; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.172251_gCymYg.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_2026-08-17.172251_P6MAXm.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.172251_P6MAXm.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_2026-08-17.172251_gCymYg.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 AT3G51540|AT3G51540 limit START_END D -500 -1 . 0 0 0 0 AT3G05515|AT3G05515 limit START_END D -500 -1 . 0 0 0 0 AT4G27700|AT4G27700 limit START_END D -500 -1 . 0 0 0 0 AT1G08743|AT1G08743 limit START_END D -500 -1 . 0 0 0 0 AT4G08555|AT4G08555 limit START_END D -500 -1 . 0 0 0 0 AT1G53200|AT1G53200 limit START_END D -500 -1 . 0 0 0 0 AT3G59280|PAM16L2 limit START_END D -500 -1 . 0 0 0 0 AT1G54570|AT1G54570 limit START_END D -500 -1 . 0 0 0 0 AT3G17480|AT3G17480 limit START_END D -500 -1 . 0 0 0 0 AT5G04660|CYP77A4 limit START_END D -500 -1 . 0 0 0 0 AT3G14470|RPPL1 limit START_END D -500 -1 . 0 0 0 0 AT2G48140|EDA4 limit START_END D -500 -1 . 0 0 0 0 AT3G04854|AT3G04854 limit START_END D -500 -1 . 0 0 0 0 AT1G26270|PI4KG5 limit START_END D -500 -1 . 0 0 0 0 AT3G16760|AT3G16760 limit START_END D -500 -1 . 0 0 0 0 AT5G04110|GYRB3 limit START_END D -500 -1 . 0 0 0 0 AT4G37130|NUP58 limit START_END D -500 -1 . 0 0 0 0 AT1G09007|AT1G09007 limit START_END D -500 -1 . 0 0 0 0 AT3G50310|MAPKKK20 limit START_END D -500 -1 . 0 0 0 0 AT5G42610|AT5G42610 limit START_END D -500 -1 . 0 0 0 0 AT4G28706|AT4G28706 limit START_END D -500 -1 . 0 0 0 0 AT5G36658|AT5G36658 limit START_END D -500 -1 . 0 0 0 0 AT4G35540|PTF2 limit START_END D -500 -1 . 0 0 0 0 AT2G41082|AT2G41082 limit START_END D -500 -1 . 0 0 0 0 AT3G51540|AT3G51540 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -229 -222 TATACCGC 5.9 3.1e-04 -8.079 3.509 AT4G27700|AT4G27700 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -235 -228 TTTACCGC 7.6 4.7e-05 -9.965 4.328 AT1G08743|AT1G08743 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -432 -425 ATAGCCGC 5.2 5.9e-04 -7.435 3.229 AT1G08743|AT1G08743 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -72 -65 TCTCCCGT 5.2 6.7e-04 -7.308 3.174 AT1G08743|AT1G08743 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -51 -44 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 AT1G53200|AT1G53200 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -339 -332 GTTCCCGA 5.3 5.1e-04 -7.581 3.292 AT1G53200|AT1G53200 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -244 -237 TTGCCCTC 4.8 8.8e-04 -7.036 3.056 AT1G53200|AT1G53200 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -101 -94 TTCACCGC 5.1 6.7e-04 -7.308 3.174 AT3G14470|RPPL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -319 -312 CTTCACGC 5.6 3.5e-04 -7.958 3.456 AT3G04854|AT3G04854 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -231 -224 AATCGCGC 5.1 6.7e-04 -7.308 3.174 AT4G37130|NUP58 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -364 -357 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 AT4G37130|NUP58 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -243 -236 TTCCCCGG 4.7 9.5e-04 -6.959 3.022 AT1G09007|AT1G09007 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -490 -483 