One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.175925_2025-05-16.175925_FDRQXr/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.2025-05-16.175925_2025-05-16.175925_FDRQXr/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m3_shift2 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --rcACACTGGGrsa ; Alignment reference a 0 0 3 0 7 0 8 0 0 1 0 1 3 0 5 c 0 0 0 6 0 9 0 9 0 0 0 0 0 3 1 g 0 0 4 2 0 0 0 0 1 8 9 8 5 4 2 t 0 0 2 1 2 0 1 0 8 0 0 0 1 2 1

oligos_7nt_mkv1_m3_shift2 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --rcACACTGGGrsa ; cor=; Ncor= a 0 0 3 0 7 0 8 0 0 1 0 1 3 0 5 c 0 0 0 6 0 9 0 9 0 0 0 0 0 3 1 g 0 0 4 2 0 0 0 0 1 8 9 8 5 4 2 t 0 0 2 1 2 0 1 0 8 0 0 0 1 2 1

oligos_6nt_mkv1_m3_rc_shift1 (oligos_6nt_mkv1_m3_rc)
; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m3_rc; m=2/3; ncol2=10; w=-1; offset=-1; strand=R; shift=1; score=0.597808; -kgCACACTrG---- ; cor=; Ncor= a 0 0 1 0 5 0 5 1 0 2 0 0 0 0 0 c 0 0 0 5 0 5 0 4 0 0 0 0 0 0 0 g 0 2 3 0 0 0 0 0 0 3 4 0 0 0 0 t 0 3 1 0 0 0 0 0 5 0 1 0 0 0 0

oligos_7nt_mkv1_m2_rc_shift0 (oligos_7nt_mkv1_m2_rc)
; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m2_rc; m=3/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.557607; kkGCACACTrG---- ; cor=; Ncor= a 0 0 0 0 3 0 3 0 0 1 0 0 0 0 0 c 0 0 0 3 0 3 0 3 0 0 0 0 0 0 0 g 2 1 3 0 0 0 0 0 0 2 3 0 0 0 0 t 1 2 0 0 0 0 0 0 3 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift3 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=3; ncol=13; ---bdCGGGGAvR ; Alignment reference a 0 0 0 0 1 0 0 0 0 0 4 1 3 c 0 0 0 1 0 4 0 0 0 0 0 2 0 g 0 0 0 2 2 0 4 4 4 4 0 1 1 t 0 0 0 1 1 0 0 0 0 0 0 0 0

oligos_6nt_mkv1_m1_shift3 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---bdCGGGGAvR ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 0 4 1 3 c 0 0 0 1 0 4 0 0 0 0 0 2 0 g 0 0 0 2 2 0 4 4 4 4 0 1 1 t 0 0 0 1 1 0 0 0 0 0 0 0 0

oligos_7nt_mkv1_m4_rc_shift0 (oligos_7nt_mkv1_m4_rc)
; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m4_rc; m=2/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.515781; MWGGSCGGGkd-- ; cor=; Ncor= a 1 1 0 0 0 0 0 0 0 0 2 0 0 c 3 0 0 0 1 4 0 0 0 0 0 0 0 g 0 0 4 4 3 0 4 4 4 2 1 0 0 t 0 3 0 0 0 0 0 0 0 2 1 0 0

oligos_6nt_mkv1_m4_rc_shift0 (oligos_6nt_mkv1_m4_rc)
; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m4_rc; m=3/3; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.443643; cwGGGCGGkg--- ; cor=; Ncor= a 1 2 0 0 0 0 0 0 0 1 0 0 0 c 3 1 0 0 0 4 0 0 0 0 0 0 0 g 1 0 5 5 5 0 5 5 3 3 0 0 0 t 0 2 0 0 0 1 0 0 2 1 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---cmCCGCCCwg ; Alignment reference a 0 0 0 1 2 0 0 1 0 0 0 2 0 c 0 0 0 3 3 5 5 0 5 5 5 0 1 g 0 0 0 0 0 0 0 4 0 0 0 1 3 t 0 0 0 1 0 0 0 0 0 0 0 2 1

oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---cmCCGCCCwg ; cor=; Ncor= a 0 0 0 1 2 0 0 1 0 0 0 2 0 c 0 0 0 3 3 5 5 0 5 5 5 0 1 g 0 0 0 0 0 0 0 4 0 0 0 1 3 t 0 0 0 1 0 0 0 0 0 0 0 2 1

