; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.163700_KdMkwl.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_2026-08-17.163700_AHU0vq.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_2026-08-17.163700_AHU0vq.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.163700_KdMkwl.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 AT3G61870 limit START_END D -500 -1 . 0 0 0 0 AT4G16545 limit START_END D -500 -1 . 0 0 0 0 AT2G05540 limit START_END D -500 -1 . 0 0 0 0 AT5G59385 limit START_END D -500 -1 . 0 0 0 0 AT4G01340 limit START_END D -500 -1 . 0 0 0 0 CXE8 limit START_END D -500 -1 . 0 0 0 0 RUS3 limit START_END D -500 -1 . 0 0 0 0 AT5G08420 limit START_END D -500 -1 . 0 0 0 0 VHA-c3 limit START_END D -500 -1 . 0 0 0 0 MED14 limit START_END D -500 -1 . 0 0 0 0 UBA1 limit START_END D -500 -1 . 0 0 0 0 DTX26 limit START_END D -500 -1 . 0 0 0 0 AT5G00815 limit START_END D -500 -1 . 0 0 0 0 AT1G56400 limit START_END D -500 -1 . 0 0 0 0 AT5G44345 limit START_END D -500 -1 . 0 0 0 0 AT5G19110 limit START_END D -500 -1 . 0 0 0 0 UBP25 limit START_END D -500 -1 . 0 0 0 0 AT5G38650 limit START_END D -500 -1 . 0 0 0 0 AT5G57760 limit START_END D -500 -1 . 0 0 0 0 AT2G48000 limit START_END D -500 -1 . 0 0 0 0 ERF13 limit START_END D -500 -1 . 0 0 0 0 AT3G52510 limit START_END D -500 -1 . 0 0 0 0 GAMMACA1 limit START_END D -500 -1 . 0 0 0 0 AT5G52115 limit START_END D -500 -1 . 0 0 0 0 AT3G42155 limit START_END D -500 -1 . 0 0 0 0 ICR4 limit START_END D -500 -1 . 0 0 0 0 LYSA1 limit START_END D -500 -1 . 0 0 0 0 GGP2 limit START_END D -500 -1 . 0 0 0 0 AT4G16545 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -387 -380 TATCCCGA 5.3 5.1e-04 -7.581 3.292 AT4G16545 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -19 -12 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 AT4G01340 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -241 -234 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 CXE8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -413 -406 TCTCCTGC 5.1 6.7e-04 -7.308 3.174 RUS3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -344 -337 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT5G08420 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -130 -123 ATATCCGC 5.1 6.7e-04 -7.308 3.174 VHA-c3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -455 -448 TATCCCAC 5.1 6.7e-04 -7.308 3.174 VHA-c3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -387 -380 GTTCCCGC 8.4 1.5e-05 -11.107 4.824 MED14 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -473 -466 TTTGCCGC 7.3 7.6e-05 -9.485 4.119 UBA1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -210 -203 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 DTX26 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -71 -64 TTACCCGC 8.3 1.8e-05 -10.925 4.745 AT5G44345 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -375 -368 GTTCCGGC 5.4 4.2e-04 -7.775 3.377 AT5G44345 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -273 -266 TCTTCCGC 5.2 5.9e-04 -7.435 3.229 AT5G19110 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -217 -210 ATACTCGC 5.2 5.9e-04 -7.435 3.229 UBP25 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -14 -7 TTACCCTC 5.1 7.4e-04 -7.209 3.131 AT2G48000 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -498 -491 TTCTCCGC 5.2 5.9e-04 -7.435 3.229 GAMMACA1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -156 -149 TTACCCGA 5.2 5.9e-04 -7.435 3.229 AT5G52115 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -413 -406 ATTCGCGC 7.4 7.6e-05 -9.485 4.119 AT5G52115 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -395 -388 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 