One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.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/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift0 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; camACACACACACACACaca ; Alignment reference a 965 3377 1678 5060 154 5244 90 5341 63 3968 63 5368 41 5276 41 5210 128 3152 571 2859 c 3349 891 3227 170 5234 40 5358 28 5333 80 5322 14 5384 26 5404 78 5174 357 3514 760 g 544 801 227 203 44 204 40 104 50 1298 40 110 29 170 32 141 100 729 639 1111 t 688 477 414 113 114 58 58 73 100 200 121 54 92 74 69 117 144 1308 822 816
klu_SANGER_10_FBgn0013469_rc_shift5 (klu_SANGER_10_FBgn0013469_rc)				; dyads_m2 versus klu_SANGER_10_FBgn0013469_rc; m=1/1; ncol2=11; w=0; offset=5; strand=R; shift=5; score=0.420483; -----mCACCCmCrCa---- ; cor=; Ncor= a 0 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 0 0 0 c 0 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 0 0 0 g 0 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 0 0 0 t 0 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0 0 0 0