oligos_7nt_mkv1_m4_shift2 (oligos_7nt_mkv1_m4)
; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=2; score=0.835305; --hmCCCGSCCWK ; cor=; Ncor= a 0 0 1 2 0 0 0 0 0 0 0 3 0 c 0 0 1 2 4 4 4 0 3 4 4 0 0 g 0 0 0 0 0 0 0 4 1 0 0 0 3 t 0 0 2 0 0 0 0 0 0 0 0 1 1

oligos_6nt_mkv1_m1_rc_shift0 (oligos_6nt_mkv1_m1_rc)
; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.443643; YbTCCCCGhv--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 1 0 0 0 c 1 1 0 4 4 4 4 0 2 2 0 0 0 g 0 2 0 0 0 0 0 4 0 1 0 0 0 t 3 1 4 0 0 0 0 0 1 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----CyAGTGTGCmm ; Alignment reference a 0 0 0 0 0 0 3 0 0 0 0 0 0 2 1 c 0 0 0 0 3 2 0 0 0 0 0 0 3 1 2 g 0 0 0 0 0 0 0 3 0 3 0 3 0 0 0 t 0 0 0 0 0 1 0 0 3 0 3 0 0 0 0

oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----CyAGTGTGCmm ; cor=; Ncor= a 0 0 0 0 0 0 3 0 0 0 0 0 0 2 1 c 0 0 0 0 3 2 0 0 0 0 0 0 3 1 2 g 0 0 0 0 0 0 0 3 0 3 0 3 0 0 0 t 0 0 0 0 0 1 0 0 3 0 3 0 0 0 0

oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)
; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.882316; ----CyAGTGTGcm- ; cor=; Ncor= a 0 0 0 0 1 0 5 0 0 0 0 0 1 3 0 c 0 0 0 0 4 3 0 0 0 0 0 0 3 2 0 g 0 0 0 0 0 0 0 4 0 5 0 5 0 0 0 t 0 0 0 0 0 2 0 1 5 0 5 0 1 0 0

oligos_7nt_mkv1_m3_rc_shift0 (oligos_7nt_mkv1_m3_rc)
; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m3_rc; m=3/3; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.557607; tsyCCCAGTGTgy-- ; cor=; Ncor= a 1 2 1 0 0 0 8 0 1 0 2 1 2 0 0 c 2 4 5 8 9 8 1 0 0 0 0 2 4 0 0 g 1 3 0 0 0 0 0 9 0 9 0 6 0 0 0 t 5 0 3 1 0 1 0 0 8 0 7 0 3 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m5_shift4 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----GrAAGGTAAym ; Alignment reference a 0 0 0 0 0 1 2 2 0 0 0 2 2 0 1 c 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 g 0 0 0 0 2 1 0 0 2 2 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0

oligos_7nt_mkv1_m5_shift4 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----GrAAGGTAAym ; cor=; Ncor= a 0 0 0 0 0 1 2 2 0 0 0 2 2 0 1 c 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 g 0 0 0 0 2 1 0 0 2 2 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0

oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc)
; oligos_7nt_mkv1_m5 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=10; w=-3; offset=-3; strand=R; shift=1; score=0.433037; -kgGGGAAGGh---- ; cor=; Ncor= a 0 1 1 0 0 0 6 6 0 0 2 0 0 0 0 c 0 1 0 0 0 0 0 0 0 1 2 0 0 0 0 g 0 2 4 6 6 6 0 0 6 5 0 0 0 0 0 t 0 2 1 0 0 0 0 0 0 0 2 0 0 0 0

oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)
; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m1_rc; m=3/3; ncol2=12; w=-4; offset=-4; strand=R; shift=0; score=0.422077; tkGGGGAAGGmw--- ; cor=; Ncor= a 1 0 1 0 0 0 5 5 0 0 2 2 0 0 0 c 1 1 0 0 0 0 0 0 0 0 2 0 0 0 0 g 1 2 4 5 5 5 0 0 5 5 0 0 0 0 0 t 2 2 0 0 0 0 0 0 0 0 1 3 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=4; ncol=14; ----CyAGTGTGcm ; Alignment reference a 0 0 0 0 1 0 5 0 0 0 0 0 1 3 c 0 0 0 0 4 3 0 0 0 0 0 0 3 2 g 0 0 0 0 0 0 0 4 0 5 0 5 0 0 t 0 0 0 0 0 2 0 1 5 0 5 0 1 0

oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----CyAGTGTGcm ; cor=; Ncor= a 0 0 0 0 1 0 5 0 0 0 0 0 1 3 c 0 0 0 0 4 3 0 0 0 0 0 0 3 2 g 0 0 0 0 0 0 0 4 0 5 0 5 0 0 t 0 0 0 0 0 2 0 1 5 0 5 0 1 0

oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)
; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.882316; ----CyAGTGTGCm ; cor=; Ncor= a 0 0 0 0 0 0 3 0 0 0 0 0 0 2 c 0 0 0 0 3 2 0 0 0 0 0 0 3 1 g 0 0 0 0 0 0 0 3 0 3 0 3 0 0 t 0 0 0 0 0 1 0 0 3 0 3 0 0 0

oligos_7nt_mkv1_m3_rc_shift0 (oligos_7nt_mkv1_m3_rc)
; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m3_rc; m=3/3; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.597808; tsyCCCAGTGTgy- ; cor=; Ncor= a 1 2 1 0 0 0 8 0 1 0 2 1 2 0 c 2 4 5 8 9 8 1 0 0 0 0 2 4 0 g 1 3 0 0 0 0 0 9 0 9 0 6 0 0 t 5 0 3 1 0 1 0 0 8 0 7 0 3 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=12; shift=3; ncol=15; ---wkCCTTCCCCma ; Alignment reference a 0 0 0 3 1 0 0 0 0 0 0 0 0 2 2 c 0 0 0 0 0 5 5 0 0 5 5 5 4 2 1 g 0 0 0 0 2 0 0 0 0 0 0 0 0 1 1 t 0 0 0 2 2 0 0 5 5 0 0 0 1 0 1

oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---wkCCTTCCCCma ; cor=; Ncor= a 0 0 0 3 1 0 0 0 0 0 0 0 0 2 2 c 0 0 0 0 0 5 5 0 0 5 5 5 4 2 1 g 0 0 0 0 2 0 0 0 0 0 0 0 0 1 1 t 0 0 0 2 2 0 0 5 5 0 0 0 1 0 1

oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=4; score=0.822016; ----dCCTTCCCcm- ; cor=; Ncor= a 0 0 0 0 2 0 0 0 0 0 0 0 1 2 0 c 0 0 0 0 0 5 6 0 0 6 6 6 4 2 0 g 0 0 0 0 2 1 0 0 0 0 0 0 0 1 0 t 0 0 0 0 2 0 0 6 6 0 0 0 1 1 0

oligos_7nt_mkv1_m5_rc_shift0 (oligos_7nt_mkv1_m5_rc)
; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m5_rc; m=3/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.422077; krTTACCTTyC---- ; cor=; Ncor= a 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 2 2 0 0 1 2 0 0 0 0 g 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 t 1 0 2 2 0 0 0 2 2 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=4; ncol=14; ----dCCTTCCCcm ; Alignment reference a 0 0 0 0 2 0 0 0 0 0 0 0 1 2 c 0 0 0 0 0 5 6 0 0 6 6 6 4 2 g 0 0 0 0 2 1 0 0 0 0 0 0 0 1 t 0 0 0 0 2 0 0 6 6 0 0 0 1 1

oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----dCCTTCCCcm ; cor=; Ncor= a 0 0 0 0 2 0 0 0 0 0 0 0 1 2 c 0 0 0 0 0 5 6 0 0 6 6 6 4 2 g 0 0 0 0 2 1 0 0 0 0 0 0 0 1 t 0 0 0 0 2 0 0 6 6 0 0 0 1 1

oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=3; score=0.822016; ---wkCCTTCCCCm ; cor=; Ncor= a 0 0 0 3 1 0 0 0 0 0 0 0 0 2 c 0 0 0 0 0 5 5 0 0 5 5 5 4 2 g 0 0 0 0 2 0 0 0 0 0 0 0 0 1 t 0 0 0 2 2 0 0 5 5 0 0 0 1 0

