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.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_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.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift4 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift4 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=4; ncol=14; ----csAGGCTGgs ; Alignment reference a 0 0 0 0 6 9 37 0 0 0 0 0 8 2 c 0 0 0 0 20 17 0 2 0 37 0 0 9 10 g 0 0 0 0 6 10 0 35 37 0 0 36 16 20 t 0 0 0 0 5 1 0 0 0 0 37 1 4 5

MA2341.1_rc_shift6 (FEZF2_rc)
; oligos_6nt_mkv1_m4 versus MA2341.1_rc (FEZF2_rc); m=1/8; ncol2=8; w=0; offset=2; strand=R; shift=6; score=0.766204; ------AGGCTGGG ; cor=; Ncor= a 0 0 0 0 0 0 233.0 9.0 5.0 0.0 5.0 3.0 45.0 36.0 c 0 0 0 0 0 0 8.0 2.0 28.0 251.0 14.0 0.0 9.0 10.0 g 0 0 0 0 0 0 10.0 247.0 224.0 8.0 15.0 258.0 206.0 202.0 t 0 0 0 0 0 0 14.0 7.0 8.0 6.0 231.0 4.0 5.0 17.0

MA2121.1_shift2 (ZNF213)
; oligos_6nt_mkv1_m4 versus MA2121.1 (ZNF213); m=2/8; ncol2=12; w=-2; offset=-2; strand=D; shift=2; score=0.709605; --gCCCAGGCwGsr ; cor=; Ncor= a 0 0 119.0 26.0 18.0 15.0 577.0 10.0 12.0 16.0 229.0 42.0 61.0 216.0 c 0 0 89.0 581.0 603.0 630.0 34.0 13.0 25.0 642.0 97.0 76.0 319.0 86.0 g 0 0 403.0 52.0 34.0 34.0 54.0 661.0 639.0 22.0 124.0 519.0 260.0 330.0 t 0 0 76.0 28.0 32.0 8.0 22.0 3.0 11.0 7.0 237.0 50.0 47.0 55.0

MA2099.1_rc_shift4 (ZNF770_rc)
; oligos_6nt_mkv1_m4 versus MA2099.1_rc (ZNF770_rc); m=3/8; ncol2=8; w=0; offset=0; strand=R; shift=4; score=0.59786; ----kGAGGCyG-- ; cor=; Ncor= a 0 0 0 0 724.0 56.0 13889.0 65.0 156.0 126.0 387.0 1052.0 0 0 c 0 0 0 0 485.0 86.0 215.0 133.0 681.0 13947.0 9119.0 374.0 0 0 g 0 0 0 0 3865.0 14154.0 140.0 14096.0 13393.0 79.0 857.0 12613.0 0 0 t 0 0 0 0 9257.0 35.0 87.0 37.0 101.0 179.0 3968.0 292.0 0 0

MA2125.1_rc_shift7 (Zfp809_rc)
; oligos_6nt_mkv1_m4 versus MA2125.1_rc (Zfp809_rc); m=4/8; ncol2=9; w=0; offset=3; strand=R; shift=7; score=0.514538; -------gGCTGGG ; cor=; Ncor= a 0 0 0 0 0 0 0 242.0 61.0 26.0 37.0 18.0 21.0 25.0 c 0 0 0 0 0 0 0 115.0 99.0 1572.0 73.0 16.0 14.0 18.0 g 0 0 0 0 0 0 0 1091.0 1218.0 35.0 26.0 1621.0 1610.0 1607.0 t 0 0 0 0 0 0 0 217.0 287.0 32.0 1529.0 10.0 20.0 15.0

MA1973.2_shift3 (ZKSCAN3)
; oligos_6nt_mkv1_m4 versus MA1973.2 (ZKSCAN3); m=5/8; ncol2=14; w=-1; offset=-1; strand=D; shift=3; score=0.514229; ---CCcAGGCTAGC ; cor=; Ncor= a 0 0 0 23.0 17.0 36.0 188.0 6.0 0.0 5.0 2.0 197.0 3.0 36.0 c 0 0 0 149.0 152.0 115.0 2.0 1.0 5.0 183.0 6.0 3.0 6.0 168.0 g 0 0 0 17.0 15.0 38.0 19.0 201.0 203.0 4.0 2.0 8.0 188.0 4.0 t 0 0 0 21.0 26.0 21.0 1.0 2.0 2.0 18.0 200.0 2.0 13.0 2.0

