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.2025-05-16.175925_2025-05-16.175925_FDRQXr/results/discovered_motifs/oligos_7nt_mkv1_m5/peak-motifs_oligos_7nt_mkv1_m5.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.2025-05-16.175925_2025-05-16.175925_FDRQXr/results/discovered_motifs/oligos_7nt_mkv1_m5/peak-motifs_oligos_7nt_mkv1_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift1 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m5_shift1 (oligos_7nt_mkv1_m5)
; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -GrAAGGTAAym ; Alignment reference a 0 0 1 2 2 0 0 0 2 2 0 1 c 0 0 0 0 0 0 0 0 0 0 1 1 g 0 2 1 0 0 2 2 0 0 0 0 0 t 0 0 0 0 0 0 0 2 0 0 1 0

MA1112.3_shift2 (NR4A1)
; oligos_7nt_mkv1_m5 versus MA1112.3 (NR4A1); m=1/9; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.560628; --AAAGGTCA-- ; cor=; Ncor= a 0 0 14313.0 15268.0 15684.0 427.0 300.0 365.0 70.0 15126.0 0 0 c 0 0 236.0 117.0 62.0 92.0 166.0 824.0 14949.0 151.0 0 0 g 0 0 823.0 333.0 128.0 12434.0 14964.0 1358.0 151.0 329.0 0 0 t 0 0 555.0 209.0 53.0 2974.0 497.0 13380.0 757.0 321.0 0 0

MA0160.3_shift2 (NR4A2)
; oligos_7nt_mkv1_m5 versus MA0160.3 (NR4A2); m=2/9; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.556688; --AAAGGTCA-- ; cor=; Ncor= a 0 0 209.0 209.0 209.0 0.0 0.0 6.0 0.0 209.0 0 0 c 0 0 0.0 0.0 5.0 0.0 0.0 22.0 209.0 4.0 0 0 g 0 0 28.0 1.0 1.0 160.0 209.0 21.0 1.0 40.0 0 0 t 0 0 22.0 18.0 0.0 49.0 2.0 209.0 14.0 0.0 0 0

MA1111.2_shift3 (NR2F2)
; oligos_7nt_mkv1_m5 versus MA1111.2 (NR2F2); m=3/9; ncol2=7; w=0; offset=2; strand=D; shift=3; score=0.516081; ---AAGGTCA-- ; cor=; Ncor= a 0 0 0 1788.0 2084.0 37.0 33.0 17.0 30.0 2111.0 0 0 c 0 0 0 37.0 15.0 16.0 12.0 22.0 1978.0 16.0 0 0 g 0 0 0 173.0 82.0 2108.0 2132.0 30.0 26.0 43.0 0 0 t 0 0 0 206.0 23.0 43.0 27.0 2135.0 170.0 34.0 0 0

MA2338.1_shift3 (Ppara)
; oligos_7nt_mkv1_m5 versus MA2338.1 (Ppara); m=4/9; ncol2=7; w=0; offset=2; strand=D; shift=3; score=0.507379; ---AAGGTCA-- ; cor=; Ncor= a 0 0 0 16299.0 17009.0 258.0 354.0 259.0 440.0 13045.0 0 0 c 0 0 0 258.0 641.0 446.0 68.0 83.0 16858.0 2036.0 0 0 g 0 0 0 788.0 328.0 17024.0 17412.0 75.0 178.0 1148.0 0 0 t 0 0 0 833.0 200.0 450.0 344.0 17761.0 702.0 1949.0 0 0

MA1121.2_rc_shift1 (TEAD2_rc)
; oligos_7nt_mkv1_m5 versus MA1121.2_rc (TEAD2_rc); m=5/9; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.469218; -GGAATGT---- ; cor=; Ncor= a 0 18.0 24.0 510.0 524.0 9.0 11.0 14.0 0 0 0 0 c 0 3.0 10.0 9.0 6.0 11.0 14.0 70.0 0 0 0 0 g 0 513.0 500.0 8.0 10.0 5.0 478.0 17.0 0 0 0 0 t 0 8.0 8.0 15.0 2.0 517.0 39.0 441.0 0 0 0 0

MA1110.3_shift4 (Nr1H4)
; oligos_7nt_mkv1_m5 versus MA1110.3 (Nr1H4); m=6/9; ncol2=6; w=0; offset=3; strand=D; shift=4; score=0.432997; ----AGGTCA-- ; cor=; Ncor= a 0 0 0 0 4597.0 13.0 31.0 1.0 163.0 4589.0 0 0 c 0 0 0 0 83.0 150.0 4.0 0.0 4351.0 29.0 0 0 g 0 0 0 0 49.0 4542.0 4671.0 0.0 10.0 118.0 0 0 t 0 0 0 0 7.0 31.0 30.0 4735.0 212.0 0.0 0 0

