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.2025-05-16.184046_2025-05-16.184046_ZEi16E/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_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.2025-05-16.184046_2025-05-16.184046_ZEi16E/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift3 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---gsGATTACAGgy ; Alignment reference a 0 0 0 2 0 0 11 0 0 11 0 11 1 1 1 c 0 0 0 0 3 0 0 1 1 0 10 0 0 2 6 g 0 0 0 8 8 12 1 0 0 1 0 0 11 8 2 t 0 0 0 2 1 0 0 11 11 0 2 1 0 1 3

MA1547.2_rc_shift3 (PITX2_rc)
; oligos_7nt_mkv2_m4 versus MA1547.2_rc (PITX2_rc); m=1/12; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.572993; ---rGGATTAr---- ; cor=; Ncor= a 0 0 0 2222.0 189.0 0.0 8019.0 0.0 0.0 8019.0 3859.0 0 0 0 0 c 0 0 0 786.0 0.0 0.0 668.0 0.0 0.0 0.0 454.0 0 0 0 0 g 0 0 0 4129.0 8019.0 8019.0 0.0 0.0 0.0 51.0 2782.0 0 0 0 0 t 0 0 0 881.0 0.0 0.0 0.0 8019.0 8019.0 0.0 924.0 0 0 0 0

MA0712.3_shift3 (OTX2)
; oligos_7nt_mkv2_m4 versus MA0712.3 (OTX2); m=2/12; ncol2=7; w=0; offset=0; strand=D; shift=3; score=0.566461; ---rGGATTA----- ; cor=; Ncor= a 0 0 0 37155.0 5435.0 2918.0 116411.0 765.0 1913.0 114798.0 0 0 0 0 0 c 0 0 0 5322.0 827.0 1620.0 2220.0 598.0 1771.0 636.0 0 0 0 0 0 g 0 0 0 55814.0 111741.0 113842.0 706.0 787.0 1407.0 1302.0 0 0 0 0 0 t 0 0 0 22388.0 2676.0 2299.0 1342.0 118529.0 115588.0 3943.0 0 0 0 0 0

MA0629.2_rc_shift6 (Rhox11_rc)
; oligos_7nt_mkv2_m4 versus MA0629.2_rc (Rhox11_rc); m=3/12; ncol2=9; w=0; offset=3; strand=R; shift=6; score=0.527764; ------wTwACAGCr ; cor=; Ncor= a 0 0 0 0 0 0 36.0 15.0 43.0 99.0 2.0 99.0 0.0 1.0 25.0 c 0 0 0 0 0 0 1.0 3.0 0.0 0.0 94.0 1.0 15.0 95.0 6.0 g 0 0 0 0 0 0 10.0 4.0 0.0 1.0 0.0 0.0 76.0 1.0 56.0 t 0 0 0 0 0 0 52.0 78.0 56.0 1.0 4.0 1.0 9.0 3.0 13.0

MA0711.2_rc_shift4 (OTX1_rc)
; oligos_7nt_mkv2_m4 versus MA0711.2_rc (OTX1_rc); m=4/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.494715; ----gGATTA----- ; cor=; Ncor= a 0 0 0 0 3363.0 378.0 23441.0 0.0 544.0 23441.0 0 0 0 0 0 c 0 0 0 0 8662.0 659.0 3160.0 0.0 254.0 0.0 0 0 0 0 0 g 0 0 0 0 23441.0 23441.0 0.0 0.0 0.0 90.0 0 0 0 0 0 t 0 0 0 0 789.0 647.0 243.0 23441.0 23441.0 745.0 0 0 0 0 0

MA0467.3_shift4 (Crx)
; oligos_7nt_mkv2_m4 versus MA0467.3 (Crx); m=5/12; ncol2=6; w=0; offset=1; strand=D; shift=4; score=0.491146; ----GGATTA----- ; cor=; Ncor= a 0 0 0 0 19.0 26.0 4227.0 11.0 50.0 4241.0 0 0 0 0 0 c 0 0 0 0 155.0 36.0 17.0 32.0 25.0 25.0 0 0 0 0 0 g 0 0 0 0 4129.0 4200.0 42.0 9.0 20.0 23.0 0 0 0 0 0 t 0 0 0 0 30.0 71.0 47.0 4281.0 4238.0 44.0 0 0 0 0 0

