One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m42/peak-motifs_local_words_6nt_m42.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_m42/peak-motifs_local_words_6nt_m42_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: local_words_6nt_m42_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| local_words_6nt_m42_shift0 (local_words_6nt_m42local_words_6nt_m42) |
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; local_words_6nt_m42 (local_words_6nt_m42local_words_6nt_m42); m=0 (reference); ncol1=24; shift=0; ncol=24; mrGCCAGCAGCaCAGCTGTCACkv
; Alignment reference
a 8 7 3 0 2 21 0 3 18 0 0 15 0 25 0 1 0 0 0 0 20 1 4 7
c 8 3 1 17 23 1 4 18 2 2 19 4 24 0 0 22 1 0 1 21 2 17 4 7
g 6 9 21 5 0 1 20 4 1 23 4 1 1 0 25 0 1 25 1 3 0 3 9 8
t 3 6 0 3 0 2 1 0 4 0 2 5 0 0 0 2 23 0 23 1 3 4 8 3
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| MA1641.1_shift9 (MYF5) |
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; local_words_6nt_m42 versus MA1641.1 (MYF5); m=1/2; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.422247; ---------gvaCAGCTGtbc---
; cor=; Ncor=
a 0 0 0 0 0 0 0 0 0 2698.0 3507.0 7490.0 95.0 10965.0 100.0 223.0 129.0 42.0 578.0 1572.0 2554.0 0 0 0
c 0 0 0 0 0 0 0 0 0 2700.0 2986.0 1368.0 10911.0 47.0 230.0 10657.0 68.0 161.0 1775.0 3146.0 3258.0 0 0 0
g 0 0 0 0 0 0 0 0 0 3258.0 3145.0 1774.0 161.0 69.0 10658.0 230.0 47.0 10912.0 1368.0 2985.0 2701.0 0 0 0
t 0 0 0 0 0 0 0 0 0 2554.0 1572.0 578.0 43.0 129.0 222.0 100.0 10966.0 95.0 7489.0 3507.0 2697.0 0 0 0
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| MA1619.1_rc_shift9 (Ptf1a(var.2)_rc) |
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; local_words_6nt_m42 versus MA1619.1_rc (Ptf1a(var.2)_rc); m=2/2; ncol2=12; w=12; offset=9; strand=R; shift=9; score=0.418981; ---------rmaCAGCTGtky---
; cor=; Ncor=
a 0 0 0 0 0 0 0 0 0 1871.0 1974.0 4341.0 49.0 7121.0 33.0 223.0 28.0 27.0 529.0 1216.0 1607.0 0 0 0
c 0 0 0 0 0 0 0 0 0 1803.0 2426.0 1065.0 7150.0 40.0 299.0 6689.0 65.0 28.0 1308.0 1629.0 1974.0 0 0 0
g 0 0 0 0 0 0 0 0 0 1977.0 1632.0 1312.0 27.0 66.0 6697.0 307.0 41.0 7149.0 1070.0 2430.0 1803.0 0 0 0
t 0 0 0 0 0 0 0 0 0 1602.0 1221.0 535.0 27.0 26.0 224.0 34.0 7119.0 49.0 4346.0 1978.0 1869.0 0 0 0
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