MA1996.2_shift4 (Nr1H2)
; oligos_7nt_mkv1_m5 versus MA1996.2 (Nr1H2); m=7/9; ncol2=6; w=0; offset=3; strand=D; shift=4; score=0.426655; ----AGGTCA-- ; cor=; Ncor= a 0 0 0 0 8549.0 88.0 91.0 61.0 147.0 8642.0 0 0 c 0 0 0 0 191.0 171.0 36.0 35.0 8483.0 51.0 0 0 g 0 0 0 0 132.0 8521.0 8740.0 41.0 72.0 241.0 0 0 t 0 0 0 0 99.0 191.0 104.0 8834.0 269.0 37.0 0 0

MA0809.3_rc_shift0 (TEAD4_rc)
; oligos_7nt_mkv1_m5 versus MA0809.3_rc (TEAD4_rc); m=8/9; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score=0.425944; TGGAATGT---- ; cor=; Ncor= a 11219.0 1494.0 2585.0 72137.0 74967.0 1502.0 1043.0 3144.0 0 0 0 0 c 1191.0 212.0 1580.0 2100.0 1025.0 569.0 3295.0 11265.0 0 0 0 0 g 3874.0 75066.0 72555.0 1176.0 1129.0 1218.0 66205.0 2414.0 0 0 0 0 t 61802.0 1314.0 1366.0 2673.0 965.0 74797.0 7543.0 61263.0 0 0 0 0

