 9 15 16 1 0 2 0 0 1 3 5 c 6 1 1 0 16 1 2 17 0 0 4 1 g 2 0 2 1 0 16 14 0 18 1 4 3 t 6 8 0 1 1 1 0 1 0 16 7 9

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; ywAACGGCGTtw ; cor=; Ncor= a 4 9 15 16 1 0 2 0 0 1 3 5 c 6 1 1 0 16 1 2 17 0 0 4 1 g 2 0 2 1 0 16 14 0 18 1 4 3 t 6 8 0 1 1 1 0 1 0 16 7 9

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m2_rc; m=2/2; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.977661; twaACGsCGTtw ; cor=; Ncor= a 5 13 15 23 1 0 2 0 0 1 3 10 c 6 1 3 0 23 1 7 24 0 0 5 1 g 4 0 5 1 0 23 14 0 25 1 5 3 t 10 11 2 1 1 1 2 1 0 23 12 11

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -waAAGAAAww ; Alignment reference a 0 35 41 89 89 0 89 89 89 39 34 c 0 20 15 0 0 0 0 0 0 12 13 g 0 9 13 0 0 89 0 0 0 13 15 t 0 25 20 0 0 0 0 0 0 25 27

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -waAAGAAAww ; cor=; Ncor= a 0 35 41 89 89 0 89 89 89 39 34 c 0 20 15 0 0 0 0 0 0 12 13 g 0 9 13 0 0 89 0 0 0 13 15 t 0 25 20 0 0 0 0 0 0 25 27

oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m5_rc; m=2/2; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.588054; awGAAGAAGAa ; cor=; Ncor= a 24 22 7 51 51 8 47 49 2 44 21 c 5 5 2 1 1 0 2 2 0 5 10 g 13 7 41 2 1 46 1 0 51 1 13 t 12 20 4 0 1 0 4 3 1 4 10

One-to-n matrix alignment; reference matrix: dyads_m5_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift3 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ctCTCTCTCwh ; Alignment reference a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26

dyads_m5_shift3 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCTCTCTCwh ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26

oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; dyads_m5 versus oligos_7nt_mkv2_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCTCTCTCwh ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26

oligos_8nt_mkv2_m5_rc_shift1 (oligos_8nt_mkv2_m5_rc)
; dyads_m5 versus oligos_8nt_mkv2_m5_rc; m=3/4; ncol2=13; w=-2; offset=-2; strand=R; shift=1; score=0.818578; -ctCTCTCTCTcth ; cor=; Ncor= a 0 20 14 8 11 4 4 2 4 5 7 12 20 24 c 0 38 19 70 7 80 1 79 2 77 2 60 8 29 g 0 12 8 4 1 1 2 2 3 4 2 6 8 13 t 0 22 51 10 73 7 85 9 83 6 81 14 56 26

dyads_m4_shift0 (dyads_m4)
; dyads_m5 versus dyads_m4; m=4/4; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.472381; wwCCCCwCTCth-- ; cor=; Ncor= a 12 10 2 1 1 2 15 0 1 2 8 11 0 0 c 5 5 28 32 30 27 4 32 1 30 3 12 0 0 g 5 5 2 0 0 1 1 0 1 0 4 1 0 0 t 12 14 2 1 3 4 14 2 31 2 19 10 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift3 ; 5 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=11; shift=3; ncol=14; ---ctCTCTCTCwh ; Alignment reference a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26

dyads_m5_shift3 (dyads_m5)
; oligos_7nt_mkv2_m4 versus dyads_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCTCTCTCwh ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26

oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCTCTCTCwh ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26

oligos_8nt_mkv2_m5_rc_shift1 (oligos_8nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m5_rc; m=3/4; ncol2=13; w=-2; offset=-2; strand=R; shift=1; score=0.818578; -ctCTCTCTCTcth ; cor=; Ncor= a 0 20 14 8 11 4 4 2 4 5 7 12 20 24 c 0 38 19 70 7 80 1 79 2 77 2 60 8 29 g 0 12 8 4 1 1 2 2 3 4 2 6 8 13 t 0 22 51 10 73 7 85 9 83 6 81 14 56 26

dyads_m4_shift0 (dyads_m4)
; oligos_7nt_mkv2_m4 versus dyads_m4; m=4/4; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.472381; wwCCCCwCTCth-- ; cor=; Ncor= a 12 10 2 1 1 2 15 0 1 2 8 11 0 0 c 5 5 28 32 30 27 4 32 1 30 3 12 0 0 g 5 5 2 0 0 1 1 0 1 0 4 1 0 0 t 12 14 2 1 3 4 14 2 31 2 19 10 0 0