oligos_7nt_mkv1_m5_rc_shift0 (oligos_7nt_mkv1_m5_rc)
; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m5_rc; m=3/3; ncol2=11; w=-4; offset=-4; strand=R; shift=0; score=0.433037; krTTACCTTyC--- ; cor=; Ncor= a 0 1 0 0 2 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 2 2 0 0 1 2 0 0 0 g 1 1 0 0 0 0 0 0 0 0 0 0 0 0 t 1 0 2 2 0 0 0 2 2 1 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m4_shift2 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --hmCCCGSCCWK ; Alignment reference a 0 0 1 2 0 0 0 0 0 0 0 3 0 c 0 0 1 2 4 4 4 0 3 4 4 0 0 g 0 0 0 0 0 0 0 4 1 0 0 0 3 t 0 0 2 0 0 0 0 0 0 0 0 1 1

oligos_7nt_mkv1_m4_shift2 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --hmCCCGSCCWK ; cor=; Ncor= a 0 0 1 2 0 0 0 0 0 0 0 3 0 c 0 0 1 2 4 4 4 0 3 4 4 0 0 g 0 0 0 0 0 0 0 4 1 0 0 0 3 t 0 0 2 0 0 0 0 0 0 0 0 1 1

oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)
; oligos_7nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.835305; ---cmCCGCCCwg ; cor=; Ncor= a 0 0 0 1 2 0 0 1 0 0 0 2 0 c 0 0 0 3 3 5 5 0 5 5 5 0 1 g 0 0 0 0 0 0 0 4 0 0 0 1 3 t 0 0 0 1 0 0 0 0 0 0 0 2 1