MA1655.2_rc_shift7 (ZNF341_rc)
; oligos_6nt_mkv1_m4 versus MA1655.2_rc (ZNF341_rc); m=6/8; ncol2=8; w=0; offset=3; strand=R; shift=7; score=0.46591; -------gGCTGTT ; cor=; Ncor= a 0 0 0 0 0 0 0 2411.0 228.0 229.0 234.0 581.0 241.0 186.0 c 0 0 0 0 0 0 0 2289.0 270.0 17972.0 468.0 1033.0 576.0 513.0 g 0 0 0 0 0 0 0 10946.0 18003.0 359.0 399.0 16813.0 211.0 955.0 t 0 0 0 0 0 0 0 3082.0 227.0 168.0 17627.0 301.0 17700.0 17074.0

MA1596.1_rc_shift0 (ZNF460_rc)
; oligos_6nt_mkv1_m4 versus MA1596.1_rc (ZNF460_rc); m=7/8; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.465279; CyyGGGAGGCkGAG ; cor=; Ncor= a 64.0 29.0 56.0 40.0 9.0 10.0 1570.0 6.0 11.0 35.0 85.0 29.0 1284.0 66.0 c 1147.0 421.0 930.0 27.0 15.0 15.0 17.0 9.0 7.0 1493.0 181.0 47.0 83.0 67.0 g 158.0 175.0 110.0 1533.0 1583.0 1584.0 12.0 1596.0 1588.0 23.0 495.0 1519.0 218.0 1460.0 t 243.0 987.0 516.0 12.0 5.0 3.0 13.0 1.0 6.0 61.0 851.0 17.0 27.0 19.0

