; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.132953_fUDFZc.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return pval -uth pval 0.001 -i $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.132953_FZxRyu.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.132953_FZxRyu.fasta ; bg $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.132953_fUDFZc.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method file ; Markov order 1 ; Strand sensitive ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.34589 ; c 0.15671 ; g 0.15366 ; t 0.34374 ; Thresholds lower upper ; pval NA 0.001 ; Output columns ; 1 seq_id ; 2 ft_type ; 3 ft_name ; 4 strand ; 5 start ; 6 end ; 7 sequence ; 8 weight #seq_id ft_type ft_name strand start end sequence weight Pval ln_Pval sig AT2G27290 limit START_END D -500 -1 . 0 0 0 0 AT3G44485 limit START_END D -500 -1 . 0 0 0 0 AT3G18170 limit START_END D -500 -1 . 0 0 0 0 MARD1 limit START_END D -500 -1 . 0 0 0 0 AT5G62830 limit START_END D -500 -1 . 0 0 0 0 AT1G63070 limit START_END D -500 -1 . 0 0 0 0 AT3G14380 limit START_END D -500 -1 . 0 0 0 0 NFYB2 limit START_END D -500 -1 . 0 0 0 0 AT2G09170 limit START_END D -500 -1 . 0 0 0 0 UGT76D1 limit START_END D -500 -1 . 0 0 0 0 SYP52 limit START_END D -500 -1 . 0 0 0 0 AT5G25100 limit START_END D -500 -1 . 0 0 0 0 AT4G04895 limit START_END D -500 -1 . 0 0 0 0 WSIP2 limit START_END D -500 -1 . 0 0 0 0 BCAT6 limit START_END D -500 -1 . 0 0 0 0 AVPL1 limit START_END D -500 -1 . 0 0 0 0 AT4G24025 limit START_END D -500 -1 . 0 0 0 0 IPUT1 limit START_END D -500 -1 . 0 0 0 0 CNGC20 limit START_END D -500 -1 . 0 0 0 0 AT3G44753 limit START_END D -500 -1 . 0 0 0 0 WIP2 limit START_END D -500 -1 . 0 0 0 0 AT1G26773 limit START_END D -500 -1 . 0 0 0 0 AT1G08153 limit START_END D -500 -1 . 0 0 0 0 AT3G03180 limit START_END D -500 -1 . 0 0 0 0 AT3G44485 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -47 -40 TCTCCCGT 5.2 6.7e-04 -7.308 3.174 AT3G18170 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -274 -267 TGTCCCGT 5.1 6.7e-04 -7.308 3.174 AT5G62830 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -357 -350 TATCCCGA 5.3 5.1e-04 -7.581 3.292 AT3G14380 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -227 -220 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 NFYB2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -326 -319 TTACCCTC 5.1 7.4e-04 -7.209 3.131 NFYB2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -284 -277 TTCCACGC 5.1 6.7e-04 -7.308 3.174 SYP52 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -341 -334 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 SYP52 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -316 -309 ATACCCGA 4.9 8.8e-04 -7.036 3.056 AT5G25100 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -9 -2 TATTCCGC 5.4 4.2e-04 -7.775 3.377 WSIP2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -144 -137 ATACACGC 5.2 6.7e-04 -7.308 3.174 AVPL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -237 -230 TCTCCGGC 5.2 5.9e-04 -7.435 3.229 AVPL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -199 -192 TTACCGGC 5.3 5.1e-04 -7.581 3.292 AT4G24025 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -243 -236 ATATCCGC 5.1 6.7e-04 -7.308 3.174 AT3G44753 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -371 -364 GTTCTCGC 5.7 3.4e-04 -7.987 3.469 AT3G44753 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -164 -157 TTGACCGC 5.1 6.7e-04 -7.308 3.174 WIP2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -200 -193 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT3G03180 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -142 -135 TTTGCCGC 7.3 7.6e-05 -9.485 4.119 AT3G03180 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -100 -93 TTACCCAC 5.0 7.4e-04 -7.209 3.131 AT3G44485 site 5015_E2Fb_Athamap_20091028_ R -47 -40 TCTCCCGT 5.1 5.8e-04 -7.452 3.237 AT3G18170 site 5015_E2Fb_Athamap_20091028_ R -274 -267 TGTCCCGT 5.0 6.5e-04 -7.339 3.187 AT5G62830 site 5015_E2Fb_Athamap_20091028_ R -357 -350 TATCCCGA 5.3 