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.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2.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.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m2/peak-motifs_oligos_7nt_mkv1_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; msAGACACACaC ; Alignment reference a 10 4 20 1 21 0 21 0 22 1 10 2 c 6 7 1 3 0 18 0 22 0 19 4 15 g 3 8 1 17 1 3 1 0 0 2 4 5 t 3 3 0 1 0 1 0 0 0 0 4 0

MA1107.3_shift3 (KLF9)
; oligos_7nt_mkv1_m2 versus MA1107.3 (KLF9); m=1/3; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.49671; ---gCCACACCC ; cor=; Ncor= a 0 0 0 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 c 0 0 0 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 g 0 0 0 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 t 0 0 0 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0

MA1153.2_rc_shift0 (Smad4_rc)
; oligos_7nt_mkv1_m2 versus MA1153.2_rc (Smad4_rc); m=2/3; ncol2=7; w=0; offset=0; strand=R; shift=0; score=0.467577; CyAGACr----- ; cor=; Ncor= a 0.0 0.0 1000.0 0.0 1000.0 0.0 581.0 0 0 0 0 0 c 1000.0 404.0 0.0 0.0 0.0 1000.0 81.0 0 0 0 0 0 g 0.0 0.0 0.0 1000.0 0.0 0.0 250.0 0 0 0 0 0 t 0.0 596.0 0.0 0.0 0.0 0.0 88.0 0 0 0 0 0

MA1964.2_shift0 (SMAD2)
; oligos_7nt_mkv1_m2 versus MA1964.2 (SMAD2); m=3/3; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.413237; CCAGAC------ ; cor=; Ncor= a 42.0 6.0 3447.0 7.0 3747.0 1.0 0 0 0 0 0 0 c 3610.0 3484.0 149.0 30.0 0.0 3757.0 0 0 0 0 0 0 g 86.0 171.0 154.0 3703.0 0.0 0.0 0 0 0 0 0 0 t 20.0 97.0 8.0 18.0 11.0 0.0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; msAGACACACaC ; Alignment reference a 10 4 20 1 21 0 21 0 22 1 10 2 c 6 7 1 3 0 18 0 22 0 19 4 15 g 3 8 1 17 1 3 1 0 0 2 4 5 t 3 3 0 1 0 1 0 0 0 0 4 0
MA1107.3_shift3 (KLF9)				; oligos_7nt_mkv1_m2 versus MA1107.3 (KLF9); m=1/3; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.49671; ---gCCACACCC ; cor=; Ncor= a 0 0 0 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 c 0 0 0 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 g 0 0 0 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 t 0 0 0 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0
MA1153.2_rc_shift0 (Smad4_rc)				; oligos_7nt_mkv1_m2 versus MA1153.2_rc (Smad4_rc); m=2/3; ncol2=7; w=0; offset=0; strand=R; shift=0; score=0.467577; CyAGACr----- ; cor=; Ncor= a 0.0 0.0 1000.0 0.0 1000.0 0.0 581.0 0 0 0 0 0 c 1000.0 404.0 0.0 0.0 0.0 1000.0 81.0 0 0 0 0 0 g 0.0 0.0 0.0 1000.0 0.0 0.0 250.0 0 0 0 0 0 t 0.0 596.0 0.0 0.0 0.0 0.0 88.0 0 0 0 0 0
MA1964.2_shift0 (SMAD2)				; oligos_7nt_mkv1_m2 versus MA1964.2 (SMAD2); m=3/3; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.413237; CCAGAC------ ; cor=; Ncor= a 42.0 6.0 3447.0 7.0 3747.0 1.0 0 0 0 0 0 0 c 3610.0 3484.0 149.0 30.0 0.0 3757.0 0 0 0 0 0 0 g 86.0 171.0 154.0 3703.0 0.0 0.0 0 0 0 0 0 0 t 20.0 97.0 8.0 18.0 11.0 0.0 0 0 0 0 0 0