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_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3.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_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_Homer

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ssCgCCCCGCCCsss ; Alignment reference a 33 30 17 22 8 15 11 8 12 7 13 13 23 35 33 c 124 125 206 45 229 211 218 231 35 242 235 233 84 124 112 g 87 96 46 197 37 47 49 36 228 33 34 30 151 90 96 t 47 40 22 27 17 18 13 16 16 9 9 15 33 42 50

homer_266_Sp1_shift2 (homer_266_Sp1)
; oligos_6nt_mkv3_m3 versus homer_266_Sp1; m=1/7; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.70989; --gGCCCCGCCCCc- ; cor=; Ncor= a 0 0 18.1 5 1.3 3.3 4.9 0.1 2.5 0.1 0.1 0.1 10.3 3.7 0 c 0 0 21.8 0.1 87 81.5 94.9 99.7 0.1 99.7 99.7 88.1 82.4 51.2 0 g 0 0 54.1 94.8 6.1 0.1 0.1 0.1 97.3 0.1 0.1 0.1 0.1 22.1 0 t 0 0 6 0.1 5.6 15.1 0.1 0.1 0.1 0.1 0.1 11.7 7.1 23 0

homer_146_KLF3_shift1 (homer_146_KLF3)
; oligos_6nt_mkv3_m3 versus homer_146_KLF3; m=2/7; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.69435; -yrrCYmCrCCChyb ; cor=; Ncor= a 0 846.28 967.73 1461.08 3.79 3.79 1548.36 3.79 1977.2 3.79 3.79 3.79 1168.86 645.15 751.41 c 0 1001.88 800.75 3.79 3783.61 2717.22 2239.05 3783.61 3.79 3783.61 3783.61 3783.61 1240.97 1240.97 979.11 g 0 823.51 1407.94 2326.34 3.79 3.79 3.79 3.79 1810.21 3.79 3.79 3.79 3.79 823.51 1073.98 t 0 1119.52 618.59 3.79 3.79 1070.19 3.79 3.79 3.79 3.79 3.79 3.79 1381.38 1085.37 990.5

homer_145_KLF14_rc_shift3 (homer_145_KLF14_rc)
; oligos_6nt_mkv3_m3 versus homer_145_KLF14_rc; m=3/7; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.668116; ---gcCmCgCCCmCy ; cor=; Ncor= a 0 0 0 5089.83 2407.76 1615.33 14995.2 152.39 7009.94 30.48 30.48 30.48 14781.8 1066.73 4724.09 c 0 0 0 5516.52 17860.1 23315.7 15208.5 29502.7 30.48 30386.6 30386.6 29350.3 12800.8 22767.1 12983.6 g 0 0 0 17646.8 3687.84 487.65 182.87 30.48 19140.2 30.48 30.48 274.3 243.82 1493.42 2316.33 t 0 0 0 2224.89 6522.29 5059.35 91.43 792.43 4297.4 30.48 30.48 822.91 2621.11 5150.78 10454

homer_149_Klf9_shift3 (homer_149_Klf9)
; oligos_6nt_mkv3_m3 versus homer_149_Klf9; m=4/7; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.603905; ---GCCACrCCCMCy ; cor=; Ncor= a 0 0 0 12 11.2 0.5 79.4 0.5 42.8 0.2 0.1 0.1 70.1 0.9 12.7 c 0 0 0 2.4 81.9 99 19.1 99 0.1 99.6 99.5 98.2 26.1 90.6 36.2 g 0 0 0 83.3 4.3 0.1 1.2 0.2 52.8 0.1 0.3 0.1 0.1 2 4.7 t 0 0 0 2.3 2.6 0.4 0.3 0.3 4.3 0.1 0.1 1.6 3.7 6.5 46.5

