One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m27/peak-motifs_oligos_6nt_mkv4_m27.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf -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 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m27/peak-motifs_oligos_6nt_mkv4_m27_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m27_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m27_shift3 (oligos_6nt_mkv4_m27oligos_6nt_mkv4_m27)
; oligos_6nt_mkv4_m27 (oligos_6nt_mkv4_m27oligos_6nt_mkv4_m27); m=0 (reference); ncol1=10; shift=3; ncol=13; ---ssCGGGTCcs ; Alignment reference a 0 0 0 310 272 0 0 0 0 0 0 571 250 c 0 0 0 815 959 2452 0 1 0 0 2452 884 947 g 0 0 0 844 840 0 2452 2451 2452 0 0 466 827 t 0 0 0 483 381 0 0 0 0 2452 0 531 428

MA1535.1_shift4 (NR2C1)
; oligos_6nt_mkv4_m27 versus MA1535.1 (NR2C1); m=1/4; ncol2=9; w=9; offset=1; strand=D; shift=4; score=0.651659; ----mrrGGTCAy ; cor=; Ncor= a 0 0 0 0 2552.0 4035.0 4866.0 0.0 0.0 0.0 0.0 9622.0 2298.0 c 0 0 0 0 2848.0 1225.0 227.0 0.0 0.0 0.0 9622.0 0.0 2786.0 g 0 0 0 0 1997.0 5587.0 4756.0 9622.0 9622.0 271.0 321.0 1716.0 2039.0 t 0 0 0 0 2225.0 1316.0 55.0 297.0 0.0 9622.0 0.0 0.0 2499.0

MA1536.1_shift5 (NR2C2(var.2))
; oligos_6nt_mkv4_m27 versus MA1536.1 (NR2C2(var.2)); m=2/4; ncol2=8; w=8; offset=2; strand=D; shift=5; score=0.569263; -----rrGGTCRh ; cor=; Ncor= a 0 0 0 0 0 6236.0 10232.0 0.0 0.0 0.0 0.0 18628.0 5065.0 c 0 0 0 0 0 3111.0 719.0 236.0 0.0 0.0 18628.0 0.0 4757.0 g 0 0 0 0 0 6420.0 8395.0 18628.0 18628.0 1588.0 1643.0 6639.0 3684.0 t 0 0 0 0 0 2861.0 0.0 1341.0 4790.0 18628.0 4406.0 0.0 5122.0

MA0767.1_shift1 (GCM2)
; oligos_6nt_mkv4_m27 versus MA0767.1 (GCM2); m=3/4; ncol2=10; w=8; offset=-2; strand=D; shift=1; score=0.469444; -bATGCGGGyr-- ; cor=; Ncor= a 0 179.0 1320.0 23.0 263.0 84.0 51.0 0.0 1.0 92.0 599.0 0 0 c 0 340.0 77.0 41.0 32.0 1320.0 1.0 0.0 0.0 533.0 140.0 0 0 g 0 375.0 299.0 24.0 1320.0 138.0 1320.0 1320.0 1320.0 91.0 341.0 0 0 t 0 427.0 45.0 1320.0 0.0 127.0 66.0 13.0 0.0 1320.0 240.0 0 0