oligos_6nt_mkv1_m1_rc_shift0 (oligos_6nt_mkv1_m1_rc)
; oligos_7nt_mkv1_m4 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.515781; YbTCCCCGhv--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 1 0 0 0 c 1 1 0 4 4 4 4 0 2 2 0 0 0 g 0 2 0 0 0 0 0 4 0 1 0 0 0 t 3 1 4 0 0 0 0 0 1 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m3_shift2 (oligos_7nt_mkv1_m3)				; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=13; shift=2; ncol=15; --rcACACTGGGrsa ; Alignment reference a 0 0 3 0 7 0 8 0 0 1 0 1 3 0 5 c 0 0 0 6 0 9 0 9 0 0 0 0 0 3 1 g 0 0 4 2 0 0 0 0 1 8 9 8 5 4 2 t 0 0 2 1 2 0 1 0 8 0 0 0 1 2 1
oligos_7nt_mkv1_m3_shift2 (oligos_7nt_mkv1_m3)				; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --rcACACTGGGrsa ; cor=; Ncor= a 0 0 3 0 7 0 8 0 0 1 0 1 3 0 5 c 0 0 0 6 0 9 0 9 0 0 0 0 0 3 1 g 0 0 4 2 0 0 0 0 1 8 9 8 5 4 2 t 0 0 2 1 2 0 1 0 8 0 0 0 1 2 1
oligos_6nt_mkv1_m3_rc_shift1 (oligos_6nt_mkv1_m3_rc)				; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m3_rc; m=2/3; ncol2=10; w=-1; offset=-1; strand=R; shift=1; score=0.597808; -kgCACACTrG---- ; cor=; Ncor= a 0 0 1 0 5 0 5 1 0 2 0 0 0 0 0 c 0 0 0 5 0 5 0 4 0 0 0 0 0 0 0 g 0 2 3 0 0 0 0 0 0 3 4 0 0 0 0 t 0 3 1 0 0 0 0 0 5 0 1 0 0 0 0
oligos_7nt_mkv1_m2_rc_shift0 (oligos_7nt_mkv1_m2_rc)				; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m2_rc; m=3/3; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.557607; kkGCACACTrG---- ; cor=; Ncor= a 0 0 0 0 3 0 3 0 0 1 0 0 0 0 0 c 0 0 0 3 0 3 0 3 0 0 0 0 0 0 0 g 2 1 3 0 0 0 0 0 0 2 3 0 0 0 0 t 1 2 0 0 0 0 0 0 3 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift3 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=3; ncol=13; ---bdCGGGGAvR ; Alignment reference a 0 0 0 0 1 0 0 0 0 0 4 1 3 c 0 0 0 1 0 4 0 0 0 0 0 2 0 g 0 0 0 2 2 0 4 4 4 4 0 1 1 t 0 0 0 1 1 0 0 0 0 0 0 0 0
oligos_6nt_mkv1_m1_shift3 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---bdCGGGGAvR ; cor=; Ncor= a 0 0 0 0 1 0 0 0 0 0 4 1 3 c 0 0 0 1 0 4 0 0 0 0 0 2 0 g 0 0 0 2 2 0 4 4 4 4 0 1 1 t 0 0 0 1 1 0 0 0 0 0 0 0 0
oligos_7nt_mkv1_m4_rc_shift0 (oligos_7nt_mkv1_m4_rc)				; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m4_rc; m=2/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.515781; MWGGSCGGGkd-- ; cor=; Ncor= a 1 1 0 0 0 0 0 0 0 0 2 0 0 c 3 0 0 0 1 4 0 0 0 0 0 0 0 g 0 0 4 4 3 0 4 4 4 2 1 0 0 t 0 3 0 0 0 0 0 0 0 2 1 0 0
oligos_6nt_mkv1_m4_rc_shift0 (oligos_6nt_mkv1_m4_rc)				; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m4_rc; m=3/3; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.443643; cwGGGCGGkg--- ; cor=; Ncor= a 1 2 0 0 0 0 0 0 0 1 0 0 0 c 3 1 0 0 0 4 0 0 0 0 0 0 0 g 1 0 5 5 5 0 5 5 3 3 0 0 0 t 0 2 0 0 0 1 0 0 2 1 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---cmCCGCCCwg ; Alignment reference a 0 0 0 1 2 0 0 1 0 0 0 2 0 c 0 0 0 3 3 5 5 0 5 5 5 0 1 g 0 0 0 0 0 0 0 4 0 0 0 1 3 t 0 0 0 1 0 0 0 0 0 0 0 2 1
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---cmCCGCCCwg ; cor=; Ncor= a 0 0 0 1 2 0 0 1 0 0 0 2 0 c 0 0 0 3 3 5 5 0 5 5 5 0 1 g 0 0 0 0 0 0 0 4 0 0 0 1 3 t 0 0 0 1 0 0 0 0 0 0 0 2 1
oligos_7nt_mkv1_m4_shift2 (oligos_7nt_mkv1_m4)				; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=2; score=0.835305; --hmCCCGSCCWK ; cor=; Ncor= a 0 0 1 2 0 0 0 0 0 0 0 3 0 c 0 0 1 2 4 4 4 0 3 4 4 0 0 g 0 0 0 0 0 0 0 4 1 0 0 0 3 t 0 0 2 0 0 0 0 0 0 0 0 1 1