MA0812.2_shift1 (TFAP2B)
; oligos_6nt_mkv1_m4 versus MA0812.2 (TFAP2B); m=8/8; ncol2=9; w=-3; offset=-3; strand=D; shift=1; score=0.428088; -GCCysAGGC---- ; cor=; Ncor= a 0 36.0 0.0 0.0 16.0 576.0 3480.0 235.0 6.0 47.0 0 0 0 0 c 0 609.0 4549.0 4549.0 1204.0 2126.0 608.0 4.0 10.0 4250.0 0 0 0 0 g 0 3940.0 4.0 1.0 612.0 1498.0 446.0 4549.0 4549.0 299.0 0 0 0 0 t 0 30.0 0.0 158.0 2716.0 348.0 14.0 2.0 1.0 25.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m4_shift4 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=4; ncol=14; ----csAGGCTGgs ; Alignment reference a 0 0 0 0 6 9 37 0 0 0 0 0 8 2 c 0 0 0 0 20 17 0 2 0 37 0 0 9 10 g 0 0 0 0 6 10 0 35 37 0 0 36 16 20 t 0 0 0 0 5 1 0 0 0 0 37 1 4 5
MA2341.1_rc_shift6 (FEZF2_rc)				; oligos_6nt_mkv1_m4 versus MA2341.1_rc (FEZF2_rc); m=1/8; ncol2=8; w=0; offset=2; strand=R; shift=6; score=0.766204; ------AGGCTGGG ; cor=; Ncor= a 0 0 0 0 0 0 233.0 9.0 5.0 0.0 5.0 3.0 45.0 36.0 c 0 0 0 0 0 0 8.0 2.0 28.0 251.0 14.0 0.0 9.0 10.0 g 0 0 0 0 0 0 10.0 247.0 224.0 8.0 15.0 258.0 206.0 202.0 t 0 0 0 0 0 0 14.0 7.0 8.0 6.0 231.0 4.0 5.0 17.0
MA2121.1_shift2 (ZNF213)				; oligos_6nt_mkv1_m4 versus MA2121.1 (ZNF213); m=2/8; ncol2=12; w=-2; offset=-2; strand=D; shift=2; score=0.709605; --gCCCAGGCwGsr ; cor=; Ncor= a 0 0 119.0 26.0 18.0 15.0 577.0 10.0 12.0 16.0 229.0 42.0 61.0 216.0 c 0 0 89.0 581.0 603.0 630.0 34.0 13.0 25.0 642.0 97.0 76.0 319.0 86.0 g 0 0 403.0 52.0 34.0 34.0 54.0 661.0 639.0 22.0 124.0 519.0 260.0 330.0 t 0 0 76.0 28.0 32.0 8.0 22.0 3.0 11.0 7.0 237.0 50.0 47.0 55.0
MA2099.1_rc_shift4 (ZNF770_rc)				; oligos_6nt_mkv1_m4 versus MA2099.1_rc (ZNF770_rc); m=3/8; ncol2=8; w=0; offset=0; strand=R; shift=4; score=0.59786; ----kGAGGCyG-- ; cor=; Ncor= a 0 0 0 0 724.0 56.0 13889.0 65.0 156.0 126.0 387.0 1052.0 0 0 c 0 0 0 0 485.0 86.0 215.0 133.0 681.0 13947.0 9119.0 374.0 0 0 g 0 0 0 0 3865.0 14154.0 140.0 14096.0 13393.0 79.0 857.0 12613.0 0 0 t 0 0 0 0 9257.0 35.0 87.0 37.0 101.0 179.0 3968.0 292.0 0 0
MA2125.1_rc_shift7 (Zfp809_rc)				; oligos_6nt_mkv1_m4 versus MA2125.1_rc (Zfp809_rc); m=4/8; ncol2=9; w=0; offset=3; strand=R; shift=7; score=0.514538; -------gGCTGGG ; cor=; Ncor= a 0 0 0 0 0 0 0 242.0 61.0 26.0 37.0 18.0 21.0 25.0 c 0 0 0 0 0 0 0 115.0 99.0 1572.0 73.0 16.0 14.0 18.0 g 0 0 0 0 0 0 0 1091.0 1218.0 35.0 26.0 1621.0 1610.0 1607.0 t 0 0 0 0 0 0 0 217.0 287.0 32.0 1529.0 10.0 20.0 15.0
MA1973.2_shift3 (ZKSCAN3)				; oligos_6nt_mkv1_m4 versus MA1973.2 (ZKSCAN3); m=5/8; ncol2=14; w=-1; offset=-1; strand=D; shift=3; score=0.514229; ---CCcAGGCTAGC ; cor=; Ncor= a 0 0 0 23.0 17.0 36.0 188.0 6.0 0.0 5.0 2.0 197.0 3.0 36.0 c 0 0 0 149.0 152.0 115.0 2.0 1.0 5.0 183.0 6.0 3.0 6.0 168.0 g 0 0 0 17.0 15.0 38.0 19.0 201.0 203.0 4.0 2.0 8.0 188.0 4.0 t 0 0 0 21.0 26.0 21.0 1.0 2.0 2.0 18.0 200.0 2.0 13.0 2.0
MA1655.2_rc_shift7 (ZNF341_rc)				; oligos_6nt_mkv1_m4 versus MA1655.2_rc (ZNF341_rc); m=6/8; ncol2=8; w=0; offset=3; strand=R; shift=7; score=0.46591; -------gGCTGTT ; cor=; Ncor= a 0 0 0 0 0 0 0 2411.0 228.0 229.0 234.0 581.0 241.0 186.0 c 0 0 0 0 0 0 0 2289.0 270.0 17972.0 468.0 1033.0 576.0 513.0 g 0 0 0 0 0 0 0 10946.0 18003.0 359.0 399.0 16813.0 211.0 955.0 t 0 0 0 0 0 0 0 3082.0 227.0 168.0 17627.0 301.0 17700.0 17074.0
MA1596.1_rc_shift0 (ZNF460_rc)				; oligos_6nt_mkv1_m4 versus MA1596.1_rc (ZNF460_rc); m=7/8; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.465279; CyyGGGAGGCkGAG ; cor=; Ncor= a 64.0 29.0 56.0 40.0 9.0 10.0 1570.0 6.0 11.0 35.0 85.0 29.0 1284.0 66.0 c 1147.0 421.0 930.0 27.0 15.0 15.0 17.0 9.0 7.0 1493.0 181.0 47.0 83.0 67.0 g 158.0 175.0 110.0 1533.0 1583.0 1584.0 12.0 1596.0 1588.0 23.0 495.0 1519.0 218.0 1460.0 t 243.0 987.0 516.0 12.0 5.0 3.0 13.0 1.0 6.0 61.0 851.0 17.0 27.0 19.0
MA0812.2_shift1 (TFAP2B)				; oligos_6nt_mkv1_m4 versus MA0812.2 (TFAP2B); m=8/8; ncol2=9; w=-3; offset=-3; strand=D; shift=1; score=0.428088; -GCCysAGGC---- ; cor=; Ncor= a 0 36.0 0.0 0.0 16.0 576.0 3480.0 235.0 6.0 47.0 0 0 0 0 c 0 609.0 4549.0 4549.0 1204.0 2126.0 608.0 4.0 10.0 4250.0 0 0 0 0 g 0 3940.0 4.0 1.0 612.0 1498.0 446.0 4549.0 4549.0 299.0 0 0 0 0 t 0 30.0 0.0 158.0 2716.0 348.0 14.0 2.0 1.0 25.0 0 0 0 0