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.2026-04-21.022353_2026-04-21.022353_CcghX5/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.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.2026-04-21.022353_2026-04-21.022353_CcghX5/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_cisBP_Caenorhabditis_elegans

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -TtTGGTGAAck ; Alignment reference a 0 19 29 3 16 3 0 0 136 151 32 21 c 0 4 22 3 0 3 0 0 0 0 101 8 g 0 18 4 0 131 147 5 150 16 2 10 83 t 0 112 98 147 6 0 148 3 1 0 10 41

M00629_2.00_shift0 (ztf-27)
; oligos_7nt_mkv2_m2 versus M00629_2.00 (ztf-27); m=1/4; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score=0.505418; bwwkGGyG---- ; cor=; Ncor= a 22.932 26.9109 34.237 5.87054 0.294779 2.59287 0.0100182 2.27366 0 0 0 0 c 25.5984 24.35 10.626 0.522018 0.0705432 0.0737382 36.1129 0.0293457 0 0 0 0 g 26.378 23.3953 18.4176 34.4651 92.6167 93.0155 0.0197748 97.65 0 0 0 0 t 25.0916 25.3438 36.7194 59.1423 7.01794 4.31789 63.8573 0.0469529 0 0 0 0

M08195_2.00_rc_shift4 (blmp-1_rc)
; oligos_7nt_mkv2_m2 versus M08195_2.00_rc (blmp-1_rc); m=2/4; ncol2=10; w=0; offset=3; strand=R; shift=4; score=0.460651; ----RGtGAAAG ; cor=; Ncor= a 0 0 0 0 68.6047 0 17.4419 3.4884 97.093 92.4418 96.5116 0 c 0 0 0 0 0 0 22.6744 0 2.907 0 3.4884 0 g 0 0 0 0 31.3953 90.6977 6.9767 96.5116 0 2.907 0 94.7674 t 0 0 0 0 0 9.3023 52.907 0 0 4.6512 0 5.2326

M02403_2.00_rc_shift5 (nhr-91_rc)
; oligos_7nt_mkv2_m2 versus M02403_2.00_rc (nhr-91_rc); m=3/4; ncol2=7; w=0; offset=4; strand=R; shift=5; score=0.446984; -----ryGamCy ; cor=; Ncor= a 0 0 0 0 0 34.3482 1.82241 19.6315 63.745 50.8264 15.3486 10.9046 c 0 0 0 0 0 15.7454 35.1688 0.261097 11.1886 42.4538 68.7876 45.5669 g 0 0 0 0 0 25.7015 0.195961 75.727 8.54111 0.495799 6.36633 7.68432 t 0 0 0 0 0 24.2048 62.8128 4.38038 16.5253 6.22402 9.49745 35.8442

M05877_2.00_rc_shift6 (nhr-91_rc)
; oligos_7nt_mkv2_m2 versus M05877_2.00_rc (nhr-91_rc); m=4/4; ncol2=8; w=0; offset=5; strand=R; shift=6; score=0.405098; ------TGAACy ; cor=; Ncor= a 0 0 0 0 0 0 1.9 17.4 82.7 89 3.2 3.4 c 0 0 0 0 0 0 7.6 2.8 8.2 7 91.9 38.6 g 0 0 0 0 0 0 1.9 74.3 3.1 2.3 2.5 2.4 t 0 0 0 0 0 0 88.6 5.5 6.1 1.7 2.4 55.5

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -TtTGGTGAAck ; Alignment reference a 0 19 29 3 16 3 0 0 136 151 32 21 c 0 4 22 3 0 3 0 0 0 0 101 8 g 0 18 4 0 131 147 5 150 16 2 10 83 t 0 112 98 147 6 0 148 3 1 0 10 41
M00629_2.00_shift0 (ztf-27)				; oligos_7nt_mkv2_m2 versus M00629_2.00 (ztf-27); m=1/4; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score=0.505418; bwwkGGyG---- ; cor=; Ncor= a 22.932 26.9109 34.237 5.87054 0.294779 2.59287 0.0100182 2.27366 0 0 0 0 c 25.5984 24.35 10.626 0.522018 0.0705432 0.0737382 36.1129 0.0293457 0 0 0 0 g 26.378 23.3953 18.4176 34.4651 92.6167 93.0155 0.0197748 97.65 0 0 0 0 t 25.0916 25.3438 36.7194 59.1423 7.01794 4.31789 63.8573 0.0469529 0 0 0 0
M08195_2.00_rc_shift4 (blmp-1_rc)				; oligos_7nt_mkv2_m2 versus M08195_2.00_rc (blmp-1_rc); m=2/4; ncol2=10; w=0; offset=3; strand=R; shift=4; score=0.460651; ----RGtGAAAG ; cor=; Ncor= a 0 0 0 0 68.6047 0 17.4419 3.4884 97.093 92.4418 96.5116 0 c 0 0 0 0 0 0 22.6744 0 2.907 0 3.4884 0 g 0 0 0 0 31.3953 90.6977 6.9767 96.5116 0 2.907 0 94.7674 t 0 0 0 0 0 9.3023 52.907 0 0 4.6512 0 5.2326
M02403_2.00_rc_shift5 (nhr-91_rc)				; oligos_7nt_mkv2_m2 versus M02403_2.00_rc (nhr-91_rc); m=3/4; ncol2=7; w=0; offset=4; strand=R; shift=5; score=0.446984; -----ryGamCy ; cor=; Ncor= a 0 0 0 0 0 34.3482 1.82241 19.6315 63.745 50.8264 15.3486 10.9046 c 0 0 0 0 0 15.7454 35.1688 0.261097 11.1886 42.4538 68.7876 45.5669 g 0 0 0 0 0 25.7015 0.195961 75.727 8.54111 0.495799 6.36633 7.68432 t 0 0 0 0 0 24.2048 62.8128 4.38038 16.5253 6.22402 9.49745 35.8442
M05877_2.00_rc_shift6 (nhr-91_rc)				; oligos_7nt_mkv2_m2 versus M05877_2.00_rc (nhr-91_rc); m=4/4; ncol2=8; w=0; offset=5; strand=R; shift=6; score=0.405098; ------TGAACy ; cor=; Ncor= a 0 0 0 0 0 0 1.9 17.4 82.7 89 3.2 3.4 c 0 0 0 0 0 0 7.6 2.8 8.2 7 91.9 38.6 g 0 0 0 0 0 0 1.9 74.3 3.1 2.3 2.5 2.4 t 0 0 0 0 0 0 88.6 5.5 6.1 1.7 2.4 55.5