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwCCCCwCTCth ; Alignment reference a 12 10 2 1 1 2 15 0 1 2 8 11 c 5 5 28 32 30 27 4 32 1 30 3 12 g 5 5 2 0 0 1 1 0 1 0 4 1 t 12 14 2 1 3 4 14 2 31 2 19 10

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwCCCCwCTCth ; cor=; Ncor= a 12 10 2 1 1 2 15 0 1 2 8 11 c 5 5 28 32 30 27 4 32 1 30 3 12 g 5 5 2 0 0 1 1 0 1 0 4 1 t 12 14 2 1 3 4 14 2 31 2 19 10

oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; dyads_m4 versus oligos_7nt_mkv2_m4; m=2/4; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.472381; ---ctCTCTCTC ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 c 0 0 0 43 17 82 4 86 1 81 2 78 g 0 0 0 14 7 4 1 1 2 3 1 4 t 0 0 0 19 51 4 87 8 88 9 90 6

dyads_m5_shift3 (dyads_m5)
; dyads_m4 versus dyads_m5; m=3/4; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.472381; ---ctCTCTCTC ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 c 0 0 0 43 17 82 4 86 1 81 2 78 g 0 0 0 14 7 4 1 1 2 3 1 4 t 0 0 0 19 51 4 87 8 88 9 90 6

oligos_8nt_mkv2_m5_rc_shift3 (oligos_8nt_mkv2_m5_rc)
; dyads_m4 versus oligos_8nt_mkv2_m5_rc; m=4/4; ncol2=13; w=0; offset=3; strand=R; shift=3; score=0.417683; ---ctCTCTCTC ; cor=; Ncor= a 0 0 0 20 14 8 11 4 4 2 4 5 c 0 0 0 38 19 70 7 80 1 79 2 77 g 0 0 0 12 8 4 1 1 2 2 3 4 t 0 0 0 22 51 10 73 7 85 9 83 6

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=12; shift=0; ncol=12; htTCTTCTTCwt ; Alignment reference a 15 10 4 1 3 4 0 1 0 4 20 12 c 14 13 1 51 0 1 46 1 2 41 7 13 g 4 10 5 0 2 2 0 1 1 2 5 5 t 21 21 44 2 49 47 8 51 51 7 22 24

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; htTCTTCTTCwt ; cor=; Ncor= a 15 10 4 1 3 4 0 1 0 4 20 12 c 14 13 1 51 0 1 46 1 2 41 7 13 g 4 10 5 0 2 2 0 1 1 2 5 5 t 21 21 44 2 49 47 8 51 51 7 22 24

oligos_6nt_mkv2_m5_rc_shift1 (oligos_6nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m5_rc; m=2/2; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.588054; -wwTTTCTTtw- ; cor=; Ncor= a 0 27 25 0 0 0 0 0 0 20 25 0 c 0 15 13 0 0 0 89 0 0 13 9 0 g 0 13 12 0 0 0 0 0 0 15 20 0 t 0 34 39 89 89 89 0 89 89 41 35 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; -ytcACCAACCCmm ; Alignment reference a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8

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; -ytcACCAACCCmm ; cor=; Ncor= a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.907614; mtTcACCAACCCmm ; cor=; Ncor= a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=3/4; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.832751; mtTCACCAACCmCm ; cor=; Ncor= a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2

