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_m1/peak-motifs_oligos_7nt_mkv1_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/2025/05/16/peak-motifs.2025-05-16.175925_2025-05-16.175925_FDRQXr/results/discovered_motifs/oligos_7nt_mkv1_m1/peak-motifs_oligos_7nt_mkv1_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)
; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wkCCTTCCCCma ; Alignment reference a 3 1 0 0 0 0 0 0 0 0 2 2 c 0 0 5 5 0 0 5 5 5 4 2 1 g 0 2 0 0 0 0 0 0 0 0 1 1 t 2 2 0 0 5 5 0 0 0 1 0 1

MA1630.3_rc_shift1 (ZNF281_rc)
; oligos_7nt_mkv1_m1 versus MA1630.3_rc (ZNF281_rc); m=1/9; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.609465; -CCCCTCCCCC- ; cor=; Ncor= a 0 7.0 18.0 1.0 105.0 96.0 1.0 1.0 1.0 1.0 1.0 0 c 0 920.0 940.0 998.0 772.0 1.0 998.0 998.0 963.0 998.0 998.0 0 g 0 27.0 1.0 1.0 1.0 183.0 1.0 1.0 1.0 1.0 1.0 0 t 0 47.0 41.0 1.0 122.0 720.0 1.0 1.0 35.0 1.0 1.0 0

MA1627.2_shift2 (Wt1)
; oligos_7nt_mkv1_m1 versus MA1627.2 (Wt1); m=2/9; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.598446; --cCTCCCCCAC ; cor=; Ncor= a 0 0 839.0 48.0 120.0 21.0 40.0 43.0 850.0 31.0 3294.0 158.0 c 0 0 2948.0 4546.0 69.0 4602.0 4354.0 4252.0 3636.0 4573.0 53.0 3749.0 g 0 0 404.0 58.0 319.0 42.0 75.0 120.0 101.0 46.0 990.0 436.0 t 0 0 500.0 39.0 4183.0 26.0 222.0 276.0 104.0 41.0 354.0 348.0

MA1122.2_rc_shift4 (TFDP1_rc)
; oligos_7nt_mkv1_m1 versus MA1122.2_rc (TFDP1_rc); m=3/9; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.491774; ----TTCCCGCs ; cor=; Ncor= a 0 0 0 0 55.0 30.0 29.0 26.0 7.0 71.0 26.0 120.0 c 0 0 0 0 137.0 98.0 1919.0 1865.0 1932.0 22.0 1862.0 940.0 g 0 0 0 0 170.0 24.0 32.0 80.0 54.0 1886.0 71.0 684.0 t 0 0 0 0 1645.0 1855.0 27.0 36.0 14.0 28.0 48.0 263.0

MA0471.3_rc_shift4 (E2F6_rc)
; oligos_7nt_mkv1_m1 versus MA0471.3_rc (E2F6_rc); m=4/9; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.475417; ----TTCCCGCC ; cor=; Ncor= a 0 0 0 0 757.0 268.0 296.0 353.0 813.0 2125.0 205.0 453.0 c 0 0 0 0 5021.0 2322.0 31614.0 31973.0 30573.0 693.0 31790.0 29387.0 g 0 0 0 0 1595.0 1171.0 834.0 434.0 539.0 26424.0 837.0 1148.0 t 0 0 0 0 25725.0 29337.0 354.0 338.0 1173.0 3856.0 266.0 2110.0

MA1117.2_shift3 (RELB)
; oligos_7nt_mkv1_m1 versus MA1117.2 (RELB); m=5/9; ncol2=7; w=0; offset=3; strand=D; shift=3; score=0.468964; ---ATTCCCC-- ; cor=; Ncor= a 0 0 0 2833.0 210.0 90.0 144.0 92.0 146.0 79.0 0 0 c 0 0 0 127.0 107.0 103.0 2928.0 3098.0 3013.0 3035.0 0 0 g 0 0 0 157.0 159.0 53.0 40.0 28.0 58.0 107.0 0 0 t 0 0 0 173.0 2814.0 3044.0 178.0 72.0 73.0 69.0 0 0

MA1154.2_shift2 (ZNF282)
; oligos_7nt_mkv1_m1 versus MA1154.2 (ZNF282); m=6/9; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.43362; --cTTTCCCmyA ; cor=; Ncor= a 0 0 21.0 39.0 16.0 3.0 0.0 0.0 0.0 140.0 12.0 256.0 c 0 0 196.0 21.0 0.0 2.0 209.0 208.0 205.0 99.0 132.0 3.0 g 0 0 50.0 7.0 8.0 3.0 2.0 0.0 3.0 0.0 2.0 37.0 t 0 0 45.0 378.0 387.0 380.0 0.0 1.0 2.0 21.0 126.0 61.0

