One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/Homer/Homer_motifs.tf -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/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_7nt_mkv4_m4/peak-motifs_oligos_7nt_mkv4_m4_vs_db_Homer

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift3 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---dtAAAGGCAyr ; Alignment reference a 0 0 0 52 44 181 150 181 3 16 4 187 39 66 c 0 0 0 30 30 3 25 3 3 2 179 0 50 33 g 0 0 0 49 30 1 4 2 179 162 3 3 38 49 t 0 0 0 63 90 9 15 8 9 14 8 4 67 46

homer_289_Tcf4_shift0 (homer_289_Tcf4)
; oligos_7nt_mkv4_m4 versus homer_289_Tcf4; m=1/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.453389; AsWTCAAAGgva-- ; cor=; Ncor= a 83.2 0.5 73.7 2.2 0.1 99.7 98.9 99.5 5.8 20.3 28 44.5 0 0 c 1.3 50.1 0.2 0.2 90.1 0.1 0.5 0.1 0.1 13.5 30.7 19.7 0 0 g 9.7 48.5 0.1 0.1 9.5 0.1 0.5 0.3 94 59.2 35.6 16.5 0 0 t 5.8 0.9 26 97.5 0.3 0.1 0.1 0.1 0.1 7 5.7 19.3 0 0

homer_262_Sox3_rc_shift2 (homer_262_Sox3_rc)
; oligos_7nt_mkv4_m4 versus homer_262_Sox3_rc; m=2/3; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.414101; --rACAAwRG---- ; cor=; Ncor= a 0 0 40.9 83 12.3 99.7 99.7 51.7 26 13.9 0 0 0 0 c 0 0 18.5 11.3 84.3 0.1 0.1 0.1 0.3 14.7 0 0 0 0 g 0 0 33 0.1 2.7 0.1 0.1 0.1 70.5 69.5 0 0 0 0 t 0 0 7.6 5.6 0.7 0.1 0.1 48.1 3.2 1.9 0 0 0 0

homer_290_TCFL2_shift0 (homer_290_TCFL2)
; oligos_7nt_mkv4_m4 versus homer_290_TCFL2; m=3/3; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.400889; ASwTCAAAGG---- ; cor=; Ncor= a 506.48 0.51 252.48 0.51 0.51 506.48 506.48 506.48 9.65 0.51 0 0 0 0 c 0.51 350.52 0.51 0.51 506.48 0.51 0.51 0.51 0.51 100.08 0 0 0 0 g 0.51 156.46 0.51 0.51 0.51 0.51 0.51 0.51 497.33 406.91 0 0 0 0 t 0.51 0.51 254.51 506.48 0.51 0.51 0.51 0.51 0.51 0.51 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift3 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---dtAAAGGCAyr ; Alignment reference a 0 0 0 52 44 181 150 181 3 16 4 187 39 66 c 0 0 0 30 30 3 25 3 3 2 179 0 50 33 g 0 0 0 49 30 1 4 2 179 162 3 3 38 49 t 0 0 0 63 90 9 15 8 9 14 8 4 67 46
homer_289_Tcf4_shift0 (homer_289_Tcf4)				; oligos_7nt_mkv4_m4 versus homer_289_Tcf4; m=1/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.453389; AsWTCAAAGgva-- ; cor=; Ncor= a 83.2 0.5 73.7 2.2 0.1 99.7 98.9 99.5 5.8 20.3 28 44.5 0 0 c 1.3 50.1 0.2 0.2 90.1 0.1 0.5 0.1 0.1 13.5 30.7 19.7 0 0 g 9.7 48.5 0.1 0.1 9.5 0.1 0.5 0.3 94 59.2 35.6 16.5 0 0 t 5.8 0.9 26 97.5 0.3 0.1 0.1 0.1 0.1 7 5.7 19.3 0 0
homer_262_Sox3_rc_shift2 (homer_262_Sox3_rc)				; oligos_7nt_mkv4_m4 versus homer_262_Sox3_rc; m=2/3; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.414101; --rACAAwRG---- ; cor=; Ncor= a 0 0 40.9 83 12.3 99.7 99.7 51.7 26 13.9 0 0 0 0 c 0 0 18.5 11.3 84.3 0.1 0.1 0.1 0.3 14.7 0 0 0 0 g 0 0 33 0.1 2.7 0.1 0.1 0.1 70.5 69.5 0 0 0 0 t 0 0 7.6 5.6 0.7 0.1 0.1 48.1 3.2 1.9 0 0 0 0
homer_290_TCFL2_shift0 (homer_290_TCFL2)				; oligos_7nt_mkv4_m4 versus homer_290_TCFL2; m=3/3; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.400889; ASwTCAAAGG---- ; cor=; Ncor= a 506.48 0.51 252.48 0.51 0.51 506.48 506.48 506.48 9.65 0.51 0 0 0 0 c 0.51 350.52 0.51 0.51 506.48 0.51 0.51 0.51 0.51 100.08 0 0 0 0 g 0.51 156.46 0.51 0.51 0.51 0.51 0.51 0.51 497.33 406.91 0 0 0 0 t 0.51 0.51 254.51 506.48 0.51 0.51 0.51 0.51 0.51 0.51 0 0 0 0