MA0682.3_rc_shift4 (PITX1_rc)
; oligos_7nt_mkv2_m4 versus MA0682.3_rc (PITX1_rc); m=6/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.489626; ----GGATTA----- ; cor=; Ncor= a 0 0 0 0 547.0 141.0 10531.0 0.0 0.0 10531.0 0 0 0 0 0 c 0 0 0 0 134.0 0.0 1039.0 0.0 0.0 0.0 0 0 0 0 0 g 0 0 0 0 10531.0 10531.0 0.0 0.0 0.0 0.0 0 0 0 0 0 t 0 0 0 0 68.0 143.0 0.0 10531.0 10531.0 0.0 0 0 0 0 0

MA0648.2_rc_shift4 (GSC_rc)
; oligos_7nt_mkv2_m4 versus MA0648.2_rc (GSC_rc); m=7/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.489392; ----GGATTA----- ; cor=; Ncor= a 0 0 0 0 1099.0 787.0 6081.0 0.0 89.0 6081.0 0 0 0 0 0 c 0 0 0 0 828.0 452.0 144.0 0.0 176.0 0.0 0 0 0 0 0 g 0 0 0 0 6081.0 6081.0 25.0 0.0 71.0 54.0 0 0 0 0 0 t 0 0 0 0 315.0 416.0 0.0 6081.0 6081.0 0.0 0 0 0 0 0

MA0891.2_rc_shift4 (GSC2_rc)
; oligos_7nt_mkv2_m4 versus MA0891.2_rc (GSC2_rc); m=8/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.488928; ----gGATTA----- ; cor=; Ncor= a 0 0 0 0 439.0 204.0 2016.0 132.0 201.0 2016.0 0 0 0 0 0 c 0 0 0 0 422.0 179.0 145.0 0.0 56.0 0.0 0 0 0 0 0 g 0 0 0 0 2016.0 2016.0 41.0 11.0 87.0 0.0 0 0 0 0 0 t 0 0 0 0 182.0 255.0 0.0 2016.0 2016.0 116.0 0 0 0 0 0

MA0714.2_rc_shift4 (PITX3_rc)
; oligos_7nt_mkv2_m4 versus MA0714.2_rc (PITX3_rc); m=9/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.48766; ----GGATTA----- ; cor=; Ncor= a 0 0 0 0 968.0 236.0 6253.0 0.0 158.0 6253.0 0 0 0 0 0 c 0 0 0 0 239.0 166.0 1101.0 15.0 260.0 9.0 0 0 0 0 0 g 0 0 0 0 6253.0 6253.0 138.0 0.0 32.0 51.0 0 0 0 0 0 t 0 0 0 0 227.0 318.0 262.0 6253.0 6253.0 493.0 0 0 0 0 0

MA0719.2_rc_shift4 (RHOXF1_rc)
; oligos_7nt_mkv2_m4 versus MA0719.2_rc (RHOXF1_rc); m=10/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.44298; ----GGmTyA----- ; cor=; Ncor= a 0 0 0 0 2275.0 0.0 7376.0 0.0 1367.0 10916.0 0 0 0 0 0 c 0 0 0 0 0.0 0.0 3540.0 0.0 5373.0 478.0 0 0 0 0 0 g 0 0 0 0 10916.0 10916.0 0.0 0.0 0.0 0.0 0 0 0 0 0 t 0 0 0 0 0.0 0.0 0.0 10916.0 5543.0 2837.0 0 0 0 0 0

MA0883.2_shift0 (Dmbx1)
; oligos_7nt_mkv2_m4 versus MA0883.2 (Dmbx1); m=11/12; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.427826; rwmmGGATTA----- ; cor=; Ncor= a 49.0 49.0 25.0 28.0 6.0 0.0 94.0 0.0 1.0 97.0 0 0 0 0 0 c 8.0 8.0 36.0 50.0 1.0 1.0 6.0 0.0 1.0 0.0 0 0 0 0 0 g 31.0 13.0 18.0 20.0 93.0 99.0 0.0 0.0 0.0 0.0 0 0 0 0 0 t 12.0 30.0 21.0 3.0 0.0 0.0 0.0 99.0 98.0 3.0 0 0 0 0 0