MA0528.3_rc_shift1 (ZNF263_rc)
; oligos_7nt_mkv1_m1 versus MA0528.3_rc (ZNF263_rc); m=7/9; ncol2=7; w=0; offset=1; strand=R; shift=1; score=0.431713; -TCCTCCC---- ; cor=; Ncor= a 0 638.0 717.0 1672.0 620.0 986.0 1192.0 1270.0 0 0 0 0 c 0 1448.0 52741.0 52875.0 163.0 53435.0 52818.0 51804.0 0 0 0 0 g 0 1758.0 2190.0 966.0 1660.0 972.0 1544.0 1659.0 0 0 0 0 t 0 52499.0 695.0 830.0 53900.0 950.0 789.0 1610.0 0 0 0 0

MA1121.2_shift1 (TEAD2)
; oligos_7nt_mkv1_m1 versus MA1121.2 (TEAD2); m=8/9; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.416732; -ACATTCC---- ; cor=; Ncor= a 0 441.0 39.0 517.0 2.0 15.0 8.0 8.0 0 0 0 0 c 0 17.0 478.0 5.0 10.0 8.0 500.0 513.0 0 0 0 0 g 0 70.0 14.0 11.0 6.0 9.0 10.0 3.0 0 0 0 0 t 0 14.0 11.0 9.0 524.0 510.0 24.0 18.0 0 0 0 0

