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.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_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.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_7nt_mkv1_m3/peak-motifs_oligos_7nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift1 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -ssCACACGCmss ; Alignment reference a 0 1 2 0 12 0 14 0 0 0 9 3 2 c 0 8 8 15 1 14 2 16 0 16 4 4 7 g 0 5 5 1 3 1 0 0 16 0 2 7 6 t 0 2 1 0 0 1 0 0 0 0 1 2 1

MA1107.3_shift1 (KLF9)
; oligos_7nt_mkv1_m3 versus MA1107.3 (KLF9); m=1/10; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.673001; -gCCACACCCAC- ; cor=; Ncor= a 0 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 18837.0 792.0 0 c 0 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 4339.0 20644.0 0 g 0 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 852.0 1778.0 0 t 0 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0 1551.0 2365.0 0

MA0472.2_shift0 (EGR2)
; oligos_7nt_mkv1_m3 versus MA0472.2 (EGR2); m=2/10; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.598681; mCGCCCACGCa-- ; cor=; Ncor= a 1157.0 0.0 295.0 6.0 24.0 0.0 2147.0 0.0 106.0 4.0 1731.0 0 0 c 679.0 1551.0 0.0 1558.0 1554.0 1468.0 110.0 1573.0 0.0 1585.0 157.0 0 0 g 94.0 28.0 3731.0 25.0 15.0 38.0 26.0 2.0 4034.0 20.0 542.0 0 0 t 142.0 73.0 222.0 29.0 13.0 277.0 2.0 23.0 171.0 115.0 430.0 0 0

MA0733.2_shift0 (EGR4)
; oligos_7nt_mkv1_m3 versus MA0733.2 (EGR4); m=3/10; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.595092; mCGCCCACGCA-- ; cor=; Ncor= a 2745.0 101.0 556.0 11.0 120.0 0.0 4500.0 44.0 233.0 10.0 4608.0 0 0 c 1924.0 4466.0 475.0 4447.0 4448.0 4403.0 1055.0 4402.0 1793.0 4354.0 839.0 0 0 g 151.0 150.0 7053.0 63.0 107.0 110.0 348.0 114.0 6862.0 183.0 829.0 0 0 t 158.0 319.0 707.0 88.0 76.0 131.0 363.0 245.0 253.0 219.0 483.0 0 0

MA0732.2_shift0 (EGR3)
; oligos_7nt_mkv1_m3 versus MA0732.2 (EGR3); m=4/10; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.592922; mCGCCCMCGCA-- ; cor=; Ncor= a 1031.0 2.0 66.0 0.0 0.0 0.0 1159.0 0.0 39.0 2.0 1262.0 0 0 c 701.0 1855.0 32.0 1856.0 1858.0 1823.0 455.0 1875.0 28.0 1899.0 54.0 0 0 g 10.0 0.0 2158.0 2.0 0.0 7.0 11.0 7.0 2152.0 1.0 168.0 0 0 t 20.0 13.0 36.0 0.0 10.0 80.0 4.0 2.0 26.0 21.0 80.0 0 0

MA0162.5_shift0 (EGR1)
; oligos_7nt_mkv1_m3 versus MA0162.5 (EGR1); m=5/10; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.530631; mCGCCCACgC--- ; cor=; Ncor= a 14508.0 642.0 5110.0 227.0 1440.0 314.0 22297.0 153.0 4696.0 969.0 0 0 0 c 10303.0 28403.0 1131.0 29338.0 27321.0 28958.0 5420.0 29507.0 2806.0 25196.0 0 0 0 g 3854.0 756.0 22237.0 665.0 1455.0 698.0 2122.0 699.0 20544.0 2157.0 0 0 0 t 1933.0 797.0 2120.0 368.0 382.0 628.0 759.0 239.0 2552.0 2276.0 0 0 0

MA0632.3_shift2 (TCFL5)
; oligos_7nt_mkv1_m3 versus MA0632.3 (TCFL5); m=6/10; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.495734; --kCrCGCGC--- ; cor=; Ncor= a 0 0 2810.0 0.0 72543.0 0.0 1566.0 1765.0 3520.0 1593.0 0 0 0 c 0 0 10582.0 72543.0 0.0 72543.0 0.0 57092.0 657.0 72543.0 0 0 0 g 0 0 22297.0 0.0 29710.0 0.0 72543.0 0.0 72543.0 4594.0 0 0 0 t 0 0 36854.0 0.0 9359.0 1643.0 0.0 15451.0 0.0 635.0 0 0 0

