One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m5/peak-motifs_local_words_8nt_m5.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_m5/peak-motifs_local_words_8nt_m5_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: local_words_8nt_m5_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| local_words_8nt_m5_shift0 (local_words_8nt_m5local_words_8nt_m5) |
 |
|
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; local_words_8nt_m5 (local_words_8nt_m5local_words_8nt_m5); m=0 (reference); ncol1=24; shift=0; ncol=24; gctGCAGCAGCTGCTGCAGCTGcw
; Alignment reference
a 44 34 55 17 11 232 5 2 249 6 6 44 3 2 51 15 6 224 10 6 36 9 41 81
c 53 169 38 27 258 11 12 294 7 3 289 6 4 279 14 18 284 21 9 283 26 17 172 68
g 161 45 55 250 31 21 285 7 7 295 2 15 295 16 13 266 9 12 275 5 10 274 57 75
t 47 57 157 11 5 41 3 2 42 1 8 240 3 8 227 6 6 48 11 11 233 5 35 81
|
| MA1485.1_shift3 (FERD3L) |
 |
|
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; local_words_8nt_m5 versus MA1485.1 (FERD3L); m=1/2; ncol2=14; w=14; offset=3; strand=D; shift=3; score=0.432527; ---GyrmCAGCTGTyAC-------
; cor=; Ncor=
a 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 0 0 0 0 0 0 0
c 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 0 0 0 0 0 0 0
g 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 0 0 0 0 0 0 0
t 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 0 0 0 0 0 0 0
|
| MA0500.2_rc_shift4 (MYOG_rc) |
 |
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; local_words_8nt_m5 versus MA0500.2_rc (MYOG_rc); m=2/2; ncol2=12; w=12; offset=4; strand=R; shift=4; score=0.416631; ----sarCAGCTGyts--------
; cor=; Ncor=
a 0 0 0 0 5310.0 8475.0 7192.0 88.0 21777.0 95.0 169.0 163.0 182.0 1678.0 4692.0 5070.0 0 0 0 0 0 0 0 0
c 0 0 0 0 6369.0 3718.0 2706.0 21985.0 179.0 131.0 21963.0 236.0 101.0 10790.0 5483.0 5596.0 0 0 0 0 0 0 0 0
g 0 0 0 0 5660.0 5497.0 10792.0 102.0 238.0 21964.0 130.0 176.0 21988.0 2730.0 3754.0 6381.0 0 0 0 0 0 0 0 0
t 0 0 0 0 5018.0 4667.0 1667.0 182.0 163.0 167.0 95.0 21782.0 86.0 7159.0 8428.0 5310.0 0 0 0 0 0 0 0 0
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