; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.111615_HHfkMU.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_2026-08-17.111615_dCA4rr.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.111615_dCA4rr.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_2026-08-17.111615_HHfkMU.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 AT5G65020|ANN2 limit START_END D -500 -1 . 0 0 0 0 ATCG01270|ycf15-B limit START_END D -500 -1 . 0 0 0 0 AT4G13660|PRR2 limit START_END D -500 -1 . 0 0 0 0 AT1G05463|AT1G05463 limit START_END D -500 -1 . 0 0 0 0 AT3G05680|EMB2016 limit START_END D -500 -1 . 0 0 0 0 AT5G58440|SNX2A limit START_END D -500 -1 . 0 0 0 0 AT3G02765|AT3G02765 limit START_END D -500 -1 . 0 0 0 0 AT4G29350|PRO2 limit START_END D -500 -1 . 0 0 0 0 AT4G39130|AT4G39130 limit START_END D -500 -1 . 0 0 0 0 AT5G15510|AT5G15510 limit START_END D -500 -1 . 0 0 0 0 AT1G21866|AT1G21866 limit START_END D -500 -1 . 0 0 0 0 AT2G22241|AT2G22241 limit START_END D -500 -1 . 0 0 0 0 AT3G44770|AT3G44770 limit START_END D -500 -1 . 0 0 0 0 AT5G02330|AT5G02330 limit START_END D -500 -1 . 0 0 0 0 AT3G02370|AT3G02370 limit START_END D -500 -1 . 0 0 0 0 AT5G29624|AT5G29624 limit START_END D -500 -1 . 0 0 0 0 AT3G19120|AT3G19120 limit START_END D -500 -1 . 0 0 0 0 AT5G59940|AT5G59940 limit START_END D -500 -1 . 0 0 0 0 AT4G32600|AT4G32600 limit START_END D -500 -1 . 0 0 0 0 AT5G16090|AT5G16090 limit START_END D -500 -1 . 0 0 0 0 AT5G10990|AT5G10990 limit START_END D -500 -1 . 0 0 0 0 AT2G02103|AT2G02103 limit START_END D -500 -1 . 0 0 0 0 AT5G03552|MIR822A limit START_END D -500 -1 . 0 0 0 0 ATCG01270|ycf15-B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -106 -99 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT1G05463|AT1G05463 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -378 -371 CTTCCAGC 5.3 5.1e-04 -7.581 3.292 AT3G05680|EMB2016 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -483 -476 ATCCTCGC 4.8 8.8e-04 -7.036 3.056 AT5G58440|SNX2A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -500 -493 TTTAGCGC 4.8 8.8e-04 -7.036 3.056 AT5G58440|SNX2A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -465 -458 GTTCCCGT 5.4 4.2e-04 -7.775 3.377 AT5G58440|SNX2A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -375 -368 CTTCTCGC 5.7 3.4e-04 -7.987 3.469 AT3G02765|AT3G02765 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -247 -240 ATCTCCGC 4.8 8.8e-04 -7.036 3.056 AT4G39130|AT4G39130 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -313 -306 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 AT4G39130|AT4G39130 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -23 -16 GTTCACGC 5.6 3.5e-04 -7.958 3.456 AT5G15510|AT5G15510 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -359 -352 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT2G22241|AT2G22241 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -238 -231 ATCCACGC 4.8 9.5e-04 -6.959 3.022 AT2G22241|AT2G22241 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -196 -189 AAACCCGC 5.2 6.7e-04 -7.308 3.174 AT2G22241|AT2G22241 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -64 -57 AATCACGC 4.8 9.5e-04 -6.959 3.022 AT3G02370|AT3G02370 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -486 -479 ATACCCGA 4.9 8.8e-04 -7.036 3.056 AT3G02370|AT3G02370 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -471 -464 ATACCCGG 4.8 8.8e-04 -7.036 3.056 AT3G02370|AT3G02370 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -420 -413 TTGCCGGC 5.1 7.4e-04 -7.209 3.131 AT3G02370|AT3G02370 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -418 -411 TTGCCGGC 5.1 