dyads_m1_shift0 (dyads_m1)
; oligos_6nt_mkv2_m1 versus dyads_m1; m=4/4; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.778017; htTCACCAACCmCm ; cor=; Ncor= a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift0 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; htTCACCAACCmCmhm ; Alignment reference a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 13 11 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 10 16 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 4 2 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2 9 7
dyads_m1_shift0 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; htTCACCAACCmCmhm ; cor=; Ncor= a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 13 11 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 10 16 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 4 2 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2 9 7
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)				; dyads_m1 versus oligos_8nt_mkv2_m1; m=2/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.932232; mtTCACCAACCmCmm- ; cor=; Ncor= a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 9 0 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 9 0 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 4 0 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2 7 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; dyads_m1 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.846547; mtTcACCAACCCmm-- ; cor=; Ncor= a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 0 0 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 0 0 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 0 0 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8 0 0
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; dyads_m1 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.778017; -ytcACCAACCCmm-- ; cor=; Ncor= a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 0 0 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 0 0 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 0 0 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8 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=14; shift=1; ncol=15; -aatgCATGCATgww ; Alignment reference a 0 19 26 7 10 3 44 3 2 2 47 5 6 14 21 c 0 10 6 9 4 41 0 3 1 49 0 3 7 12 6 g 0 11 10 1 29 1 5 0 47 1 1 0 35 8 10 t 0 12 10 35 9 7 3 46 2 0 4 44 4 18 15
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -aatgCATGCATgww ; cor=; Ncor= a 0 19 26 7 10 3 44 3 2 2 47 5 6 14 21 c 0 10 6 9 4 41 0 3 1 49 0 3 7 12 6 g 0 11 10 1 29 1 5 0 47 1 1 0 35 8 10 t 0 12 10 35 9 7 3 46 2 0 4 44 4 18 15
oligos_8nt_mkv2_m4_rc_shift0 (oligos_8nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m4_rc; m=2/4; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.77123; wrrTGCATGCAyyw- ; cor=; Ncor= a 9 8 11 2 2 0 27 2 1 1 24 6 7 14 0 c 4 6 1 2 2 28 0 0 0 25 1 11 8 3 0 g 3 9 11 1 24 0 0 0 28 1 2 1 6 4 0 t 13 6 6 24 1 1 2 27 0 2 2 11 8 8 0
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=3/4; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.659079; ---wrCATGCAtr-- ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 0 0 c 0 0 0 12 8 49 0 3 0 50 3 8 6 0 0 g 0 0 0 5 17 0 2 0 50 0 2 4 14 0 0 t 0 0 0 20 10 1 2 47 0 0 4 26 12 0 0
dyads_m3_shift3 (dyads_m3)				; oligos_7nt_mkv2_m3 versus dyads_m3; m=4/4; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.659079; ---wrCATGCAtr-- ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 0 0 c 0 0 0 12 8 49 0 3 0 50 3 8 6 0 0 g 0 0 0 5 17 0 2 0 50 0 2 4 14 0 0 t 0 0 0 20 10 1 2 47 0 0 4 26 12 0 0

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=15; shift=0; ncol=15; mtTCACCAACCmCmm ; Alignment reference a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 9 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 9 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 4 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2 7
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=1/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; mtTCACCAACCmCmm ; cor=; Ncor= a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 9 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 9 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 4 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2 7
dyads_m1_shift0 (dyads_m1)				; oligos_8nt_mkv2_m1 versus dyads_m1; m=2/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.932232; htTCACCAACCmCmh ; cor=; Ncor= a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 13 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 10 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 4 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2 9
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/4; ncol2=14; w=0; offset=0; strand=D; shift=0; score=0.904395; mtTcACCAACCCmm- ; cor=; Ncor= a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 0 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 0 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 0 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8 0
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.832751; -ytcACCAACCCmm- ; cor=; Ncor= a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 0 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 0 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 0 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m4_shift1 (oligos_8nt_mkv2_m4)				; oligos_8nt_mkv2_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -wrrTGCATGCAyyw ; Alignment reference a 0 8 8 11 2 2 0 27 2 1 1 24 6 6 13 c 0 4 6 1 2 1 28 0 0 0 24 1 11 9 3 g 0 3 8 11 1 25 0 0 0 28 2 2 1 6 4 t 0 14 7 6 24 1 1 2 27 0 2 2 11 8 9
oligos_8nt_mkv2_m4_shift1 (oligos_8nt_mkv2_m4)				; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m4; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wrrTGCATGCAyyw ; cor=; Ncor= a 0 8 8 11 2 2 0 27 2 1 1 24 6 6 13 c 0 4 6 1 2 1 28 0 0 0 24 1 11 9 3 g 0 3 8 11 1 25 0 0 0 28 2 2 1 6 4 t 0 14 7 6 24 1 1 2 27 0 2 2 11 8 9
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_8nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=2/4; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.77123; wwcATGCATGcatt- ; cor=; Ncor= a 15 18 4 44 4 0 2 46 3 7 9 35 10 12 0 c 10 8 35 0 1 1 47 0 5 1 29 1 10 11 0 g 6 12 7 3 0 49 1 3 0 41 4 9 6 10 0 t 21 14 6 5 47 2 2 3 44 3 10 7 26 19 0
dyads_m3_rc_shift2 (dyads_m3_rc)				; oligos_8nt_mkv2_m4 versus dyads_m3_rc; m=3/4; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.654056; --yaTGCATGyw--- ; cor=; Ncor= a 0 0 12 26 4 0 0 47 2 1 10 20 0 0 0 c 0 0 14 4 2 0 50 0 2 0 17 5 0 0 0 g 0 0 6 8 3 50 0 3 0 49 8 12 0 0 0 t 0 0 18 12 41 0 0 0 46 0 15 13 0 0 0
oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)				; oligos_8nt_mkv2_m4 versus oligos_6nt_mkv2_m2_rc; m=4/4; ncol2=10; w=0; offset=1; strand=R; shift=2; score=0.654056; --yaTGCATGyw--- ; cor=; Ncor= a 0 0 12 26 4 0 0 47 2 1 10 20 0 0 0 c 0 0 14 4 2 0 50 0 2 0 17 5 0 0 0 g 0 0 6 8 3 50 0 3 0 49 8 12 0 0 0 t 0 0 18 12 41 0 0 0 46 0 15 13 0 0 0

