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_m3/peak-motifs_oligos_7nt_mkv2_m3.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_m3/peak-motifs_oligos_7nt_mkv2_m3_vs_db_cisBP_Caenorhabditis_elegans

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; mhGCACTCCGy ; Alignment reference a 32 19 16 0 72 16 0 0 0 4 18 c 33 32 0 75 3 54 0 75 75 3 19 g 3 1 59 0 0 3 0 0 0 52 3 t 7 23 0 0 0 2 75 0 0 16 35

M05824_2.00_rc_shift1 (egl-44_rc)
; oligos_7nt_mkv2_m3 versus M05824_2.00_rc (egl-44_rc); m=1/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.684183; -crCATTCCaw ; cor=; Ncor= a 0 8.59961 49.0702 0 99.8326 0 17.1059 0 0 57.1327 28.37 c 0 59.5661 0.216472 100 0.118145 0 0 99.5582 96.8112 0.797347 24.6524 g 0 10.9467 50.7134 0 0.0492271 0 0.921584 0.441826 0.496467 19.1442 16.0536 t 0 20.8876 0 0 0 100 81.9725 0 2.69238 22.9257 30.924

M03995_2.00_rc_shift0 (egl-44_rc)
; oligos_7nt_mkv2_m3 versus M03995_2.00_rc (egl-44_rc); m=2/7; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.673047; ccrCATTCCw- ; cor=; Ncor= a 18.4925 11.5686 46.7626 8.40052 99.1037 0 20.5274 0.112786 0 54.5111 0 c 41.1324 55.3848 0.406392 90.8234 0 0 0 99.1582 99.0574 2.75232 0 g 18.9281 12.1484 52.2187 0.776053 0.896294 0 2.38039 0.321853 0.104427 16.0557 0 t 21.447 20.8983 0.612335 0 0 100 77.0922 0.40713 0.838165 26.6809 0

M03996_2.00_rc_shift0 (egl-44_rc)
; oligos_7nt_mkv2_m3 versus M03996_2.00_rc (egl-44_rc); m=3/7; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.672893; ycrCATTCCww ; cor=; Ncor= a 18.7614 11.2376 49.4598 5.73884 99.5802 0.0210194 12.9367 0.370561 0 63.2431 32.0922 c 37.8144 52.5275 0.561093 94.1058 0.174905 0.115607 0.252131 97.6737 99.3335 1.35742 19.7134 g 18.094 11.5748 49.7491 0.155372 0.244867 0.136626 1.36571 0.408303 0.279154 9.40416 10.6541 t 25.3302 24.6601 0.230013 0 0 99.7267 85.4454 1.54744 0.380348 25.9953 37.5404

M05823_2.00_rc_shift1 (egl-44_rc)
; oligos_7nt_mkv2_m3 versus M05823_2.00_rc (egl-44_rc); m=4/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.671161; -crCATTCCww ; cor=; Ncor= a 0 10.6867 50.811 7.11351 99.9705 0 16.1711 0 0 58.3822 26.7682 c 0 55.685 0 92.8865 0 0 0 100 95.4624 0.642463 24.6547 g 0 11.4732 49.189 0 0.029484 0 0.625741 0 0 11.6376 16.9673 t 0 22.155 0 0 0 100 83.2031 0 4.53756 29.3377 31.6097

M05826_2.00_rc_shift1 (egl-44_rc)
; oligos_7nt_mkv2_m3 versus M05826_2.00_rc (egl-44_rc); m=5/7; ncol2=9; w=0; offset=1; strand=R; shift=1; score=0.58862; -crCATwCCd- ; cor=; Ncor= a 0 13.0974 46.3913 2.60955 100 0 39.0024 0.796432 1.32194 41.007 0 c 0 50.1898 1.6542 97.3905 0 0 0 95.1152 89.0269 8.02724 0 g 0 14.1469 47.9823 0 0 0 10.2865 4.08835 0 25.935 0 t 0 22.5659 3.97218 0 0 100 50.7111 0 9.65113 25.0307 0

M05825_2.00_rc_shift1 (egl-44_rc)
; oligos_7nt_mkv2_m3 versus M05825_2.00_rc (egl-44_rc); m=6/7; ncol2=9; w=0; offset=1; strand=R; shift=1; score=0.587413; -crCATwCCr- ; cor=; Ncor= a 0 13.1722 40.6114 1.16064 92.5142 0 39.9864 0.743938 0 41.7801 0 c 0 45.4563 3.11259 98.8394 0 0 0 93.0749 92.0854 4.92402 0 g 0 17.849 52.9879 0 7.48585 0 13.5988 6.18112 0.417992 29.1889 0 t 0 23.5224 3.28808 0 0 100 46.4149 0 7.49659 24.107 0

