One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_6nt_mkv3_m27/peak-motifs_oligos_6nt_mkv3_m27.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_6nt_mkv3_m27/peak-motifs_oligos_6nt_mkv3_m27_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m27_shift3 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv3_m27_shift3 (oligos_6nt_mkv3_m27oligos_6nt_mkv3_m27) |
 |
|
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; oligos_6nt_mkv3_m27 (oligos_6nt_mkv3_m27oligos_6nt_mkv3_m27); m=0 (reference); ncol1=11; shift=3; ncol=14; ---awAAAGCAAah
; Alignment reference
a 0 0 0 63 53 140 148 149 9 28 146 150 53 42
c 0 0 0 27 22 0 0 1 7 110 1 1 29 39
g 0 0 0 31 33 2 0 0 129 4 3 0 37 32
t 0 0 0 31 44 10 4 2 7 10 2 1 33 39
|
| MA0508.3_rc_shift0 (PRDM1_rc) |
 |
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; oligos_6nt_mkv3_m27 versus MA0508.3_rc (PRDM1_rc); m=1/2; ncol2=11; w=8; offset=-3; strand=R; shift=0; score=0.420495; raGAGAAAGwr---
; cor=; Ncor=
a 19978.0 27294.0 660.0 49466.0 432.0 52619.0 50943.0 52905.0 829.0 17272.0 22293.0 0 0 0
c 7861.0 4098.0 290.0 1390.0 207.0 561.0 1011.0 826.0 701.0 8768.0 6638.0 0 0 0
g 17518.0 13567.0 52821.0 1076.0 53465.0 488.0 1346.0 467.0 52752.0 12288.0 17788.0 0 0 0
t 10124.0 10522.0 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0 1199.0 17153.0 8762.0 0 0 0
|
| MA0442.2_shift0 (SOX10) |
 |
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; oligos_6nt_mkv3_m27 versus MA0442.2 (SOX10); m=2/2; ncol2=11; w=8; offset=-3; strand=D; shift=0; score=0.406805; rraACAAAGvm---
; cor=; Ncor=
a 683.0 723.0 1118.0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 666.0 638.0 0 0 0
c 397.0 283.0 372.0 4.0 1989.0 7.0 28.0 23.0 13.0 552.0 555.0 0 0 0
g 527.0 571.0 317.0 3.0 11.0 7.0 20.0 12.0 2012.0 619.0 505.0 0 0 0
t 448.0 478.0 248.0 25.0 52.0 12.0 39.0 61.0 20.0 218.0 357.0 0 0 0
|