oligos_6nt_mkv1_m1_rc_shift0 (oligos_6nt_mkv1_m1_rc)				; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.443643; YbTCCCCGhv--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 1 0 0 0 c 1 1 0 4 4 4 4 0 2 2 0 0 0 g 0 2 0 0 0 0 0 4 0 1 0 0 0 t 3 1 4 0 0 0 0 0 1 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----CyAGTGTGCmm ; Alignment reference a 0 0 0 0 0 0 3 0 0 0 0 0 0 2 1 c 0 0 0 0 3 2 0 0 0 0 0 0 3 1 2 g 0 0 0 0 0 0 0 3 0 3 0 3 0 0 0 t 0 0 0 0 0 1 0 0 3 0 3 0 0 0 0
oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----CyAGTGTGCmm ; cor=; Ncor= a 0 0 0 0 0 0 3 0 0 0 0 0 0 2 1 c 0 0 0 0 3 2 0 0 0 0 0 0 3 1 2 g 0 0 0 0 0 0 0 3 0 3 0 3 0 0 0 t 0 0 0 0 0 1 0 0 3 0 3 0 0 0 0
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)				; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m3; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score=0.882316; ----CyAGTGTGcm- ; cor=; Ncor= a 0 0 0 0 1 0 5 0 0 0 0 0 1 3 0 c 0 0 0 0 4 3 0 0 0 0 0 0 3 2 0 g 0 0 0 0 0 0 0 4 0 5 0 5 0 0 0 t 0 0 0 0 0 2 0 1 5 0 5 0 1 0 0
oligos_7nt_mkv1_m3_rc_shift0 (oligos_7nt_mkv1_m3_rc)				; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m3_rc; m=3/3; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.557607; tsyCCCAGTGTgy-- ; cor=; Ncor= a 1 2 1 0 0 0 8 0 1 0 2 1 2 0 0 c 2 4 5 8 9 8 1 0 0 0 0 2 4 0 0 g 1 3 0 0 0 0 0 9 0 9 0 6 0 0 0 t 5 0 3 1 0 1 0 0 8 0 7 0 3 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m5_shift4 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=4; ncol=15; ----GrAAGGTAAym ; Alignment reference a 0 0 0 0 0 1 2 2 0 0 0 2 2 0 1 c 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 g 0 0 0 0 2 1 0 0 2 2 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0
oligos_7nt_mkv1_m5_shift4 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----GrAAGGTAAym ; cor=; Ncor= a 0 0 0 0 0 1 2 2 0 0 0 2 2 0 1 c 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 g 0 0 0 0 2 1 0 0 2 2 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 2 0 0 1 0
oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc)				; oligos_7nt_mkv1_m5 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=10; w=-3; offset=-3; strand=R; shift=1; score=0.433037; -kgGGGAAGGh---- ; cor=; Ncor= a 0 1 1 0 0 0 6 6 0 0 2 0 0 0 0 c 0 1 0 0 0 0 0 0 0 1 2 0 0 0 0 g 0 2 4 6 6 6 0 0 6 5 0 0 0 0 0 t 0 2 1 0 0 0 0 0 0 0 2 0 0 0 0
oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc)				; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m1_rc; m=3/3; ncol2=12; w=-4; offset=-4; strand=R; shift=0; score=0.422077; tkGGGGAAGGmw--- ; cor=; Ncor= a 1 0 1 0 0 0 5 5 0 0 2 2 0 0 0 c 1 1 0 0 0 0 0 0 0 0 2 0 0 0 0 g 1 2 4 5 5 5 0 0 5 5 0 0 0 0 0 t 2 2 0 0 0 0 0 0 0 0 1 3 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=4; ncol=14; ----CyAGTGTGcm ; Alignment reference a 0 0 0 0 1 0 5 0 0 0 0 0 1 3 c 0 0 0 0 4 3 0 0 0 0 0 0 3 2 g 0 0 0 0 0 0 0 4 0 5 0 5 0 0 t 0 0 0 0 0 2 0 1 5 0 5 0 1 0
oligos_6nt_mkv1_m3_shift4 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----CyAGTGTGcm ; cor=; Ncor= a 0 0 0 0 1 0 5 0 0 0 0 0 1 3 c 0 0 0 0 4 3 0 0 0 0 0 0 3 2 g 0 0 0 0 0 0 0 4 0 5 0 5 0 0 t 0 0 0 0 0 2 0 1 5 0 5 0 1 0
oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2)				; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.882316; ----CyAGTGTGCm ; cor=; Ncor= a 0 0 0 0 0 0 3 0 0 0 0 0 0 2 c 0 0 0 0 3 2 0 0 0 0 0 0 3 1 g 0 0 0 0 0 0 0 3 0 3 0 3 0 0 t 0 0 0 0 0 1 0 0 3 0 3 0 0 0