M03576_2.00_rc_shift2 (egl-44_rc)
; oligos_7nt_mkv2_m3 versus M03576_2.00_rc (egl-44_rc); m=7/7; ncol2=8; w=0; offset=2; strand=R; shift=2; score=0.534359; --rCATTCCw- ; cor=; Ncor= a 0 0 55.3984 11.533 100 0 20.3512 0 0 47.8661 0 c 0 0 0.291803 86.4519 0 0 0.102514 100 99.9814 2.3192 0 g 0 0 39.4067 2.01508 0 0 4.31895 0 0 19.317 0 t 0 0 4.90317 0 0 100 75.2273 0 0.0186498 30.4978 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; mhGCACTCCGy ; Alignment reference a 32 19 16 0 72 16 0 0 0 4 18 c 33 32 0 75 3 54 0 75 75 3 19 g 3 1 59 0 0 3 0 0 0 52 3 t 7 23 0 0 0 2 75 0 0 16 35
M05824_2.00_rc_shift1 (egl-44_rc)				; oligos_7nt_mkv2_m3 versus M05824_2.00_rc (egl-44_rc); m=1/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.684183; -crCATTCCaw ; cor=; Ncor= a 0 8.59961 49.0702 0 99.8326 0 17.1059 0 0 57.1327 28.37 c 0 59.5661 0.216472 100 0.118145 0 0 99.5582 96.8112 0.797347 24.6524 g 0 10.9467 50.7134 0 0.0492271 0 0.921584 0.441826 0.496467 19.1442 16.0536 t 0 20.8876 0 0 0 100 81.9725 0 2.69238 22.9257 30.924
M03995_2.00_rc_shift0 (egl-44_rc)				; oligos_7nt_mkv2_m3 versus M03995_2.00_rc (egl-44_rc); m=2/7; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.673047; ccrCATTCCw- ; cor=; Ncor= a 18.4925 11.5686 46.7626 8.40052 99.1037 0 20.5274 0.112786 0 54.5111 0 c 41.1324 55.3848 0.406392 90.8234 0 0 0 99.1582 99.0574 2.75232 0 g 18.9281 12.1484 52.2187 0.776053 0.896294 0 2.38039 0.321853 0.104427 16.0557 0 t 21.447 20.8983 0.612335 0 0 100 77.0922 0.40713 0.838165 26.6809 0
M03996_2.00_rc_shift0 (egl-44_rc)				; oligos_7nt_mkv2_m3 versus M03996_2.00_rc (egl-44_rc); m=3/7; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.672893; ycrCATTCCww ; cor=; Ncor= a 18.7614 11.2376 49.4598 5.73884 99.5802 0.0210194 12.9367 0.370561 0 63.2431 32.0922 c 37.8144 52.5275 0.561093 94.1058 0.174905 0.115607 0.252131 97.6737 99.3335 1.35742 19.7134 g 18.094 11.5748 49.7491 0.155372 0.244867 0.136626 1.36571 0.408303 0.279154 9.40416 10.6541 t 25.3302 24.6601 0.230013 0 0 99.7267 85.4454 1.54744 0.380348 25.9953 37.5404
M05823_2.00_rc_shift1 (egl-44_rc)				; oligos_7nt_mkv2_m3 versus M05823_2.00_rc (egl-44_rc); m=4/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.671161; -crCATTCCww ; cor=; Ncor= a 0 10.6867 50.811 7.11351 99.9705 0 16.1711 0 0 58.3822 26.7682 c 0 55.685 0 92.8865 0 0 0 100 95.4624 0.642463 24.6547 g 0 11.4732 49.189 0 0.029484 0 0.625741 0 0 11.6376 16.9673 t 0 22.155 0 0 0 100 83.2031 0 4.53756 29.3377 31.6097
M05826_2.00_rc_shift1 (egl-44_rc)				; oligos_7nt_mkv2_m3 versus M05826_2.00_rc (egl-44_rc); m=5/7; ncol2=9; w=0; offset=1; strand=R; shift=1; score=0.58862; -crCATwCCd- ; cor=; Ncor= a 0 13.0974 46.3913 2.60955 100 0 39.0024 0.796432 1.32194 41.007 0 c 0 50.1898 1.6542 97.3905 0 0 0 95.1152 89.0269 8.02724 0 g 0 14.1469 47.9823 0 0 0 10.2865 4.08835 0 25.935 0 t 0 22.5659 3.97218 0 0 100 50.7111 0 9.65113 25.0307 0
M05825_2.00_rc_shift1 (egl-44_rc)				; oligos_7nt_mkv2_m3 versus M05825_2.00_rc (egl-44_rc); m=6/7; ncol2=9; w=0; offset=1; strand=R; shift=1; score=0.587413; -crCATwCCr- ; cor=; Ncor= a 0 13.1722 40.6114 1.16064 92.5142 0 39.9864 0.743938 0 41.7801 0 c 0 45.4563 3.11259 98.8394 0 0 0 93.0749 92.0854 4.92402 0 g 0 17.849 52.9879 0 7.48585 0 13.5988 6.18112 0.417992 29.1889 0 t 0 23.5224 3.28808 0 0 100 46.4149 0 7.49659 24.107 0
M03576_2.00_rc_shift2 (egl-44_rc)				; oligos_7nt_mkv2_m3 versus M03576_2.00_rc (egl-44_rc); m=7/7; ncol2=8; w=0; offset=2; strand=R; shift=2; score=0.534359; --rCATTCCw- ; cor=; Ncor= a 0 0 55.3984 11.533 100 0 20.3512 0 0 47.8661 0 c 0 0 0.291803 86.4519 0 0 0.102514 100 99.9814 2.3192 0 g 0 0 39.4067 2.01508 0 0 4.31895 0 0 19.317 0 t 0 0 4.90317 0 0 100 75.2273 0 0.0186498 30.4978 0