MA1116.2_rc_shift4 (RBPJ_rc)
; oligos_7nt_mkv1_m1 versus MA1116.2_rc (RBPJ_rc); m=9/9; ncol2=6; w=0; offset=4; strand=R; shift=4; score=0.40085; ----TTCCCA-- ; cor=; Ncor= a 0 0 0 0 4.0 29.0 78.0 60.0 1.0 2386.0 0 0 c 0 0 0 0 1.0 4.0 2309.0 2313.0 2341.0 2.0 0 0 g 0 0 0 0 15.0 0.0 8.0 20.0 25.0 12.0 0 0 t 0 0 0 0 2382.0 2369.0 7.0 9.0 35.0 2.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1)				; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wkCCTTCCCCma ; Alignment reference a 3 1 0 0 0 0 0 0 0 0 2 2 c 0 0 5 5 0 0 5 5 5 4 2 1 g 0 2 0 0 0 0 0 0 0 0 1 1 t 2 2 0 0 5 5 0 0 0 1 0 1
MA1630.3_rc_shift1 (ZNF281_rc)				; oligos_7nt_mkv1_m1 versus MA1630.3_rc (ZNF281_rc); m=1/9; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.609465; -CCCCTCCCCC- ; cor=; Ncor= a 0 7.0 18.0 1.0 105.0 96.0 1.0 1.0 1.0 1.0 1.0 0 c 0 920.0 940.0 998.0 772.0 1.0 998.0 998.0 963.0 998.0 998.0 0 g 0 27.0 1.0 1.0 1.0 183.0 1.0 1.0 1.0 1.0 1.0 0 t 0 47.0 41.0 1.0 122.0 720.0 1.0 1.0 35.0 1.0 1.0 0
MA1627.2_shift2 (Wt1)				; oligos_7nt_mkv1_m1 versus MA1627.2 (Wt1); m=2/9; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.598446; --cCTCCCCCAC ; cor=; Ncor= a 0 0 839.0 48.0 120.0 21.0 40.0 43.0 850.0 31.0 3294.0 158.0 c 0 0 2948.0 4546.0 69.0 4602.0 4354.0 4252.0 3636.0 4573.0 53.0 3749.0 g 0 0 404.0 58.0 319.0 42.0 75.0 120.0 101.0 46.0 990.0 436.0 t 0 0 500.0 39.0 4183.0 26.0 222.0 276.0 104.0 41.0 354.0 348.0
MA1122.2_rc_shift4 (TFDP1_rc)				; oligos_7nt_mkv1_m1 versus MA1122.2_rc (TFDP1_rc); m=3/9; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.491774; ----TTCCCGCs ; cor=; Ncor= a 0 0 0 0 55.0 30.0 29.0 26.0 7.0 71.0 26.0 120.0 c 0 0 0 0 137.0 98.0 1919.0 1865.0 1932.0 22.0 1862.0 940.0 g 0 0 0 0 170.0 24.0 32.0 80.0 54.0 1886.0 71.0 684.0 t 0 0 0 0 1645.0 1855.0 27.0 36.0 14.0 28.0 48.0 263.0
MA0471.3_rc_shift4 (E2F6_rc)				; oligos_7nt_mkv1_m1 versus MA0471.3_rc (E2F6_rc); m=4/9; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.475417; ----TTCCCGCC ; cor=; Ncor= a 0 0 0 0 757.0 268.0 296.0 353.0 813.0 2125.0 205.0 453.0 c 0 0 0 0 5021.0 2322.0 31614.0 31973.0 30573.0 693.0 31790.0 29387.0 g 0 0 0 0 1595.0 1171.0 834.0 434.0 539.0 26424.0 837.0 1148.0 t 0 0 0 0 25725.0 29337.0 354.0 338.0 1173.0 3856.0 266.0 2110.0
MA1117.2_shift3 (RELB)				; oligos_7nt_mkv1_m1 versus MA1117.2 (RELB); m=5/9; ncol2=7; w=0; offset=3; strand=D; shift=3; score=0.468964; ---ATTCCCC-- ; cor=; Ncor= a 0 0 0 2833.0 210.0 90.0 144.0 92.0 146.0 79.0 0 0 c 0 0 0 127.0 107.0 103.0 2928.0 3098.0 3013.0 3035.0 0 0 g 0 0 0 157.0 159.0 53.0 40.0 28.0 58.0 107.0 0 0 t 0 0 0 173.0 2814.0 3044.0 178.0 72.0 73.0 69.0 0 0
MA1154.2_shift2 (ZNF282)				; oligos_7nt_mkv1_m1 versus MA1154.2 (ZNF282); m=6/9; ncol2=15; w=0; offset=2; strand=D; shift=2; score=0.43362; --cTTTCCCmyA ; cor=; Ncor= a 0 0 21.0 39.0 16.0 3.0 0.0 0.0 0.0 140.0 12.0 256.0 c 0 0 196.0 21.0 0.0 2.0 209.0 208.0 205.0 99.0 132.0 3.0 g 0 0 50.0 7.0 8.0 3.0 2.0 0.0 3.0 0.0 2.0 37.0 t 0 0 45.0 378.0 387.0 380.0 0.0 1.0 2.0 21.0 126.0 61.0
MA0528.3_rc_shift1 (ZNF263_rc)				; oligos_7nt_mkv1_m1 versus MA0528.3_rc (ZNF263_rc); m=7/9; ncol2=7; w=0; offset=1; strand=R; shift=1; score=0.431713; -TCCTCCC---- ; cor=; Ncor= a 0 638.0 717.0 1672.0 620.0 986.0 1192.0 1270.0 0 0 0 0 c 0 1448.0 52741.0 52875.0 163.0 53435.0 52818.0 51804.0 0 0 0 0 g 0 1758.0 2190.0 966.0 1660.0 972.0 1544.0 1659.0 0 0 0 0 t 0 52499.0 695.0 830.0 53900.0 950.0 789.0 1610.0 0 0 0 0
MA1121.2_shift1 (TEAD2)				; oligos_7nt_mkv1_m1 versus MA1121.2 (TEAD2); m=8/9; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.416732; -ACATTCC---- ; cor=; Ncor= a 0 441.0 39.0 517.0 2.0 15.0 8.0 8.0 0 0 0 0 c 0 17.0 478.0 5.0 10.0 8.0 500.0 513.0 0 0 0 0 g 0 70.0 14.0 11.0 6.0 9.0 10.0 3.0 0 0 0 0 t 0 14.0 11.0 9.0 524.0 510.0 24.0 18.0 0 0 0 0
MA1116.2_rc_shift4 (RBPJ_rc)				; oligos_7nt_mkv1_m1 versus MA1116.2_rc (RBPJ_rc); m=9/9; ncol2=6; w=0; offset=4; strand=R; shift=4; score=0.40085; ----TTCCCA-- ; cor=; Ncor= a 0 0 0 0 4.0 29.0 78.0 60.0 1.0 2386.0 0 0 c 0 0 0 0 1.0 4.0 2309.0 2313.0 2341.0 2.0 0 0 g 0 0 0 0 15.0 0.0 8.0 20.0 25.0 12.0 0 0 t 0 0 0 0 2382.0 2369.0 7.0 9.0 35.0 2.0 0 0