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_m2/peak-motifs_oligos_7nt_mkv1_m2.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_m2/peak-motifs_oligos_7nt_mkv1_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift1 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -CyAGTGTGCmm ; Alignment reference a 0 0 0 3 0 0 0 0 0 0 2 1 c 0 3 2 0 0 0 0 0 0 3 1 2 g 0 0 0 0 3 0 3 0 3 0 0 0 t 0 0 1 0 0 3 0 3 0 0 0 0

MA0143.5_rc_shift1 (SOX2_rc)
; oligos_7nt_mkv1_m2 versus MA0143.5_rc (SOX2_rc); m=1/5; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.482431; -cCATTGT---- ; cor=; Ncor= a 0 10304.0 1656.0 79277.0 1185.0 2412.0 4848.0 1385.0 0 0 0 0 c 0 54414.0 73372.0 930.0 2002.0 550.0 1243.0 418.0 0 0 0 0 g 0 6264.0 800.0 732.0 1742.0 1205.0 78356.0 436.0 0 0 0 0 t 0 14772.0 9926.0 4815.0 80825.0 81587.0 1307.0 83515.0 0 0 0 0

MA0514.3_rc_shift1 (Sox3_rc)
; oligos_7nt_mkv1_m2 versus MA0514.3_rc (Sox3_rc); m=2/5; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.480115; -cCATTGT---- ; cor=; Ncor= a 0 973.0 187.0 11151.0 69.0 289.0 525.0 89.0 0 0 0 0 c 0 7664.0 10041.0 104.0 143.0 93.0 178.0 76.0 0 0 0 0 g 0 1582.0 133.0 150.0 143.0 312.0 11125.0 52.0 0 0 0 0 t 0 1759.0 1617.0 573.0 11623.0 11284.0 150.0 11761.0 0 0 0 0

MA1120.2_rc_shift1 (SOX13_rc)
; oligos_7nt_mkv1_m2 versus MA1120.2_rc (SOX13_rc); m=3/5; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.476649; -cCATTGT---- ; cor=; Ncor= a 0 461.0 73.0 4291.0 51.0 118.0 161.0 39.0 0 0 0 0 c 0 2666.0 3837.0 28.0 63.0 50.0 60.0 40.0 0 0 0 0 g 0 647.0 57.0 77.0 48.0 55.0 4276.0 22.0 0 0 0 0 t 0 778.0 585.0 156.0 4390.0 4329.0 55.0 4451.0 0 0 0 0

MA0738.2_shift6 (HIC2)
; oligos_7nt_mkv1_m2 versus MA0738.2 (HIC2); m=4/5; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.440006; ------rTGCCM ; cor=; Ncor= a 0 0 0 0 0 0 2606.0 0.0 494.0 23.0 435.0 1466.0 c 0 0 0 0 0 0 394.0 117.0 354.0 4891.0 4891.0 3425.0 g 0 0 0 0 0 0 2285.0 0.0 4891.0 14.0 0.0 0.0 t 0 0 0 0 0 0 367.0 4891.0 151.0 0.0 59.0 0.0

MA1994.2_rc_shift0 (Nkx2-1_rc)
; oligos_7nt_mkv1_m2 versus MA1994.2_rc (Nkx2-1_rc); m=5/5; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.407725; TCAAGTG----- ; cor=; Ncor= a 541.0 518.0 15157.0 15106.0 316.0 343.0 886.0 0 0 0 0 0 c 213.0 14172.0 315.0 605.0 118.0 146.0 181.0 0 0 0 0 0 g 243.0 657.0 518.0 162.0 15640.0 275.0 14886.0 0 0 0 0 0 t 15245.0 895.0 252.0 369.0 168.0 15478.0 289.0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m2_shift1 (oligos_7nt_mkv1_m2)				; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=1; ncol=12; -CyAGTGTGCmm ; Alignment reference a 0 0 0 3 0 0 0 0 0 0 2 1 c 0 3 2 0 0 0 0 0 0 3 1 2 g 0 0 0 0 3 0 3 0 3 0 0 0 t 0 0 1 0 0 3 0 3 0 0 0 0
MA0143.5_rc_shift1 (SOX2_rc)				; oligos_7nt_mkv1_m2 versus MA0143.5_rc (SOX2_rc); m=1/5; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.482431; -cCATTGT---- ; cor=; Ncor= a 0 10304.0 1656.0 79277.0 1185.0 2412.0 4848.0 1385.0 0 0 0 0 c 0 54414.0 73372.0 930.0 2002.0 550.0 1243.0 418.0 0 0 0 0 g 0 6264.0 800.0 732.0 1742.0 1205.0 78356.0 436.0 0 0 0 0 t 0 14772.0 9926.0 4815.0 80825.0 81587.0 1307.0 83515.0 0 0 0 0
MA0514.3_rc_shift1 (Sox3_rc)				; oligos_7nt_mkv1_m2 versus MA0514.3_rc (Sox3_rc); m=2/5; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.480115; -cCATTGT---- ; cor=; Ncor= a 0 973.0 187.0 11151.0 69.0 289.0 525.0 89.0 0 0 0 0 c 0 7664.0 10041.0 104.0 143.0 93.0 178.0 76.0 0 0 0 0 g 0 1582.0 133.0 150.0 143.0 312.0 11125.0 52.0 0 0 0 0 t 0 1759.0 1617.0 573.0 11623.0 11284.0 150.0 11761.0 0 0 0 0
MA1120.2_rc_shift1 (SOX13_rc)				; oligos_7nt_mkv1_m2 versus MA1120.2_rc (SOX13_rc); m=3/5; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.476649; -cCATTGT---- ; cor=; Ncor= a 0 461.0 73.0 4291.0 51.0 118.0 161.0 39.0 0 0 0 0 c 0 2666.0 3837.0 28.0 63.0 50.0 60.0 40.0 0 0 0 0 g 0 647.0 57.0 77.0 48.0 55.0 4276.0 22.0 0 0 0 0 t 0 778.0 585.0 156.0 4390.0 4329.0 55.0 4451.0 0 0 0 0
MA0738.2_shift6 (HIC2)				; oligos_7nt_mkv1_m2 versus MA0738.2 (HIC2); m=4/5; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.440006; ------rTGCCM ; cor=; Ncor= a 0 0 0 0 0 0 2606.0 0.0 494.0 23.0 435.0 1466.0 c 0 0 0 0 0 0 394.0 117.0 354.0 4891.0 4891.0 3425.0 g 0 0 0 0 0 0 2285.0 0.0 4891.0 14.0 0.0 0.0 t 0 0 0 0 0 0 367.0 4891.0 151.0 0.0 59.0 0.0
MA1994.2_rc_shift0 (Nkx2-1_rc)				; oligos_7nt_mkv1_m2 versus MA1994.2_rc (Nkx2-1_rc); m=5/5; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.407725; TCAAGTG----- ; cor=; Ncor= a 541.0 518.0 15157.0 15106.0 316.0 343.0 886.0 0 0 0 0 0 c 213.0 14172.0 315.0 605.0 118.0 146.0 181.0 0 0 0 0 0 g 243.0 657.0 518.0 162.0 15640.0 275.0 14886.0 0 0 0 0 0 t 15245.0 895.0 252.0 369.0 168.0 15478.0 289.0 0 0 0 0 0