4.4e-04 -7.729 3.357 AT3G14380 site 5015_E2Fb_Athamap_20091028_ D -227 -220 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 NFYB2 site 5015_E2Fb_Athamap_20091028_ D -326 -319 TTACCCTC 5.0 6.5e-04 -7.339 3.187 NFYB2 site 5015_E2Fb_Athamap_20091028_ D -284 -277 TTCCACGC 5.1 6.5e-04 -7.339 3.187 SYP52 site 5015_E2Fb_Athamap_20091028_ R -341 -334 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT5G25100 site 5015_E2Fb_Athamap_20091028_ R -9 -2 TATTCCGC 5.4 3.9e-04 -7.849 3.409 WSIP2 site 5015_E2Fb_Athamap_20091028_ D -144 -137 ATACACGC 4.7 7.9e-04 -7.143 3.102 AVPL1 site 5015_E2Fb_Athamap_20091028_ R -237 -230 TCTCCGGC 5.1 5.8e-04 -7.452 3.237 AVPL1 site 5015_E2Fb_Athamap_20091028_ R -199 -192 TTACCGGC 5.3 5.1e-04 -7.581 3.292 AT4G24025 site 5015_E2Fb_Athamap_20091028_ R -243 -236 ATATCCGC 4.7 8.2e-04 -7.106 3.086 AT3G44753 site 5015_E2Fb_Athamap_20091028_ R -371 -364 GTTCTCGC 5.5 3.6e-04 -7.929 3.444 AT3G44753 site 5015_E2Fb_Athamap_20091028_ R -164 -157 TTGACCGC 5.1 6.5e-04 -7.339 3.187 WIP2 site 5015_E2Fb_Athamap_20091028_ D -200 -193 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT3G03180 site 5015_E2Fb_Athamap_20091028_ R -142 -135 TTTGCCGC 7.5 6.2e-05 -9.688 4.208 AT3G03180 site 5015_E2Fb_Athamap_20091028_ D -100 -93 TTACCCAC 4.9 6.9e-04 -7.279 3.161 AT3G44485 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -460 -450 ATCCGGCGCAA 7.3 9.0e-05 -9.316 4.046 AT3G18170 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -16 -6 TCCCCACGATT 4.5 9.8e-04 -6.928 3.009 AT5G62830 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -361 -351 ATCCCGAGATT 6.1 2.5e-04 -8.294 3.602 AT3G14380 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -226 -216 TTCCCTCTTAT 4.6 9.1e-04 -7.002 3.041 AT3G14380 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -207 -197 TTGCCACCATA 4.9 6.5e-04 -7.339 3.187 NFYB2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -389 -379 TACGAGCGAAT 5.9 2.9e-04 -8.146 3.538 NFYB2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -388 -378 TTCGCTCGTAA 4.9 6.5e-04 -7.339 3.187 NFYB2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -283 -273 TCCACGCGCTA 6.3 2.1e-04 -8.468 3.678 SYP52 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -320 -310 TACCCGAAAAA 4.5 9.1e-04 -7.002 3.041 AT4G04895 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -97 -87 GTCCCACCAAA 5.7 3.3e-04 -8.016 3.481 WSIP2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -189 -179 TCCCCACTATA 4.6 9.1e-04 -7.002 3.041 BCAT6 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -390 -380 TTCACCCGATA 4.4 9.8e-04 -6.928 3.009 AVPL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -203 -193 TACCGGCCCGA 6.1 2.5e-04 -8.294 3.602 CNGC20 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -268 -258 TTTCGGCCCAT 5.1 5.4e-04 -7.524 3.268 CNGC20 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -128 -118 TTGCCTCCAAT 4.7 8.3e-04 -7.094 3.081 AT3G44753 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -375 -365 TTCTCGCCAAT 8.7 1.9e-05 -10.871 4.721 AT3G44753 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -125 -115 AATCCGCGAAA 5.6 3.6e-04 -7.929 3.444 AT3G03180 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -220 -210 GTCCAGCCCAT 6.2 2.3e-04 -8.377 3.638 AT3G03180 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -146 -136 TTGCCGCAAAA 5.5 3.9e-04 -7.849 3.409 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 8 4 0 -11.100 10.500 21.600 a:0.346 c:0.157 g:0.154 t:0.344 ; 2 5015_E2Fb_Athamap_20091028_ 8 4 0 -12.900 10.900 23.800 a:0.346 c:0.157 g:0.154 t:0.344 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 11 4 0 -19.800 12.800 32.600 a:0.346 c:0.157 g:0.154 t:0.344 ; Number of sequences scanned 24 ; Sum of sequence lengths 12000 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 18 0 ; 2 5015_E2Fb_Athamap_20091028_ 17 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 19 0 ; TOTAL 54 0 ; Host name rsat ; Job started 2026-08-17.132953 ; Job done 2026-08-17.132954 ; Seconds 0.43 ; user 0.43 ; system 0.05 ; cuser 0.8 ; csystem 0.07