One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3) |
 |
|
|
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=15; shift=1; ncol=16; -raAAATGAGAAAyay
; Alignment reference
a 0 1085 2150 3072 3068 3125 201 127 3239 240 3238 3160 3082 439 1833 776
c 0 259 394 149 159 142 47 125 33 91 49 114 133 1796 338 1047
g 0 1545 423 112 101 64 241 3083 68 2972 106 93 128 197 598 354
t 0 553 475 109 114 111 2953 107 102 139 49 75 99 1010 673 1265
|
| MA0050.4_shift0 (Irf1) |
 |
|
|
; oligos_6nt_mkv4_m3 versus MA0050.4 (Irf1); m=1/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.454549; tGAAAcTGAAA-----
; cor=; Ncor=
a 3724.0 1661.0 13772.0 14795.0 14878.0 1939.0 1900.0 1017.0 14145.0 14424.0 14172.0 0 0 0 0 0
c 1292.0 637.0 361.0 253.0 176.0 9822.0 933.0 314.0 298.0 353.0 365.0 0 0 0 0 0
g 2035.0 12682.0 1024.0 258.0 240.0 3315.0 274.0 14013.0 775.0 499.0 607.0 0 0 0 0 0
t 8589.0 660.0 483.0 334.0 346.0 564.0 12533.0 296.0 422.0 364.0 496.0 0 0 0 0 0
|
| MA0508.4_rc_shift7 (PRDM1_rc) |
 |
|
|
; oligos_6nt_mkv4_m3 versus MA0508.4_rc (PRDM1_rc); m=2/2; ncol2=7; w=0; offset=6; strand=R; shift=7; score=0.400865; -------GAGAAAG--
; cor=; Ncor=
a 0 0 0 0 0 0 0 660.0 49466.0 432.0 52619.0 50943.0 52905.0 829.0 0 0
c 0 0 0 0 0 0 0 290.0 1390.0 207.0 561.0 1011.0 826.0 701.0 0 0
g 0 0 0 0 0 0 0 52821.0 1076.0 53465.0 488.0 1346.0 467.0 52752.0 0 0
t 0 0 0 0 0 0 0 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0 1199.0 0 0
|