One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m23/peak-motifs_oligos_7nt_mkv4_m23.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_m23/peak-motifs_oligos_7nt_mkv4_m23_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m23_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv4_m23_shift0 (oligos_7nt_mkv4_m23oligos_7nt_mkv4_m23) |
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; oligos_7nt_mkv4_m23 (oligos_7nt_mkv4_m23oligos_7nt_mkv4_m23); m=0 (reference); ncol1=12; shift=0; ncol=13; ssAGGCTGGCsg-
; Alignment reference
a 21 27 147 1 0 0 0 0 4 0 34 23 0
c 60 67 8 4 1 159 8 4 0 160 47 37 0
g 56 53 4 156 160 2 14 157 156 1 43 70 0
t 24 14 2 0 0 0 139 0 1 0 37 31 0
|
| MA0739.1_rc_shift3 (Hic1_rc) |
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|
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; oligos_7nt_mkv4_m23 versus MA0739.1_rc (Hic1_rc); m=1/2; ncol2=9; w=9; offset=3; strand=R; shift=3; score=0.535846; ---gGtTGGCAy-
; cor=; Ncor=
a 0 0 0 2692.0 1488.0 614.0 317.0 68.0 0.0 183.0 11007.0 666.0 0
c 0 0 0 1884.0 1629.0 2267.0 3.0 31.0 121.0 11007.0 73.0 4670.0 0
g 0 0 0 4822.0 11007.0 1986.0 1999.0 11007.0 11007.0 588.0 422.0 719.0 0
t 0 0 0 1610.0 1220.0 6140.0 9008.0 88.0 50.0 950.0 62.0 6337.0 0
|
| MA0671.1_rc_shift4 (NFIX_rc) |
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; oligos_7nt_mkv4_m23 versus MA0671.1_rc (NFIX_rc); m=2/2; ncol2=9; w=8; offset=4; strand=R; shift=4; score=0.452809; ----byTGGCacs
; cor=; Ncor=
a 0 0 0 0 6439.0 2399.0 110.0 0.0 29.0 2539.0 32864.0 8043.0 7378.0
c 0 0 0 0 9135.0 12688.0 180.0 0.0 3257.0 32864.0 5911.0 10855.0 8725.0
g 0 0 0 0 9039.0 1356.0 2230.0 32864.0 32864.0 186.0 9695.0 6134.0 8810.0
t 0 0 0 0 8251.0 32864.0 32864.0 0.0 3.0 132.0 11279.0 7832.0 7951.0
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