; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.172524_1SwnUw.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_2026-08-17.172524_5fImL4.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.172524_5fImL4.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_2026-08-17.172524_1SwnUw.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 AT1G49832|AT1G49832 limit START_END D -500 -1 . 0 0 0 0 AT4G26670|TIM22-2 limit START_END D -500 -1 . 0 0 0 0 AT1G07127|AT1G07127 limit START_END D -500 -1 . 0 0 0 0 AT1G78160|APUM7 limit START_END D -500 -1 . 0 0 0 0 AT5G48920|TED7 limit START_END D -500 -1 . 0 0 0 0 AT1G80740|CMT1 limit START_END D -500 -1 . 0 0 0 0 AT4G33630|EX1 limit START_END D -500 -1 . 0 0 0 0 AT1G55020|LOX1 limit START_END D -500 -1 . 0 0 0 0 ATCG00810|RPL22 limit START_END D -500 -1 . 0 0 0 0 AT2G21180|AT2G21180 limit START_END D -500 -1 . 0 0 0 0 AT1G14140|PUMP3 limit START_END D -500 -1 . 0 0 0 0 AT2G40410|CAN2 limit START_END D -500 -1 . 0 0 0 0 AT5G29560|AT5G29560 limit START_END D -500 -1 . 0 0 0 0 AT5G33399|AT5G33399 limit START_END D -500 -1 . 0 0 0 0 AT1G66080|AT1G66080 limit START_END D -500 -1 . 0 0 0 0 AT3G24517|AT3G24517 limit START_END D -500 -1 . 0 0 0 0 AT1G08933|AT1G08933 limit START_END D -500 -1 . 0 0 0 0 AT2G21840|AT2G21840 limit START_END D -500 -1 . 0 0 0 0 AT5G06635|AT5G06635 limit START_END D -500 -1 . 0 0 0 0 AT1G48160|SRP19 limit START_END D -500 -1 . 0 0 0 0 AT5G00850|AT5G00850 limit START_END D -500 -1 . 0 0 0 0 AT5G22520|AT5G22520 limit START_END D -500 -1 . 0 0 0 0 AT4G13630|AT4G13630 limit START_END D -500 -1 . 0 0 0 0 AT1G12820|AFB3 limit START_END D -500 -1 . 0 0 0 0 AT1G49832|AT1G49832 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -457 -450 CTTCGCGC 6.0 3.1e-04 -8.079 3.509 AT5G48920|TED7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -486 -479 TCTCCGGC 5.2 5.9e-04 -7.435 3.229 AT5G48920|TED7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -466 -459 GTTACCGC 5.8 3.1e-04 -8.079 3.509 AT5G48920|TED7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -459 -452 TCTCCCGG 5.0 7.4e-04 -7.209 3.131 AT5G48920|TED7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -75 -68 AGTCACGC 4.9 8.0e-04 -7.131 3.097 AT1G80740|CMT1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -277 -270 TCTCCCGC 8.2 1.9e-05 -10.871 4.721 ATCG00810|RPL22 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -465 -458 TATCCTGC 5.3 5.1e-04 -7.581 3.292 ATCG00810|RPL22 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -259 -252 TTTTCCGC 7.2 1.0e-04 -9.210 4.000 ATCG00810|RPL22 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -163 -156 TTACCCGT 5.3 5.1e-04 -7.581 3.292 AT1G14140|PUMP3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -386 -379 TCTCCGGC 5.2 5.9e-04 -7.435 3.229 AT1G14140|PUMP3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -380 -373 TCACCCGC 5.9 3.1e-04 -8.079 3.509 AT2G40410|CAN2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -242 -235 GTTCTCGC 5.7 3.4e-04 -7.987 3.469 AT2G40410|CAN2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -205 -198 ATGGCCGC 4.7 9.5e-04 -6.959 3.022 AT5G29560|AT5G29560 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -441 -434 TTACCAGC 5.2 5.9e-04 -7.435 3.229 AT5G29560|AT5G29560 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -101 -94 ACTCCCGC 7.7 3.5e-05 -10.260 4.456 AT2G21840|AT2G21840 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -165 -158 AGTCCCGC 7.7 3.5e-05 -10.260 4.456 AT2G21840|AT2G21840 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -159 -152 TATACCGC 5.9 3.1e-04 -8.079 3.509 AT5G00850|AT5G00850 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -471 -464 TCTCCCGC 8.2 1.9e-05 -10.871 4.721 AT5G00850|AT5G00850 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -207 -200 TTGCCAGC 5.0 8.0e-04 -7.131 3.097 AT5G22520|AT5G22520 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -337 -330 GGTCCCGC 6.2 2.9e-04 -8.146 3.538 AT5G22520|AT5G22520 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -294 -287 TATCCCTC 5.2 5.9e-04 -7.435 3.229 AT4G13630|AT4G13630 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -432 -425 CTTCCAGC 5.3 5.1e-04 -7.581 3.292 AT1G49832|AT1G49832 site 5015_E2Fb_Athamap_20091028_ R -457 -450 CTTCGCGC 5.8 3.1e-04 -8.079 3.509 AT5G48920|TED7 site 5015_E2Fb_Athamap_20091028_ R -486 -479 TCTCCGGC 5.1 5.8e-04 -7.452 3.237 AT5G48920|TED7 site 5015_E2Fb_Athamap_20091028_ D -466 -459 