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=10; shift=3; ncol=13; ---wrCATGCAtr ; Alignment reference a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12
dyads_m3_shift3 (dyads_m3)				; oligos_6nt_mkv2_m2 versus dyads_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wrCATGCAtr ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wrCATGCAtr ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3; m=3/4; ncol2=14; w=-2; offset=-2; strand=D; shift=1; score=0.659079; -aatgCATGCATg ; cor=; Ncor= a 0 19 26 7 10 3 44 3 2 2 47 5 6 c 0 10 6 9 4 41 0 3 1 49 0 3 7 g 0 11 10 1 29 1 5 0 47 1 1 0 35 t 0 12 10 35 9 7 3 46 2 0 4 44 4
oligos_8nt_mkv2_m4_rc_shift0 (oligos_8nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m4_rc; m=4/4; ncol2=14; w=-3; offset=-3; strand=R; shift=0; score=0.654056; wrrTGCATGCAyy ; cor=; Ncor= a 9 8 11 2 2 0 27 2 1 1 24 6 7 c 4 6 1 2 2 28 0 0 0 25 1 11 8 g 3 9 11 1 24 0 0 0 28 1 2 1 6 t 13 6 6 24 1 1 2 27 0 2 2 11 8

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=13; shift=0; ncol=13; dagAGAGAGAGag ; Alignment reference a 26 56 14 81 6 83 9 85 7 73 10 51 22 c 13 8 6 2 4 3 2 2 1 1 4 8 12 g 29 8 60 2 77 2 79 1 80 7 70 19 38 t 24 20 12 7 5 4 2 4 4 11 8 14 20
oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m5; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; dagAGAGAGAGag ; cor=; Ncor= a 26 56 14 81 6 83 9 85 7 73 10 51 22 c 13 8 6 2 4 3 2 2 1 1 4 8 12 g 29 8 60 2 77 2 79 1 80 7 70 19 38 t 24 20 12 7 5 4 2 4 4 11 8 14 20
dyads_m5_rc_shift0 (dyads_m5_rc)				; oligos_8nt_mkv2_m5 versus dyads_m5_rc; m=2/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.818578; dwGAGAGAGag-- ; cor=; Ncor= a 26 54 6 90 9 88 8 87 4 51 19 0 0 c 10 6 4 1 3 2 1 1 4 7 14 0 0 g 33 11 78 2 81 1 86 4 82 17 43 0 0 t 26 24 7 2 2 4 0 3 5 20 19 0 0
oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)				; oligos_8nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=3/4; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.818578; dwGAGAGAGag-- ; cor=; Ncor= a 26 54 6 90 9 88 8 87 4 51 19 0 0 c 10 6 4 1 3 2 1 1 4 7 14 0 0 g 33 11 78 2 81 1 86 4 82 17 43 0 0 t 26 24 7 2 2 4 0 3 5 20 19 0 0
dyads_m4_rc_shift4 (dyads_m4_rc)				; oligos_8nt_mkv2_m5 versus dyads_m4_rc; m=4/4; ncol2=12; w=0; offset=4; strand=R; shift=4; score=0.417683; ----daGAGwGGG ; cor=; Ncor= a 0 0 0 0 10 19 2 31 2 14 4 3 1 c 0 0 0 0 1 4 0 1 0 1 1 0 0 g 0 0 0 0 12 3 30 1 32 4 27 30 32 t 0 0 0 0 11 8 2 1 0 15 2 1 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift3 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=10; shift=3; ncol=13; ---wrCATGCAtr ; Alignment reference a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12
dyads_m3_shift3 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wrCATGCAtr ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; dyads_m3 versus oligos_6nt_mkv2_m2; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wrCATGCAtr ; cor=; Ncor= a 0 0 0 13 15 0 46 0 0 0 41 12 18 c 0 0 0 12 8 49 0 3 0 50 3 8 6 g 0 0 0 5 17 0 2 0 50 0 2 4 14 t 0 0 0 20 10 1 2 47 0 0 4 26 12
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; dyads_m3 versus oligos_7nt_mkv2_m3; m=3/4; ncol2=14; w=-2; offset=-2; strand=D; shift=1; score=0.659079; -aatgCATGCATg ; cor=; Ncor= a 0 19 26 7 10 3 44 3 2 2 47 5 6 c 0 10 6 9 4 41 0 3 1 49 0 3 7 g 0 11 10 1 29 1 5 0 47 1 1 0 35 t 0 12 10 35 9 7 3 46 2 0 4 44 4
oligos_8nt_mkv2_m4_rc_shift0 (oligos_8nt_mkv2_m4_rc)				; dyads_m3 versus oligos_8nt_mkv2_m4_rc; m=4/4; ncol2=14; w=-3; offset=-3; strand=R; shift=0; score=0.654056; wrrTGCATGCAyy ; cor=; Ncor= a 9 8 11 2 2 0 27 2 1 1 24 6 7 c 4 6 1 2 2 28 0 0 0 25 1 11 8 g 3 9 11 1 24 0 0 0 28 1 2 1 6 t 13 6 6 24 1 1 2 27 0 2 2 11 8

