; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.170244_MrKA34.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_2026-08-17.170244_nla2MV.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; bg $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.170244_nla2MV.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.170244_MrKA34.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 AT1G29550|EIF4E3 limit START_END D -500 -1 . 0 0 0 0 AT1G71790|AT1G71790 limit START_END D -500 -1 . 0 0 0 0 AT1G48950|AT1G48950 limit START_END D -500 -1 . 0 0 0 0 AT1G21925|AT1G21925 limit START_END D -500 -1 . 0 0 0 0 AT1G20180|AT1G20180 limit START_END D -500 -1 . 0 0 0 0 AT5G60700|AT5G60700 limit START_END D -500 -1 . 0 0 0 0 AT5G48060|AT5G48060 limit START_END D -500 -1 . 0 0 0 0 AT1G33355|AT1G33355 limit START_END D -500 -1 . 0 0 0 0 AT2G35240|MORF6 limit START_END D -500 -1 . 0 0 0 0 AT1G08403|AT1G08403 limit START_END D -500 -1 . 0 0 0 0 AT3G01730|AT3G01730 limit START_END D -500 -1 . 0 0 0 0 AT1G61920|AT1G61920 limit START_END D -500 -1 . 0 0 0 0 AT1G15215|AT1G15215 limit START_END D -500 -1 . 0 0 0 0 AT3G44769|AT3G44769 limit START_END D -500 -1 . 0 0 0 0 AT3G17900|AT3G17900 limit START_END D -500 -1 . 0 0 0 0 AT2G33435|AT2G33435 limit START_END D -500 -1 . 0 0 0 0 AT5G16950|AT5G16950 limit START_END D -500 -1 . 0 0 0 0 AT5G46880|HDG5 limit START_END D -500 -1 . 0 0 0 0 AT2G38480|AT2G38480 limit START_END D -500 -1 . 0 0 0 0 AT1G59590|ZCF37 limit START_END D -500 -1 . 0 0 0 0 AT4G07805|AT4G07805 limit START_END D -500 -1 . 0 0 0 0 AT5G02875|AT5G02875 limit START_END D -500 -1 . 0 0 0 0 AT5G62290|AT5G62290 limit START_END D -500 -1 . 0 0 0 0 AT3G05495|AT3G05495 limit START_END D -500 -1 . 0 0 0 0 AT1G29550|EIF4E3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -91 -84 ACACCCGC 5.4 4.2e-04 -7.775 3.377 AT1G71790|AT1G71790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -376 -369 ATAACCGC 5.0 8.0e-04 -7.131 3.097 AT1G71790|AT1G71790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -297 -290 TTCGCCGC 5.4 4.2e-04 -7.775 3.377 AT1G48950|AT1G48950 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -284 -277 TATCCCTC 5.2 5.9e-04 -7.435 3.229 AT1G20180|AT1G20180 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -241 -234 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT1G20180|AT1G20180 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -58 -51 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 AT5G60700|AT5G60700 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -316 -309 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 AT1G33355|AT1G33355 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -375 -368 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT3G01730|AT3G01730 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -335 -328 AATCTCGC 4.8 8.8e-04 -7.036 3.056 AT3G01730|AT3G01730 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -70 -63 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT3G01730|AT3G01730 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -49 -42 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 AT1G15215|AT1G15215 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -234 -227 TTCCCCGC 7.9 2.8e-05 -10.483 4.553 AT1G15215|AT1G15215 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -220 -213 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 AT3G17900|AT3G17900 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -395 -388 ATTCCCAC 6.5 2.7e-04 -8.217 3.569 AT3G17900|AT3G17900 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -106 -99 TTACCCTC 5.1 7.4e-04 -7.209 3.131 AT2G33435|AT2G33435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -424 -417 ACTCTCGC 5.0 8.0e-04 -7.131 3.097 AT2G33435|AT2G33435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -305 -298 ACTGCCGC 4.9 8.8e-04 -7.036 3.056 AT2G33435|AT2G33435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -116 -109 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT5G16950|AT5G16950 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -366 -359 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT5G16950|AT5G16950 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -114 -107 AGTCTCGC 5.0 8.0e-04 -7.131 3.097 AT5G46880|HDG5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -275 -268 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT5G46880|HDG5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -198 -191 TTACCCTC 5.1 7.4e-04 -7.209 3.131 AT1G59590|ZCF37 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -393 -386 TTACCCGA 5.2 5.9e-04 -7.435 3.229 AT4G07805|AT4G07805 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -296 -289 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 AT4G07805|AT4G07805 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -191 -184 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT1G29550|EIF4E3 site 5015_E2Fb_Athamap_20091028_ D -91 -84 ACACCCGC 5.0 6.5e-04 -7.339 3.187 AT1G71790|AT1G71790 site 5015_E2Fb_Athamap_20091028_ D -376 -369 ATAACCGC 4.5 9.4e-04 -6.970 3.027 AT1G71790|AT1G71790 site 5015_E2Fb_Athamap_20091028_ D -297 -290 TTCGCCGC 5.4 4.4e-04 -7.729 3.357 AT1G48950|AT1G48950 site 5015_E2Fb_Athamap_20091028_ R -284 -277 TATCCCTC 5.1 5.8e-04 -7.452 3.237 AT1G48950|AT1G48950 site 5015_E2Fb_Athamap_20091028_ R -143 -136 TTTAACGC 4.5 9.4e-04 -6.970 3.027 AT1G20180|AT1G20180 site 5015_E2Fb_Athamap_20091028_ D -241 -234 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT1G20180|AT1G20180 site 5015_E2Fb_Athamap_20091028_ D -58 -51 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT5G60700|AT5G60700 site 5015_E2Fb_Athamap_20091028_ D -316 -309 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 AT1G33355|AT1G33355 site 5015_E2Fb_Athamap_20091028_ D -375 -368 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT3G01730|AT3G01730 site 5015_E2Fb_Athamap_20091028_ D -70 -63 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT3G01730|AT3G01730 site 5015_E2Fb_Athamap_20091028_ D -49 -42 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 AT1G15215|AT1G15215 site 5015_E2Fb_Athamap_20091028_ D -234 -227 TTCCCCGC 8.1 2.5e-05 -10.597 4.602 AT1G15215|AT1G15215 site 5015_E2Fb_Athamap_20091028_ D -220 -213 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT3G17900|AT3G17900 site 5015_E2Fb_Athamap_20091028_ D -395 -388 ATTCCCAC 6.3 2.7e-04 -8.217 3.569 AT3G17900|AT3G17900 site 5015_E2Fb_Athamap_20091028_ D -106 -99 TTACCCTC 5.0 6.5e-04 -7.339 3.187 AT2G33435|AT2G33435 site 5015_E2Fb_Athamap_20091028_ D -424 -417 ACTCTCGC 4.5 9.4e-04 -6.970 3.027 AT2G33435|AT2G33435 site 5015_E2Fb_Athamap_20091028_ R -116 -109 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT5G16950|AT5G16950 site 5015_E2Fb_Athamap_20091028_ D -366 -359 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT5G16950|AT5G16950 site 5015_E2Fb_Athamap_20091028_ D -175 -168 TTTCGCGA 4.5 9.4e-04 -6.970 3.027 AT5G16950|AT5G16950 site 5015_E2Fb_Athamap_20091028_ R -114 -107 AGTCTCGC 4.5 9.4e-04 -6.970 3.027 AT5G46880|HDG5 site 5015_E2Fb_Athamap_20091028_ R -275 -268 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT5G46880|HDG5 site 5015_E2Fb_Athamap_20091028_ R -198 -191 TTACCCTC 5.0 6.5e-04 -7.339 3.187 AT1G59590|ZCF37 site 5015_E2Fb_Athamap_20091028_ D -393 -386 TTACCCGA 5.2 5.8e-04 -7.452 3.237 AT4G07805|AT4G07805 site 5015_E2Fb_Athamap_20091028_ R -296 -289 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 AT4G07805|AT4G07805 site 5015_E2Fb_Athamap_20091028_ R -191 -184 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT1G29550|EIF4E3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -90 -80 CACCCGCGCAT 8.1 3.9e-05 -10.152 4.409 AT1G71790|AT1G71790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -426 -416 TTCAAGCCATA 5.2 5.0e-04 -7.601 3.301 AT1G71790|AT1G71790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -385 -375 ATCCTGCTCAT 6.2 2.3e-04 -8.377 3.638 AT1G48950|AT1G48950 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -410 -400 ATCCCTCGATA 6.7 1.5e-04 -8.805 3.824 AT1G20180|AT1G20180 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -57 -47 TTCCCTCTAAC 4.9 7.2e-04 -7.236 3.143 AT1G20180|AT1G20180 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -47 -37 CTTGCGCCAAA 4.9 6.5e-04 -7.339 3.187 AT5G60700|AT5G60700 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -337 -327 TATACGCCAAT 4.7 7.7e-04 -7.169 3.114 AT5G48060|AT5G48060 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -230 -220 TTTCCTCCAAA 4.6 8.3e-04 -7.094 3.081 AT1G33355|AT1G33355 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -70 -60 TACACGCGAAT 7.3 9.0e-05 -9.316 4.046 AT2G35240|MORF6 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -384 -374 ATGTCGCCCTA 4.8 7.2e-04 -7.236 3.143 AT3G01730|AT3G01730 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -69 -59 TTCCCTCGAAT 7.4 8.1e-05 -9.421 4.092 AT1G15215|AT1G15215 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -233 -223 TCCCCGCGGAC 4.4 9.8e-04 -6.928 3.009 AT1G15215|AT1G15215 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -47 -37 AACCCACTAAA 4.6 8.3e-04 -7.094 3.081 AT3G17900|AT3G17900 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -497 -487 TTCAAGCGCAT 4.8 7.7e-04 -7.169 3.114 AT3G17900|AT3G17900 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -272 -262 TACAAGCCCAA 4.6 8.3e-04 -7.094 3.081 AT3G17900|AT3G17900 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -105 -95 TACCCTCCTAA 5.6 3.6e-04 -7.929 3.444 AT3G17900|AT3G17900 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -63 -53 AACCCCCTAAA 4.4 9.8e-04 -6.928 3.009 AT2G33435|AT2G33435 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -490 -480 AACCCGCCTCT 5.2 5.4e-04 -7.524 3.268 AT5G16950|AT5G16950 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -174 -164 TTCGCGATCGA 4.7 8.3e-04 -7.094 3.081 AT5G46880|HDG5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -219 -209 ACCCCTCCATA 4.7 7.7e-04 -7.169 3.114 AT5G46880|HDG5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -202 -192 TACCCTCGAAA 6.8 1.5e-04 -8.805 3.824 AT5G46880|HDG5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -182 -172 CTCCCACTAAT 4.4 9.8e-04 -6.928 3.009 AT4G07805|AT4G07805 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -195 -185 TTCCCTCTCTC 4.7 7.7e-04 -7.169 3.114 ; ; 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_ 25 0 ; 2 5015_E2Fb_Athamap_20091028_ 25 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 23 0 ; TOTAL 73 0 ; Host name rsat ; Job started 2026-08-17.170245 ; Job done 2026-08-17.170246 ; Seconds 0.48 ; user 0.48 ; system 0.05 ; cuser 0.79 ; csystem 0.09