7.4e-04 -7.209 3.131 AT5G29624|AT5G29624 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -137 -130 TGTCCTGC 5.0 7.4e-04 -7.209 3.131 AT5G29624|AT5G29624 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -11 -4 ATTCCAGC 6.7 2.5e-04 -8.294 3.602 AT3G19120|AT3G19120 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -427 -420 TTGCCAGC 5.0 8.0e-04 -7.131 3.097 AT5G59940|AT5G59940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -436 -429 TTCACCGC 5.1 6.7e-04 -7.308 3.174 AT5G59940|AT5G59940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -422 -415 TTTACCGC 7.6 4.7e-05 -9.965 4.328 AT5G59940|AT5G59940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -301 -294 TTATCCGC 5.4 4.2e-04 -7.775 3.377 AT5G59940|AT5G59940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -289 -282 ATCACCGC 4.8 9.5e-04 -6.959 3.022 AT4G32600|AT4G32600 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -128 -121 TTACGCGC 5.8 3.1e-04 -8.079 3.509 AT4G32600|AT4G32600 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -50 -43 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT5G16090|AT5G16090 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -298 -291 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT5G16090|AT5G16090 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -17 -10 TTACTCGC 5.6 3.5e-04 -7.958 3.456 AT5G10990|AT5G10990 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -184 -177 TCTCCCGA 5.1 6.7e-04 -7.308 3.174 AT5G03552|MIR822A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -371 -364 ATACCGGC 5.0 7.4e-04 -7.209 3.131 AT5G03552|MIR822A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -314 -307 CTCCCCGC 6.2 2.9e-04 -8.146 3.538 AT5G03552|MIR822A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -263 -256 ATACTCGC 5.2 5.9e-04 -7.435 3.229 ATCG01270|ycf15-B site 5015_E2Fb_Athamap_20091028_ R -106 -99 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT1G05463|AT1G05463 site 5015_E2Fb_Athamap_20091028_ R -378 -371 CTTCCAGC 5.2 5.1e-04 -7.581 3.292 AT5G58440|SNX2A site 5015_E2Fb_Athamap_20091028_ D -500 -493 TTTAGCGC 4.7 7.9e-04 -7.143 3.102 AT5G58440|SNX2A site 5015_E2Fb_Athamap_20091028_ D -465 -458 GTTCCCGT 5.3 5.1e-04 -7.581 3.292 AT5G58440|SNX2A site 5015_E2Fb_Athamap_20091028_ R -375 -368 CTTCTCGC 5.5 3.6e-04 -7.929 3.444 AT4G39130|AT4G39130 site 5015_E2Fb_Athamap_20091028_ D -313 -306 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 AT4G39130|AT4G39130 site 5015_E2Fb_Athamap_20091028_ D -23 -16 GTTCACGC 5.5 3.6e-04 -7.929 3.444 AT5G15510|AT5G15510 site 5015_E2Fb_Athamap_20091028_ R -359 -352 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT2G22241|AT2G22241 site 5015_E2Fb_Athamap_20091028_ R -196 -189 AAACCCGC 4.8 7.9e-04 -7.143 3.102 AT3G02370|AT3G02370 site 5015_E2Fb_Athamap_20091028_ D -420 -413 TTGCCGGC 5.0 6.5e-04 -7.339 3.187 AT3G02370|AT3G02370 site 5015_E2Fb_Athamap_20091028_ R -418 -411 TTGCCGGC 5.0 6.5e-04 -7.339 3.187 AT5G29624|AT5G29624 site 5015_E2Fb_Athamap_20091028_ R -137 -130 TGTCCTGC 4.9 6.9e-04 -7.279 3.161 AT5G29624|AT5G29624 site 5015_E2Fb_Athamap_20091028_ D -11 -4 ATTCCAGC 6.6 2.4e-04 -8.335 3.620 AT3G19120|AT3G19120 site 5015_E2Fb_Athamap_20091028_ R -427 -420 TTGCCAGC 4.9 6.9e-04 -7.279 3.161 AT5G59940|AT5G59940 site 5015_E2Fb_Athamap_20091028_ R -436 -429 TTCACCGC 5.1 6.5e-04 -7.339 3.187 AT5G59940|AT5G59940 site 5015_E2Fb_Athamap_20091028_ D -422 -415 TTTACCGC 7.8 3.7e-05 -10.205 4.432 AT5G59940|AT5G59940 site 5015_E2Fb_Athamap_20091028_ R -301 -294 TTATCCGC 5.4 3.9e-04 -7.849 3.409 AT4G32600|AT4G32600 site 5015_E2Fb_Athamap_20091028_ D -128 -121 TTACGCGC 5.8 3.1e-04 -8.079 3.509 