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=14; shift=0; ncol=14; mtTcACCAACCCmm ; Alignment reference a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8
oligos_7nt_mkv2_m1_shift0 (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=0; score= 1; mtTcACCAACCCmm ; cor=; Ncor= a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8
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=1; strand=D; shift=1; score=0.907614; -ytcACCAACCCmm ; cor=; Ncor= a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=3/4; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.904395; mtTCACCAACCmCm ; cor=; Ncor= a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2
dyads_m1_shift0 (dyads_m1)				; oligos_7nt_mkv2_m1 versus dyads_m1; m=4/4; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.846547; htTCACCAACCmCm ; cor=; Ncor= a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift3 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ctCTCTCTCwh ; Alignment reference a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26
dyads_m5_shift3 (dyads_m5)				; dyads_m5 versus dyads_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCTCTCTCwh ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; dyads_m5 versus oligos_7nt_mkv2_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCTCTCTCwh ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26
oligos_8nt_mkv2_m5_rc_shift1 (oligos_8nt_mkv2_m5_rc)				; dyads_m5 versus oligos_8nt_mkv2_m5_rc; m=3/4; ncol2=13; w=-2; offset=-2; strand=R; shift=1; score=0.818578; -ctCTCTCTCTcth ; cor=; Ncor= a 0 20 14 8 11 4 4 2 4 5 7 12 20 24 c 0 38 19 70 7 80 1 79 2 77 2 60 8 29 g 0 12 8 4 1 1 2 2 3 4 2 6 8 13 t 0 22 51 10 73 7 85 9 83 6 81 14 56 26
dyads_m4_shift0 (dyads_m4)				; dyads_m5 versus dyads_m4; m=4/4; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.472381; wwCCCCwCTCth-- ; cor=; Ncor= a 12 10 2 1 1 2 15 0 1 2 8 11 0 0 c 5 5 28 32 30 27 4 32 1 30 3 12 0 0 g 5 5 2 0 0 1 1 0 1 0 4 1 0 0 t 12 14 2 1 3 4 14 2 31 2 19 10 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=11; shift=3; ncol=14; ---ctCTCTCTCwh ; Alignment reference a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26
dyads_m5_shift3 (dyads_m5)				; oligos_7nt_mkv2_m4 versus dyads_m5; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCTCTCTCwh ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ctCTCTCTCwh ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 24 26 c 0 0 0 43 17 82 4 86 1 81 2 78 11 33 g 0 0 0 14 7 4 1 1 2 3 1 4 6 10 t 0 0 0 19 51 4 87 8 88 9 90 6 54 26
oligos_8nt_mkv2_m5_rc_shift1 (oligos_8nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m5_rc; m=3/4; ncol2=13; w=-2; offset=-2; strand=R; shift=1; score=0.818578; -ctCTCTCTCTcth ; cor=; Ncor= a 0 20 14 8 11 4 4 2 4 5 7 12 20 24 c 0 38 19 70 7 80 1 79 2 77 2 60 8 29 g 0 12 8 4 1 1 2 2 3 4 2 6 8 13 t 0 22 51 10 73 7 85 9 83 6 81 14 56 26
