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_m4/peak-motifs_oligos_7nt_mkv2_m4.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_m4/peak-motifs_oligos_7nt_mkv2_m4_vs_db_cisBP_Caenorhabditis_elegans

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; TCTGGCTTCAym ; Alignment reference a 11 1 0 0 0 0 0 0 0 48 0 28 c 0 44 0 0 0 57 11 0 59 9 31 19 g 0 13 0 59 59 0 0 0 0 0 1 0 t 48 1 59 0 0 2 48 59 0 2 27 12

M00609_2.00_rc_shift0 (che-1_rc)
; oligos_7nt_mkv2_m4 versus M00609_2.00_rc (che-1_rc); m=1/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.657888; wagGGcTTCm-- ; cor=; Ncor= a 25.4183 47.4945 22.8171 7.68239 8.90882 14.5768 3.05199 0.728178 2.1474 28.5277 0 0 c 16.0462 13.6074 11.7931 2.50661 0.0088004 64.0352 0.79915 0.0136065 86.8567 33.4776 0 0 g 13.1375 21.7718 41.1618 77.3957 77.2496 2.48291 0.0100096 4.36139 2.95725 14.1664 0 0 t 45.3981 17.1263 24.228 12.4153 13.8328 18.9051 96.1389 94.8968 8.03864 23.8283 0 0

M01867_2.00_shift2 (ztf-28)
; oligos_7nt_mkv2_m4 versus M01867_2.00 (ztf-28); m=2/4; ncol2=10; w=0; offset=2; strand=D; shift=2; score= 0.6178; --rrGCTTcwtc ; cor=; Ncor= a 0 0 37.7203 39.8642 2.69874 4.31048 5.72006 1.71209 21.6595 50.6966 21.8415 18.2303 c 0 0 20.9094 6.02235 1.94019 92.8559 0.0207332 1.62859 48.6887 8.3801 24.3811 47.1383 g 0 0 30.8827 41.491 93.9522 0.896774 0.194754 1.29397 11.1948 5.90536 19.1789 21.3935 t 0 0 10.4876 12.6225 1.40887 1.93682 94.0644 95.3653 18.457 35.0179 34.5985 13.2379

M00624_2.00_shift2 (lsy-27)
; oligos_7nt_mkv2_m4 versus M00624_2.00 (lsy-27); m=3/4; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.600999; --rrGCTTcwsc ; cor=; Ncor= a 0 0 34.2803 38.5544 5.78911 0.318041 1.89381 0.95431 18.6879 44.7311 22.6935 22.0752 c 0 0 23.6786 9.2264 0.0559094 98.9312 0.0184736 0.0489593 45.9648 11.0305 28.2778 37.8813 g 0 0 26.1689 30.6327 93.3147 0.627774 0.710767 0.183275 11.1103 7.24759 27.4421 24.6421 t 0 0 15.8722 21.5865 0.840278 0.122999 97.377 98.8135 24.2369 36.9908 21.5867 15.4014

M08451_2.00_shift3 (che-1)
; oligos_7nt_mkv2_m4 versus M08451_2.00 (che-1); m=4/4; ncol2=6; w=0; offset=3; strand=D; shift=3; score=0.455367; ---SGyTTC--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 29.7297 0 48.6486 0 0 100 0 0 0 g 0 0 0 70.2703 100 0 0 0 0 0 0 0 t 0 0 0 0 0 51.3514 100 100 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; TCTGGCTTCAym ; Alignment reference a 11 1 0 0 0 0 0 0 0 48 0 28 c 0 44 0 0 0 57 11 0 59 9 31 19 g 0 13 0 59 59 0 0 0 0 0 1 0 t 48 1 59 0 0 2 48 59 0 2 27 12
M00609_2.00_rc_shift0 (che-1_rc)				; oligos_7nt_mkv2_m4 versus M00609_2.00_rc (che-1_rc); m=1/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.657888; wagGGcTTCm-- ; cor=; Ncor= a 25.4183 47.4945 22.8171 7.68239 8.90882 14.5768 3.05199 0.728178 2.1474 28.5277 0 0 c 16.0462 13.6074 11.7931 2.50661 0.0088004 64.0352 0.79915 0.0136065 86.8567 33.4776 0 0 g 13.1375 21.7718 41.1618 77.3957 77.2496 2.48291 0.0100096 4.36139 2.95725 14.1664 0 0 t 45.3981 17.1263 24.228 12.4153 13.8328 18.9051 96.1389 94.8968 8.03864 23.8283 0 0
M01867_2.00_shift2 (ztf-28)				; oligos_7nt_mkv2_m4 versus M01867_2.00 (ztf-28); m=2/4; ncol2=10; w=0; offset=2; strand=D; shift=2; score= 0.6178; --rrGCTTcwtc ; cor=; Ncor= a 0 0 37.7203 39.8642 2.69874 4.31048 5.72006 1.71209 21.6595 50.6966 21.8415 18.2303 c 0 0 20.9094 6.02235 1.94019 92.8559 0.0207332 1.62859 48.6887 8.3801 24.3811 47.1383 g 0 0 30.8827 41.491 93.9522 0.896774 0.194754 1.29397 11.1948 5.90536 19.1789 21.3935 t 0 0 10.4876 12.6225 1.40887 1.93682 94.0644 95.3653 18.457 35.0179 34.5985 13.2379
M00624_2.00_shift2 (lsy-27)				; oligos_7nt_mkv2_m4 versus M00624_2.00 (lsy-27); m=3/4; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.600999; --rrGCTTcwsc ; cor=; Ncor= a 0 0 34.2803 38.5544 5.78911 0.318041 1.89381 0.95431 18.6879 44.7311 22.6935 22.0752 c 0 0 23.6786 9.2264 0.0559094 98.9312 0.0184736 0.0489593 45.9648 11.0305 28.2778 37.8813 g 0 0 26.1689 30.6327 93.3147 0.627774 0.710767 0.183275 11.1103 7.24759 27.4421 24.6421 t 0 0 15.8722 21.5865 0.840278 0.122999 97.377 98.8135 24.2369 36.9908 21.5867 15.4014
M08451_2.00_shift3 (che-1)				; oligos_7nt_mkv2_m4 versus M08451_2.00 (che-1); m=4/4; ncol2=6; w=0; offset=3; strand=D; shift=3; score=0.455367; ---SGyTTC--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 29.7297 0 48.6486 0 0 100 0 0 0 g 0 0 0 70.2703 100 0 0 0 0 0 0 0 t 0 0 0 0 0 51.3514 100 100 0 0 0 0