; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.163845_i9lWEh.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_2026-08-17.163845_GGFZlh.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.163845_GGFZlh.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_2026-08-17.163845_i9lWEh.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 PKSB limit START_END D -500 -1 . 0 0 0 0 AT3G16120 limit START_END D -500 -1 . 0 0 0 0 AT5G53710 limit START_END D -500 -1 . 0 0 0 0 RSH2 limit START_END D -500 -1 . 0 0 0 0 PBL18 limit START_END D -500 -1 . 0 0 0 0 KIN14I limit START_END D -500 -1 . 0 0 0 0 PYL5 limit START_END D -500 -1 . 0 0 0 0 SD113 limit START_END D -500 -1 . 0 0 0 0 NEAP4 limit START_END D -500 -1 . 0 0 0 0 LOI1 limit START_END D -500 -1 . 0 0 0 0 AT2G34740 limit START_END D -500 -1 . 0 0 0 0 AT2G33180 limit START_END D -500 -1 . 0 0 0 0 AT1G50820 limit START_END D -500 -1 . 0 0 0 0 ENODL11 limit START_END D -500 -1 . 0 0 0 0 AT2G28320 limit START_END D -500 -1 . 0 0 0 0 U60.1F limit START_END D -500 -1 . 0 0 0 0 DEK1 limit START_END D -500 -1 . 0 0 0 0 AT3G02115 limit START_END D -500 -1 . 0 0 0 0 NFS2 limit START_END D -500 -1 . 0 0 0 0 XRN2 limit START_END D -500 -1 . 0 0 0 0 AT1G09187 limit START_END D -500 -1 . 0 0 0 0 AT3G60810 limit START_END D -500 -1 . 0 0 0 0 AT5G09890 limit START_END D -500 -1 . 0 0 0 0 AT3G49550 limit START_END D -500 -1 . 0 0 0 0 AtGH9B8 limit START_END D -500 -1 . 0 0 0 0 AT3G30385 limit START_END D -500 -1 . 0 0 0 0 SEC limit START_END D -500 -1 . 0 0 0 0 AT5G28824 limit START_END D -500 -1 . 0 0 0 0 PKSB site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -481 -474 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT3G16120 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -449 -442 CTTGCCGC 5.6 3.5e-04 -7.958 3.456 AT5G53710 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -459 -452 TTACCAGC 5.2 5.9e-04 -7.435 3.229 AT5G53710 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -132 -125 ATTCCCAC 6.5 2.7e-04 -8.217 3.569 PBL18 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -449 -442 CTTTCCGC 5.4 4.2e-04 -7.775 3.377 KIN14I site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -62 -55 ATTCTCGC 7.1 1.4e-04 -8.874 3.854 KIN14I site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -8 -1 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 NEAP4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -288 -281 ATTGCCGC 7.0 1.6e-04 -8.740 3.796 NEAP4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -176 -169 TTTGCCGC 7.3 7.6e-05 -9.485 4.119 LOI1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -253 -246 ATTCCTGC 6.7 2.5e-04 -8.294 3.602 AT2G33180 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -238 -231 TTGCACGC 5.3 5.9e-04 -7.435 3.229 AT2G33180 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -13 -6 GTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT1G50820 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -479 -472 TTTCCCGG 7.0 1.6e-04 -8.740 3.796 AT3G02115 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -450 -443 ATCCGCGC 5.1 6.7e-04 -7.308 3.174 AT3G02115 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -135 -128 TATCCCAC 5.1 6.7e-04 -7.308 3.174 AT5G09890 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -438 -431 TTCCCTGC 4.8 8.8e-04 -7.036 3.056 AT3G49550 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -273 -266 TTTCCTGC 7.1 1.4e-04 -8.874 3.854 AT3G49550 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -168 -161 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AtGH9B8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -468 -461 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 SEC site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -225 -218 AGTGCCGC 4.9 8.8e-04 -7.036 3.056 PKSB site 5015_E2Fb_Athamap_20091028_ R -481 -474 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT3G16120 site 5015_E2Fb_Athamap_20091028_ R -449 -442 CTTGCCGC 5.4 3.9e-04 -7.849 3.409 AT5G53710 site 5015_E2Fb_Athamap_20091028_ R -459 -452 TTACCAGC 5.1 5.8e-04 -7.452 3.237 AT5G53710 site 5015_E2Fb_Athamap_20091028_ D -132 -125 ATTCCCAC 6.3 2.7e-04 -8.217 3.569 PBL18 site 5015_E2Fb_Athamap_20091028_ R -449 -442 CTTTCCGC 5.3 4.4e-04 -7.729 3.357 KIN14I site 5015_E2Fb_Athamap_20091028_ D -62 -55 ATTCTCGC 6.9 1.9e-04 -8.568 3.721 KIN14I site 5015_E2Fb_Athamap_20091028_ R -8 -1 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 NEAP4 site 5015_E2Fb_Athamap_20091028_ R -288 -281 ATTGCCGC 6.8 1.9e-04 -8.568 3.721 NEAP4 site 5015_E2Fb_Athamap_20091028_ D -176 -169 TTTGCCGC 7.5 6.2e-05 -9.688 4.208 LOI1 site 5015_E2Fb_Athamap_20091028_ D -253 -246 ATTCCTGC 6.6 2.5e-04 -8.294 3.602 AT2G33180 site 5015_E2Fb_Athamap_20091028_ R -238 -231 TTGCACGC 5.2 5.1e-04 -7.581 3.292 AT2G33180 site 5015_E2Fb_Athamap_20091028_ R -13 -6 GTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT1G50820 site 5015_E2Fb_Athamap_20091028_ R -479 -472 TTTCCCGG 7.2 1.4e-04 -8.874 3.854 AT3G02115 site 5015_E2Fb_Athamap_20091028_ D -450 -443 ATCCGCGC 4.7 8.2e-04 -7.106 3.086 AT3G02115 site 5015_E2Fb_Athamap_20091028_ D -135 -128 TATCCCAC 5.1 6.5e-04 -7.339 3.187 AT5G09890 site 5015_E2Fb_Athamap_20091028_ R -438 -431 TTCCCTGC 4.7 7.9e-04 -7.143 3.102 AT3G49550 site 5015_E2Fb_Athamap_20091028_ D -273 -266 TTTCCTGC 7.3 1.3e-04 -8.948 3.886 AT3G49550 site 5015_E2Fb_Athamap_20091028_ D -168 -161 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AtGH9B8 site 5015_E2Fb_Athamap_20091028_ D -468 -461 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 PKSB site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -376 -366 TTCCCTACCTA 5.5 3.9e-04 -7.849 3.409 AT3G16120 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -453 -443 TTGCCGCTATT 6.9 1.3e-04 -8.948 3.886 PBL18 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -453 -443 TTTCCGCACAA 6.0 2.9e-04 -8.146 3.538 KIN14I site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -60 -50 ATCACGCGAGA 5.2 5.0e-04 -7.601 3.301 KIN14I site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -12 -2 TTCCCTCCCTA 8.6 2.1e-05 -10.771 4.678 NEAP4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -175 -165 TTGCCGCGCTA 8.6 2.1e-05 -10.771 4.678 NEAP4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -46 -36 TAGCCGTCAAA 4.4 9.8e-04 -6.928 3.009 LOI1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -252 -242 TTCCTGCGATA 7.9 4.8e-05 -9.944 4.319 AT2G33180 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -338 -328 AACGCGCCTAT 6.9 1.3e-04 -8.948 3.886 DEK1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -389 -379 TTCCTACCATA 5.2 5.0e-04 -7.601 3.301 DEK1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -135 -125 TACACGCTCTG 4.6 8.3e-04 -7.094 3.081 DEK1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -91 -81 TACACGCGCGT 5.8 3.1e-04 -8.079 3.509 AT3G02115 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -449 -439 TCCGCGCTCAA 7.6 6.6e-05 -9.626 4.180 NFS2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -275 -265 TTCCTTCGCAT 4.4 9.8e-04 -6.928 3.009 XRN2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -409 -399 AACCCACCCAT 6.0 2.7e-04 -8.217 3.569 AT3G60810 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -269 -259 TTCGAGCCCCA 5.5 3.9e-04 -7.849 3.409 AT5G09890 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -397 -387 TTGCCACCAAA 4.7 7.7e-04 -7.169 3.114 AT3G49550 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -272 -262 TTCCTGCCCAC 6.6 1.6e-04 -8.740 3.796 AT3G49550 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -167 -157 TAACCGCCAAG 5.6 3.9e-04 -7.849 3.409 AtGH9B8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -467 -457 CTCTCGCCTAA 4.7 7.7e-04 -7.169 3.114 AtGH9B8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -47 -37 TTACGGCCATT 4.8 7.2e-04 -7.236 3.143 ; ; 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 28 ; Sum of sequence lengths 14000 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 20 0 ; 2 5015_E2Fb_Athamap_20091028_ 19 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 21 0 ; TOTAL 60 0 ; Host name rsat ; Job started 2026-08-17.163845 ; Job done 2026-08-17.163846 ; Seconds 0.45 ; user 0.45 ; system 0.04 ; cuser 0.73 ; csystem 0.09