MA1717.2_rc_shift0 (ZNF784_rc)
; oligos_7nt_mkv1_m5 versus MA1717.2_rc (ZNF784_rc); m=9/9; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score=0.411604; cGGTArGT---- ; cor=; Ncor= a 1746.0 154.0 124.0 22.0 6529.0 2182.0 69.0 0.0 0 0 0 0 c 4783.0 555.0 10.0 42.0 96.0 77.0 0.0 0.0 0 0 0 0 g 559.0 6529.0 6529.0 35.0 229.0 4347.0 6529.0 6.0 0 0 0 0 t 680.0 135.0 39.0 6529.0 206.0 71.0 26.0 6529.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m5_shift1 (oligos_7nt_mkv1_m5)				; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -GrAAGGTAAym ; Alignment reference a 0 0 1 2 2 0 0 0 2 2 0 1 c 0 0 0 0 0 0 0 0 0 0 1 1 g 0 2 1 0 0 2 2 0 0 0 0 0 t 0 0 0 0 0 0 0 2 0 0 1 0
MA1112.3_shift2 (NR4A1)				; oligos_7nt_mkv1_m5 versus MA1112.3 (NR4A1); m=1/9; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.560628; --AAAGGTCA-- ; cor=; Ncor= a 0 0 14313.0 15268.0 15684.0 427.0 300.0 365.0 70.0 15126.0 0 0 c 0 0 236.0 117.0 62.0 92.0 166.0 824.0 14949.0 151.0 0 0 g 0 0 823.0 333.0 128.0 12434.0 14964.0 1358.0 151.0 329.0 0 0 t 0 0 555.0 209.0 53.0 2974.0 497.0 13380.0 757.0 321.0 0 0
MA0160.3_shift2 (NR4A2)				; oligos_7nt_mkv1_m5 versus MA0160.3 (NR4A2); m=2/9; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.556688; --AAAGGTCA-- ; cor=; Ncor= a 0 0 209.0 209.0 209.0 0.0 0.0 6.0 0.0 209.0 0 0 c 0 0 0.0 0.0 5.0 0.0 0.0 22.0 209.0 4.0 0 0 g 0 0 28.0 1.0 1.0 160.0 209.0 21.0 1.0 40.0 0 0 t 0 0 22.0 18.0 0.0 49.0 2.0 209.0 14.0 0.0 0 0
MA1111.2_shift3 (NR2F2)				; oligos_7nt_mkv1_m5 versus MA1111.2 (NR2F2); m=3/9; ncol2=7; w=0; offset=2; strand=D; shift=3; score=0.516081; ---AAGGTCA-- ; cor=; Ncor= a 0 0 0 1788.0 2084.0 37.0 33.0 17.0 30.0 2111.0 0 0 c 0 0 0 37.0 15.0 16.0 12.0 22.0 1978.0 16.0 0 0 g 0 0 0 173.0 82.0 2108.0 2132.0 30.0 26.0 43.0 0 0 t 0 0 0 206.0 23.0 43.0 27.0 2135.0 170.0 34.0 0 0
MA2338.1_shift3 (Ppara)				; oligos_7nt_mkv1_m5 versus MA2338.1 (Ppara); m=4/9; ncol2=7; w=0; offset=2; strand=D; shift=3; score=0.507379; ---AAGGTCA-- ; cor=; Ncor= a 0 0 0 16299.0 17009.0 258.0 354.0 259.0 440.0 13045.0 0 0 c 0 0 0 258.0 641.0 446.0 68.0 83.0 16858.0 2036.0 0 0 g 0 0 0 788.0 328.0 17024.0 17412.0 75.0 178.0 1148.0 0 0 t 0 0 0 833.0 200.0 450.0 344.0 17761.0 702.0 1949.0 0 0
MA1121.2_rc_shift1 (TEAD2_rc)				; oligos_7nt_mkv1_m5 versus MA1121.2_rc (TEAD2_rc); m=5/9; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.469218; -GGAATGT---- ; cor=; Ncor= a 0 18.0 24.0 510.0 524.0 9.0 11.0 14.0 0 0 0 0 c 0 3.0 10.0 9.0 6.0 11.0 14.0 70.0 0 0 0 0 g 0 513.0 500.0 8.0 10.0 5.0 478.0 17.0 0 0 0 0 t 0 8.0 8.0 15.0 2.0 517.0 39.0 441.0 0 0 0 0
MA1110.3_shift4 (Nr1H4)				; oligos_7nt_mkv1_m5 versus MA1110.3 (Nr1H4); m=6/9; ncol2=6; w=0; offset=3; strand=D; shift=4; score=0.432997; ----AGGTCA-- ; cor=; Ncor= a 0 0 0 0 4597.0 13.0 31.0 1.0 163.0 4589.0 0 0 c 0 0 0 0 83.0 150.0 4.0 0.0 4351.0 29.0 0 0 g 0 0 0 0 49.0 4542.0 4671.0 0.0 10.0 118.0 0 0 t 0 0 0 0 7.0 31.0 30.0 4735.0 212.0 0.0 0 0
MA1996.2_shift4 (Nr1H2)				; oligos_7nt_mkv1_m5 versus MA1996.2 (Nr1H2); m=7/9; ncol2=6; w=0; offset=3; strand=D; shift=4; score=0.426655; ----AGGTCA-- ; cor=; Ncor= a 0 0 0 0 8549.0 88.0 91.0 61.0 147.0 8642.0 0 0 c 0 0 0 0 191.0 171.0 36.0 35.0 8483.0 51.0 0 0 g 0 0 0 0 132.0 8521.0 8740.0 41.0 72.0 241.0 0 0 t 0 0 0 0 99.0 191.0 104.0 8834.0 269.0 37.0 0 0
MA0809.3_rc_shift0 (TEAD4_rc)				; oligos_7nt_mkv1_m5 versus MA0809.3_rc (TEAD4_rc); m=8/9; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score=0.425944; TGGAATGT---- ; cor=; Ncor= a 11219.0 1494.0 2585.0 72137.0 74967.0 1502.0 1043.0 3144.0 0 0 0 0 c 1191.0 212.0 1580.0 2100.0 1025.0 569.0 3295.0 11265.0 0 0 0 0 g 3874.0 75066.0 72555.0 1176.0 1129.0 1218.0 66205.0 2414.0 0 0 0 0 t 61802.0 1314.0 1366.0 2673.0 965.0 74797.0 7543.0 61263.0 0 0 0 0
MA1717.2_rc_shift0 (ZNF784_rc)				; oligos_7nt_mkv1_m5 versus MA1717.2_rc (ZNF784_rc); m=9/9; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score=0.411604; cGGTArGT---- ; cor=; Ncor= a 1746.0 154.0 124.0 22.0 6529.0 2182.0 69.0 0.0 0 0 0 0 c 4783.0 555.0 10.0 42.0 96.0 77.0 0.0 0.0 0 0 0 0 g 559.0 6529.0 6529.0 35.0 229.0 4347.0 6529.0 6.0 0 0 0 0 t 680.0 135.0 39.0 6529.0 206.0 71.0 26.0 6529.0 0 0 0 0