One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_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_Rep2_motifs50/results/discovered_motifs/oligos_6nt_mkv3_m4/peak-motifs_oligos_6nt_mkv3_m4_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4oligos_6nt_mkv3_m4) |
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; oligos_6nt_mkv3_m4 (oligos_6nt_mkv3_m4oligos_6nt_mkv3_m4); m=0 (reference); ncol1=12; shift=0; ncol=17; svAAAGCCACms-----
; Alignment reference
a 82 90 239 326 325 20 4 3 327 20 127 60 0 0 0 0 0
c 88 115 32 4 6 4 322 330 3 259 92 112 0 0 0 0 0
g 102 89 41 4 2 312 7 3 8 50 84 100 0 0 0 0 0
t 68 46 28 6 7 4 7 4 2 11 37 68 0 0 0 0 0
|
| MA0002.2_rc_shift3 (RUNX1_rc) |
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; oligos_6nt_mkv3_m4 versus MA0002.2_rc (RUNX1_rc); m=1/2; ncol2=11; w=9; offset=3; strand=R; shift=3; score=0.486465; ---waaCCACAram---
; cor=; Ncor=
a 0 0 0 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 0 0 0
c 0 0 0 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 0 0 0
g 0 0 0 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 0 0 0
t 0 0 0 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0 0 0 0
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| MA0079.4_shift2 (SP1) |
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; oligos_6nt_mkv3_m4 versus MA0079.4 (SP1); m=2/2; ncol2=15; w=10; offset=2; strand=D; shift=2; score=0.425046; --ywrRCCACGCCCmCh
; cor=; Ncor=
a 0 0 7866.0 28233.0 28895.0 14584.0 962.0 55.0 42154.0 0.0 959.0 0.0 8.0 0.0 24666.0 1195.0 12598.0
c 0 0 13273.0 1872.0 1530.0 0.0 48854.0 49649.0 12672.0 49660.0 0.0 49666.0 49662.0 48772.0 24196.0 37612.0 15606.0
g 0 0 9691.0 999.0 19477.0 37543.0 82.0 0.0 0.0 0.0 48957.0 0.0 0.0 0.0 15.0 919.0 3044.0
t 0 0 18833.0 19877.0 1184.0 153.0 124.0 1670.0 0.0 31.0 867.0 17.0 0.0 1440.0 1373.0 10717.0 18415.0
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