MA0056.3_rc_shift1 (MZF1_rc)
; oligos_7nt_mkv2_m4 versus MA0056.3_rc (MZF1_rc); m=12/12; ncol2=8; w=-2; offset=-2; strand=R; shift=1; score=0.405882; -TGGGGATT------ ; cor=; Ncor= a 0 1111.0 369.0 154.0 114.0 93.0 7982.0 282.0 372.0 0 0 0 0 0 0 c 0 484.0 83.0 58.0 54.0 100.0 98.0 385.0 999.0 0 0 0 0 0 0 g 0 611.0 7673.0 7919.0 7939.0 7949.0 56.0 426.0 1016.0 0 0 0 0 0 0 t 0 6036.0 117.0 111.0 135.0 100.0 106.0 7149.0 5855.0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift3 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---gsGATTACAGgy ; Alignment reference a 0 0 0 2 0 0 11 0 0 11 0 11 1 1 1 c 0 0 0 0 3 0 0 1 1 0 10 0 0 2 6 g 0 0 0 8 8 12 1 0 0 1 0 0 11 8 2 t 0 0 0 2 1 0 0 11 11 0 2 1 0 1 3
MA1547.2_rc_shift3 (PITX2_rc)				; oligos_7nt_mkv2_m4 versus MA1547.2_rc (PITX2_rc); m=1/12; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.572993; ---rGGATTAr---- ; cor=; Ncor= a 0 0 0 2222.0 189.0 0.0 8019.0 0.0 0.0 8019.0 3859.0 0 0 0 0 c 0 0 0 786.0 0.0 0.0 668.0 0.0 0.0 0.0 454.0 0 0 0 0 g 0 0 0 4129.0 8019.0 8019.0 0.0 0.0 0.0 51.0 2782.0 0 0 0 0 t 0 0 0 881.0 0.0 0.0 0.0 8019.0 8019.0 0.0 924.0 0 0 0 0
MA0712.3_shift3 (OTX2)				; oligos_7nt_mkv2_m4 versus MA0712.3 (OTX2); m=2/12; ncol2=7; w=0; offset=0; strand=D; shift=3; score=0.566461; ---rGGATTA----- ; cor=; Ncor= a 0 0 0 37155.0 5435.0 2918.0 116411.0 765.0 1913.0 114798.0 0 0 0 0 0 c 0 0 0 5322.0 827.0 1620.0 2220.0 598.0 1771.0 636.0 0 0 0 0 0 g 0 0 0 55814.0 111741.0 113842.0 706.0 787.0 1407.0 1302.0 0 0 0 0 0 t 0 0 0 22388.0 2676.0 2299.0 1342.0 118529.0 115588.0 3943.0 0 0 0 0 0
MA0629.2_rc_shift6 (Rhox11_rc)				; oligos_7nt_mkv2_m4 versus MA0629.2_rc (Rhox11_rc); m=3/12; ncol2=9; w=0; offset=3; strand=R; shift=6; score=0.527764; ------wTwACAGCr ; cor=; Ncor= a 0 0 0 0 0 0 36.0 15.0 43.0 99.0 2.0 99.0 0.0 1.0 25.0 c 0 0 0 0 0 0 1.0 3.0 0.0 0.0 94.0 1.0 15.0 95.0 6.0 g 0 0 0 0 0 0 10.0 4.0 0.0 1.0 0.0 0.0 76.0 1.0 56.0 t 0 0 0 0 0 0 52.0 78.0 56.0 1.0 4.0 1.0 9.0 3.0 13.0
MA0711.2_rc_shift4 (OTX1_rc)				; oligos_7nt_mkv2_m4 versus MA0711.2_rc (OTX1_rc); m=4/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.494715; ----gGATTA----- ; cor=; Ncor= a 0 0 0 0 3363.0 378.0 23441.0 0.0 544.0 23441.0 0 0 0 0 0 c 0 0 0 0 8662.0 659.0 3160.0 0.0 254.0 0.0 0 0 0 0 0 g 0 0 0 0 23441.0 23441.0 0.0 0.0 0.0 90.0 0 0 0 0 0 t 0 0 0 0 789.0 647.0 243.0 23441.0 23441.0 745.0 0 0 0 0 0
MA0467.3_shift4 (Crx)				; oligos_7nt_mkv2_m4 versus MA0467.3 (Crx); m=5/12; ncol2=6; w=0; offset=1; strand=D; shift=4; score=0.491146; ----GGATTA----- ; cor=; Ncor= a 0 0 0 0 19.0 26.0 4227.0 11.0 50.0 4241.0 0 0 0 0 0 c 0 0 0 0 155.0 36.0 17.0 32.0 25.0 25.0 0 0 0 0 0 g 0 0 0 0 4129.0 4200.0 42.0 9.0 20.0 23.0 0 0 0 0 0 t 0 0 0 0 30.0 71.0 47.0 4281.0 4238.0 44.0 0 0 0 0 0
