One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/positions_6-8nt_m2/peak-motifs_positions_6-8nt_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.180830_2026-01-25.180830_qbHDLg/results/discovered_motifs/positions_6-8nt_m2/peak-motifs_positions_6-8nt_m2_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6-8nt_m2_shift0 (positions_6-8nt_m2) |
 |
|
|
; positions_6-8nt_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; wwaAAATAAAAcAtww
; Alignment reference
a 1833 1979 3158 4568 4567 4506 530 4561 4453 4442 4323 1244 3602 1255 2091 1905
c 901 832 545 143 140 193 316 137 201 184 248 2350 409 586 790 884
g 922 995 498 125 95 152 222 155 132 136 156 458 425 577 847 865
t 1443 1293 898 263 297 248 4031 246 313 337 372 1047 663 2681 1371 1445
|
| hb_shift4 (hb) |
 |
|
|
; positions_6-8nt_m2 versus hb; m=1/1; ncol2=9; w=0; offset=4; strand=D; shift=4; score=0.434193; ----mayAAAAAa---
; cor=; Ncor=
a 0 0 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0
c 0 0 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0
g 0 0 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0
t 0 0 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0
|