AT4G32600|AT4G32600 site 5015_E2Fb_Athamap_20091028_ R -50 -43 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT5G16090|AT5G16090 site 5015_E2Fb_Athamap_20091028_ D -298 -291 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT5G16090|AT5G16090 site 5015_E2Fb_Athamap_20091028_ D -17 -10 TTACTCGC 5.5 3.6e-04 -7.929 3.444 AT5G10990|AT5G10990 site 5015_E2Fb_Athamap_20091028_ D -184 -177 TCTCCCGA 5.0 6.5e-04 -7.339 3.187 AT5G03552|MIR822A site 5015_E2Fb_Athamap_20091028_ D -371 -364 ATACCGGC 4.6 9.4e-04 -6.970 3.027 AT5G03552|MIR822A site 5015_E2Fb_Athamap_20091028_ R -314 -307 CTCCCCGC 6.1 2.9e-04 -8.146 3.538 AT5G03552|MIR822A site 5015_E2Fb_Athamap_20091028_ D -263 -256 ATACTCGC 4.8 7.5e-04 -7.195 3.125 ATCG01270|ycf15-B site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -110 -100 TTCCGGCTAAG 5.1 5.4e-04 -7.524 3.268 AT1G05463|AT1G05463 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -442 -432 TTCTCTCCCTT 4.9 6.5e-04 -7.339 3.187 AT1G05463|AT1G05463 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -382 -372 TTCCAGCTCAT 7.1 1.1e-04 -9.115 3.959 AT3G05680|EMB2016 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -292 -282 ATCACGCTCTG 4.4 9.8e-04 -6.928 3.009 AT5G58440|SNX2A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -379 -369 TTCTCGCTAAG 5.6 3.6e-04 -7.929 3.444 AT5G58440|SNX2A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -284 -274 CACCCGCTAAC 5.0 6.0e-04 -7.419 3.222 AT5G58440|SNX2A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -240 -230 TTTCCGACAAA 5.0 6.5e-04 -7.339 3.187 AT4G29350|PRO2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -176 -166 AACCCGAGAAA 5.3 4.6e-04 -7.684 3.337 AT5G15510|AT5G15510 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -363 -353 TTCCCACTCTT 6.5 1.8e-04 -8.623 3.745 AT1G21866|AT1G21866 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -99 -89 TTCTCACCAAA 5.1 6.0e-04 -7.419 3.222 AT2G22241|AT2G22241 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -242 -232 TCCACGCTCTT 4.7 7.7e-04 -7.169 3.114 AT2G22241|AT2G22241 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -200 -190 AACCCGCCACG 5.6 3.6e-04 -7.929 3.444 AT2G22241|AT2G22241 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -162 -152 TTCGAGCCCAG 5.7 3.3e-04 -8.016 3.481 AT5G02330|AT5G02330 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -71 -61 TTCTCACCCTT 4.9 7.2e-04 -7.236 3.143 AT3G02370|AT3G02370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -421 -411 TTGCCGGCAAT 4.9 6.5e-04 -7.339 3.187 AT3G02370|AT3G02370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -420 -410 TTGCCGGCAAA 5.1 6.0e-04 -7.419 3.222 AT3G02370|AT3G02370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -44 -34 TTTCCGACAAA 5.0 6.5e-04 -7.339 3.187 AT5G59940|AT5G59940 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -440 -430 TCACCGCGAAT 5.3 4.6e-04 -7.684 3.337 AT5G59940|AT5G59940 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -309 -299 CGCCCGCCCAT 7.5 7.5e-05 -9.498 4.125 AT5G16090|AT5G16090 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -493 -483 TACGAGCCTTA 4.5 9.1e-04 -7.002 3.041 AT2G02103|AT2G02103 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -455 -445 TAAGCGCCCTT 6.4 1.9e-04 -8.568 3.721 ; ; 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 23 ; Sum of sequence lengths 11500 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 32 0 ; 2 5015_E2Fb_Athamap_20091028_ 25 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 21 0 ; TOTAL 78 0 ; Host name rsat ; Job started 2026-08-17.111615 ; Job done 2026-08-17.111616 ; Seconds 0.48 ; user 0.48 ; system 0.04 ; cuser 0.77 ; csystem 0.14