One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m28/peak-motifs_local_words_8nt_m28.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_8nt_m28/peak-motifs_local_words_8nt_m28_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: local_words_8nt_m28_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| local_words_8nt_m28_shift0 (local_words_8nt_m28local_words_8nt_m28) |
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; local_words_8nt_m28 (local_words_8nt_m28local_words_8nt_m28); m=0 (reference); ncol1=24; shift=0; ncol=24; rsTGACAGCTGCAGCAGCTGagrs
; Alignment reference
a 18 12 8 3 52 1 58 3 2 6 1 3 58 1 2 52 4 1 8 1 32 6 17 13
c 15 22 4 1 5 58 0 0 59 2 0 57 0 3 54 4 2 52 1 2 8 15 14 21
g 26 20 8 58 4 2 1 60 2 5 60 1 1 57 6 0 54 6 5 60 11 38 20 16
t 4 9 43 1 2 2 4 0 0 50 2 2 4 2 1 7 3 4 49 0 12 4 12 13
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| MA1485.1_shift10 (FERD3L) |
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; local_words_8nt_m28 versus MA1485.1 (FERD3L); m=1/2; ncol2=14; w=14; offset=10; strand=D; shift=10; score=0.424031; ----------GyrmCAGCTGTyAC
; cor=; Ncor=
a 0 0 0 0 0 0 0 0 0 0 2158.0 450.0 14384.0 15390.0 36.0 29605.0 0.0 3649.0 81.0 0.0 1268.0 103.0 29605.0 0.0
c 0 0 0 0 0 0 0 0 0 0 68.0 20049.0 2443.0 9363.0 29605.0 126.0 841.0 29605.0 129.0 0.0 3878.0 8664.0 809.0 29605.0
g 0 0 0 0 0 0 0 0 0 0 29605.0 348.0 12703.0 3142.0 0.0 118.0 29605.0 471.0 210.0 29605.0 3395.0 5920.0 9815.0 0.0
t 0 0 0 0 0 0 0 0 0 0 225.0 9557.0 74.0 1710.0 0.0 144.0 4691.0 0.0 29605.0 0.0 21065.0 14919.0 958.0 48.0
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| MA0499.2_rc_shift1 (MYOD1_rc) |
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; local_words_8nt_m28 versus MA0499.2_rc (MYOD1_rc); m=2/2; ncol2=13; w=13; offset=1; strand=R; shift=1; score=0.421989; -rkrACAGGTGcwg----------
; cor=; Ncor=
a 0 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 0 0 0 0 0 0 0 0 0 0
c 0 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 0 0 0 0 0 0 0 0 0 0
g 0 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 0 0 0 0 0 0 0 0 0 0
t 0 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0 0 0 0 0 0 0 0 0 0 0
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