AT5G52115 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -137 -130 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 ICR4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -450 -443 TTACACGC 5.5 3.9e-04 -7.849 3.409 ICR4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -106 -99 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 ICR4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -58 -51 CTTCCCCC 4.9 8.0e-04 -7.131 3.097 LYSA1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -489 -482 TATGCCGC 5.6 3.5e-04 -7.958 3.456 LYSA1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -357 -350 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 LYSA1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -85 -78 TTTTCCGC 7.2 1.0e-04 -9.210 4.000 GGP2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -276 -269 TTTCCCGG 7.0 1.6e-04 -8.740 3.796 GGP2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -248 -241 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT4G16545 site 5015_E2Fb_Athamap_20091028_ R -387 -380 TATCCCGA 5.3 4.4e-04 -7.729 3.357 AT4G16545 site 5015_E2Fb_Athamap_20091028_ D -19 -12 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT4G01340 site 5015_E2Fb_Athamap_20091028_ R -241 -234 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 CXE8 site 5015_E2Fb_Athamap_20091028_ D -413 -406 TCTCCTGC 5.0 6.5e-04 -7.339 3.187 RUS3 site 5015_E2Fb_Athamap_20091028_ D -344 -337 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT5G08420 site 5015_E2Fb_Athamap_20091028_ D -130 -123 ATATCCGC 4.7 8.2e-04 -7.106 3.086 VHA-c3 site 5015_E2Fb_Athamap_20091028_ D -455 -448 TATCCCAC 5.1 6.5e-04 -7.339 3.187 VHA-c3 site 5015_E2Fb_Athamap_20091028_ R -387 -380 GTTCCCGC 8.6 1.5e-05 -11.107 4.824 MED14 site 5015_E2Fb_Athamap_20091028_ D -473 -466 TTTGCCGC 7.5 6.2e-05 -9.688 4.208 UBA1 site 5015_E2Fb_Athamap_20091028_ R -210 -203 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 UBA1 site 5015_E2Fb_Athamap_20091028_ D -24 -17 TGTCCCCC 4.5 9.4e-04 -6.970 3.027 DTX26 site 5015_E2Fb_Athamap_20091028_ D -71 -64 TTACCCGC 8.5 1.8e-05 -10.925 4.745 AT5G44345 site 5015_E2Fb_Athamap_20091028_ R -375 -368 GTTCCGGC 5.3 4.4e-04 -7.729 3.357 AT5G44345 site 5015_E2Fb_Athamap_20091028_ D -273 -266 TCTTCCGC 5.1 5.8e-04 -7.452 3.237 AT5G19110 site 5015_E2Fb_Athamap_20091028_ R -217 -210 ATACTCGC 4.8 7.5e-04 -7.195 3.125 UBP25 site 5015_E2Fb_Athamap_20091028_ R -14 -7 TTACCCTC 5.0 6.5e-04 -7.339 3.187 AT2G48000 site 5015_E2Fb_Athamap_20091028_ R -498 -491 TTCTCCGC 5.1 5.8e-04 -7.452 3.237 GAMMACA1 site 5015_E2Fb_Athamap_20091028_ D -156 -149 TTACCCGA 5.2 5.8e-04 -7.452 3.237 AT5G52115 site 5015_E2Fb_Athamap_20091028_ R -413 -406 ATTCGCGC 7.2 1.4e-04 -8.874 3.854 AT5G52115 site 5015_E2Fb_Athamap_20091028_ R -395 -388 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 AT5G52115 site 5015_E2Fb_Athamap_20091028_ D -137 -130 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 ICR4 site 5015_E2Fb_Athamap_20091028_ R -450 -443 TTACACGC 5.5 3.9e-04 -7.849 3.409 ICR4 site 5015_E2Fb_Athamap_20091028_ R -106 -99 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 ICR4 site 5015_E2Fb_Athamap_20091028_ D -58 -51 CTTCCCCC 4.8 7.9e-04 -7.143 3.102 LYSA1 site 5015_E2Fb_Athamap_20091028_ D -489 -482 TATGCCGC 5.5 3.6e-04 -7.929 3.444 LYSA1 site 5015_E2Fb_Athamap_20091028_ R -357 -350 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 LYSA1 site 5015_E2Fb_Athamap_20091028_ D -85 -78 TTTTCCGC 7.4 9.3e-05 -9.283 4.032 GGP2 site 5015_E2Fb_Athamap_20091028_ R -276 -269 TTTCCCGG 7.2 1.4e-04 -8.874 3.854 GGP2 site 5015_E2Fb_Athamap_20091028_ D -248 -241 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT3G61870 