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.2025-05-16.175517_2025-05-16.175517_w6aMRg/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_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.2025-05-16.175517_2025-05-16.175517_w6aMRg/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; mtsmCmwCmC ; Alignment reference a 18 6 2 14 0 18 8 2 13 1 c 8 3 12 9 27 10 3 22 10 25 g 1 6 13 6 1 0 2 2 1 1 t 2 14 2 0 1 1 16 3 5 2

MA0018.5_rc_shift1 (CREB1_rc)
; oligos_6nt_mkv1_m4 versus MA0018.5_rc (CREB1_rc); m=1/8; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.649893; -TGACATCA- ; cor=; Ncor= a 0 1485.0 1852.0 68217.0 1831.0 56875.0 2279.0 2963.0 75554.0 0 c 0 1222.0 2177.0 1207.0 74401.0 6339.0 2012.0 72555.0 1109.0 0 g 0 1018.0 71982.0 1231.0 1895.0 14144.0 1748.0 2298.0 970.0 0 t 0 75819.0 3533.0 8889.0 1417.0 2186.0 73505.0 1728.0 1911.0 0

MA0734.4_shift2 (Gli2)
; oligos_6nt_mkv1_m4 versus MA0734.4 (Gli2); m=2/8; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.511433; --GACCACCC ; cor=; Ncor= a 0 0 60.0 1920.0 44.0 8.0 2216.0 9.0 313.0 59.0 c 0 0 96.0 227.0 2404.0 2464.0 40.0 2451.0 2145.0 2288.0 g 0 0 2251.0 337.0 27.0 13.0 82.0 12.0 20.0 77.0 t 0 0 85.0 8.0 17.0 7.0 154.0 20.0 14.0 68.0

MA1630.3_rc_shift2 (ZNF281_rc)
; oligos_6nt_mkv1_m4 versus MA1630.3_rc (ZNF281_rc); m=3/8; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.474552; --CCCCTCCC ; cor=; Ncor= a 0 0 7.0 18.0 1.0 105.0 96.0 1.0 1.0 1.0 c 0 0 920.0 940.0 998.0 772.0 1.0 998.0 998.0 963.0 g 0 0 27.0 1.0 1.0 1.0 183.0 1.0 1.0 1.0 t 0 0 47.0 41.0 1.0 122.0 720.0 1.0 1.0 35.0

MA1965.2_shift4 (SP5)
; oligos_6nt_mkv1_m4 versus MA1965.2 (SP5); m=4/8; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.463247; ----CCTCCC ; cor=; Ncor= a 0 0 0 0 6.0 7.0 0.0 47.0 11.0 0.0 c 0 0 0 0 20683.0 20286.0 0.0 20649.0 20451.0 20604.0 g 0 0 0 0 3.0 403.0 231.0 0.0 234.0 92.0 t 0 0 0 0 4.0 0.0 20465.0 0.0 0.0 0.0

MA2337.1_rc_shift1 (Nr1h3_rc)
; oligos_6nt_mkv1_m4 versus MA2337.1_rc (Nr1h3_rc); m=5/8; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.429071; -TGmCCT--- ; cor=; Ncor= a 0 1.0 5.0 2247.0 4.0 3.0 0.0 0 0 0 c 0 19.0 1.0 1600.0 3839.0 3832.0 35.0 0 0 0 g 0 6.0 3851.0 5.0 17.0 27.0 31.0 0 0 0 t 0 3836.0 5.0 10.0 2.0 0.0 3796.0 0 0 0

MA1996.2_rc_shift1 (Nr1H2_rc)
; oligos_6nt_mkv1_m4 versus MA1996.2_rc (Nr1H2_rc); m=6/8; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.424654; -TGACCT--- ; cor=; Ncor= a 0 37.0 269.0 8834.0 104.0 191.0 99.0 0 0 0 c 0 241.0 72.0 41.0 8740.0 8521.0 132.0 0 0 0 g 0 51.0 8483.0 35.0 36.0 171.0 191.0 0 0 0 t 0 8642.0 147.0 61.0 91.0 88.0 8549.0 0 0 0

MA1110.3_rc_shift1 (Nr1H4_rc)
; oligos_6nt_mkv1_m4 versus MA1110.3_rc (Nr1H4_rc); m=7/8; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.422632; -TGACCT--- ; cor=; Ncor= a 0 0.0 212.0 4735.0 30.0 31.0 7.0 0 0 0 c 0 118.0 10.0 0.0 4671.0 4542.0 49.0 0 0 0 g 0 29.0 4351.0 0.0 4.0 150.0 83.0 0 0 0 t 0 4589.0 163.0 1.0 31.0 13.0 4597.0 0 0 0