MA1512.2_shift4 (KLF11)
; oligos_7nt_mkv1_m3 versus MA1512.2 (KLF11); m=7/10; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.485635; ----cCACGCCCm ; cor=; Ncor= a 0 0 0 0 2022.0 650.0 8655.0 0.0 2426.0 11.0 1.0 0.0 4689.0 c 0 0 0 0 5549.0 8662.0 1289.0 9142.0 52.0 9161.0 9166.0 8941.0 4226.0 g 0 0 0 0 401.0 156.0 115.0 0.0 8291.0 18.0 20.0 4.0 69.0 t 0 0 0 0 1192.0 506.0 27.0 38.0 349.0 23.0 7.0 885.0 761.0

MA1099.3_rc_shift5 (HES1_rc)
; oligos_7nt_mkv1_m3 versus MA1099.3_rc (HES1_rc); m=8/10; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.485476; -----CACGyGcc ; cor=; Ncor= a 0 0 0 0 0 53.0 18526.0 0.0 791.0 232.0 18.0 8007.0 4239.0 c 0 0 0 0 0 18526.0 0.0 18526.0 0.0 9081.0 0.0 18526.0 18526.0 g 0 0 0 0 0 0.0 4057.0 0.0 18526.0 0.0 18526.0 2072.0 3492.0 t 0 0 0 0 0 1.0 253.0 21.0 0.0 9446.0 464.0 5858.0 3321.0

MA0006.2_rc_shift5 (Ahr::Arnt_rc)
; oligos_7nt_mkv1_m3 versus MA0006.2_rc (Ahr::Arnt_rc); m=9/10; ncol2=5; w=0; offset=4; strand=R; shift=5; score=0.412874; -----CACGC--- ; cor=; Ncor= a 0 0 0 0 0 0.0 24.0 1.0 1.0 1.0 0 0 0 c 0 0 0 0 0 24.0 0.0 23.0 0.0 23.0 0 0 0 g 0 0 0 0 0 0.0 0.0 0.0 23.0 0.0 0 0 0 t 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0 0 0

