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_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1.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_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift5 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift5 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=10; shift=5; ncol=15; -----wtATGTAGww ; Alignment reference a 0 0 0 0 0 1449 1012 4118 51 373 18 4017 89 1337 1269 c 0 0 0 0 0 871 973 54 478 24 10 254 127 962 910 g 0 0 0 0 0 909 931 102 68 3899 15 21 3788 813 896 t 0 0 0 0 0 1094 1407 49 3726 27 4280 31 319 1211 1248

MA0610.2_shift8 (DMRT3)
; oligos_6nt_test_vs_ctrl_m1 versus MA0610.2 (DMRT3); m=1/5; ncol2=7; w=0; offset=3; strand=D; shift=8; score=0.500146; --------TGTATCa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 106.0 0.0 0.0 999.0 202.0 0.0 618.0 c 0 0 0 0 0 0 0 0 22.0 0.0 0.0 0.0 0.0 999.0 188.0 g 0 0 0 0 0 0 0 0 22.0 999.0 0.0 0.0 104.0 0.0 97.0 t 0 0 0 0 0 0 0 0 851.0 0.0 999.0 0.0 694.0 0.0 97.0

MA1479.2_rc_shift7 (DMRTC2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus MA1479.2_rc (DMRTC2_rc); m=2/5; ncol2=11; w=0; offset=2; strand=R; shift=7; score=0.46537; -------aTGTAkCA ; cor=; Ncor= a 0 0 0 0 0 0 0 873.0 73.0 0.0 5.0 873.0 147.0 0.0 873.0 c 0 0 0 0 0 0 0 80.0 40.0 2.0 0.0 7.0 1.0 873.0 134.0 g 0 0 0 0 0 0 0 165.0 0.0 873.0 6.0 80.0 267.0 12.0 90.0 t 0 0 0 0 0 0 0 242.0 873.0 0.0 873.0 100.0 459.0 0.0 48.0

MA1573.2_rc_shift0 (Thap11_rc)
; oligos_6nt_test_vs_ctrl_m1 versus MA1573.2_rc (Thap11_rc); m=3/5; ncol2=14; w=-5; offset=-5; strand=R; shift=0; score=0.456725; cTGGGAvtTGTAGT- ; cor=; Ncor= a 97.0 22.0 19.0 5.0 22.0 603.0 216.0 144.0 9.0 8.0 6.0 610.0 19.0 14.0 0 c 421.0 147.0 10.0 5.0 2.0 19.0 165.0 56.0 29.0 9.0 10.0 6.0 18.0 20.0 0 g 68.0 16.0 622.0 642.0 631.0 20.0 209.0 46.0 13.0 639.0 17.0 39.0 603.0 38.0 0 t 74.0 475.0 9.0 8.0 5.0 18.0 70.0 414.0 609.0 4.0 627.0 5.0 20.0 588.0 0

MA1478.2_rc_shift8 (DMRTA2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus MA1478.2_rc (DMRTA2_rc); m=4/5; ncol2=6; w=0; offset=3; strand=R; shift=8; score=0.437748; --------TGTAwC- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 261.0 3.0 13.0 1710.0 983.0 6.0 0 c 0 0 0 0 0 0 0 0 78.0 0.0 71.0 29.0 10.0 1710.0 0 g 0 0 0 0 0 0 0 0 23.0 1710.0 9.0 147.0 527.0 1.0 0 t 0 0 0 0 0 0 0 0 1710.0 0.0 1710.0 578.0 727.0 0.0 0