MA0682.3_rc_shift4 (PITX1_rc)				; oligos_7nt_mkv2_m4 versus MA0682.3_rc (PITX1_rc); m=6/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.489626; ----GGATTA----- ; cor=; Ncor= a 0 0 0 0 547.0 141.0 10531.0 0.0 0.0 10531.0 0 0 0 0 0 c 0 0 0 0 134.0 0.0 1039.0 0.0 0.0 0.0 0 0 0 0 0 g 0 0 0 0 10531.0 10531.0 0.0 0.0 0.0 0.0 0 0 0 0 0 t 0 0 0 0 68.0 143.0 0.0 10531.0 10531.0 0.0 0 0 0 0 0
MA0648.2_rc_shift4 (GSC_rc)				; oligos_7nt_mkv2_m4 versus MA0648.2_rc (GSC_rc); m=7/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.489392; ----GGATTA----- ; cor=; Ncor= a 0 0 0 0 1099.0 787.0 6081.0 0.0 89.0 6081.0 0 0 0 0 0 c 0 0 0 0 828.0 452.0 144.0 0.0 176.0 0.0 0 0 0 0 0 g 0 0 0 0 6081.0 6081.0 25.0 0.0 71.0 54.0 0 0 0 0 0 t 0 0 0 0 315.0 416.0 0.0 6081.0 6081.0 0.0 0 0 0 0 0
MA0891.2_rc_shift4 (GSC2_rc)				; oligos_7nt_mkv2_m4 versus MA0891.2_rc (GSC2_rc); m=8/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.488928; ----gGATTA----- ; cor=; Ncor= a 0 0 0 0 439.0 204.0 2016.0 132.0 201.0 2016.0 0 0 0 0 0 c 0 0 0 0 422.0 179.0 145.0 0.0 56.0 0.0 0 0 0 0 0 g 0 0 0 0 2016.0 2016.0 41.0 11.0 87.0 0.0 0 0 0 0 0 t 0 0 0 0 182.0 255.0 0.0 2016.0 2016.0 116.0 0 0 0 0 0
MA0714.2_rc_shift4 (PITX3_rc)				; oligos_7nt_mkv2_m4 versus MA0714.2_rc (PITX3_rc); m=9/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.48766; ----GGATTA----- ; cor=; Ncor= a 0 0 0 0 968.0 236.0 6253.0 0.0 158.0 6253.0 0 0 0 0 0 c 0 0 0 0 239.0 166.0 1101.0 15.0 260.0 9.0 0 0 0 0 0 g 0 0 0 0 6253.0 6253.0 138.0 0.0 32.0 51.0 0 0 0 0 0 t 0 0 0 0 227.0 318.0 262.0 6253.0 6253.0 493.0 0 0 0 0 0
MA0719.2_rc_shift4 (RHOXF1_rc)				; oligos_7nt_mkv2_m4 versus MA0719.2_rc (RHOXF1_rc); m=10/12; ncol2=6; w=0; offset=1; strand=R; shift=4; score=0.44298; ----GGmTyA----- ; cor=; Ncor= a 0 0 0 0 2275.0 0.0 7376.0 0.0 1367.0 10916.0 0 0 0 0 0 c 0 0 0 0 0.0 0.0 3540.0 0.0 5373.0 478.0 0 0 0 0 0 g 0 0 0 0 10916.0 10916.0 0.0 0.0 0.0 0.0 0 0 0 0 0 t 0 0 0 0 0.0 0.0 0.0 10916.0 5543.0 2837.0 0 0 0 0 0
MA0883.2_shift0 (Dmbx1)				; oligos_7nt_mkv2_m4 versus MA0883.2 (Dmbx1); m=11/12; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.427826; rwmmGGATTA----- ; cor=; Ncor= a 49.0 49.0 25.0 28.0 6.0 0.0 94.0 0.0 1.0 97.0 0 0 0 0 0 c 8.0 8.0 36.0 50.0 1.0 1.0 6.0 0.0 1.0 0.0 0 0 0 0 0 g 31.0 13.0 18.0 20.0 93.0 99.0 0.0 0.0 0.0 0.0 0 0 0 0 0 t 12.0 30.0 21.0 3.0 0.0 0.0 0.0 99.0 98.0 3.0 0 0 0 0 0
MA0056.3_rc_shift1 (MZF1_rc)				; oligos_7nt_mkv2_m4 versus MA0056.3_rc (MZF1_rc); m=12/12; ncol2=8; w=-2; offset=-2; strand=R; shift=1; score=0.405882; -TGGGGATT------ ; cor=; Ncor= a 0 1111.0 369.0 154.0 114.0 93.0 7982.0 282.0 372.0 0 0 0 0 0 0 c 0 484.0 83.0 58.0 54.0 100.0 98.0 385.0 999.0 0 0 0 0 0 0 g 0 611.0 7673.0 7919.0 7939.0 7949.0 56.0 426.0 1016.0 0 0 0 0 0 0 t 0 6036.0 117.0 111.0 135.0 100.0 106.0 7149.0 5855.0 0 0 0 0 0 0