One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.014834_2026-04-21.014834_X2uSrl/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/cisBP2/cisBP_Caenorhabditis_elegans_2019.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/2026/04/21/peak-motifs.2026-04-21.014834_2026-04-21.014834_X2uSrl/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_cisBP_Caenorhabditis_elegans

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 6 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=11; shift=0; ncol=11; wAATACTAAwa ; Alignment reference a 48 118 138 2 162 0 16 169 141 73 86 c 37 17 0 0 0 173 2 2 6 6 35 g 3 6 5 27 0 0 0 2 12 9 25 t 85 32 30 144 11 0 155 0 14 85 27

M00651_2.00_rc_shift0 (mex-6_rc)
; oligos_7nt_mkv2_m1 versus M00651_2.00_rc (mex-6_rc); m=1/5; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.667066; waATAATAAr- ; cor=; Ncor= a 29.2863 66.3373 79.0552 17.5069 99.9633 99.9633 12.0422 99.9633 76.2969 39.2485 0 c 20.5145 8.16601 12.1974 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 4.49775 16.8462 0 g 20.5145 8.16601 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 14.7076 27.0591 0 t 29.6848 17.3306 8.73512 82.4686 0.0122303 0.0122303 87.9333 0.0122303 4.49775 16.8462 0

M06329_2.00_shift3 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15)
; oligos_7nt_mkv2_m1 versus M06329_2.00 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15); m=2/5; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.477299; ---yryTAATk ; cor=; Ncor= a 0 0 0 4.7619 42.8571 0 0 100 100 0 0 c 0 0 0 42.8571 19.0476 57.1429 0 0 0 0 0 g 0 0 0 9.52381 28.5714 0 0 0 0 4.7619 38.0952 t 0 0 0 42.8571 9.52381 42.8571 100 0 0 95.2381 61.9048

M02745_2.00_shift3 (mef-2)
; oligos_7nt_mkv2_m1 versus M02745_2.00 (mef-2); m=3/5; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.464342; ---TaCTAwAA ; cor=; Ncor= a 0 0 0 2.00391 61.8663 0.100301 0.100301 99.5994 62.6062 97.5478 96.6942 c 0 0 0 0.342131 0.870918 99.7492 0.0501505 0.0500751 0.125905 0 0.194458 g 0 0 0 0.439883 12.4106 0.100301 0.100301 0.2003 0.283286 0.147131 0.0486145 t 0 0 0 97.2141 24.8523 0.0501505 99.7492 0.150225 36.9846 2.30505 3.06271

M00282_2.00_rc_shift4 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-43,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15_rc)
; oligos_7nt_mkv2_m1 versus M00282_2.00_rc (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-43,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15_rc); m=4/5; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.425346; ----acYAATT ; cor=; Ncor= a 0 0 0 0 57.8256 10.7347 0.0285388 99.919 99.919 0.0269978 0.0269978 c 0 0 0 0 10.5567 64.2297 25.7135 0.0269978 0.0269978 0.0269978 2.72678 g 0 0 0 0 21.0609 10.7347 0.0285388 0.0269978 0.0269978 0.0269978 0.0269978 t 0 0 0 0 10.5567 14.301 74.2295 0.0269978 0.0269978 99.919 97.2192

M06350_2.00_shift4 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15)
; oligos_7nt_mkv2_m1 versus M06350_2.00 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15); m=5/5; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.410441; ----ayTAATT ; cor=; Ncor= a 0 0 0 0 55 10 0 90 100 0 0 c 0 0 0 0 10 45 0 0 0 0 0 g 0 0 0 0 20 15 0 0 0 0 5 t 0 0 0 0 15 30 100 10 0 100 95

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=11; shift=0; ncol=11; wAATACTAAwa ; Alignment reference a 48 118 138 2 162 0 16 169 141 73 86 c 37 17 0 0 0 173 2 2 6 6 35 g 3 6 5 27 0 0 0 2 12 9 25 t 85 32 30 144 11 0 155 0 14 85 27
M00651_2.00_rc_shift0 (mex-6_rc)				; oligos_7nt_mkv2_m1 versus M00651_2.00_rc (mex-6_rc); m=1/5; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.667066; waATAATAAr- ; cor=; Ncor= a 29.2863 66.3373 79.0552 17.5069 99.9633 99.9633 12.0422 99.9633 76.2969 39.2485 0 c 20.5145 8.16601 12.1974 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 4.49775 16.8462 0 g 20.5145 8.16601 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 0.0122303 14.7076 27.0591 0 t 29.6848 17.3306 8.73512 82.4686 0.0122303 0.0122303 87.9333 0.0122303 4.49775 16.8462 0
M06329_2.00_shift3 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15)				; oligos_7nt_mkv2_m1 versus M06329_2.00 (alr-1,ceh-1,ceh-12,ceh-13,ceh-16,ceh-17,ceh-2,ceh-43,ceh-7,ceh-8,ceh-9,mls-2,tab-1,unc-4,unc-42,vab-15); m=2/5; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.477299; ---yryTAATk ; cor=; Ncor= a 0 0 0 4.7619 42.8571 0 0 100 100 0 0 c 0 0 0 42.8571 19.0476 57.1429 0 0 0 0 0 g 0 0 0 9.52381 28.5714 0 0 0 0 4.7619 38.0952 t 0 0 0 42.8571 9.52381 42.8571 100 0 0 95.2381 61.9048
M02745_2.00_shift3 (mef-2)				; oligos_7nt_mkv2_m1 versus M02745_2.00 (mef-2); m=3/5; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.464342; ---TaCTAwAA ; cor=; Ncor= a 0 0 0 2.00391 61.8663 0.100301 0.100301 99.5994 62.6062 97.5478 96.6942 c 0 0 0 0.342131 0.870918 99.7492 0.0501505 0.0500751 0.125905 0 0.194458 g 0 0 0 0.439883 12.4106 0.100301 0.100301 0.2003 0.283286 0.147131 0.0486145 t 0 0 0 97.2141 24.8523 0.0501505 99.7492 0.150225 36.9846 2.30505 3.06271
M00282_2.00_rc_shift4 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-43,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15_rc)				; oligos_7nt_mkv2_m1 versus M00282_2.00_rc (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-43,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15_rc); m=4/5; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.425346; ----acYAATT ; cor=; Ncor= a 0 0 0 0 57.8256 10.7347 0.0285388 99.919 99.919 0.0269978 0.0269978 c 0 0 0 0 10.5567 64.2297 25.7135 0.0269978 0.0269978 0.0269978 2.72678 g 0 0 0 0 21.0609 10.7347 0.0285388 0.0269978 0.0269978 0.0269978 0.0269978 t 0 0 0 0 10.5567 14.301 74.2295 0.0269978 0.0269978 99.919 97.2192
M06350_2.00_shift4 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15)				; oligos_7nt_mkv2_m1 versus M06350_2.00 (alr-1,ceh-1,ceh-10,ceh-12,ceh-14,ceh-16,ceh-17,ceh-2,ceh-8,dsc-1,lim-6,lin-11,mec-3,tab-1,ttx-3,unc-4,unc-42,vab-15); m=5/5; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.410441; ----ayTAATT ; cor=; Ncor= a 0 0 0 0 55 10 0 90 100 0 0 c 0 0 0 0 10 45 0 0 0 0 0 g 0 0 0 0 20 15 0 0 0 0 5 t 0 0 0 0 15 30 100 10 0 100 95