; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.172422_I81hhh.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_2026-08-17.172422_tvvKfG.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_2026-08-17.172422_tvvKfG.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.172422_I81hhh.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 AT5G16940|AT5G16940 limit START_END D -500 -1 . 0 0 0 0 AT5G19810|AT5G19810 limit START_END D -500 -1 . 0 0 0 0 AT5G56810|AT5G56810 limit START_END D -500 -1 . 0 0 0 0 AT5G52230|MBD13 limit START_END D -500 -1 . 0 0 0 0 AT2G28930|APK1B limit START_END D -500 -1 . 0 0 0 0 AT1G68250|AT1G68250 limit START_END D -500 -1 . 0 0 0 0 ATCG00190|RPOB limit START_END D -500 -1 . 0 0 0 0 AT1G08240|AT1G08240 limit START_END D -500 -1 . 0 0 0 0 AT5G41630|AT5G41630 limit START_END D -500 -1 . 0 0 0 0 AT1G12530|AT1G12530 limit START_END D -500 -1 . 0 0 0 0 AT1G73000|PYL3 limit START_END D -500 -1 . 0 0 0 0 AT1G75160|AT1G75160 limit START_END D -500 -1 . 0 0 0 0 AT4G09530|AT4G09530 limit START_END D -500 -1 . 0 0 0 0 AT2G13100|AT2G13100 limit START_END D -500 -1 . 0 0 0 0 AT3G05840|ASK3 limit START_END D -500 -1 . 0 0 0 0 AT1G36310|TRM9 limit START_END D -500 -1 . 0 0 0 0 AT5G54225|LCR83 limit START_END D -500 -1 . 0 0 0 0 AT1G20650|PBL21 limit START_END D -500 -1 . 0 0 0 0 AT1G19500|AT1G19500 limit START_END D -500 -1 . 0 0 0 0 AT4G34290|AT4G34290 limit START_END D -500 -1 . 0 0 0 0 AT1G31555|AT1G31555 limit START_END D -500 -1 . 0 0 0 0 AT3G48970|HIPP31 limit START_END D -500 -1 . 0 0 0 0 AT3G53690|AT3G53690 limit START_END D -500 -1 . 0 0 0 0 AT1G10920|LOV1 limit START_END D -500 -1 . 0 0 0 0 AT5G16940|AT5G16940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -464 -457 ATACCAGC 4.9 8.8e-04 -7.036 3.056 AT5G16940|AT5G16940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -397 -390 CCTCCCGC 6.2 2.9e-04 -8.146 3.538 AT5G16940|AT5G16940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -347 -340 TTCCTCGC 5.2 5.9e-04 -7.435 3.229 AT5G16940|AT5G16940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -11 -4 AGTCTCGC 5.0 8.0e-04 -7.131 3.097 AT2G28930|APK1B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -25 -18 GGTCCCGC 6.2 2.9e-04 -8.146 3.538 ATCG00190|RPOB site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -254 -247 GTTCCAGC 5.3 5.1e-04 -7.581 3.292 ATCG00190|RPOB site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -248 -241 AATACCGC 5.0 8.0e-04 -7.131 3.097 AT1G08240|AT1G08240 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -255 -248 TATCACGC 5.6 3.5e-04 -7.958 3.456 AT5G41630|AT5G41630 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -279 -272 TTATCCGC 5.4 4.2e-04 -7.775 3.377 AT1G73000|PYL3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -499 -492 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT1G73000|PYL3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -318 -311 ATACACGC 5.2 6.7e-04 -7.308 3.174 AT1G75160|AT1G75160 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -360 -353 TCTCCCAC 4.9 8.8e-04 -7.036 3.056 AT2G13100|AT2G13100 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -189 -182 ATATCCGC 5.1 6.7e-04 -7.308 3.174 AT3G05840|ASK3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -490 -483 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT3G05840|ASK3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -271 -264 ATACTCGC 5.2 5.9e-04 -7.435 3.229 AT3G05840|ASK3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -195 -188 ATTCCCAC 6.5 2.7e-04 -8.217 3.569 AT1G20650|PBL21 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -340 -333 TTCCCCGC 7.9 2.8e-05 -10.483 4.553 AT1G20650|PBL21 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -95 -88 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT1G31555|AT1G31555 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -68 -61 TTTCCTGC 7.1 1.4e-04 -8.874 3.854 AT1G10920|LOV1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -271 -264 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 AT5G16940|AT5G16940 site 5015_E2Fb_Athamap_20091028_ R -397 -390 CCTCCCGC 6.1 2.9e-04 -8.146 3.538 AT5G16940|AT5G16940 site 5015_E2Fb_Athamap_20091028_ D -347 -340 TTCCTCGC 5.1 5.8e-04 -7.452 