dyads_m4_shift0 (dyads_m4)				; oligos_7nt_mkv2_m4 versus dyads_m4; m=4/4; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.472381; wwCCCCwCTCth-- ; cor=; Ncor= a 12 10 2 1 1 2 15 0 1 2 8 11 0 0 c 5 5 28 32 30 27 4 32 1 30 3 12 0 0 g 5 5 2 0 0 1 1 0 1 0 4 1 0 0 t 12 14 2 1 3 4 14 2 31 2 19 10 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift0 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wwCCCCwCTCth ; Alignment reference a 12 10 2 1 1 2 15 0 1 2 8 11 c 5 5 28 32 30 27 4 32 1 30 3 12 g 5 5 2 0 0 1 1 0 1 0 4 1 t 12 14 2 1 3 4 14 2 31 2 19 10
dyads_m4_shift0 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wwCCCCwCTCth ; cor=; Ncor= a 12 10 2 1 1 2 15 0 1 2 8 11 c 5 5 28 32 30 27 4 32 1 30 3 12 g 5 5 2 0 0 1 1 0 1 0 4 1 t 12 14 2 1 3 4 14 2 31 2 19 10
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; dyads_m4 versus oligos_7nt_mkv2_m4; m=2/4; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.472381; ---ctCTCTCTC ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 c 0 0 0 43 17 82 4 86 1 81 2 78 g 0 0 0 14 7 4 1 1 2 3 1 4 t 0 0 0 19 51 4 87 8 88 9 90 6
dyads_m5_shift3 (dyads_m5)				; dyads_m4 versus dyads_m5; m=3/4; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.472381; ---ctCTCTCTC ; cor=; Ncor= a 0 0 0 19 20 5 3 0 4 2 2 7 c 0 0 0 43 17 82 4 86 1 81 2 78 g 0 0 0 14 7 4 1 1 2 3 1 4 t 0 0 0 19 51 4 87 8 88 9 90 6
oligos_8nt_mkv2_m5_rc_shift3 (oligos_8nt_mkv2_m5_rc)				; dyads_m4 versus oligos_8nt_mkv2_m5_rc; m=4/4; ncol2=13; w=0; offset=3; strand=R; shift=3; score=0.417683; ---ctCTCTCTC ; cor=; Ncor= a 0 0 0 20 14 8 11 4 4 2 4 5 c 0 0 0 38 19 70 7 80 1 79 2 77 g 0 0 0 12 8 4 1 1 2 2 3 4 t 0 0 0 22 51 10 73 7 85 9 83 6

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; -ytcACCAACCCmm ; Alignment reference a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8
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; -ytcACCAACCCmm ; cor=; Ncor= a 0 9 11 11 46 0 0 44 45 11 1 11 19 18 c 0 14 6 27 1 50 47 1 2 38 42 34 18 17 g 0 4 7 5 0 0 1 1 2 1 0 4 5 7 t 0 23 26 7 3 0 2 4 1 0 7 1 8 8
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/4; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.907614; mtTcACCAACCCmm ; cor=; Ncor= a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=3/4; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.832751; mtTCACCAACCmCm ; cor=; Ncor= a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2
dyads_m1_shift0 (dyads_m1)				; oligos_6nt_mkv2_m1 versus dyads_m1; m=4/4; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.778017; htTCACCAACCmCm ; cor=; Ncor= a 14 8 4 1 33 2 0 32 33 5 1 12 5 11 c 11 6 4 25 1 34 35 0 1 30 30 20 25 17 g 2 3 0 3 0 0 0 0 2 1 2 3 2 6 t 9 19 28 7 2 0 1 4 0 0 3 1 4 2