One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/local_words_8nt_m3/peak-motifs_local_words_8nt_m3.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/local_words_8nt_m3/peak-motifs_local_words_8nt_m3_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: local_words_8nt_m3_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| local_words_8nt_m3_shift0 (local_words_8nt_m3local_words_8nt_m3) |
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|
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; local_words_8nt_m3 (local_words_8nt_m3local_words_8nt_m3); m=0 (reference); ncol1=24; shift=0; ncol=24; vbswGACAGCTGCAGCTGTCwsvb
; Alignment reference
a 6 2 4 6 0 19 0 22 0 1 4 1 0 19 0 0 0 1 1 0 14 2 8 4
c 6 7 6 0 1 1 21 1 1 21 1 0 23 0 2 23 1 2 3 23 4 12 7 8
g 8 7 12 4 23 3 2 1 23 2 0 23 0 1 21 1 1 21 1 1 0 6 7 6
t 4 8 2 14 0 1 1 0 0 0 19 0 1 4 1 0 22 0 19 0 6 4 2 6
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| MA1485.1_rc_shift2 (FERD3L_rc) |
 |
|
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; local_words_8nt_m3 versus MA1485.1_rc (FERD3L_rc); m=1/2; ncol2=14; w=14; offset=2; strand=R; shift=2; score=0.434461; --GTrACAGCTGkyrC--------
; cor=; Ncor=
a 0 0 48.0 958.0 14919.0 21065.0 0.0 29605.0 0.0 4691.0 144.0 0.0 1710.0 74.0 9557.0 225.0 0 0 0 0 0 0 0 0
c 0 0 0.0 9815.0 5920.0 3395.0 29605.0 210.0 471.0 29605.0 118.0 0.0 3142.0 12703.0 348.0 29605.0 0 0 0 0 0 0 0 0
g 0 0 29605.0 809.0 8664.0 3878.0 0.0 129.0 29605.0 841.0 126.0 29605.0 9363.0 2443.0 20049.0 68.0 0 0 0 0 0 0 0 0
t 0 0 0.0 29605.0 103.0 1268.0 0.0 81.0 3649.0 0.0 29605.0 36.0 15390.0 14384.0 450.0 2158.0 0 0 0 0 0 0 0 0
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| MA0499.2_shift9 (MYOD1) |
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; local_words_8nt_m3 versus MA0499.2 (MYOD1); m=2/2; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.433839; ---------cwgCACCTGTymy--
; cor=; Ncor=
a 0 0 0 0 0 0 0 0 0 7175.0 9462.0 4549.0 349.0 32281.0 463.0 534.0 241.0 208.0 402.0 1808.0 9462.0 5687.0 0 0
c 0 0 0 0 0 0 0 0 0 11279.0 7103.0 5622.0 33328.0 583.0 25275.0 32504.0 563.0 386.0 2555.0 19052.0 10485.0 11760.0 0 0
g 0 0 0 0 0 0 0 0 0 8118.0 8444.0 21884.0 354.0 849.0 7336.0 932.0 366.0 33468.0 1699.0 4440.0 6202.0 7495.0 0 0
t 0 0 0 0 0 0 0 0 0 7728.0 9291.0 2245.0 269.0 587.0 1226.0 330.0 33130.0 238.0 29644.0 9000.0 8151.0 9358.0 0 0
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