MA1121.2_rc_shift4 (TEAD2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus MA1121.2_rc (TEAD2_rc); m=5/5; ncol2=7; w=-1; offset=-1; strand=R; shift=4; score=0.42293; ----GGAATGT---- ; cor=; Ncor= a 0 0 0 0 18.0 24.0 510.0 524.0 9.0 11.0 14.0 0 0 0 0 c 0 0 0 0 3.0 10.0 9.0 6.0 11.0 14.0 70.0 0 0 0 0 g 0 0 0 0 513.0 500.0 8.0 10.0 5.0 478.0 17.0 0 0 0 0 t 0 0 0 0 8.0 8.0 15.0 2.0 517.0 39.0 441.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift5 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=10; shift=5; ncol=15; -----wtATGTAGww ; Alignment reference a 0 0 0 0 0 1449 1012 4118 51 373 18 4017 89 1337 1269 c 0 0 0 0 0 871 973 54 478 24 10 254 127 962 910 g 0 0 0 0 0 909 931 102 68 3899 15 21 3788 813 896 t 0 0 0 0 0 1094 1407 49 3726 27 4280 31 319 1211 1248
MA0610.2_shift8 (DMRT3)				; oligos_6nt_test_vs_ctrl_m1 versus MA0610.2 (DMRT3); m=1/5; ncol2=7; w=0; offset=3; strand=D; shift=8; score=0.500146; --------TGTATCa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 106.0 0.0 0.0 999.0 202.0 0.0 618.0 c 0 0 0 0 0 0 0 0 22.0 0.0 0.0 0.0 0.0 999.0 188.0 g 0 0 0 0 0 0 0 0 22.0 999.0 0.0 0.0 104.0 0.0 97.0 t 0 0 0 0 0 0 0 0 851.0 0.0 999.0 0.0 694.0 0.0 97.0
MA1479.2_rc_shift7 (DMRTC2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus MA1479.2_rc (DMRTC2_rc); m=2/5; ncol2=11; w=0; offset=2; strand=R; shift=7; score=0.46537; -------aTGTAkCA ; cor=; Ncor= a 0 0 0 0 0 0 0 873.0 73.0 0.0 5.0 873.0 147.0 0.0 873.0 c 0 0 0 0 0 0 0 80.0 40.0 2.0 0.0 7.0 1.0 873.0 134.0 g 0 0 0 0 0 0 0 165.0 0.0 873.0 6.0 80.0 267.0 12.0 90.0 t 0 0 0 0 0 0 0 242.0 873.0 0.0 873.0 100.0 459.0 0.0 48.0
MA1573.2_rc_shift0 (Thap11_rc)				; oligos_6nt_test_vs_ctrl_m1 versus MA1573.2_rc (Thap11_rc); m=3/5; ncol2=14; w=-5; offset=-5; strand=R; shift=0; score=0.456725; cTGGGAvtTGTAGT- ; cor=; Ncor= a 97.0 22.0 19.0 5.0 22.0 603.0 216.0 144.0 9.0 8.0 6.0 610.0 19.0 14.0 0 c 421.0 147.0 10.0 5.0 2.0 19.0 165.0 56.0 29.0 9.0 10.0 6.0 18.0 20.0 0 g 68.0 16.0 622.0 642.0 631.0 20.0 209.0 46.0 13.0 639.0 17.0 39.0 603.0 38.0 0 t 74.0 475.0 9.0 8.0 5.0 18.0 70.0 414.0 609.0 4.0 627.0 5.0 20.0 588.0 0
MA1478.2_rc_shift8 (DMRTA2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus MA1478.2_rc (DMRTA2_rc); m=4/5; ncol2=6; w=0; offset=3; strand=R; shift=8; score=0.437748; --------TGTAwC- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 261.0 3.0 13.0 1710.0 983.0 6.0 0 c 0 0 0 0 0 0 0 0 78.0 0.0 71.0 29.0 10.0 1710.0 0 g 0 0 0 0 0 0 0 0 23.0 1710.0 9.0 147.0 527.0 1.0 0 t 0 0 0 0 0 0 0 0 1710.0 0.0 1710.0 578.0 727.0 0.0 0
MA1121.2_rc_shift4 (TEAD2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus MA1121.2_rc (TEAD2_rc); m=5/5; ncol2=7; w=-1; offset=-1; strand=R; shift=4; score=0.42293; ----GGAATGT---- ; cor=; Ncor= a 0 0 0 0 18.0 24.0 510.0 524.0 9.0 11.0 14.0 0 0 0 0 c 0 0 0 0 3.0 10.0 9.0 6.0 11.0 14.0 70.0 0 0 0 0 g 0 0 0 0 513.0 500.0 8.0 10.0 5.0 478.0 17.0 0 0 0 0 t 0 0 0 0 8.0 8.0 15.0 2.0 517.0 39.0 441.0 0 0 0 0