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT3G50310|MAPKKK20 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -122 -115 ATATCCGC 5.1 6.7e-04 -7.308 3.174 AT5G36658|AT5G36658 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -495 -488 ATACCCGA 4.9 8.8e-04 -7.036 3.056 AT5G36658|AT5G36658 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -463 -456 TAACCCGC 6.1 3.0e-04 -8.112 3.523 AT2G41082|AT2G41082 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -476 -469 TTTCTCGC 7.4 6.6e-05 -9.626 4.180 AT2G41082|AT2G41082 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -403 -396 AAACCCGC 5.2 6.7e-04 -7.308 3.174 AT2G41082|AT2G41082 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -287 -280 ATCGCCGC 5.1 6.7e-04 -7.308 3.174 AT2G41082|AT2G41082 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -200 -193 CTTCCCGA 5.3 5.1e-04 -7.581 3.292 AT2G41082|AT2G41082 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -148 -141 CTACCCGC 6.6 2.6e-04 -8.255 3.585 AT2G41082|AT2G41082 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -46 -39 ATCTCCGC 4.8 8.8e-04 -7.036 3.056 AT3G51540|AT3G51540 site 5015_E2Fb_Athamap_20091028_ R -229 -222 TATACCGC 5.8 3.1e-04 -8.079 3.509 AT4G27700|AT4G27700 site 5015_E2Fb_Athamap_20091028_ R -235 -228 TTTACCGC 7.8 3.7e-05 -10.205 4.432 AT1G08743|AT1G08743 site 5015_E2Fb_Athamap_20091028_ D -432 -425 ATAGCCGC 4.8 7.9e-04 -7.143 3.102 AT1G08743|AT1G08743 site 5015_E2Fb_Athamap_20091028_ R -72 -65 TCTCCCGT 5.1 5.8e-04 -7.452 3.237 AT1G08743|AT1G08743 site 5015_E2Fb_Athamap_20091028_ R -51 -44 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 AT1G53200|AT1G53200 site 5015_E2Fb_Athamap_20091028_ R -339 -332 GTTCCCGA 5.2 5.1e-04 -7.581 3.292 AT1G53200|AT1G53200 site 5015_E2Fb_Athamap_20091028_ R -244 -237 TTGCCCTC 4.7 7.9e-04 -7.143 3.102 AT1G53200|AT1G53200 site 5015_E2Fb_Athamap_20091028_ R -101 -94 TTCACCGC 5.1 6.5e-04 -7.339 3.187 AT3G14470|RPPL1 site 5015_E2Fb_Athamap_20091028_ D -319 -312 CTTCACGC 5.5 3.6e-04 -7.929 3.444 AT3G04854|AT3G04854 site 5015_E2Fb_Athamap_20091028_ R -231 -224 AATCGCGC 4.7 8.2e-04 -7.106 3.086 AT4G37130|NUP58 site 5015_E2Fb_Athamap_20091028_ R -364 -357 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT4G37130|NUP58 site 5015_E2Fb_Athamap_20091028_ D -243 -236 TTCCCCGG 4.7 8.2e-04 -7.106 3.086 AT1G09007|AT1G09007 site 5015_E2Fb_Athamap_20091028_ R -490 -483 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT3G50310|MAPKKK20 site 5015_E2Fb_Athamap_20091028_ D -122 -115 ATATCCGC 4.7 8.2e-04 -7.106 3.086 AT5G36658|AT5G36658 site 5015_E2Fb_Athamap_20091028_ D -463 -456 TAACCCGC 6.0 2.9e-04 -8.146 3.538 AT2G41082|AT2G41082 site 5015_E2Fb_Athamap_20091028_ R -476 -469 TTTCTCGC 7.6 5.8e-05 -9.755 4.237 AT2G41082|AT2G41082 site 5015_E2Fb_Athamap_20091028_ R -403 -396 AAACCCGC 4.8 7.9e-04 -7.143 3.102 AT2G41082|AT2G41082 site 5015_E2Fb_Athamap_20091028_ R -287 -280 ATCGCCGC 4.7 8.2e-04 -7.106 3.086 AT2G41082|AT2G41082 site 5015_E2Fb_Athamap_20091028_ R -200 -193 CTTCCCGA 5.2 5.1e-04 -7.581 3.292 AT2G41082|AT2G41082 site 5015_E2Fb_Athamap_20091028_ R -148 -141 CTACCCGC 6.4 2.6e-04 -8.255 3.585 AT3G51540|AT3G51540 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -417 -407 ATCCAGCTCTA 6.4 1.9e-04 -8.568 3.721 AT3G51540|AT3G51540 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -233 -223 ATACCGCGGAT 4.8 7.2e-04 -7.236 3.143 AT3G51540|AT3G51540 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -82 -72 TACACGTCATA 4.8 7.2e-04 -7.236 3.143 AT4G27700|AT4G27700 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -458 -448 TACACGACCAA 5.0 6.0e-04 -7.419 3.222 AT4G27700|AT4G27700 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -239 -229 TTACCGCCTTA 6.7 1.5e-04 -8.805 3.824 AT4G27700|AT4G27700 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -35 -25 ATTGCGCCATT 5.8 3.1e-04 -8.079 3.509 AT1G08743|AT1G08743 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -431 -421 TAGCCGCCATC 5.5 3.9e-04 -7.849 3.409 AT1G08743|AT1G08743 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -55 -45 TTCCCGCTTCT 5.8 3.1e-04 -8.079 3.509 AT1G53200|AT1G53200 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -278 -268 TACGCGGCCAC 5.2 5.4e-04 -7.524 3.268 AT1G53200|AT1G53200 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -216 -206 TTGCCGACATT 4.6 8.3e-04 -7.094 3.081 AT1G53200|AT1G53200 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -105 -95 TCACCGCTCTT 4.5 9.1e-04 -7.002 3.041 AT3G59280|PAM16L2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -66 -56 TAGCAGCCCAA 4.6 8.3e-04 -7.094 3.081 AT2G48140|EDA4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -418 -408 TACGCTCCATA 6.8 1.4e-04 -8.874 3.854 AT3G04854|AT3G04854 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -235 -225 ATCGCGCTTAG 4.7 8.3e-04 -7.094 3.081 AT3G04854|AT3G04854 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -234 -224 TAAGCGCGATT 5.5 4.2e-04 -7.775 3.377 AT3G16760|AT3G16760 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -281 -271 AACCAGCTCAA 5.0 6.0e-04 -7.419 3.222 AT1G09007|AT1G09007 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -494 -484 TAACCGCCATT 7.2 1.1e-04 -9.115 3.959 AT3G50310|MAPKKK20 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -148 -138 TAGCAGCCCAA 4.6 8.3e-04 -7.094 3.081 AT5G42610|AT5G42610 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -18 -8 TTCTTGCCAAA 5.0 6.0e-04 -7.419 3.222 AT5G36658|AT5G36658 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -462 -452 AACCCGCTATC 6.1 2.5e-04 -8.294 3.602 AT4G35540|PTF2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -487 -477 AACCTGCCCAA 6.4 1.9e-04 -8.568 3.721 AT4G35540|PTF2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -378 -368 AACGCACGCAT 4.8 7.2e-04 -7.236 3.143 AT2G41082|AT2G41082 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -456 -446 TTTGCGCTCAT 6.1 2.5e-04 -8.294 3.602 AT2G41082|AT2G41082 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -204 -194 TTCCCGATCCA 5.1 6.0e-04 -7.419 3.222 AT2G41082|AT2G41082 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -22 -12 TTCGCGTTATT 5.8 3.1e-04 -8.079 3.509 ; ; 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_ 20 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 25 0 ; TOTAL 67 0 ; Host name rsat ; Job started 2026-08-17.172251 ; Job done 2026-08-17.172253 ; Seconds 0.45 ; user 0.45 ; system 0.07 ; cuser 0.79 ; csystem 0.11