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -122 -112 AGCCCGTCATA 5.2 5.0e-04 -7.601 3.301 AT4G16545 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -18 -8 TTCCCTCCCAT 8.4 2.7e-05 -10.520 4.569 AT2G05540 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -218 -208 TTCACCCCCAA 5.2 5.0e-04 -7.601 3.301 CXE8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -81 -71 TTCGGGCTAAA 6.0 2.7e-04 -8.217 3.569 AT5G08420 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -129 -119 TATCCGCCAAC 5.7 3.3e-04 -8.016 3.481 VHA-c3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -391 -381 TTCCCGCGTAT 9.3 9.4e-06 -11.575 5.027 MED14 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -472 -462 TTGCCGCCCAA 8.9 1.4e-05 -11.176 4.854 UBA1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -214 -204 TTCCAGCTATG 4.8 7.7e-04 -7.169 3.114 DTX26 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -70 -60 TACCCGCTAGC 5.8 3.1e-04 -8.079 3.509 AT5G44345 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -379 -369 TTCCGGCCTTA 6.3 2.1e-04 -8.468 3.678 AT5G44345 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -105 -95 CACGCGACCAA 4.5 9.1e-04 -7.002 3.041 AT5G19110 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -86 -76 ATTCCGCGTAA 5.0 6.5e-04 -7.339 3.187 AT5G57760 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -317 -307 GTCCGGCCCAT 6.3 2.1e-04 -8.468 3.678 AT5G57760 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -67 -57 TTCCTTCCATA 4.8 7.2e-04 -7.236 3.143 AT2G48000 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -225 -215 TTCTCGTGCAA 5.0 6.5e-04 -7.339 3.187 AT3G52510 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -389 -379 TACTCGCGAGA 5.5 3.9e-04 -7.849 3.409 AT5G52115 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -430 -420 CTCGCGCCCAA 9.2 1.0e-05 -11.513 5.000 AT5G52115 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -417 -407 TTCGCGCTACA 7.9 4.8e-05 -9.944 4.319 AT5G52115 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -416 -406 GTAGCGCGAAT 4.6 8.3e-04 -7.094 3.081 AT5G52115 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -399 -389 TTCCCGTTCCA 4.9 6.5e-04 -7.339 3.187 AT5G52115 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -327 -317 TATCCGCCATT 7.3 9.0e-05 -9.316 4.046 AT5G52115 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -136 -126 TTCCCGCCATC 9.6 7.4e-06 -11.814 5.131 AT3G42155 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -73 -63 TTCCTCCCCAA 5.0 6.0e-04 -7.419 3.222 ICR4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -461 -451 TACCCACACAT 4.7 7.7e-04 -7.169 3.114 ICR4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -369 -359 TACGAGCTAAA 5.5 4.2e-04 -7.775 3.377 ICR4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -296 -286 TTTACGCCAAA 5.5 3.9e-04 -7.849 3.409 LYSA1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -361 -351 TTCCCACTGTA 4.5 9.1e-04 -7.002 3.041 LYSA1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -84 -74 TTTCCGCCAAT 8.3 3.1e-05 -10.382 4.509 LYSA1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -55 -45 GTCCGGCCCAA 6.4 1.9e-04 -8.568 3.721 GGP2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -280 -270 TTCCCGGTTTA 4.4 9.8e-04 -6.928 3.009 GGP2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -247 -237 TTCCCTCTATG 4.6 8.3e-04 -7.094 3.081 ; ; 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_ 28 0 ; 2 5015_E2Fb_Athamap_20091028_ 29 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 31 0 ; TOTAL 88 0 ; Host name rsat ; Job started 2026-08-17.163701 ; Job done 2026-08-17.163702 ; Seconds 0.43 ; user 0.43 ; system 0.05 ; cuser 0.77 ; csystem 0.06