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_6nt_mkv1_m3/peak-motifs_oligos_6nt_mkv1_m3.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_6nt_mkv1_m3/peak-motifs_oligos_6nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -CyAGTGTGcm ; Alignment reference a 0 1 0 5 0 0 0 0 0 1 3 c 0 4 3 0 0 0 0 0 0 3 2 g 0 0 0 0 4 0 5 0 5 0 0 t 0 0 2 0 1 5 0 5 0 1 0

MA0143.5_rc_shift1 (SOX2_rc)
; oligos_6nt_mkv1_m3 versus MA0143.5_rc (SOX2_rc); m=1/8; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.578064; -cCATTGT--- ; cor=; Ncor= a 0 10304.0 1656.0 79277.0 1185.0 2412.0 4848.0 1385.0 0 0 0 c 0 54414.0 73372.0 930.0 2002.0 550.0 1243.0 418.0 0 0 0 g 0 6264.0 800.0 732.0 1742.0 1205.0 78356.0 436.0 0 0 0 t 0 14772.0 9926.0 4815.0 80825.0 81587.0 1307.0 83515.0 0 0 0

MA0514.3_rc_shift1 (Sox3_rc)
; oligos_6nt_mkv1_m3 versus MA0514.3_rc (Sox3_rc); m=2/8; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.575414; -cCATTGT--- ; cor=; Ncor= a 0 973.0 187.0 11151.0 69.0 289.0 525.0 89.0 0 0 0 c 0 7664.0 10041.0 104.0 143.0 93.0 178.0 76.0 0 0 0 g 0 1582.0 133.0 150.0 143.0 312.0 11125.0 52.0 0 0 0 t 0 1759.0 1617.0 573.0 11623.0 11284.0 150.0 11761.0 0 0 0

MA1120.2_rc_shift1 (SOX13_rc)
; oligos_6nt_mkv1_m3 versus MA1120.2_rc (SOX13_rc); m=3/8; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.573594; -cCATTGT--- ; cor=; Ncor= a 0 461.0 73.0 4291.0 51.0 118.0 161.0 39.0 0 0 0 c 0 2666.0 3837.0 28.0 63.0 50.0 60.0 40.0 0 0 0 g 0 647.0 57.0 77.0 48.0 55.0 4276.0 22.0 0 0 0 t 0 778.0 585.0 156.0 4390.0 4329.0 55.0 4451.0 0 0 0

MA1152.2_shift1 (SOX15)
; oligos_6nt_mkv1_m3 versus MA1152.2 (SOX15); m=4/8; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.536612; -yywTTGT--- ; cor=; Ncor= a 0 32.0 62.0 631.0 3.0 3.0 83.0 24.0 0 0 0 c 0 554.0 412.0 3.0 3.0 2.0 21.0 2.0 0 0 0 g 0 147.0 26.0 5.0 6.0 2.0 890.0 3.0 0 0 0 t 0 267.0 501.0 362.0 988.0 994.0 5.0 971.0 0 0 0

MA0102.5_rc_shift3 (CEBPA_rc)
; oligos_6nt_mkv1_m3 versus MA0102.5_rc (CEBPA_rc); m=5/8; ncol2=10; w=0; offset=2; strand=R; shift=3; score= 0.5276; ---aTTGTGCA ; cor=; Ncor= a 0 0 0 50992.0 1411.0 1092.0 9787.0 6308.0 2053.0 10928.0 75354.0 c 0 0 0 7312.0 1381.0 340.0 1583.0 6751.0 678.0 57887.0 2365.0 g 0 0 0 16193.0 1034.0 5655.0 61538.0 3535.0 75124.0 936.0 282.0 t 0 0 0 4506.0 75177.0 71916.0 6095.0 62409.0 1148.0 9252.0 1002.0

MA0836.3_rc_shift4 (CEBPD_rc)
; oligos_6nt_mkv1_m3 versus MA0836.3_rc (CEBPD_rc); m=6/8; ncol2=8; w=0; offset=3; strand=R; shift=4; score=0.498385; ----TTGTGCA ; cor=; Ncor= a 0 0 0 0 359.0 185.0 2276.0 1831.0 292.0 1977.0 20939.0 c 0 0 0 0 404.0 75.0 377.0 2625.0 214.0 17309.0 233.0 g 0 0 0 0 315.0 652.0 17458.0 1022.0 20683.0 299.0 81.0 t 0 0 0 0 20374.0 20540.0 1341.0 15974.0 263.0 1867.0 199.0

MA1994.2_rc_shift0 (Nkx2-1_rc)
; oligos_6nt_mkv1_m3 versus MA1994.2_rc (Nkx2-1_rc); m=7/8; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.431759; TCAAGTG---- ; cor=; Ncor= a 541.0 518.0 15157.0 15106.0 316.0 343.0 886.0 0 0 0 0 c 213.0 14172.0 315.0 605.0 118.0 146.0 181.0 0 0 0 0 g 243.0 657.0 518.0 162.0 15640.0 275.0 14886.0 0 0 0 0 t 15245.0 895.0 252.0 369.0 168.0 15478.0 289.0 0 0 0 0

