One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m32/peak-motifs_local_words_6nt_m32.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/local_words_6nt_m32/peak-motifs_local_words_6nt_m32_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m32_shift0 ; 5 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
local_words_6nt_m32_shift0 (local_words_6nt_m32local_words_6nt_m32)     
; local_words_6nt_m32 (local_words_6nt_m32local_words_6nt_m32); m=0 (reference); ncol1=24; shift=0; ncol=25; srcaGCTGCCAGCAGCAsCTGtss-
; Alignment reference
a	10	20	4	34	2	4	2	0	3	2	49	1	2	45	6	0	47	3	2	2	0	1	10	12	0
c	17	12	38	5	7	44	1	2	45	50	1	2	47	1	1	54	1	36	51	1	1	8	20	15	0
g	18	14	9	5	46	7	5	50	1	2	4	51	3	0	49	2	2	16	1	0	55	9	17	17	0
t	11	10	5	12	1	1	48	4	7	2	2	2	4	10	0	0	6	1	2	53	0	38	9	12	0
MA0499.2_shift12 (MYOD1) 
; local_words_6nt_m32 versus MA0499.2 (MYOD1); m=1/4; ncol2=13; w=12; offset=12; strand=D; shift=12; score=0.429621; ------------cwgCACCTGTymy
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0	0	0	0	7175.0	9462.0	4549.0	349.0	32281.0	463.0	534.0	241.0	208.0	402.0	1808.0	9462.0	5687.0
c	0	0	0	0	0	0	0	0	0	0	0	0	11279.0	7103.0	5622.0	33328.0	583.0	25275.0	32504.0	563.0	386.0	2555.0	19052.0	10485.0	11760.0
g	0	0	0	0	0	0	0	0	0	0	0	0	8118.0	8444.0	21884.0	354.0	849.0	7336.0	932.0	366.0	33468.0	1699.0	4440.0	6202.0	7495.0
t	0	0	0	0	0	0	0	0	0	0	0	0	7728.0	9291.0	2245.0	269.0	587.0	1226.0	330.0	33130.0	238.0	29644.0	9000.0	8151.0	9358.0
MA0745.2_shift12 (SNAI2) 
; local_words_6nt_m32 versus MA0745.2 (SNAI2); m=2/4; ncol2=13; w=12; offset=12; strand=D; shift=12; score=0.407806; ------------aygCACCTGTmry
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0	0	0	0	14658.0	7668.0	10322.0	408.0	44963.0	112.0	246.0	78.0	179.0	814.0	12017.0	13586.0	6215.0
c	0	0	0	0	0	0	0	0	0	0	0	0	10031.0	12314.0	6393.0	44463.0	202.0	45144.0	44739.0	313.0	254.0	6467.0	18771.0	11016.0	13476.0
g	0	0	0	0	0	0	0	0	0	0	0	0	11169.0	9490.0	26742.0	323.0	424.0	326.0	487.0	196.0	45257.0	1263.0	6281.0	12297.0	8219.0
t	0	0	0	0	0	0	0	0	0	0	0	0	9958.0	16344.0	2359.0	622.0	227.0	234.0	344.0	45229.0	126.0	37272.0	8747.0	8917.0	17906.0
MA1485.1_shift11 (FERD3L) 
; local_words_6nt_m32 versus MA1485.1 (FERD3L); m=3/4; ncol2=14; w=13; offset=11; strand=D; shift=11; score=0.405006; -----------GyrmCAGCTGTyAC
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0	0	0	2158.0	450.0	14384.0	15390.0	36.0	29605.0	0.0	3649.0	81.0	0.0	1268.0	103.0	29605.0	0.0
c	0	0	0	0	0	0	0	0	0	0	0	68.0	20049.0	2443.0	9363.0	29605.0	126.0	841.0	29605.0	129.0	0.0	3878.0	8664.0	809.0	29605.0
g	0	0	0	0	0	0	0	0	0	0	0	29605.0	348.0	12703.0	3142.0	0.0	118.0	29605.0	471.0	210.0	29605.0	3395.0	5920.0	9815.0	0.0
t	0	0	0	0	0	0	0	0	0	0	0	225.0	9557.0	74.0	1710.0	0.0	144.0	4691.0	0.0	29605.0	0.0	21065.0	14919.0	958.0	48.0
MA1621.1_shift11 (Rbpjl) 
; local_words_6nt_m32 versus MA1621.1 (Rbpjl); m=4/4; ncol2=14; w=13; offset=11; strand=D; shift=11; score=0.400754; -----------svmaCACCTGtsyc
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0	0	0	2006.0	2466.0	3369.0	6005.0	139.0	9386.0	84.0	234.0	63.0	102.0	569.0	1539.0	2273.0	2082.0
c	0	0	0	0	0	0	0	0	0	0	0	2881.0	2427.0	3117.0	1373.0	9273.0	70.0	8533.0	9005.0	144.0	131.0	1718.0	3247.0	2884.0	3003.0
g	0	0	0	0	0	0	0	0	0	0	0	2476.0	2549.0	1802.0	1492.0	103.0	110.0	672.0	317.0	132.0	9295.0	1581.0	2687.0	1958.0	2281.0
t	0	0	0	0	0	0	0	0	0	0	0	2289.0	2210.0	1364.0	782.0	137.0	86.0	363.0	96.0	9313.0	124.0	5784.0	2179.0	2537.0	2286.0