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.2025-05-16.175823_2025-05-16.175823_YJjJog/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_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.2025-05-16.175823_2025-05-16.175823_YJjJog/results/discovered_motifs/oligos_6nt_mkv2_m4/peak-motifs_oligos_6nt_mkv2_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift1 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=1; ncol=13; -sscCGCCGCGss ; Alignment reference a 0 17 9 16 4 11 4 5 6 4 5 17 11 c 0 49 37 60 97 8 97 88 3 101 14 37 49 g 0 34 56 20 9 91 8 16 100 6 87 46 40 t 0 14 12 18 4 4 5 5 5 3 8 14 14

MA1713.2_shift3 (ZNF610)
; oligos_6nt_mkv2_m4 versus MA1713.2 (ZNF610); m=1/7; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.616738; ---scGCCGCTCC ; cor=; Ncor= a 0 0 0 176.0 354.0 68.0 37.0 18.0 18.0 4.0 18.0 6.0 123.0 c 0 0 0 1222.0 1347.0 121.0 2245.0 2312.0 45.0 2357.0 34.0 2315.0 1976.0 g 0 0 0 738.0 392.0 2118.0 84.0 41.0 2312.0 21.0 45.0 62.0 186.0 t 0 0 0 250.0 293.0 79.0 20.0 15.0 11.0 4.0 2289.0 3.0 101.0

MA2328.1_shift2 (ZBED4)
; oligos_6nt_mkv2_m4 versus MA2328.1 (ZBED4); m=2/7; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.588425; --CcCGCyCCGC- ; cor=; Ncor= a 0 0 41.0 26.0 29.0 17.0 6.0 11.0 14.0 12.0 22.0 19.0 0 c 0 0 479.0 419.0 549.0 14.0 621.0 391.0 598.0 604.0 19.0 589.0 0 g 0 0 80.0 65.0 62.0 608.0 26.0 28.0 34.0 23.0 580.0 35.0 0 t 0 0 60.0 150.0 20.0 21.0 7.0 230.0 14.0 21.0 39.0 17.0 0

MA0516.3_rc_shift1 (SP2_rc)
; oligos_6nt_mkv2_m4 versus MA0516.3_rc (SP2_rc); m=3/7; ncol2=9; w=0; offset=0; strand=R; shift=1; score=0.532693; -cCCCGCCCC--- ; cor=; Ncor= a 0 18.3284 0.733138 24.1935 0.733138 0.733138 0.733138 0.733138 0.733138 79.912 0 0 0 c 0 610.704 877.566 974.34 997.801 0.733138 997.801 997.801 830.645 766.129 0 0 0 g 0 164.956 0.733138 0.733138 0.733138 886.364 0.733138 0.733138 0.733138 0.733138 0 0 0 t 0 206.012 120.968 0.733138 0.733138 112.17 0.733138 0.733138 167.889 153.226 0 0 0

MA1721.2_rc_shift3 (ZNF93_rc)
; oligos_6nt_mkv2_m4 versus MA1721.2_rc (ZNF93_rc); m=4/7; ncol2=14; w=0; offset=2; strand=R; shift=3; score=0.453681; ---CCGCTGCyGm ; cor=; Ncor= a 0 0 0 37.0 126.0 44.0 10.0 57.0 44.0 10.0 32.0 50.0 730.0 c 0 0 0 2145.0 1784.0 33.0 2328.0 576.0 42.0 2334.0 1263.0 22.0 1483.0 g 0 0 0 134.0 138.0 2292.0 20.0 96.0 2279.0 26.0 92.0 2278.0 114.0 t 0 0 0 72.0 340.0 19.0 30.0 1659.0 23.0 18.0 1001.0 38.0 61.0

MA1727.2_rc_shift1 (ZNF417_rc)
; oligos_6nt_mkv2_m4 versus MA1727.2_rc (ZNF417_rc); m=5/7; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.413548; -TGGCGCC----- ; cor=; Ncor= a 0 1.0 13.0 7.0 1.0 55.0 1.0 1.0 0 0 0 0 0 c 0 1.0 1.0 1.0 996.0 1.0 996.0 996.0 0 0 0 0 0 g 0 13.0 954.0 990.0 1.0 936.0 1.0 1.0 0 0 0 0 0 t 0 984.0 31.0 1.0 1.0 7.0 1.0 1.0 0 0 0 0 0

MA0471.3_rc_shift0 (E2F6_rc)
; oligos_6nt_mkv2_m4 versus MA0471.3_rc (E2F6_rc); m=6/7; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score=0.409607; TTCCCGCC----- ; cor=; Ncor= a 757.0 268.0 296.0 353.0 813.0 2125.0 205.0 453.0 0 0 0 0 0 c 5021.0 2322.0 31614.0 31973.0 30573.0 693.0 31790.0 29387.0 0 0 0 0 0 g 1595.0 1171.0 834.0 434.0 539.0 26424.0 837.0 1148.0 0 0 0 0 0 t 25725.0 29337.0 354.0 338.0 1173.0 3856.0 266.0 2110.0 0 0 0 0 0