MA0479.2_rc_shift5 (FOXH1_rc)
; oligos_6nt_mkv1_m3 versus MA0479.2_rc (FOXH1_rc); m=8/8; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.406626; -----TGTGKA ; cor=; Ncor= a 0 0 0 0 0 1073.0 0.0 0.0 0.0 64.0 8211.0 c 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 g 0 0 0 0 0 0.0 8211.0 0.0 6797.0 5773.0 0.0 t 0 0 0 0 0 7138.0 0.0 8211.0 1414.0 2374.0 0.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3)				; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -CyAGTGTGcm ; Alignment reference a 0 1 0 5 0 0 0 0 0 1 3 c 0 4 3 0 0 0 0 0 0 3 2 g 0 0 0 0 4 0 5 0 5 0 0 t 0 0 2 0 1 5 0 5 0 1 0
MA0143.5_rc_shift1 (SOX2_rc)				; oligos_6nt_mkv1_m3 versus MA0143.5_rc (SOX2_rc); m=1/8; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.578064; -cCATTGT--- ; cor=; Ncor= a 0 10304.0 1656.0 79277.0 1185.0 2412.0 4848.0 1385.0 0 0 0 c 0 54414.0 73372.0 930.0 2002.0 550.0 1243.0 418.0 0 0 0 g 0 6264.0 800.0 732.0 1742.0 1205.0 78356.0 436.0 0 0 0 t 0 14772.0 9926.0 4815.0 80825.0 81587.0 1307.0 83515.0 0 0 0
MA0514.3_rc_shift1 (Sox3_rc)				; oligos_6nt_mkv1_m3 versus MA0514.3_rc (Sox3_rc); m=2/8; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.575414; -cCATTGT--- ; cor=; Ncor= a 0 973.0 187.0 11151.0 69.0 289.0 525.0 89.0 0 0 0 c 0 7664.0 10041.0 104.0 143.0 93.0 178.0 76.0 0 0 0 g 0 1582.0 133.0 150.0 143.0 312.0 11125.0 52.0 0 0 0 t 0 1759.0 1617.0 573.0 11623.0 11284.0 150.0 11761.0 0 0 0
MA1120.2_rc_shift1 (SOX13_rc)				; oligos_6nt_mkv1_m3 versus MA1120.2_rc (SOX13_rc); m=3/8; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.573594; -cCATTGT--- ; cor=; Ncor= a 0 461.0 73.0 4291.0 51.0 118.0 161.0 39.0 0 0 0 c 0 2666.0 3837.0 28.0 63.0 50.0 60.0 40.0 0 0 0 g 0 647.0 57.0 77.0 48.0 55.0 4276.0 22.0 0 0 0 t 0 778.0 585.0 156.0 4390.0 4329.0 55.0 4451.0 0 0 0
MA1152.2_shift1 (SOX15)				; oligos_6nt_mkv1_m3 versus MA1152.2 (SOX15); m=4/8; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.536612; -yywTTGT--- ; cor=; Ncor= a 0 32.0 62.0 631.0 3.0 3.0 83.0 24.0 0 0 0 c 0 554.0 412.0 3.0 3.0 2.0 21.0 2.0 0 0 0 g 0 147.0 26.0 5.0 6.0 2.0 890.0 3.0 0 0 0 t 0 267.0 501.0 362.0 988.0 994.0 5.0 971.0 0 0 0
MA0102.5_rc_shift3 (CEBPA_rc)				; oligos_6nt_mkv1_m3 versus MA0102.5_rc (CEBPA_rc); m=5/8; ncol2=10; w=0; offset=2; strand=R; shift=3; score= 0.5276; ---aTTGTGCA ; cor=; Ncor= a 0 0 0 50992.0 1411.0 1092.0 9787.0 6308.0 2053.0 10928.0 75354.0 c 0 0 0 7312.0 1381.0 340.0 1583.0 6751.0 678.0 57887.0 2365.0 g 0 0 0 16193.0 1034.0 5655.0 61538.0 3535.0 75124.0 936.0 282.0 t 0 0 0 4506.0 75177.0 71916.0 6095.0 62409.0 1148.0 9252.0 1002.0
MA0836.3_rc_shift4 (CEBPD_rc)				; oligos_6nt_mkv1_m3 versus MA0836.3_rc (CEBPD_rc); m=6/8; ncol2=8; w=0; offset=3; strand=R; shift=4; score=0.498385; ----TTGTGCA ; cor=; Ncor= a 0 0 0 0 359.0 185.0 2276.0 1831.0 292.0 1977.0 20939.0 c 0 0 0 0 404.0 75.0 377.0 2625.0 214.0 17309.0 233.0 g 0 0 0 0 315.0 652.0 17458.0 1022.0 20683.0 299.0 81.0 t 0 0 0 0 20374.0 20540.0 1341.0 15974.0 263.0 1867.0 199.0
MA1994.2_rc_shift0 (Nkx2-1_rc)				; oligos_6nt_mkv1_m3 versus MA1994.2_rc (Nkx2-1_rc); m=7/8; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.431759; TCAAGTG---- ; cor=; Ncor= a 541.0 518.0 15157.0 15106.0 316.0 343.0 886.0 0 0 0 0 c 213.0 14172.0 315.0 605.0 118.0 146.0 181.0 0 0 0 0 g 243.0 657.0 518.0 162.0 15640.0 275.0 14886.0 0 0 0 0 t 15245.0 895.0 252.0 369.0 168.0 15478.0 289.0 0 0 0 0
MA0479.2_rc_shift5 (FOXH1_rc)				; oligos_6nt_mkv1_m3 versus MA0479.2_rc (FOXH1_rc); m=8/8; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.406626; -----TGTGKA ; cor=; Ncor= a 0 0 0 0 0 1073.0 0.0 0.0 0.0 64.0 8211.0 c 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 g 0 0 0 0 0 0.0 8211.0 0.0 6797.0 5773.0 0.0 t 0 0 0 0 0 7138.0 0.0 8211.0 1414.0 2374.0 0.0