One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/08/peak-motifs.2026-01-08.113908_2026-01-08.113908_nI4Dk5/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/2026/01/08/peak-motifs.2026-01-08.113908_2026-01-08.113908_nI4Dk5/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; cgyCCGtCCGtCCkyss ; Alignment reference a 2 1 0 0 0 0 0 0 0 0 1 2 0 0 0 3 0 c 9 2 8 12 12 0 2 12 13 1 3 10 11 1 9 6 5 g 3 9 2 2 2 14 3 2 0 13 1 2 3 8 0 5 6 t 0 2 4 0 0 0 9 0 1 0 9 0 0 5 5 0 3

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/2; ncol2=17; w=0; offset=0; strand=D; shift=0; score= 1; cgyCCGtCCGtCCkyss ; cor=; Ncor= a 2 1 0 0 0 0 0 0 0 0 1 2 0 0 0 3 0 c 9 2 8 12 12 0 2 12 13 1 3 10 11 1 9 6 5 g 3 9 2 2 2 14 3 2 0 13 1 2 3 8 0 5 6 t 0 2 4 0 0 0 9 0 1 0 9 0 0 5 5 0 3

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.576003; -syCCGTCCkys----- ; cor=; Ncor= a 0 0 5 0 0 0 1 0 0 0 3 3 0 0 0 0 0 c 0 6 7 20 21 0 1 19 19 1 7 10 0 0 0 0 0 g 0 11 3 0 0 19 3 1 1 9 2 6 0 0 0 0 0 t 0 4 6 1 0 2 16 1 1 11 9 2 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; scCGrsCGCGGCCsgkcS ; Alignment reference a 1 2 1 1 4 1 0 1 1 1 0 0 0 1 1 1 2 0 c 5 5 7 0 2 3 10 0 8 0 0 10 9 4 1 1 5 7 g 4 1 1 8 3 6 0 8 1 9 10 0 1 4 6 4 1 3 t 0 2 1 1 1 0 0 1 0 0 0 0 0 1 2 4 2 0

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/4; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; scCGrsCGCGGCCsgkcS ; cor=; Ncor= a 1 2 1 1 4 1 0 1 1 1 0 0 0 1 1 1 2 0 c 5 5 7 0 2 3 10 0 8 0 0 10 9 4 1 1 5 7 g 4 1 1 8 3 6 0 8 1 9 10 0 1 4 6 4 1 3 t 0 2 1 1 1 0 0 1 0 0 0 0 0 1 2 4 2 0

oligos_7nt_test_vs_ctrl_m3_rc_shift1 (oligos_7nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/4; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.655873; -sCgaGCGmGGCssv--- ; cor=; Ncor= a 0 1 1 2 5 0 0 0 5 0 0 1 0 1 3 0 0 0 c 0 4 7 2 2 0 10 0 3 0 0 9 5 5 4 0 0 0 g 0 3 2 4 2 10 0 10 1 10 10 0 5 3 3 0 0 0 t 0 2 0 2 1 0 0 0 1 0 0 0 0 1 0 0 0 0

oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/4; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.618845; ----sgCCCGGCCGGGcs ; cor=; Ncor= a 0 0 0 0 3 4 1 1 2 2 0 2 0 1 0 1 5 1 c 0 0 0 0 10 5 17 16 17 1 0 20 19 2 5 3 8 8 g 0 0 0 0 8 8 3 5 2 19 20 0 1 17 16 17 5 10 t 0 0 0 0 1 5 1 0 1 0 2 0 2 2 1 1 4 3

oligos_6nt_test_vs_ctrl_m3_rc_shift3 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=4/4; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.560962; ---smGCGrGGCsys--- ; cor=; Ncor= a 0 0 0 1 5 0 0 0 4 0 0 0 0 1 2 0 0 0 c 0 0 0 4 5 0 13 2 3 0 0 14 9 7 7 0 0 0 g 0 0 0 6 3 13 1 12 6 14 14 0 5 2 4 0 0 0 t 0 0 0 3 1 1 0 0 1 0 0 0 0 4 1 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -syCCGTCCkys ; Alignment reference a 0 0 5 0 0 0 1 0 0 0 3 3 c 0 6 7 20 21 0 1 19 19 1 7 10 g 0 11 3 0 0 19 3 1 1 9 2 6 t 0 4 6 1 0 2 16 1 1 11 9 2

oligos_6nt_test_vs_ctrl_m1_shift1 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -syCCGTCCkys ; cor=; Ncor= a 0 0 5 0 0 0 1 0 0 0 3 3 c 0 6 7 20 21 0 1 19 19 1 7 10 g 0 11 3 0 0 19 3 1 1 9 2 6 t 0 4 6 1 0 2 16 1 1 11 9 2

oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=2/2; ncol2=17; w=-1; offset=-1; strand=D; shift=0; score=0.576003; cgyCCGtCCGtC ; cor=; Ncor= a 2 1 0 0 0 0 0 0 0 0 1 2 c 9 2 8 12 12 0 2 12 13 1 3 10 g 3 9 2 2 2 14 3 2 0 13 1 2 t 0 2 4 0 0 0 9 0 1 0 9 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift4 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=14; shift=4; ncol=18; ----sgCCCGGCCGGGcs ; Alignment reference a 0 0 0 0 3 4 1 1 2 2 0 2 0 1 0 1 5 1 c 0 0 0 0 10 5 17 16 17 1 0 20 19 2 5 3 8 8 g 0 0 0 0 8 8 3 5 2 19 20 0 1 17 16 17 5 10 t 0 0 0 0 1 5 1 0 1 0 2 0 2 2 1 1 4 3

oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=4; score= 1; ----sgCCCGGCCGGGcs ; cor=; Ncor= a 0 0 0 0 3 4 1 1 2 2 0 2 0 1 0 1 5 1 c 0 0 0 0 10 5 17 16 17 1 0 20 19 2 5 3 8 8 g 0 0 0 0 8 8 3 5 2 19 20 0 1 17 16 17 5 10 t 0 0 0 0 1 5 1 0 1 0 2 0 2 2 1 1 4 3

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=2/2; ncol2=18; w=-4; offset=-4; strand=D; shift=0; score=0.618845; scCGrsCGCGGCCsgkcS ; cor=; Ncor= a 1 2 1 1 4 1 0 1 1 1 0 0 0 1 1 1 2 0 c 5 5 7 0 2 3 10 0 8 0 0 10 9 4 1 1 5 7 g 4 1 1 8 3 6 0 8 1 9 10 0 1 4 6 4 1 3 t 0 2 1 1 1 0 0 1 0 0 0 0 0 1 2 4 2 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=14; shift=3; ncol=17; ---bssGCCkCGCtcGs ; Alignment reference a 0 0 0 0 1 0 0 0 0 1 0 0 0 1 2 0 2 c 0 0 0 3 3 5 0 10 10 1 10 0 10 2 4 2 3 g 0 0 0 4 5 5 9 0 0 3 0 10 0 2 2 7 4 t 0 0 0 3 1 0 1 0 0 5 0 0 0 5 2 1 1

oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---bssGCCkCGCtcGs ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 1 0 0 0 1 2 0 2 c 0 0 0 3 3 5 0 10 10 1 10 0 10 2 4 2 3 g 0 0 0 4 5 5 9 0 0 3 0 10 0 2 2 7 4 t 0 0 0 3 1 0 1 0 0 5 0 0 0 5 2 1 1

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.817296; ---srsGCCyCGCks-- ; cor=; Ncor= a 0 0 0 1 4 0 0 0 0 1 0 0 1 1 3 0 0 c 0 0 0 4 2 5 0 14 14 6 12 1 13 3 6 0 0 g 0 0 0 7 7 9 14 0 0 3 2 13 0 5 4 0 0 t 0 0 0 2 1 0 0 0 0 4 0 0 0 5 1 0 0

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.655873; SgmcsGGCCGCGsyCGg ; cor=; Ncor= a 0 2 4 2 1 0 0 0 0 0 1 0 0 1 1 1 2 c 3 1 4 6 4 1 0 10 9 1 8 0 6 3 8 1 1 g 7 5 1 1 4 9 10 0 0 8 0 10 3 2 0 7 5 t 0 2 1 1 1 0 0 0 1 1 1 0 1 4 1 1 2

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; TdTGTrAAGth ; Alignment reference a 0 3 0 1 0 4 9 10 0 2 3 c 1 0 0 0 0 0 0 0 1 0 3 g 1 3 0 9 0 6 0 0 7 2 0 t 8 4 10 0 10 0 1 0 2 6 4

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; TdTGTrAAGth ; cor=; Ncor= a 0 3 0 1 0 4 9 10 0 2 3 c 1 0 0 0 0 0 0 0 1 0 3 g 1 3 0 9 0 6 0 0 7 2 0 t 8 4 10 0 10 0 1 0 2 6 4