homer_148_KLF5_rc_shift3 (homer_148_KLF5_rc)
; oligos_6nt_mkv3_m3 versus homer_148_KLF5_rc; m=5/7; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.553498; ---GCCmCrCCCw-- ; cor=; Ncor= a 0 0 0 14.8 18.4 2.2 52.6 1.2 49 0.1 0.1 0.1 35.7 0 0 c 0 0 0 1.9 69.4 92.2 40.5 97.2 0.1 99.7 99.7 88.2 22.4 0 0 g 0 0 0 75.6 6 0.1 2.3 0.1 42.8 0.1 0.1 0.1 5.5 0 0 t 0 0 0 7.7 6.2 5.5 4.6 1.5 8.1 0.1 0.1 11.6 36.4 0 0

homer_160_Maz_rc_shift4 (homer_160_Maz_rc)
; oligos_6nt_mkv3_m3 versus homer_160_Maz_rc; m=6/7; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.470177; ----CCCCcCCC--- ; cor=; Ncor= a 0 0 0 0 0.1 0.1 0.1 0.1 5.4 8.4 0.1 0.1 0 0 0 c 0 0 0 0 99.7 95.6 89.4 84.8 60.7 70.2 99.7 98.9 0 0 0 g 0 0 0 0 0.1 0.1 5.8 6.1 14.9 8.2 0.1 0.1 0 0 0 t 0 0 0 0 0.1 4.2 4.7 9 19 13.2 0.1 0.9 0 0 0

homer_63_Egr2_rc_shift5 (homer_63_Egr2_rc)
; oligos_6nt_mkv3_m3 versus homer_63_Egr2_rc; m=7/7; ncol2=12; w=0; offset=5; strand=R; shift=5; score=0.425711; -----cmCrCCCACr ; cor=; Ncor= a 0 0 0 0 0 20.4 32.9 1.4 25.3 0.1 0.1 0.1 86.1 0.1 25.5 c 0 0 0 0 0 35.7 51.3 95.3 0.1 99.7 99.7 94.3 13.7 99.7 3.5 g 0 0 0 0 0 19.2 6.6 0.1 58.7 0.1 0.1 0.1 0.1 0.1 55.2 t 0 0 0 0 0 24.8 9.2 3.2 15.9 0.1 0.1 5.5 0.1 0.1 15.8

