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.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_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.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift2 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --msCTAGGCra ; Alignment reference a 0 0 16 10 0 0 46 1 2 1 16 18 c 0 0 18 14 46 0 2 3 1 45 10 11 g 0 0 8 14 2 0 0 42 41 0 12 10 t 0 0 6 10 0 48 0 2 4 2 10 9

MA1979.2_shift1 (ZNF416)
; oligos_6nt_mkv2_m4 versus MA1979.2 (ZNF416); m=1/4; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.577801; -TaTCTGGGCa- ; cor=; Ncor= a 0 47.0 197.0 48.0 1.0 2.0 1.0 2.0 0.0 4.0 212.0 0 c 0 32.0 25.0 28.0 334.0 6.0 7.0 5.0 1.0 320.0 38.0 0 g 0 26.0 77.0 15.0 7.0 1.0 335.0 335.0 341.0 3.0 29.0 0 t 0 240.0 46.0 254.0 3.0 336.0 2.0 3.0 3.0 18.0 66.0 0

MA1153.2_rc_shift4 (Smad4_rc)
; oligos_6nt_mkv2_m4 versus MA1153.2_rc (Smad4_rc); m=2/4; ncol2=7; w=0; offset=2; strand=R; shift=4; score=0.51455; ----CyAGACr- ; cor=; Ncor= a 0 0 0 0 0.0 0.0 1000.0 0.0 1000.0 0.0 581.0 0 c 0 0 0 0 1000.0 404.0 0.0 0.0 0.0 1000.0 81.0 0 g 0 0 0 0 0.0 0.0 0.0 1000.0 0.0 0.0 250.0 0 t 0 0 0 0 0.0 596.0 0.0 0.0 0.0 0.0 88.0 0

MA0161.3_shift4 (NFIC)
; oligos_6nt_mkv2_m4 versus MA0161.3 (NFIC); m=3/4; ncol2=7; w=0; offset=2; strand=D; shift=4; score=0.512735; ----CTTGGCA- ; cor=; Ncor= a 0 0 0 0 412.0 154.0 352.0 310.0 223.0 264.0 10158.0 0 c 0 0 0 0 10542.0 303.0 333.0 129.0 121.0 10725.0 397.0 0 g 0 0 0 0 329.0 369.0 177.0 11087.0 10973.0 88.0 478.0 0 t 0 0 0 0 324.0 10781.0 10745.0 81.0 290.0 530.0 574.0 0

MA1724.2_rc_shift0 (Rfx6_rc)
; oligos_6nt_mkv2_m4 versus MA1724.2_rc (Rfx6_rc); m=4/4; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.456973; GTTGCTAGG--- ; cor=; Ncor= a 635.0 213.0 216.0 339.0 54.0 66.0 6994.0 810.0 272.0 0 0 0 c 552.0 339.0 132.0 359.0 8215.0 1205.0 146.0 242.0 232.0 0 0 0 g 6811.0 258.0 117.0 7474.0 102.0 64.0 1066.0 6405.0 7859.0 0 0 0 t 552.0 7740.0 8085.0 378.0 179.0 7215.0 344.0 1093.0 187.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift2 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --msCTAGGCra ; Alignment reference a 0 0 16 10 0 0 46 1 2 1 16 18 c 0 0 18 14 46 0 2 3 1 45 10 11 g 0 0 8 14 2 0 0 42 41 0 12 10 t 0 0 6 10 0 48 0 2 4 2 10 9
MA1979.2_shift1 (ZNF416)				; oligos_6nt_mkv2_m4 versus MA1979.2 (ZNF416); m=1/4; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.577801; -TaTCTGGGCa- ; cor=; Ncor= a 0 47.0 197.0 48.0 1.0 2.0 1.0 2.0 0.0 4.0 212.0 0 c 0 32.0 25.0 28.0 334.0 6.0 7.0 5.0 1.0 320.0 38.0 0 g 0 26.0 77.0 15.0 7.0 1.0 335.0 335.0 341.0 3.0 29.0 0 t 0 240.0 46.0 254.0 3.0 336.0 2.0 3.0 3.0 18.0 66.0 0
MA1153.2_rc_shift4 (Smad4_rc)				; oligos_6nt_mkv2_m4 versus MA1153.2_rc (Smad4_rc); m=2/4; ncol2=7; w=0; offset=2; strand=R; shift=4; score=0.51455; ----CyAGACr- ; cor=; Ncor= a 0 0 0 0 0.0 0.0 1000.0 0.0 1000.0 0.0 581.0 0 c 0 0 0 0 1000.0 404.0 0.0 0.0 0.0 1000.0 81.0 0 g 0 0 0 0 0.0 0.0 0.0 1000.0 0.0 0.0 250.0 0 t 0 0 0 0 0.0 596.0 0.0 0.0 0.0 0.0 88.0 0
MA0161.3_shift4 (NFIC)				; oligos_6nt_mkv2_m4 versus MA0161.3 (NFIC); m=3/4; ncol2=7; w=0; offset=2; strand=D; shift=4; score=0.512735; ----CTTGGCA- ; cor=; Ncor= a 0 0 0 0 412.0 154.0 352.0 310.0 223.0 264.0 10158.0 0 c 0 0 0 0 10542.0 303.0 333.0 129.0 121.0 10725.0 397.0 0 g 0 0 0 0 329.0 369.0 177.0 11087.0 10973.0 88.0 478.0 0 t 0 0 0 0 324.0 10781.0 10745.0 81.0 290.0 530.0 574.0 0
MA1724.2_rc_shift0 (Rfx6_rc)				; oligos_6nt_mkv2_m4 versus MA1724.2_rc (Rfx6_rc); m=4/4; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.456973; GTTGCTAGG--- ; cor=; Ncor= a 635.0 213.0 216.0 339.0 54.0 66.0 6994.0 810.0 272.0 0 0 0 c 552.0 339.0 132.0 359.0 8215.0 1205.0 146.0 242.0 232.0 0 0 0 g 6811.0 258.0 117.0 7474.0 102.0 64.0 1066.0 6405.0 7859.0 0 0 0 t 552.0 7740.0 8085.0 378.0 179.0 7215.0 344.0 1093.0 187.0 0 0 0