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=10; shift=1; ncol=11; -mcCTTCCCmk ; Alignment reference a 0 4 2 0 0 0 0 0 0 3 2 c 0 3 3 9 0 0 9 7 9 3 0 g 0 2 2 0 0 0 0 0 0 1 4 t 0 0 2 0 9 9 0 2 0 2 3

oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -mcCTTCCCmk ; cor=; Ncor= a 0 4 2 0 0 0 0 0 0 3 2 c 0 3 3 9 0 0 9 7 9 3 0 g 0 2 2 0 0 0 0 0 0 1 4 t 0 0 2 0 9 9 0 2 0 2 3

oligos_7nt_test_vs_ctrl_m5_rc_shift0 (oligos_7nt_test_vs_ctrl_m5_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m5_rc; m=2/2; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.572954; ssCCtTCCCCG ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 1 0 c 6 5 13 13 2 3 11 14 10 11 0 g 8 6 0 1 3 1 1 0 2 2 14 t 0 3 1 0 8 10 2 0 2 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---srsGCCyCGCks ; Alignment reference a 0 0 0 1 4 0 0 0 0 1 0 0 1 1 3 c 0 0 0 4 2 5 0 14 14 6 12 1 13 3 6 g 0 0 0 7 7 9 14 0 0 3 2 13 0 5 4 t 0 0 0 2 1 0 0 0 0 4 0 0 0 5 1

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---srsGCCyCGCks ; cor=; Ncor= a 0 0 0 1 4 0 0 0 0 1 0 0 1 1 3 c 0 0 0 4 2 5 0 14 14 6 12 1 13 3 6 g 0 0 0 7 7 9 14 0 0 3 2 13 0 5 4 t 0 0 0 2 1 0 0 0 0 4 0 0 0 5 1

oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.817296; ---bssGCCkCGCtc ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 1 0 0 0 1 2 c 0 0 0 3 3 5 0 10 10 1 10 0 10 2 4 g 0 0 0 4 5 5 9 0 0 3 0 10 0 2 2 t 0 0 0 3 1 0 1 0 0 5 0 0 0 5 2

oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.560962; SgmcsGGCCGCGsyC ; cor=; Ncor= a 0 2 4 2 1 0 0 0 0 0 1 0 0 1 1 c 3 1 4 6 4 1 0 10 9 1 8 0 6 3 8 g 7 5 1 1 4 9 10 0 0 8 0 10 3 2 0 t 0 2 1 1 1 0 0 0 1 1 1 0 1 4 1

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; wwATAAACAva ; Alignment reference a 7 7 17 1 20 15 19 2 19 5 10 c 3 4 1 4 0 4 1 17 0 7 2 g 4 3 1 1 0 1 0 1 0 7 4 t 6 6 1 14 0 0 0 0 1 1 4

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwATAAACAva ; cor=; Ncor= a 7 7 17 1 20 15 19 2 19 5 10 c 3 4 1 4 0 4 1 17 0 7 2 g 4 3 1 1 0 1 0 1 0 7 4 t 6 6 1 14 0 0 0 0 1 1 4

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; ssCGGGGAaGGss ; Alignment reference a 0 3 0 0 2 0 2 10 8 0 1 3 0 c 6 4 14 2 2 0 1 1 3 1 0 6 8 g 7 5 0 11 10 14 11 3 2 13 13 5 6 t 1 2 0 1 0 0 0 0 1 0 0 0 0

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; ssCGGGGAaGGss ; cor=; Ncor= a 0 3 0 0 2 0 2 10 8 0 1 3 0 c 6 4 14 2 2 0 1 1 3 1 0 6 8 g 7 5 0 11 10 14 11 3 2 13 13 5 6 t 1 2 0 1 0 0 0 0 1 0 0 0 0