MA0498.3_shift1 (MEIS1)
; oligos_6nt_mkv1_m4 versus MA0498.3 (MEIS1); m=8/8; ncol2=5; w=0; offset=1; strand=D; shift=1; score=0.404785; -TGACA---- ; cor=; Ncor= a 0 8690.0 0.0 77159.0 0.0 77159.0 0 0 0 0 c 0 5575.0 1249.0 2903.0 77159.0 0.0 0 0 0 0 g 0 3174.0 77159.0 672.0 0.0 9263.0 0 0 0 0 t 0 77159.0 0.0 0.0 1155.0 3861.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; mtsmCmwCmC ; Alignment reference a 18 6 2 14 0 18 8 2 13 1 c 8 3 12 9 27 10 3 22 10 25 g 1 6 13 6 1 0 2 2 1 1 t 2 14 2 0 1 1 16 3 5 2
MA0018.5_rc_shift1 (CREB1_rc)				; oligos_6nt_mkv1_m4 versus MA0018.5_rc (CREB1_rc); m=1/8; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.649893; -TGACATCA- ; cor=; Ncor= a 0 1485.0 1852.0 68217.0 1831.0 56875.0 2279.0 2963.0 75554.0 0 c 0 1222.0 2177.0 1207.0 74401.0 6339.0 2012.0 72555.0 1109.0 0 g 0 1018.0 71982.0 1231.0 1895.0 14144.0 1748.0 2298.0 970.0 0 t 0 75819.0 3533.0 8889.0 1417.0 2186.0 73505.0 1728.0 1911.0 0
MA0734.4_shift2 (Gli2)				; oligos_6nt_mkv1_m4 versus MA0734.4 (Gli2); m=2/8; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.511433; --GACCACCC ; cor=; Ncor= a 0 0 60.0 1920.0 44.0 8.0 2216.0 9.0 313.0 59.0 c 0 0 96.0 227.0 2404.0 2464.0 40.0 2451.0 2145.0 2288.0 g 0 0 2251.0 337.0 27.0 13.0 82.0 12.0 20.0 77.0 t 0 0 85.0 8.0 17.0 7.0 154.0 20.0 14.0 68.0
MA1630.3_rc_shift2 (ZNF281_rc)				; oligos_6nt_mkv1_m4 versus MA1630.3_rc (ZNF281_rc); m=3/8; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.474552; --CCCCTCCC ; cor=; Ncor= a 0 0 7.0 18.0 1.0 105.0 96.0 1.0 1.0 1.0 c 0 0 920.0 940.0 998.0 772.0 1.0 998.0 998.0 963.0 g 0 0 27.0 1.0 1.0 1.0 183.0 1.0 1.0 1.0 t 0 0 47.0 41.0 1.0 122.0 720.0 1.0 1.0 35.0
MA1965.2_shift4 (SP5)				; oligos_6nt_mkv1_m4 versus MA1965.2 (SP5); m=4/8; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.463247; ----CCTCCC ; cor=; Ncor= a 0 0 0 0 6.0 7.0 0.0 47.0 11.0 0.0 c 0 0 0 0 20683.0 20286.0 0.0 20649.0 20451.0 20604.0 g 0 0 0 0 3.0 403.0 231.0 0.0 234.0 92.0 t 0 0 0 0 4.0 0.0 20465.0 0.0 0.0 0.0
MA2337.1_rc_shift1 (Nr1h3_rc)				; oligos_6nt_mkv1_m4 versus MA2337.1_rc (Nr1h3_rc); m=5/8; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.429071; -TGmCCT--- ; cor=; Ncor= a 0 1.0 5.0 2247.0 4.0 3.0 0.0 0 0 0 c 0 19.0 1.0 1600.0 3839.0 3832.0 35.0 0 0 0 g 0 6.0 3851.0 5.0 17.0 27.0 31.0 0 0 0 t 0 3836.0 5.0 10.0 2.0 0.0 3796.0 0 0 0
MA1996.2_rc_shift1 (Nr1H2_rc)				; oligos_6nt_mkv1_m4 versus MA1996.2_rc (Nr1H2_rc); m=6/8; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.424654; -TGACCT--- ; cor=; Ncor= a 0 37.0 269.0 8834.0 104.0 191.0 99.0 0 0 0 c 0 241.0 72.0 41.0 8740.0 8521.0 132.0 0 0 0 g 0 51.0 8483.0 35.0 36.0 171.0 191.0 0 0 0 t 0 8642.0 147.0 61.0 91.0 88.0 8549.0 0 0 0
MA1110.3_rc_shift1 (Nr1H4_rc)				; oligos_6nt_mkv1_m4 versus MA1110.3_rc (Nr1H4_rc); m=7/8; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.422632; -TGACCT--- ; cor=; Ncor= a 0 0.0 212.0 4735.0 30.0 31.0 7.0 0 0 0 c 0 118.0 10.0 0.0 4671.0 4542.0 49.0 0 0 0 g 0 29.0 4351.0 0.0 4.0 150.0 83.0 0 0 0 t 0 4589.0 163.0 1.0 31.0 13.0 4597.0 0 0 0
MA0498.3_shift1 (MEIS1)				; oligos_6nt_mkv1_m4 versus MA0498.3 (MEIS1); m=8/8; ncol2=5; w=0; offset=1; strand=D; shift=1; score=0.404785; -TGACA---- ; cor=; Ncor= a 0 8690.0 0.0 77159.0 0.0 77159.0 0 0 0 0 c 0 5575.0 1249.0 2903.0 77159.0 0.0 0 0 0 0 g 0 3174.0 77159.0 672.0 0.0 9263.0 0 0 0 0 t 0 77159.0 0.0 0.0 1155.0 3861.0 0 0 0 0