One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/04/peak-motifs.2026-01-04.175405_2026-01-04.175405_YulKOI/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_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/2026/01/04/peak-motifs.2026-01-04.175405_2026-01-04.175405_YulKOI/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --asAGAGAGar ; Alignment reference a 0 0 3254 1954 7916 11 7890 19 7997 10 3447 2295 c 0 0 1515 2150 354 33 431 11 337 131 1538 1515 g 0 0 1957 3079 95 8316 25 8318 34 8234 1953 2927 t 0 0 1676 1219 37 42 56 54 34 27 1464 1665

MA1731.2_rc_shift3 (ZNF768_rc)
; oligos_6nt_test_vs_ctrl_m2 versus MA1731.2_rc (ZNF768_rc); m=1/3; ncol2=9; w=0; offset=1; strand=R; shift=3; score=0.766345; ---CAGAGAgGs ; cor=; Ncor= a 0 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 43.0 c 0 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 268.0 g 0 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 478.0 t 0 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0 211.0

MA0508.4_rc_shift3 (PRDM1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus MA0508.4_rc (PRDM1_rc); m=2/3; ncol2=7; w=0; offset=1; strand=R; shift=3; score=0.516452; ---GAGAAAG-- ; cor=; Ncor= a 0 0 0 660.0 49466.0 432.0 52619.0 50943.0 52905.0 829.0 0 0 c 0 0 0 290.0 1390.0 207.0 561.0 1011.0 826.0 701.0 0 0 g 0 0 0 52821.0 1076.0 53465.0 488.0 1346.0 467.0 52752.0 0 0 t 0 0 0 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0 1199.0 0 0

MA1982.2_shift0 (ZNF574)
; oligos_6nt_test_vs_ctrl_m2 versus MA1982.2 (ZNF574); m=3/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.510873; ksCTAGAGmGGC ; cor=; Ncor= a 97.0 33.0 68.0 43.0 997.0 1.0 983.0 58.0 302.0 19.0 58.0 121.0 c 26.0 409.0 877.0 231.0 1.0 4.0 8.0 12.0 512.0 15.0 118.0 802.0 g 618.0 540.0 54.0 19.0 1.0 994.0 8.0 930.0 129.0 965.0 689.0 12.0 t 260.0 19.0 1.0 707.0 1.0 1.0 1.0 1.0 58.0 1.0 136.0 65.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --asAGAGAGar ; Alignment reference a 0 0 3254 1954 7916 11 7890 19 7997 10 3447 2295 c 0 0 1515 2150 354 33 431 11 337 131 1538 1515 g 0 0 1957 3079 95 8316 25 8318 34 8234 1953 2927 t 0 0 1676 1219 37 42 56 54 34 27 1464 1665
MA1731.2_rc_shift3 (ZNF768_rc)				; oligos_6nt_test_vs_ctrl_m2 versus MA1731.2_rc (ZNF768_rc); m=1/3; ncol2=9; w=0; offset=1; strand=R; shift=3; score=0.766345; ---CAGAGAgGs ; cor=; Ncor= a 0 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 43.0 c 0 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 268.0 g 0 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 478.0 t 0 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0 211.0
MA0508.4_rc_shift3 (PRDM1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus MA0508.4_rc (PRDM1_rc); m=2/3; ncol2=7; w=0; offset=1; strand=R; shift=3; score=0.516452; ---GAGAAAG-- ; cor=; Ncor= a 0 0 0 660.0 49466.0 432.0 52619.0 50943.0 52905.0 829.0 0 0 c 0 0 0 290.0 1390.0 207.0 561.0 1011.0 826.0 701.0 0 0 g 0 0 0 52821.0 1076.0 53465.0 488.0 1346.0 467.0 52752.0 0 0 t 0 0 0 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0 1199.0 0 0
MA1982.2_shift0 (ZNF574)				; oligos_6nt_test_vs_ctrl_m2 versus MA1982.2 (ZNF574); m=3/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.510873; ksCTAGAGmGGC ; cor=; Ncor= a 97.0 33.0 68.0 43.0 997.0 1.0 983.0 58.0 302.0 19.0 58.0 121.0 c 26.0 409.0 877.0 231.0 1.0 4.0 8.0 12.0 512.0 15.0 118.0 802.0 g 618.0 540.0 54.0 19.0 1.0 994.0 8.0 930.0 129.0 965.0 689.0 12.0 t 260.0 19.0 1.0 707.0 1.0 1.0 1.0 1.0 58.0 1.0 136.0 65.0