One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m30/peak-motifs_oligos_7nt_mkv4_m30.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_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m30/peak-motifs_oligos_7nt_mkv4_m30_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m30_shift2 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv4_m30_shift2 (oligos_7nt_mkv4_m30oligos_7nt_mkv4_m30) |
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; oligos_7nt_mkv4_m30 (oligos_7nt_mkv4_m30oligos_7nt_mkv4_m30); m=0 (reference); ncol1=11; shift=2; ncol=13; --ssCGmGCCGss
; Alignment reference
a 0 0 25 28 0 1 126 4 11 0 1 25 29
c 0 0 100 79 222 0 76 12 199 224 5 104 79
g 0 0 78 98 8 229 22 207 13 6 224 74 93
t 0 0 27 25 0 0 6 7 7 0 0 27 29
|
| MA1099.2_rc_shift0 (HES1_rc) |
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; oligos_7nt_mkv4_m30 versus MA1099.2_rc (HES1_rc); m=1/2; ncol2=10; w=8; offset=-2; strand=R; shift=0; score=0.448518; gvCACGyGcc---
; cor=; Ncor=
a 3216.0 4837.0 53.0 18526.0 0.0 791.0 232.0 18.0 8007.0 4239.0 0 0 0
c 6013.0 6360.0 18526.0 0.0 18526.0 0.0 9081.0 0.0 18526.0 18526.0 0 0 0
g 12513.0 6203.0 0.0 4057.0 0.0 18526.0 0.0 18526.0 2072.0 3492.0 0 0 0
t 2742.0 1126.0 1.0 253.0 21.0 0.0 9446.0 464.0 5858.0 3321.0 0 0 0
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| MA0616.2_rc_shift0 (HES2_rc) |
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; oligos_7nt_mkv4_m30 versus MA0616.2_rc (HES2_rc); m=2/2; ncol2=10; w=8; offset=-2; strand=R; shift=0; score=0.44384; grCACGTGcC---
; cor=; Ncor=
a 1319.0 3849.0 0.0 8483.0 0.0 129.0 0.0 73.0 1581.0 798.0 0 0 0
c 1735.0 1289.0 8483.0 0.0 8483.0 0.0 2028.0 85.0 8483.0 8483.0 0 0 0
g 4464.0 4634.0 15.0 1098.0 0.0 8483.0 0.0 8483.0 1107.0 1193.0 0 0 0
t 966.0 512.0 53.0 0.0 0.0 0.0 6455.0 118.0 1501.0 775.0 0 0 0
|