oligos_7nt_mkv1_m3_rc_shift0 (oligos_7nt_mkv1_m3_rc)				; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m3_rc; m=3/3; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.597808; tsyCCCAGTGTgy- ; cor=; Ncor= a 1 2 1 0 0 0 8 0 1 0 2 1 2 0 c 2 4 5 8 9 8 1 0 0 0 0 2 4 0 g 1 3 0 0 0 0 0 9 0 9 0 6 0 0 t 5 0 3 1 0 1 0 0 8 0 7 0 3 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=12; shift=3; ncol=15; ---wkCCTTCCCCma ; Alignment reference a 0 0 0 3 1 0 0 0 0 0 0 0 0 2 2 c 0 0 0 0 0 5 5 0 0 5 5 5 4 2 1 g 0 0 0 0 2 0 0 0 0 0 0 0 0 1 1 t 0 0 0 2 2 0 0 5 5 0 0 0 1 0 1
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=3; score= 1; ---wkCCTTCCCCma ; cor=; Ncor= a 0 0 0 3 1 0 0 0 0 0 0 0 0 2 2 c 0 0 0 0 0 5 5 0 0 5 5 5 4 2 1 g 0 0 0 0 2 0 0 0 0 0 0 0 0 1 1 t 0 0 0 2 2 0 0 5 5 0 0 0 1 0 1
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)				; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=4; score=0.822016; ----dCCTTCCCcm- ; cor=; Ncor= a 0 0 0 0 2 0 0 0 0 0 0 0 1 2 0 c 0 0 0 0 0 5 6 0 0 6 6 6 4 2 0 g 0 0 0 0 2 1 0 0 0 0 0 0 0 1 0 t 0 0 0 0 2 0 0 6 6 0 0 0 1 1 0
oligos_7nt_mkv1_m5_rc_shift0 (oligos_7nt_mkv1_m5_rc)				; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m5_rc; m=3/3; ncol2=11; w=-3; offset=-3; strand=R; shift=0; score=0.422077; krTTACCTTyC---- ; cor=; Ncor= a 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 2 2 0 0 1 2 0 0 0 0 g 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 t 1 0 2 2 0 0 0 2 2 1 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=4; ncol=14; ----dCCTTCCCcm ; Alignment reference a 0 0 0 0 2 0 0 0 0 0 0 0 1 2 c 0 0 0 0 0 5 6 0 0 6 6 6 4 2 g 0 0 0 0 2 1 0 0 0 0 0 0 0 1 t 0 0 0 0 2 0 0 6 6 0 0 0 1 1
oligos_6nt_mkv1_m2_shift4 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=4; score= 1; ----dCCTTCCCcm ; cor=; Ncor= a 0 0 0 0 2 0 0 0 0 0 0 0 1 2 c 0 0 0 0 0 5 6 0 0 6 6 6 4 2 g 0 0 0 0 2 1 0 0 0 0 0 0 0 1 t 0 0 0 0 2 0 0 6 6 0 0 0 1 1
oligos_7nt_mkv1_m1_shift3 (oligos_7nt_mkv1_m1)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=3; score=0.822016; ---wkCCTTCCCCm ; cor=; Ncor= a 0 0 0 3 1 0 0 0 0 0 0 0 0 2 c 0 0 0 0 0 5 5 0 0 5 5 5 4 2 g 0 0 0 0 2 0 0 0 0 0 0 0 0 1 t 0 0 0 2 2 0 0 5 5 0 0 0 1 0
oligos_7nt_mkv1_m5_rc_shift0 (oligos_7nt_mkv1_m5_rc)				; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m5_rc; m=3/3; ncol2=11; w=-4; offset=-4; strand=R; shift=0; score=0.433037; krTTACCTTyC--- ; cor=; Ncor= a 0 1 0 0 2 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 2 2 0 0 1 2 0 0 0 g 1 1 0 0 0 0 0 0 0 0 0 0 0 0 t 1 0 2 2 0 0 0 2 2 1 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m4_shift2 (oligos_7nt_mkv1_m4)				; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --hmCCCGSCCWK ; Alignment reference a 0 0 1 2 0 0 0 0 0 0 0 3 0 c 0 0 1 2 4 4 4 0 3 4 4 0 0 g 0 0 0 0 0 0 0 4 1 0 0 0 3 t 0 0 2 0 0 0 0 0 0 0 0 1 1
oligos_7nt_mkv1_m4_shift2 (oligos_7nt_mkv1_m4)				; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --hmCCCGSCCWK ; cor=; Ncor= a 0 0 1 2 0 0 0 0 0 0 0 3 0 c 0 0 1 2 4 4 4 0 3 4 4 0 0 g 0 0 0 0 0 0 0 4 1 0 0 0 3 t 0 0 2 0 0 0 0 0 0 0 0 1 1
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)				; oligos_7nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=3; score=0.835305; ---cmCCGCCCwg ; cor=; Ncor= a 0 0 0 1 2 0 0 1 0 0 0 2 0 c 0 0 0 3 3 5 5 0 5 5 5 0 1 g 0 0 0 0 0 0 0 4 0 0 0 1 3 t 0 0 0 1 0 0 0 0 0 0 0 2 1
oligos_6nt_mkv1_m1_rc_shift0 (oligos_6nt_mkv1_m1_rc)				; oligos_7nt_mkv1_m4 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.515781; YbTCCCCGhv--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 1 0 0 0 c 1 1 0 4 4 4 4 0 2 2 0 0 0 g 0 2 0 0 0 0 0 4 0 1 0 0 0 t 3 1 4 0 0 0 0 0 1 0 0 0 0