One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184201_2025-05-16.184201_aBOVlS/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2025/05/16/peak-motifs.2025-05-16.184201_2025-05-16.184201_aBOVlS/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=11; shift=1; ncol=12; -aaAAAGCCGcg ; Alignment reference a 0 45 40 73 78 74 2 3 5 3 17 12 c 0 10 15 0 2 1 4 76 75 1 33 12 g 0 14 15 7 1 6 72 1 2 75 14 49 t 0 13 12 2 1 1 4 2 0 3 18 9

MA0442.3_shift1 (SOX10)
; oligos_7nt_mkv2_m4 versus MA0442.3 (SOX10); m=1/3; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.46273; -ACAAAG----- ; cor=; Ncor= a 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 0 0 c 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 0 0 g 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 0 0 t 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0 0 0

MA0146.3_rc_shift4 (Zfx_rc)
; oligos_7nt_mkv2_m4 versus MA0146.3_rc (Zfx_rc); m=2/3; ncol2=10; w=0; offset=3; strand=R; shift=4; score=0.433377; ----AGGCCbvG ; cor=; Ncor= a 0 0 0 0 480.0 1.0 0.0 1.0 1.0 15.0 144.0 112.0 c 0 0 0 0 0.0 0.0 0.0 477.0 470.0 122.0 183.0 2.0 g 0 0 0 0 1.0 480.0 481.0 3.0 2.0 153.0 124.0 361.0 t 0 0 0 0 0.0 0.0 0.0 0.0 8.0 191.0 30.0 6.0

MA0508.4_rc_shift0 (PRDM1_rc)
; oligos_7nt_mkv2_m4 versus MA0508.4_rc (PRDM1_rc); m=3/3; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.423864; GAGAAAG----- ; cor=; Ncor= a 660.0 49466.0 432.0 52619.0 50943.0 52905.0 829.0 0 0 0 0 0 c 290.0 1390.0 207.0 561.0 1011.0 826.0 701.0 0 0 0 0 0 g 52821.0 1076.0 53465.0 488.0 1346.0 467.0 52752.0 0 0 0 0 0 t 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0 1199.0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=11; shift=1; ncol=12; -aaAAAGCCGcg ; Alignment reference a 0 45 40 73 78 74 2 3 5 3 17 12 c 0 10 15 0 2 1 4 76 75 1 33 12 g 0 14 15 7 1 6 72 1 2 75 14 49 t 0 13 12 2 1 1 4 2 0 3 18 9
MA0442.3_shift1 (SOX10)				; oligos_7nt_mkv2_m4 versus MA0442.3 (SOX10); m=1/3; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.46273; -ACAAAG----- ; cor=; Ncor= a 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 0 0 c 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 0 0 g 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 0 0 t 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0 0 0
MA0146.3_rc_shift4 (Zfx_rc)				; oligos_7nt_mkv2_m4 versus MA0146.3_rc (Zfx_rc); m=2/3; ncol2=10; w=0; offset=3; strand=R; shift=4; score=0.433377; ----AGGCCbvG ; cor=; Ncor= a 0 0 0 0 480.0 1.0 0.0 1.0 1.0 15.0 144.0 112.0 c 0 0 0 0 0.0 0.0 0.0 477.0 470.0 122.0 183.0 2.0 g 0 0 0 0 1.0 480.0 481.0 3.0 2.0 153.0 124.0 361.0 t 0 0 0 0 0.0 0.0 0.0 0.0 8.0 191.0 30.0 6.0
MA0508.4_rc_shift0 (PRDM1_rc)				; oligos_7nt_mkv2_m4 versus MA0508.4_rc (PRDM1_rc); m=3/3; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.423864; GAGAAAG----- ; cor=; Ncor= a 660.0 49466.0 432.0 52619.0 50943.0 52905.0 829.0 0 0 0 0 0 c 290.0 1390.0 207.0 561.0 1011.0 826.0 701.0 0 0 0 0 0 g 52821.0 1076.0 53465.0 488.0 1346.0 467.0 52752.0 0 0 0 0 0 t 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0 1199.0 0 0 0 0 0