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_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_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.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; gAaTGGAATGGAAtg ; Alignment reference a 12 50 44 5 0 4 64 49 1 0 7 63 53 12 7 c 5 5 3 2 7 1 1 2 3 7 1 1 0 9 10 g 44 8 15 1 57 61 1 10 3 52 59 2 8 3 41 t 6 4 5 59 3 1 1 6 60 8 0 1 6 43 9

MA0152.3_shift6 (Nfatc2)
; oligos_7nt_mkv2_m2 versus MA0152.3 (Nfatc2); m=1/4; ncol2=8; w=0; offset=6; strand=D; shift=6; score=0.459531; ------aATGGAAA- ; cor=; Ncor= a 0 0 0 0 0 0 2166.0 2583.0 170.0 78.0 33.0 3095.0 3140.0 2944.0 0 c 0 0 0 0 0 0 460.0 206.0 124.0 17.0 27.0 38.0 19.0 104.0 0 g 0 0 0 0 0 0 292.0 329.0 101.0 3118.0 3133.0 65.0 45.0 79.0 0 t 0 0 0 0 0 0 321.0 121.0 2844.0 26.0 46.0 41.0 35.0 112.0 0

MA0090.4_rc_shift2 (TEAD1_rc)
; oligos_7nt_mkv2_m2 versus MA0090.4_rc (TEAD1_rc); m=2/4; ncol2=9; w=0; offset=2; strand=R; shift=2; score=0.449666; --CTGGAATGT---- ; cor=; Ncor= a 0 0 7203.0 9428.0 1687.0 1332.0 63590.0 68517.0 700.0 1103.0 1941.0 0 0 0 0 c 0 0 47856.0 2051.0 374.0 765.0 1210.0 646.0 946.0 1923.0 9179.0 0 0 0 0 g 0 0 6215.0 1729.0 67635.0 66953.0 622.0 700.0 646.0 61276.0 1248.0 0 0 0 0 t 0 0 9124.0 57190.0 702.0 1348.0 4976.0 535.0 68106.0 6096.0 58030.0 0 0 0 0

MA0809.3_rc_shift3 (TEAD4_rc)
; oligos_7nt_mkv2_m2 versus MA0809.3_rc (TEAD4_rc); m=3/4; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.440988; ---TGGAATGT---- ; cor=; Ncor= a 0 0 0 11219.0 1494.0 2585.0 72137.0 74967.0 1502.0 1043.0 3144.0 0 0 0 0 c 0 0 0 1191.0 212.0 1580.0 2100.0 1025.0 569.0 3295.0 11265.0 0 0 0 0 g 0 0 0 3874.0 75066.0 72555.0 1176.0 1129.0 1218.0 66205.0 2414.0 0 0 0 0 t 0 0 0 61802.0 1314.0 1366.0 2673.0 965.0 74797.0 7543.0 61263.0 0 0 0 0

MA0808.1_rc_shift3 (TEAD3_rc)
; oligos_7nt_mkv2_m2 versus MA0808.1_rc (TEAD3_rc); m=4/4; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.421904; ---wGGAATGy---- ; cor=; Ncor= a 0 0 0 13663.0 4.0 0.0 16878.0 21444.0 0.0 0.0 1109.0 0 0 0 0 c 0 0 0 8654.0 0.0 0.0 969.0 0.0 0.0 441.0 8913.0 0 0 0 0 g 0 0 0 1039.0 21444.0 21444.0 23.0 0.0 0.0 18920.0 66.0 0 0 0 0 t 0 0 0 21444.0 0.0 0.0 4566.0 0.0 21444.0 2524.0 12530.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; gAaTGGAATGGAAtg ; Alignment reference a 12 50 44 5 0 4 64 49 1 0 7 63 53 12 7 c 5 5 3 2 7 1 1 2 3 7 1 1 0 9 10 g 44 8 15 1 57 61 1 10 3 52 59 2 8 3 41 t 6 4 5 59 3 1 1 6 60 8 0 1 6 43 9
MA0152.3_shift6 (Nfatc2)				; oligos_7nt_mkv2_m2 versus MA0152.3 (Nfatc2); m=1/4; ncol2=8; w=0; offset=6; strand=D; shift=6; score=0.459531; ------aATGGAAA- ; cor=; Ncor= a 0 0 0 0 0 0 2166.0 2583.0 170.0 78.0 33.0 3095.0 3140.0 2944.0 0 c 0 0 0 0 0 0 460.0 206.0 124.0 17.0 27.0 38.0 19.0 104.0 0 g 0 0 0 0 0 0 292.0 329.0 101.0 3118.0 3133.0 65.0 45.0 79.0 0 t 0 0 0 0 0 0 321.0 121.0 2844.0 26.0 46.0 41.0 35.0 112.0 0
MA0090.4_rc_shift2 (TEAD1_rc)				; oligos_7nt_mkv2_m2 versus MA0090.4_rc (TEAD1_rc); m=2/4; ncol2=9; w=0; offset=2; strand=R; shift=2; score=0.449666; --CTGGAATGT---- ; cor=; Ncor= a 0 0 7203.0 9428.0 1687.0 1332.0 63590.0 68517.0 700.0 1103.0 1941.0 0 0 0 0 c 0 0 47856.0 2051.0 374.0 765.0 1210.0 646.0 946.0 1923.0 9179.0 0 0 0 0 g 0 0 6215.0 1729.0 67635.0 66953.0 622.0 700.0 646.0 61276.0 1248.0 0 0 0 0 t 0 0 9124.0 57190.0 702.0 1348.0 4976.0 535.0 68106.0 6096.0 58030.0 0 0 0 0
MA0809.3_rc_shift3 (TEAD4_rc)				; oligos_7nt_mkv2_m2 versus MA0809.3_rc (TEAD4_rc); m=3/4; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.440988; ---TGGAATGT---- ; cor=; Ncor= a 0 0 0 11219.0 1494.0 2585.0 72137.0 74967.0 1502.0 1043.0 3144.0 0 0 0 0 c 0 0 0 1191.0 212.0 1580.0 2100.0 1025.0 569.0 3295.0 11265.0 0 0 0 0 g 0 0 0 3874.0 75066.0 72555.0 1176.0 1129.0 1218.0 66205.0 2414.0 0 0 0 0 t 0 0 0 61802.0 1314.0 1366.0 2673.0 965.0 74797.0 7543.0 61263.0 0 0 0 0
MA0808.1_rc_shift3 (TEAD3_rc)				; oligos_7nt_mkv2_m2 versus MA0808.1_rc (TEAD3_rc); m=4/4; ncol2=8; w=0; offset=3; strand=R; shift=3; score=0.421904; ---wGGAATGy---- ; cor=; Ncor= a 0 0 0 13663.0 4.0 0.0 16878.0 21444.0 0.0 0.0 1109.0 0 0 0 0 c 0 0 0 8654.0 0.0 0.0 969.0 0.0 0.0 441.0 8913.0 0 0 0 0 g 0 0 0 1039.0 21444.0 21444.0 23.0 0.0 0.0 18920.0 66.0 0 0 0 0 t 0 0 0 21444.0 0.0 0.0 4566.0 0.0 21444.0 2524.0 12530.0 0 0 0 0