One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m34/peak-motifs_local_words_6nt_m34.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_m34/peak-motifs_local_words_6nt_m34_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: local_words_6nt_m34_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| local_words_6nt_m34_shift0 (local_words_6nt_m34local_words_6nt_m34) |
 |
|
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; local_words_6nt_m34 (local_words_6nt_m34local_words_6nt_m34); m=0 (reference); ncol1=24; shift=0; ncol=24; bcAGCTGgCAGCAGCTGCCACcmm
; Alignment reference
a 9 11 37 0 1 2 1 5 1 43 3 0 45 1 2 1 1 3 4 41 3 8 16 13
c 16 27 3 2 41 2 4 8 47 3 2 51 0 2 47 0 5 44 44 1 36 31 15 18
g 13 10 6 45 7 2 44 33 2 2 46 0 0 48 1 3 45 1 1 8 7 8 12 12
t 13 3 5 4 2 45 2 5 1 3 0 0 6 0 1 47 0 3 2 1 5 4 8 8
|
| MA1485.1_shift7 (FERD3L) |
 |
|
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; local_words_6nt_m34 versus MA1485.1 (FERD3L); m=1/2; ncol2=14; w=14; offset=7; strand=D; shift=7; score=0.447288; -------GyrmCAGCTGTyAC---
; cor=; Ncor=
a 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 0
c 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 0
g 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 0
t 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 0
|
| MA0500.2_rc_shift8 (MYOG_rc) |
 |
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; local_words_6nt_m34 versus MA0500.2_rc (MYOG_rc); m=2/2; ncol2=12; w=12; offset=8; strand=R; shift=8; score=0.403441; --------sarCAGCTGyts----
; cor=; Ncor=
a 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 0
c 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 0
g 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 0
t 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 0
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