One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m4/peak-motifs_local_words_6nt_m4.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_m4/peak-motifs_local_words_6nt_m4_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: local_words_6nt_m4_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| local_words_6nt_m4_shift0 (local_words_6nt_m4local_words_6nt_m4) |
 |
|
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; local_words_6nt_m4 (local_words_6nt_m4local_words_6nt_m4); m=0 (reference); ncol1=24; shift=0; ncol=25; sbCTGGCAGCAGCTGCAsCTGTyg-
; Alignment reference
a 9 5 2 5 2 4 2 32 2 0 34 1 0 3 1 1 33 1 3 4 1 1 6 4 0
c 14 15 30 5 2 1 39 1 1 40 2 2 42 1 1 39 2 28 36 2 1 8 12 8 0
g 13 11 7 2 36 35 0 4 37 2 3 39 0 2 40 1 3 11 1 0 38 0 10 21 0
t 6 11 3 30 2 2 1 5 2 0 3 0 0 36 0 1 4 2 2 36 2 33 14 9 0
|
| MA0500.2_rc_shift6 (MYOG_rc) |
 |
|
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; local_words_6nt_m4 versus MA0500.2_rc (MYOG_rc); m=1/2; ncol2=12; w=12; offset=6; strand=R; shift=6; score=0.410676; ------sarCAGCTGyts-------
; cor=; Ncor=
a 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 0 0 0 0
c 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 0 0 0 0
g 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 0 0 0 0
t 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 0 0 0 0
|
| MA0499.2_shift12 (MYOD1) |
 |
|
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; local_words_6nt_m4 versus MA0499.2 (MYOD1); m=2/2; ncol2=13; w=12; offset=12; strand=D; shift=12; score=0.405357; ------------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
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