GTTACCGC 5.7 3.1e-04 -8.079 3.509 AT5G48920|TED7 site 5015_E2Fb_Athamap_20091028_ R -459 -452 TCTCCCGG 4.9 6.9e-04 -7.279 3.161 AT5G48920|TED7 site 5015_E2Fb_Athamap_20091028_ D -75 -68 AGTCACGC 4.5 9.4e-04 -6.970 3.027 AT1G80740|CMT1 site 5015_E2Fb_Athamap_20091028_ D -277 -270 TCTCCCGC 8.4 2.1e-05 -10.771 4.678 ATCG00810|RPL22 site 5015_E2Fb_Athamap_20091028_ D -465 -458 TATCCTGC 5.3 5.1e-04 -7.581 3.292 ATCG00810|RPL22 site 5015_E2Fb_Athamap_20091028_ R -259 -252 TTTTCCGC 7.4 9.3e-05 -9.283 4.032 ATCG00810|RPL22 site 5015_E2Fb_Athamap_20091028_ D -163 -156 TTACCCGT 5.2 5.1e-04 -7.581 3.292 AT1G14140|PUMP3 site 5015_E2Fb_Athamap_20091028_ D -464 -457 TGTCCCCC 4.5 9.4e-04 -6.970 3.027 AT1G14140|PUMP3 site 5015_E2Fb_Athamap_20091028_ D -386 -379 TCTCCGGC 5.1 5.8e-04 -7.452 3.237 AT1G14140|PUMP3 site 5015_E2Fb_Athamap_20091028_ R -380 -373 TCACCCGC 5.8 3.1e-04 -8.079 3.509 AT2G40410|CAN2 site 5015_E2Fb_Athamap_20091028_ R -242 -235 GTTCTCGC 5.5 3.6e-04 -7.929 3.444 AT5G29560|AT5G29560 site 5015_E2Fb_Athamap_20091028_ R -441 -434 TTACCAGC 5.1 5.8e-04 -7.452 3.237 AT5G29560|AT5G29560 site 5015_E2Fb_Athamap_20091028_ D -101 -94 ACTCCCGC 7.6 5.8e-05 -9.755 4.237 AT2G21840|AT2G21840 site 5015_E2Fb_Athamap_20091028_ D -165 -158 AGTCCCGC 7.6 5.8e-05 -9.755 4.237 AT2G21840|AT2G21840 site 5015_E2Fb_Athamap_20091028_ R -159 -152 TATACCGC 5.8 3.1e-04 -8.079 3.509 AT5G00850|AT5G00850 site 5015_E2Fb_Athamap_20091028_ D -471 -464 TCTCCCGC 8.4 2.1e-05 -10.771 4.678 AT5G00850|AT5G00850 site 5015_E2Fb_Athamap_20091028_ D -207 -200 TTGCCAGC 4.9 6.9e-04 -7.279 3.161 AT5G22520|AT5G22520 site 5015_E2Fb_Athamap_20091028_ R -337 -330 GGTCCCGC 6.0 2.9e-04 -8.146 3.538 AT5G22520|AT5G22520 site 5015_E2Fb_Athamap_20091028_ D -294 -287 TATCCCTC 5.1 5.8e-04 -7.452 3.237 AT4G13630|AT4G13630 site 5015_E2Fb_Athamap_20091028_ D -432 -425 CTTCCAGC 5.2 5.1e-04 -7.581 3.292 AT1G49832|AT1G49832 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -110 -100 ATCGCACCTAA 4.6 9.1e-04 -7.002 3.041 AT1G80740|CMT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -446 -436 GTCCCGAGAAT 5.0 6.0e-04 -7.419 3.222 AT1G80740|CMT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -296 -286 TCCGAGCGCAT 4.6 8.3e-04 -7.094 3.081 AT1G80740|CMT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -276 -266 CTCCCGCTCAC 6.4 1.9e-04 -8.568 3.721 ATCG00810|RPL22 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -263 -253 TTTCCGCCTTT 5.6 3.6e-04 -7.929 3.444 ATCG00810|RPL22 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -233 -223 GTCCCGGGCAT 5.3 4.6e-04 -7.684 3.337 ATCG00810|RPL22 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -177 -167 TTCCCTTCCAT 4.9 7.2e-04 -7.236 3.143 AT2G40410|CAN2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -327 -317 TTCGCTACCAT 4.5 9.1e-04 -7.002 3.041 AT2G40410|CAN2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -209 -199 TGGCCGCGCAA 5.9 2.9e-04 -8.146 3.538 AT2G40410|CAN2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -208 -198 TGCGCGGCCAT 5.5 3.9e-04 -7.849 3.409 AT5G29560|AT5G29560 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -100 -90 CTCCCGCGACT 6.7 1.5e-04 -8.805 3.824 AT1G66080|AT1G66080 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -162 -152 ATCTCACCCTA 4.6 9.1e-04 -7.002 3.041 AT1G08933|AT1G08933 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -51 -41 TATGCGCTATA 5.6 3.6e-04 -7.929 3.444 AT2G21840|AT2G21840 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -164 -154 GTCCCGCGGTA 6.7 1.5e-04 -8.805 3.824 AT1G48160|SRP19 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -280 -270 TACGCGCAATG 5.0 6.0e-04 -7.419 3.222 AT1G48160|SRP19 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -85 -75 ATTCCGCCAAA 7.4 8.1e-05 -9.421 4.092 AT5G00850|AT5G00850 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -470 -460 CTCCCGCTAAT 8.2 3.4e-05 -10.289 4.469 AT5G22520|AT5G22520 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -341 -331 GTCCCGCCTCT 5.1 5.4e-04 -7.524 3.268 AT5G22520|AT5G22520 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -293 -283 ATCCCTCCCAC 5.4 4.2e-04 -7.775 3.377 ; ; 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_ 22 0 ; 2 5015_E2Fb_Athamap_20091028_ 22 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 19 0 ; TOTAL 63 0 ; Host name rsat ; Job started 2026-08-17.172524 ; Job done 2026-08-17.172526 ; Seconds 0.47 ; user 0.47 ; system 0.04 ; cuser 0.71 ; csystem 0.14