3.237 AT5G16940|AT5G16940 site 5015_E2Fb_Athamap_20091028_ D -283 -276 TTCCCCAC 4.5 9.4e-04 -6.970 3.027 AT5G16940|AT5G16940 site 5015_E2Fb_Athamap_20091028_ D -11 -4 AGTCTCGC 4.5 9.4e-04 -6.970 3.027 AT2G28930|APK1B site 5015_E2Fb_Athamap_20091028_ R -25 -18 GGTCCCGC 6.0 2.9e-04 -8.146 3.538 ATCG00190|RPOB site 5015_E2Fb_Athamap_20091028_ D -254 -247 GTTCCAGC 5.2 5.8e-04 -7.452 3.237 ATCG00190|RPOB site 5015_E2Fb_Athamap_20091028_ R -248 -241 AATACCGC 4.5 9.4e-04 -6.970 3.027 AT1G08240|AT1G08240 site 5015_E2Fb_Athamap_20091028_ R -255 -248 TATCACGC 5.6 3.3e-04 -8.016 3.481 AT5G41630|AT5G41630 site 5015_E2Fb_Athamap_20091028_ R -279 -272 TTATCCGC 5.4 3.9e-04 -7.849 3.409 AT1G12530|AT1G12530 site 5015_E2Fb_Athamap_20091028_ R -467 -460 TTGCCCCC 4.5 9.4e-04 -6.970 3.027 AT1G73000|PYL3 site 5015_E2Fb_Athamap_20091028_ R -499 -492 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT1G73000|PYL3 site 5015_E2Fb_Athamap_20091028_ D -318 -311 ATACACGC 4.7 7.9e-04 -7.143 3.102 AT1G75160|AT1G75160 site 5015_E2Fb_Athamap_20091028_ D -360 -353 TCTCCCAC 4.8 7.5e-04 -7.195 3.125 AT2G13100|AT2G13100 site 5015_E2Fb_Athamap_20091028_ R -189 -182 ATATCCGC 4.7 8.2e-04 -7.106 3.086 AT3G05840|ASK3 site 5015_E2Fb_Athamap_20091028_ R -490 -483 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT3G05840|ASK3 site 5015_E2Fb_Athamap_20091028_ R -271 -264 ATACTCGC 4.8 7.5e-04 -7.195 3.125 AT3G05840|ASK3 site 5015_E2Fb_Athamap_20091028_ D -195 -188 ATTCCCAC 6.3 2.7e-04 -8.217 3.569 AT3G05840|ASK3 site 5015_E2Fb_Athamap_20091028_ R -21 -14 TTGCCCCC 4.5 9.4e-04 -6.970 3.027 AT1G20650|PBL21 site 5015_E2Fb_Athamap_20091028_ R -340 -333 TTCCCCGC 8.1 2.5e-05 -10.597 4.602 AT1G20650|PBL21 site 5015_E2Fb_Athamap_20091028_ R -95 -88 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT1G31555|AT1G31555 site 5015_E2Fb_Athamap_20091028_ R -68 -61 TTTCCTGC 7.3 1.3e-04 -8.948 3.886 AT1G10920|LOV1 site 5015_E2Fb_Athamap_20091028_ R -271 -264 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT5G16940|AT5G16940 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -452 -442 ATCCCACCAAG 5.0 6.0e-04 -7.419 3.222 AT5G16940|AT5G16940 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -401 -391 CTCCCGCGAAA 8.9 1.4e-05 -11.176 4.854 AT5G19810|AT5G19810 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -201 -191 TGCGCACCAAT 4.8 7.2e-04 -7.236 3.143 AT5G19810|AT5G19810 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -46 -36 CTCCCTCTAAA 4.6 8.3e-04 -7.094 3.081 AT2G28930|APK1B site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -29 -19 GTCCCGCCTTT 6.7 1.5e-04 -8.805 3.824 ATCG00190|RPOB site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -253 -243 TTCCAGCGGTA 5.5 3.9e-04 -7.849 3.409 AT1G12530|AT1G12530 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -471 -461 TGCCCCCTATA 4.5 9.1e-04 -7.002 3.041 AT1G75160|AT1G75160 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -96 -86 TTCTCACGATA 4.6 8.3e-04 -7.094 3.081 AT3G05840|ASK3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -494 -484 TTCCAGCCAAA 8.3 3.1e-05 -10.382 4.509 AT3G05840|ASK3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -194 -184 TTCCCACTAAA 6.9 1.3e-04 -8.948 3.886 AT1G36310|TRM9 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -349 -339 AACCCGCATAA 4.9 6.5e-04 -7.339 3.187 AT1G20650|PBL21 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -343 -333 TTCCCCGCATT 4.4 9.8e-04 -6.928 3.009 AT1G20650|PBL21 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -99 -89 TTCCCACAAAA 5.1 5.4e-04 -7.524 3.268 AT4G34290|AT4G34290 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -177 -167 TTCCTACCCTT 4.9 7.2e-04 -7.236 3.143 AT1G31555|AT1G31555 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -72 -62 TTCCTGCGTTT 4.8 7.2e-04 -7.236 3.143 AT3G53690|AT3G53690 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -322 -312 AACCTGCTCTA 5.1 5.4e-04 -7.524 3.268 ; ; 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_ 20 0 ; 2 5015_E2Fb_Athamap_20091028_ 22 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 16 0 ; TOTAL 58 0 ; Host name rsat ; Job started 2026-08-17.172422 ; Job done 2026-08-17.172424 ; Seconds 0.49 ; user 0.49 ; system 0.05 ; cuser 0.78 ; csystem 0.12