MA1650.2_shift6 (ZBTB14)
; oligos_6nt_mkv2_m4 versus MA1650.2 (ZBTB14); m=7/7; ncol2=8; w=0; offset=5; strand=D; shift=6; score=0.409158; ------CCGCGCA ; cor=; Ncor= a 0 0 0 0 0 0 335.0 41.0 93.0 68.0 132.0 56.0 4500.0 c 0 0 0 0 0 0 3525.0 4292.0 294.0 4078.0 305.0 4178.0 37.0 g 0 0 0 0 0 0 614.0 155.0 4098.0 319.0 4043.0 261.0 10.0 t 0 0 0 0 0 0 73.0 59.0 62.0 82.0 67.0 52.0 0.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=1; ncol=13; -sscCGCCGCGss ; Alignment reference a 0 17 9 16 4 11 4 5 6 4 5 17 11 c 0 49 37 60 97 8 97 88 3 101 14 37 49 g 0 34 56 20 9 91 8 16 100 6 87 46 40 t 0 14 12 18 4 4 5 5 5 3 8 14 14
MA1713.2_shift3 (ZNF610)				; oligos_6nt_mkv2_m4 versus MA1713.2 (ZNF610); m=1/7; ncol2=10; w=0; offset=2; strand=D; shift=3; score=0.616738; ---scGCCGCTCC ; cor=; Ncor= a 0 0 0 176.0 354.0 68.0 37.0 18.0 18.0 4.0 18.0 6.0 123.0 c 0 0 0 1222.0 1347.0 121.0 2245.0 2312.0 45.0 2357.0 34.0 2315.0 1976.0 g 0 0 0 738.0 392.0 2118.0 84.0 41.0 2312.0 21.0 45.0 62.0 186.0 t 0 0 0 250.0 293.0 79.0 20.0 15.0 11.0 4.0 2289.0 3.0 101.0
MA2328.1_shift2 (ZBED4)				; oligos_6nt_mkv2_m4 versus MA2328.1 (ZBED4); m=2/7; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.588425; --CcCGCyCCGC- ; cor=; Ncor= a 0 0 41.0 26.0 29.0 17.0 6.0 11.0 14.0 12.0 22.0 19.0 0 c 0 0 479.0 419.0 549.0 14.0 621.0 391.0 598.0 604.0 19.0 589.0 0 g 0 0 80.0 65.0 62.0 608.0 26.0 28.0 34.0 23.0 580.0 35.0 0 t 0 0 60.0 150.0 20.0 21.0 7.0 230.0 14.0 21.0 39.0 17.0 0
MA0516.3_rc_shift1 (SP2_rc)				; oligos_6nt_mkv2_m4 versus MA0516.3_rc (SP2_rc); m=3/7; ncol2=9; w=0; offset=0; strand=R; shift=1; score=0.532693; -cCCCGCCCC--- ; cor=; Ncor= a 0 18.3284 0.733138 24.1935 0.733138 0.733138 0.733138 0.733138 0.733138 79.912 0 0 0 c 0 610.704 877.566 974.34 997.801 0.733138 997.801 997.801 830.645 766.129 0 0 0 g 0 164.956 0.733138 0.733138 0.733138 886.364 0.733138 0.733138 0.733138 0.733138 0 0 0 t 0 206.012 120.968 0.733138 0.733138 112.17 0.733138 0.733138 167.889 153.226 0 0 0
MA1721.2_rc_shift3 (ZNF93_rc)				; oligos_6nt_mkv2_m4 versus MA1721.2_rc (ZNF93_rc); m=4/7; ncol2=14; w=0; offset=2; strand=R; shift=3; score=0.453681; ---CCGCTGCyGm ; cor=; Ncor= a 0 0 0 37.0 126.0 44.0 10.0 57.0 44.0 10.0 32.0 50.0 730.0 c 0 0 0 2145.0 1784.0 33.0 2328.0 576.0 42.0 2334.0 1263.0 22.0 1483.0 g 0 0 0 134.0 138.0 2292.0 20.0 96.0 2279.0 26.0 92.0 2278.0 114.0 t 0 0 0 72.0 340.0 19.0 30.0 1659.0 23.0 18.0 1001.0 38.0 61.0
MA1727.2_rc_shift1 (ZNF417_rc)				; oligos_6nt_mkv2_m4 versus MA1727.2_rc (ZNF417_rc); m=5/7; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.413548; -TGGCGCC----- ; cor=; Ncor= a 0 1.0 13.0 7.0 1.0 55.0 1.0 1.0 0 0 0 0 0 c 0 1.0 1.0 1.0 996.0 1.0 996.0 996.0 0 0 0 0 0 g 0 13.0 954.0 990.0 1.0 936.0 1.0 1.0 0 0 0 0 0 t 0 984.0 31.0 1.0 1.0 7.0 1.0 1.0 0 0 0 0 0
MA0471.3_rc_shift0 (E2F6_rc)				; oligos_6nt_mkv2_m4 versus MA0471.3_rc (E2F6_rc); m=6/7; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score=0.409607; TTCCCGCC----- ; cor=; Ncor= a 757.0 268.0 296.0 353.0 813.0 2125.0 205.0 453.0 0 0 0 0 0 c 5021.0 2322.0 31614.0 31973.0 30573.0 693.0 31790.0 29387.0 0 0 0 0 0 g 1595.0 1171.0 834.0 434.0 539.0 26424.0 837.0 1148.0 0 0 0 0 0 t 25725.0 29337.0 354.0 338.0 1173.0 3856.0 266.0 2110.0 0 0 0 0 0
MA1650.2_shift6 (ZBTB14)				; oligos_6nt_mkv2_m4 versus MA1650.2 (ZBTB14); m=7/7; ncol2=8; w=0; offset=5; strand=D; shift=6; score=0.409158; ------CCGCGCA ; cor=; Ncor= a 0 0 0 0 0 0 335.0 41.0 93.0 68.0 132.0 56.0 4500.0 c 0 0 0 0 0 0 3525.0 4292.0 294.0 4078.0 305.0 4178.0 37.0 g 0 0 0 0 0 0 614.0 155.0 4098.0 319.0 4043.0 261.0 10.0 t 0 0 0 0 0 0 73.0 59.0 62.0 82.0 67.0 52.0 0.0