MA0039.5_shift0 (KLF4)
; oligos_7nt_mkv1_m3 versus MA0039.5 (KLF4); m=10/10; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score=0.401412; CCCCACCC----- ; cor=; Ncor= a 2465.0 2105.0 7021.0 1173.0 45602.0 852.0 1617.0 1202.0 0 0 0 0 0 c 49209.0 47865.0 45405.0 52875.0 161.0 52366.0 51112.0 51045.0 0 0 0 0 0 g 1583.0 1214.0 1422.0 793.0 6598.0 1470.0 1870.0 1005.0 0 0 0 0 0 t 2560.0 4633.0 1969.0 976.0 3456.0 1129.0 1218.0 2565.0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3)				; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -ssCACACGCmss ; Alignment reference a 0 1 2 0 12 0 14 0 0 0 9 3 2 c 0 8 8 15 1 14 2 16 0 16 4 4 7 g 0 5 5 1 3 1 0 0 16 0 2 7 6 t 0 2 1 0 0 1 0 0 0 0 1 2 1
MA1107.3_shift1 (KLF9)				; oligos_7nt_mkv1_m3 versus MA1107.3 (KLF9); m=1/10; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.673001; -gCCACACCCAC- ; cor=; Ncor= a 0 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 18837.0 792.0 0 c 0 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 4339.0 20644.0 0 g 0 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 852.0 1778.0 0 t 0 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0 1551.0 2365.0 0
MA0472.2_shift0 (EGR2)				; oligos_7nt_mkv1_m3 versus MA0472.2 (EGR2); m=2/10; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.598681; mCGCCCACGCa-- ; cor=; Ncor= a 1157.0 0.0 295.0 6.0 24.0 0.0 2147.0 0.0 106.0 4.0 1731.0 0 0 c 679.0 1551.0 0.0 1558.0 1554.0 1468.0 110.0 1573.0 0.0 1585.0 157.0 0 0 g 94.0 28.0 3731.0 25.0 15.0 38.0 26.0 2.0 4034.0 20.0 542.0 0 0 t 142.0 73.0 222.0 29.0 13.0 277.0 2.0 23.0 171.0 115.0 430.0 0 0
MA0733.2_shift0 (EGR4)				; oligos_7nt_mkv1_m3 versus MA0733.2 (EGR4); m=3/10; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.595092; mCGCCCACGCA-- ; cor=; Ncor= a 2745.0 101.0 556.0 11.0 120.0 0.0 4500.0 44.0 233.0 10.0 4608.0 0 0 c 1924.0 4466.0 475.0 4447.0 4448.0 4403.0 1055.0 4402.0 1793.0 4354.0 839.0 0 0 g 151.0 150.0 7053.0 63.0 107.0 110.0 348.0 114.0 6862.0 183.0 829.0 0 0 t 158.0 319.0 707.0 88.0 76.0 131.0 363.0 245.0 253.0 219.0 483.0 0 0
MA0732.2_shift0 (EGR3)				; oligos_7nt_mkv1_m3 versus MA0732.2 (EGR3); m=4/10; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.592922; mCGCCCMCGCA-- ; cor=; Ncor= a 1031.0 2.0 66.0 0.0 0.0 0.0 1159.0 0.0 39.0 2.0 1262.0 0 0 c 701.0 1855.0 32.0 1856.0 1858.0 1823.0 455.0 1875.0 28.0 1899.0 54.0 0 0 g 10.0 0.0 2158.0 2.0 0.0 7.0 11.0 7.0 2152.0 1.0 168.0 0 0 t 20.0 13.0 36.0 0.0 10.0 80.0 4.0 2.0 26.0 21.0 80.0 0 0
MA0162.5_shift0 (EGR1)				; oligos_7nt_mkv1_m3 versus MA0162.5 (EGR1); m=5/10; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.530631; mCGCCCACgC--- ; cor=; Ncor= a 14508.0 642.0 5110.0 227.0 1440.0 314.0 22297.0 153.0 4696.0 969.0 0 0 0 c 10303.0 28403.0 1131.0 29338.0 27321.0 28958.0 5420.0 29507.0 2806.0 25196.0 0 0 0 g 3854.0 756.0 22237.0 665.0 1455.0 698.0 2122.0 699.0 20544.0 2157.0 0 0 0 t 1933.0 797.0 2120.0 368.0 382.0 628.0 759.0 239.0 2552.0 2276.0 0 0 0
MA0632.3_shift2 (TCFL5)				; oligos_7nt_mkv1_m3 versus MA0632.3 (TCFL5); m=6/10; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.495734; --kCrCGCGC--- ; cor=; Ncor= a 0 0 2810.0 0.0 72543.0 0.0 1566.0 1765.0 3520.0 1593.0 0 0 0 c 0 0 10582.0 72543.0 0.0 72543.0 0.0 57092.0 657.0 72543.0 0 0 0 g 0 0 22297.0 0.0 29710.0 0.0 72543.0 0.0 72543.0 4594.0 0 0 0 t 0 0 36854.0 0.0 9359.0 1643.0 0.0 15451.0 0.0 635.0 0 0 0
MA1512.2_shift4 (KLF11)				; oligos_7nt_mkv1_m3 versus MA1512.2 (KLF11); m=7/10; ncol2=10; w=0; offset=3; strand=D; shift=4; score=0.485635; ----cCACGCCCm ; cor=; Ncor= a 0 0 0 0 2022.0 650.0 8655.0 0.0 2426.0 11.0 1.0 0.0 4689.0 c 0 0 0 0 5549.0 8662.0 1289.0 9142.0 52.0 9161.0 9166.0 8941.0 4226.0 g 0 0 0 0 401.0 156.0 115.0 0.0 8291.0 18.0 20.0 4.0 69.0 t 0 0 0 0 1192.0 506.0 27.0 38.0 349.0 23.0 7.0 885.0 761.0
MA1099.3_rc_shift5 (HES1_rc)				; oligos_7nt_mkv1_m3 versus MA1099.3_rc (HES1_rc); m=8/10; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.485476; -----CACGyGcc ; cor=; Ncor= a 0 0 0 0 0 53.0 18526.0 0.0 791.0 232.0 18.0 8007.0 4239.0 c 0 0 0 0 0 18526.0 0.0 18526.0 0.0 9081.0 0.0 18526.0 18526.0 g 0 0 0 0 0 0.0 4057.0 0.0 18526.0 0.0 18526.0 2072.0 3492.0 t 0 0 0 0 0 1.0 253.0 21.0 0.0 9446.0 464.0 5858.0 3321.0
MA0006.2_rc_shift5 (Ahr::Arnt_rc)				; oligos_7nt_mkv1_m3 versus MA0006.2_rc (Ahr::Arnt_rc); m=9/10; ncol2=5; w=0; offset=4; strand=R; shift=5; score=0.412874; -----CACGC--- ; cor=; Ncor= a 0 0 0 0 0 0.0 24.0 1.0 1.0 1.0 0 0 0 c 0 0 0 0 0 24.0 0.0 23.0 0.0 23.0 0 0 0 g 0 0 0 0 0 0.0 0.0 0.0 23.0 0.0 0 0 0 t 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 0 0 0
MA0039.5_shift0 (KLF4)				; oligos_7nt_mkv1_m3 versus MA0039.5 (KLF4); m=10/10; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score=0.401412; CCCCACCC----- ; cor=; Ncor= a 2465.0 2105.0 7021.0 1173.0 45602.0 852.0 1617.0 1202.0 0 0 0 0 0 c 49209.0 47865.0 45405.0 52875.0 161.0 52366.0 51112.0 51045.0 0 0 0 0 0 g 1583.0 1214.0 1422.0 793.0 6598.0 1470.0 1870.0 1005.0 0 0 0 0 0 t 2560.0 4633.0 1969.0 976.0 3456.0 1129.0 1218.0 2565.0 0 0 0 0 0