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ssCgCCCCGCCCsss ; Alignment reference a 33 30 17 22 8 15 11 8 12 7 13 13 23 35 33 c 124 125 206 45 229 211 218 231 35 242 235 233 84 124 112 g 87 96 46 197 37 47 49 36 228 33 34 30 151 90 96 t 47 40 22 27 17 18 13 16 16 9 9 15 33 42 50
homer_266_Sp1_shift2 (homer_266_Sp1)				; oligos_6nt_mkv3_m3 versus homer_266_Sp1; m=1/7; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.70989; --gGCCCCGCCCCc- ; cor=; Ncor= a 0 0 18.1 5 1.3 3.3 4.9 0.1 2.5 0.1 0.1 0.1 10.3 3.7 0 c 0 0 21.8 0.1 87 81.5 94.9 99.7 0.1 99.7 99.7 88.1 82.4 51.2 0 g 0 0 54.1 94.8 6.1 0.1 0.1 0.1 97.3 0.1 0.1 0.1 0.1 22.1 0 t 0 0 6 0.1 5.6 15.1 0.1 0.1 0.1 0.1 0.1 11.7 7.1 23 0
homer_146_KLF3_shift1 (homer_146_KLF3)				; oligos_6nt_mkv3_m3 versus homer_146_KLF3; m=2/7; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.69435; -yrrCYmCrCCChyb ; cor=; Ncor= a 0 846.28 967.73 1461.08 3.79 3.79 1548.36 3.79 1977.2 3.79 3.79 3.79 1168.86 645.15 751.41 c 0 1001.88 800.75 3.79 3783.61 2717.22 2239.05 3783.61 3.79 3783.61 3783.61 3783.61 1240.97 1240.97 979.11 g 0 823.51 1407.94 2326.34 3.79 3.79 3.79 3.79 1810.21 3.79 3.79 3.79 3.79 823.51 1073.98 t 0 1119.52 618.59 3.79 3.79 1070.19 3.79 3.79 3.79 3.79 3.79 3.79 1381.38 1085.37 990.5
homer_145_KLF14_rc_shift3 (homer_145_KLF14_rc)				; oligos_6nt_mkv3_m3 versus homer_145_KLF14_rc; m=3/7; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.668116; ---gcCmCgCCCmCy ; cor=; Ncor= a 0 0 0 5089.83 2407.76 1615.33 14995.2 152.39 7009.94 30.48 30.48 30.48 14781.8 1066.73 4724.09 c 0 0 0 5516.52 17860.1 23315.7 15208.5 29502.7 30.48 30386.6 30386.6 29350.3 12800.8 22767.1 12983.6 g 0 0 0 17646.8 3687.84 487.65 182.87 30.48 19140.2 30.48 30.48 274.3 243.82 1493.42 2316.33 t 0 0 0 2224.89 6522.29 5059.35 91.43 792.43 4297.4 30.48 30.48 822.91 2621.11 5150.78 10454
homer_149_Klf9_shift3 (homer_149_Klf9)				; oligos_6nt_mkv3_m3 versus homer_149_Klf9; m=4/7; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.603905; ---GCCACrCCCMCy ; cor=; Ncor= a 0 0 0 12 11.2 0.5 79.4 0.5 42.8 0.2 0.1 0.1 70.1 0.9 12.7 c 0 0 0 2.4 81.9 99 19.1 99 0.1 99.6 99.5 98.2 26.1 90.6 36.2 g 0 0 0 83.3 4.3 0.1 1.2 0.2 52.8 0.1 0.3 0.1 0.1 2 4.7 t 0 0 0 2.3 2.6 0.4 0.3 0.3 4.3 0.1 0.1 1.6 3.7 6.5 46.5
homer_148_KLF5_rc_shift3 (homer_148_KLF5_rc)				; oligos_6nt_mkv3_m3 versus homer_148_KLF5_rc; m=5/7; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.553498; ---GCCmCrCCCw-- ; cor=; Ncor= a 0 0 0 14.8 18.4 2.2 52.6 1.2 49 0.1 0.1 0.1 35.7 0 0 c 0 0 0 1.9 69.4 92.2 40.5 97.2 0.1 99.7 99.7 88.2 22.4 0 0 g 0 0 0 75.6 6 0.1 2.3 0.1 42.8 0.1 0.1 0.1 5.5 0 0 t 0 0 0 7.7 6.2 5.5 4.6 1.5 8.1 0.1 0.1 11.6 36.4 0 0
homer_160_Maz_rc_shift4 (homer_160_Maz_rc)				; oligos_6nt_mkv3_m3 versus homer_160_Maz_rc; m=6/7; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.470177; ----CCCCcCCC--- ; cor=; Ncor= a 0 0 0 0 0.1 0.1 0.1 0.1 5.4 8.4 0.1 0.1 0 0 0 c 0 0 0 0 99.7 95.6 89.4 84.8 60.7 70.2 99.7 98.9 0 0 0 g 0 0 0 0 0.1 0.1 5.8 6.1 14.9 8.2 0.1 0.1 0 0 0 t 0 0 0 0 0.1 4.2 4.7 9 19 13.2 0.1 0.9 0 0 0
homer_63_Egr2_rc_shift5 (homer_63_Egr2_rc)				; oligos_6nt_mkv3_m3 versus homer_63_Egr2_rc; m=7/7; ncol2=12; w=0; offset=5; strand=R; shift=5; score=0.425711; -----cmCrCCCACr ; cor=; Ncor= a 0 0 0 0 0 20.4 32.9 1.4 25.3 0.1 0.1 0.1 86.1 0.1 25.5 c 0 0 0 0 0 35.7 51.3 95.3 0.1 99.7 99.7 94.3 13.7 99.7 3.5 g 0 0 0 0 0 19.2 6.6 0.1 58.7 0.1 0.1 0.1 0.1 0.1 55.2 t 0 0 0 0 0 24.8 9.2 3.2 15.9 0.1 0.1 5.5 0.1 0.1 15.8