One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m2/peak-motifs_local_words_8nt_m2.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_8nt_m2/peak-motifs_local_words_8nt_m2_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
local_words_8nt_m2_shift0 (local_words_8nt_m2local_words_8nt_m2)     
; local_words_8nt_m2 (local_words_8nt_m2local_words_8nt_m2); m=0 (reference); ncol1=24; shift=0; ncol=24; srGsAACAGCTGCTGCAGCTGTsg
; Alignment reference
a	4	10	4	2	26	30	1	36	1	2	3	1	1	2	1	3	26	0	0	1	1	1	3	8
c	13	9	4	11	5	0	34	2	0	34	0	0	35	1	2	32	2	1	37	0	3	6	10	6
g	16	10	26	23	6	8	2	0	34	0	1	36	1	1	34	2	4	35	0	2	32	3	16	17
t	5	9	4	2	1	0	1	0	3	2	34	1	1	34	1	1	6	2	1	35	2	28	9	7
MA1485.1_rc_shift2 (FERD3L_rc) 
; local_words_8nt_m2 versus MA1485.1_rc (FERD3L_rc); m=1/4; ncol2=14; w=14; offset=2; strand=R; shift=2; score=0.473477; --GTrACAGCTGkyrC--------
; cor=; Ncor=
a	0	0	48.0	958.0	14919.0	21065.0	0.0	29605.0	0.0	4691.0	144.0	0.0	1710.0	74.0	9557.0	225.0	0	0	0	0	0	0	0	0
c	0	0	0.0	9815.0	5920.0	3395.0	29605.0	210.0	471.0	29605.0	118.0	0.0	3142.0	12703.0	348.0	29605.0	0	0	0	0	0	0	0	0
g	0	0	29605.0	809.0	8664.0	3878.0	0.0	129.0	29605.0	841.0	126.0	29605.0	9363.0	2443.0	20049.0	68.0	0	0	0	0	0	0	0	0
t	0	0	0.0	29605.0	103.0	1268.0	0.0	81.0	3649.0	0.0	29605.0	36.0	15390.0	14384.0	450.0	2158.0	0	0	0	0	0	0	0	0
MA0832.1_shift2 (Tcf21) 
; local_words_8nt_m2 versus MA0832.1 (Tcf21); m=2/4; ncol2=14; w=14; offset=2; strand=D; shift=2; score=0.460273; --ryAACAGCTGTTry--------
; cor=; Ncor=
a	0	0	55.0	28.0	171.0	171.0	0.0	171.0	0.0	0.0	0.0	0.0	0.0	5.0	50.0	30.0	0	0	0	0	0	0	0	0
c	0	0	29.0	76.0	1.0	10.0	171.0	1.0	0.0	171.0	0.0	0.0	4.0	23.0	23.0	49.0	0	0	0	0	0	0	0	0
g	0	0	70.0	22.0	23.0	0.0	0.0	0.0	171.0	1.0	0.0	171.0	20.0	0.0	80.0	32.0	0	0	0	0	0	0	0	0
t	0	0	17.0	46.0	3.0	0.0	0.0	0.0	2.0	1.0	171.0	0.0	171.0	171.0	19.0	60.0	0	0	0	0	0	0	0	0
MA0500.2_rc_shift3 (MYOG_rc) 
; local_words_8nt_m2 versus MA0500.2_rc (MYOG_rc); m=3/4; ncol2=12; w=12; offset=3; strand=R; shift=3; score=0.418502; ---sarCAGCTGyts---------
; cor=; Ncor=
a	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	0	0	0	0	0	0
c	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	0	0	0	0	0	0
g	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	0	0	0	0	0	0
t	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	0	0	0	0	0	0
MA0499.2_rc_shift2 (MYOD1_rc) 
; local_words_8nt_m2 versus MA0499.2_rc (MYOD1_rc); m=4/4; ncol2=13; w=13; offset=2; strand=R; shift=2; score=0.408963; --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