MA1513.1_rc_shift0 (KLF15_rc)
; oligos_6nt_mkv4_m27 versus MA1513.1_rc (KLF15_rc); m=4/4; ncol2=11; w=8; offset=-3; strand=R; shift=0; score=0.431114; sgGGGCGGGgs-- ; cor=; Ncor= a 2165.0 1602.0 3.0 1.0 11.0 0.0 0.0 3.0 9.0 1809.0 1744.0 0 0 c 3124.0 1934.0 100.0 359.0 2.0 11369.0 1.0 333.0 86.0 2117.0 5538.0 0 0 g 5013.0 6267.0 11254.0 10954.0 11345.0 0.0 11368.0 10940.0 11234.0 6506.0 2903.0 0 0 t 1067.0 1566.0 12.0 55.0 11.0 0.0 0.0 93.0 40.0 937.0 1184.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m27_shift3 (oligos_6nt_mkv4_m27oligos_6nt_mkv4_m27)				; oligos_6nt_mkv4_m27 (oligos_6nt_mkv4_m27oligos_6nt_mkv4_m27); m=0 (reference); ncol1=10; shift=3; ncol=13; ---ssCGGGTCcs ; Alignment reference a 0 0 0 310 272 0 0 0 0 0 0 571 250 c 0 0 0 815 959 2452 0 1 0 0 2452 884 947 g 0 0 0 844 840 0 2452 2451 2452 0 0 466 827 t 0 0 0 483 381 0 0 0 0 2452 0 531 428
MA1535.1_shift4 (NR2C1)				; oligos_6nt_mkv4_m27 versus MA1535.1 (NR2C1); m=1/4; ncol2=9; w=9; offset=1; strand=D; shift=4; score=0.651659; ----mrrGGTCAy ; cor=; Ncor= a 0 0 0 0 2552.0 4035.0 4866.0 0.0 0.0 0.0 0.0 9622.0 2298.0 c 0 0 0 0 2848.0 1225.0 227.0 0.0 0.0 0.0 9622.0 0.0 2786.0 g 0 0 0 0 1997.0 5587.0 4756.0 9622.0 9622.0 271.0 321.0 1716.0 2039.0 t 0 0 0 0 2225.0 1316.0 55.0 297.0 0.0 9622.0 0.0 0.0 2499.0
MA1536.1_shift5 (NR2C2(var.2))				; oligos_6nt_mkv4_m27 versus MA1536.1 (NR2C2(var.2)); m=2/4; ncol2=8; w=8; offset=2; strand=D; shift=5; score=0.569263; -----rrGGTCRh ; cor=; Ncor= a 0 0 0 0 0 6236.0 10232.0 0.0 0.0 0.0 0.0 18628.0 5065.0 c 0 0 0 0 0 3111.0 719.0 236.0 0.0 0.0 18628.0 0.0 4757.0 g 0 0 0 0 0 6420.0 8395.0 18628.0 18628.0 1588.0 1643.0 6639.0 3684.0 t 0 0 0 0 0 2861.0 0.0 1341.0 4790.0 18628.0 4406.0 0.0 5122.0
MA0767.1_shift1 (GCM2)				; oligos_6nt_mkv4_m27 versus MA0767.1 (GCM2); m=3/4; ncol2=10; w=8; offset=-2; strand=D; shift=1; score=0.469444; -bATGCGGGyr-- ; cor=; Ncor= a 0 179.0 1320.0 23.0 263.0 84.0 51.0 0.0 1.0 92.0 599.0 0 0 c 0 340.0 77.0 41.0 32.0 1320.0 1.0 0.0 0.0 533.0 140.0 0 0 g 0 375.0 299.0 24.0 1320.0 138.0 1320.0 1320.0 1320.0 91.0 341.0 0 0 t 0 427.0 45.0 1320.0 0.0 127.0 66.0 13.0 0.0 1320.0 240.0 0 0
MA1513.1_rc_shift0 (KLF15_rc)				; oligos_6nt_mkv4_m27 versus MA1513.1_rc (KLF15_rc); m=4/4; ncol2=11; w=8; offset=-3; strand=R; shift=0; score=0.431114; sgGGGCGGGgs-- ; cor=; Ncor= a 2165.0 1602.0 3.0 1.0 11.0 0.0 0.0 3.0 9.0 1809.0 1744.0 0 0 c 3124.0 1934.0 100.0 359.0 2.0 11369.0 1.0 333.0 86.0 2117.0 5538.0 0 0 g 5013.0 6267.0 11254.0 10954.0 11345.0 0.0 11368.0 10940.0 11234.0 6506.0 2903.0 0 0 t 1067.0 1566.0 12.0 55.0 11.0 0.0 0.0 93.0 40.0 937.0 1184.0 0 0