One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m6/peak-motifs_local_words_6nt_m6.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_m6/peak-motifs_local_words_6nt_m6_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m6_shift0 ; 5 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
local_words_6nt_m6_shift0 (local_words_6nt_m6local_words_6nt_m6)     
; local_words_6nt_m6 (local_words_6nt_m6local_words_6nt_m6); m=0 (reference); ncol1=24; shift=0; ncol=24; drgTGACAGgTGCAGCTGTCACar
; Alignment reference
a	17	14	6	4	2	35	4	46	3	4	7	3	2	48	0	1	3	0	3	1	36	2	18	13
c	7	9	10	4	4	10	42	0	4	9	1	3	49	1	0	48	1	1	3	46	5	37	12	9
g	14	17	31	3	43	5	4	2	41	34	3	45	0	1	51	2	0	48	4	3	4	10	12	18
t	13	11	4	40	2	1	1	3	3	4	40	0	0	1	0	0	47	2	41	1	6	2	9	11
MA1485.1_shift8 (FERD3L) 
; local_words_6nt_m6 versus MA1485.1 (FERD3L); m=1/4; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.440136; --------GyrmCAGCTGTyAC--
; cor=; Ncor=
a	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	0	0
c	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	0	0
g	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	0	0
t	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	0	0
MA0499.2_rc_shift2 (MYOD1_rc) 
; local_words_6nt_m6 versus MA0499.2_rc (MYOD1_rc); m=2/4; ncol2=13; w=13; offset=2; strand=R; shift=2; score= 0.4356; --rkrACAGGTGcwg---------
; cor=; Ncor=
a	0	0	9358.0	8151.0	9000.0	29644.0	238.0	33130.0	330.0	1226.0	587.0	269.0	2245.0	9291.0	7728.0	0	0	0	0	0	0	0	0	0
c	0	0	7495.0	6202.0	4440.0	1699.0	33468.0	366.0	932.0	7336.0	849.0	354.0	21884.0	8444.0	8118.0	0	0	0	0	0	0	0	0	0
g	0	0	11760.0	10485.0	19052.0	2555.0	386.0	563.0	32504.0	25275.0	583.0	33328.0	5622.0	7103.0	11279.0	0	0	0	0	0	0	0	0	0
t	0	0	5687.0	9462.0	1808.0	402.0	208.0	241.0	534.0	463.0	32281.0	349.0	4549.0	9462.0	7175.0	0	0	0	0	0	0	0	0	0
MA0745.2_rc_shift2 (SNAI2_rc) 
; local_words_6nt_m6 versus MA0745.2_rc (SNAI2_rc); m=3/4; ncol2=13; w=13; offset=2; strand=R; shift=2; score=0.414246; --rykACAGGTGcrt---------
; cor=; Ncor=
a	0	0	17906.0	8917.0	8747.0	37272.0	126.0	45229.0	344.0	234.0	227.0	622.0	2359.0	16344.0	9958.0	0	0	0	0	0	0	0	0	0
c	0	0	8219.0	12297.0	6281.0	1263.0	45257.0	196.0	487.0	326.0	424.0	323.0	26742.0	9490.0	11169.0	0	0	0	0	0	0	0	0	0
g	0	0	13476.0	11016.0	18771.0	6467.0	254.0	313.0	44739.0	45144.0	202.0	44463.0	6393.0	12314.0	10031.0	0	0	0	0	0	0	0	0	0
t	0	0	6215.0	13586.0	12017.0	814.0	179.0	78.0	246.0	112.0	44963.0	408.0	10322.0	7668.0	14658.0	0	0	0	0	0	0	0	0	0
MA0500.2_rc_shift9 (MYOG_rc) 
; local_words_6nt_m6 versus MA0500.2_rc (MYOG_rc); m=4/4; ncol2=12; w=12; offset=9; strand=R; shift=9; score=0.401793; ---------sarCAGCTGyts---
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0	5310.0	8475.0	7192.0	88.0	21777.0	95.0	169.0	163.0	182.0	1678.0	4692.0	5070.0	0	0	0
c	0	0	0	0	0	0	0	0	0	6369.0	3718.0	2706.0	21985.0	179.0	131.0	21963.0	236.0	101.0	10790.0	5483.0	5596.0	0	0	0
g	0	0	0	0	0	0	0	0	0	5660.0	5497.0	10792.0	102.0	238.0	21964.0	130.0	176.0	21988.0	2730.0	3754.0	6381.0	0	0	0
t	0	0	0	0	0	0	0	0	0	5018.0	4667.0	1667.0	182.0	163.0	167.0	95.0	21782.0	86.0	7159.0	8428.0	5310.0	0	0	0