oligos_6nt_test_vs_ctrl_m2_rc_shift2 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/2; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.572954; --mkGGGAAGgk- ; cor=; Ncor= a 0 0 3 2 0 2 0 9 9 0 2 0 0 c 0 0 4 1 0 0 0 0 0 0 2 2 0 g 0 0 0 3 9 7 9 0 0 9 3 3 0 t 0 0 2 3 0 0 0 0 0 0 2 4 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; scCGrsCGCGGCCsgkcS ; Alignment reference a 1 2 1 1 4 1 0 1 1 1 0 0 0 1 1 1 2 0 c 5 5 7 0 2 3 10 0 8 0 0 10 9 4 1 1 5 7 g 4 1 1 8 3 6 0 8 1 9 10 0 1 4 6 4 1 3 t 0 2 1 1 1 0 0 1 0 0 0 0 0 1 2 4 2 0
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/4; ncol2=18; w=0; offset=0; strand=D; shift=0; score= 1; scCGrsCGCGGCCsgkcS ; cor=; Ncor= a 1 2 1 1 4 1 0 1 1 1 0 0 0 1 1 1 2 0 c 5 5 7 0 2 3 10 0 8 0 0 10 9 4 1 1 5 7 g 4 1 1 8 3 6 0 8 1 9 10 0 1 4 6 4 1 3 t 0 2 1 1 1 0 0 1 0 0 0 0 0 1 2 4 2 0
oligos_7nt_test_vs_ctrl_m3_rc_shift1 (oligos_7nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/4; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.655873; -sCgaGCGmGGCssv--- ; cor=; Ncor= a 0 1 1 2 5 0 0 0 5 0 0 1 0 1 3 0 0 0 c 0 4 7 2 2 0 10 0 3 0 0 9 5 5 4 0 0 0 g 0 3 2 4 2 10 0 10 1 10 10 0 5 3 3 0 0 0 t 0 2 0 2 1 0 0 0 1 0 0 0 0 1 0 0 0 0
oligos_7nt_test_vs_ctrl_m4_shift4 (oligos_7nt_test_vs_ctrl_m4)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/4; ncol2=14; w=0; offset=4; strand=D; shift=4; score=0.618845; ----sgCCCGGCCGGGcs ; cor=; Ncor= a 0 0 0 0 3 4 1 1 2 2 0 2 0 1 0 1 5 1 c 0 0 0 0 10 5 17 16 17 1 0 20 19 2 5 3 8 8 g 0 0 0 0 8 8 3 5 2 19 20 0 1 17 16 17 5 10 t 0 0 0 0 1 5 1 0 1 0 2 0 2 2 1 1 4 3
oligos_6nt_test_vs_ctrl_m3_rc_shift3 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=4/4; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.560962; ---smGCGrGGCsys--- ; cor=; Ncor= a 0 0 0 1 5 0 0 0 4 0 0 0 0 1 2 0 0 0 c 0 0 0 4 5 0 13 2 3 0 0 14 9 7 7 0 0 0 g 0 0 0 6 3 13 1 12 6 14 14 0 5 2 4 0 0 0 t 0 0 0 3 1 1 0 0 1 0 0 0 0 4 1 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=14; shift=3; ncol=17; ---bssGCCkCGCtcGs ; Alignment reference a 0 0 0 0 1 0 0 0 0 1 0 0 0 1 2 0 2 c 0 0 0 3 3 5 0 10 10 1 10 0 10 2 4 2 3 g 0 0 0 4 5 5 9 0 0 3 0 10 0 2 2 7 4 t 0 0 0 3 1 0 1 0 0 5 0 0 0 5 2 1 1
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=3; score= 1; ---bssGCCkCGCtcGs ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 1 0 0 0 1 2 0 2 c 0 0 0 3 3 5 0 10 10 1 10 0 10 2 4 2 3 g 0 0 0 4 5 5 9 0 0 3 0 10 0 2 2 7 4 t 0 0 0 3 1 0 1 0 0 5 0 0 0 5 2 1 1
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score=0.817296; ---srsGCCyCGCks-- ; cor=; Ncor= a 0 0 0 1 4 0 0 0 0 1 0 0 1 1 3 0 0 c 0 0 0 4 2 5 0 14 14 6 12 1 13 3 6 0 0 g 0 0 0 7 7 9 14 0 0 3 2 13 0 5 4 0 0 t 0 0 0 2 1 0 0 0 0 4 0 0 0 5 1 0 0
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.655873; SgmcsGGCCGCGsyCGg ; cor=; Ncor= a 0 2 4 2 1 0 0 0 0 0 1 0 0 1 1 1 2 c 3 1 4 6 4 1 0 10 9 1 8 0 6 3 8 1 1 g 7 5 1 1 4 9 10 0 0 8 0 10 3 2 0 7 5 t 0 2 1 1 1 0 0 0 1 1 1 0 1 4 1 1 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---srsGCCyCGCks ; Alignment reference a 0 0 0 1 4 0 0 0 0 1 0 0 1 1 3 c 0 0 0 4 2 5 0 14 14 6 12 1 13 3 6 g 0 0 0 7 7 9 14 0 0 3 2 13 0 5 4 t 0 0 0 2 1 0 0 0 0 4 0 0 0 5 1
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---srsGCCyCGCks ; cor=; Ncor= a 0 0 0 1 4 0 0 0 0 1 0 0 1 1 3 c 0 0 0 4 2 5 0 14 14 6 12 1 13 3 6 g 0 0 0 7 7 9 14 0 0 3 2 13 0 5 4 t 0 0 0 2 1 0 0 0 0 4 0 0 0 5 1
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=3; score=0.817296; ---bssGCCkCGCtc ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 1 0 0 0 1 2 c 0 0 0 3 3 5 0 10 10 1 10 0 10 2 4 g 0 0 0 4 5 5 9 0 0 3 0 10 0 2 2 t 0 0 0 3 1 0 1 0 0 5 0 0 0 5 2
oligos_7nt_test_vs_ctrl_m2_rc_shift0 (oligos_7nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2_rc; m=3/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.560962; SgmcsGGCCGCGsyC ; cor=; Ncor= a 0 2 4 2 1 0 0 0 0 0 1 0 0 1 1 c 3 1 4 6 4 1 0 10 9 1 8 0 6 3 8 g 7 5 1 1 4 9 10 0 0 8 0 10 3 2 0 t 0 2 1 1 1 0 0 0 1 1 1 0 1 4 1