; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.132448_w0IKZf.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_2026-08-17.132448_jNEumA.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_2026-08-17.132448_jNEumA.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.132448_w0IKZf.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 RPS2 limit START_END D -500 -1 . 0 0 0 0 PAP11 limit START_END D -500 -1 . 0 0 0 0 ATPAP15 limit START_END D -500 -1 . 0 0 0 0 U2.4 limit START_END D -500 -1 . 0 0 0 0 VHA-A limit START_END D -500 -1 . 0 0 0 0 PLDALPHA1 limit START_END D -500 -1 . 0 0 0 0 AT5G45480 limit START_END D -500 -1 . 0 0 0 0 RRF limit START_END D -500 -1 . 0 0 0 0 AT4G05730 limit START_END D -500 -1 . 0 0 0 0 PGK3 limit START_END D -500 -1 . 0 0 0 0 CRRSP48 limit START_END D -500 -1 . 0 0 0 0 RPL10B limit START_END D -500 -1 . 0 0 0 0 AT2G37435 limit START_END D -500 -1 . 0 0 0 0 EMB1687 limit START_END D -500 -1 . 0 0 0 0 AT5G38640 limit START_END D -500 -1 . 0 0 0 0 AT4G14360 limit START_END D -500 -1 . 0 0 0 0 AT4G10700 limit START_END D -500 -1 . 0 0 0 0 AT3G61118 limit START_END D -500 -1 . 0 0 0 0 AT3G08715 limit START_END D -500 -1 . 0 0 0 0 WRKY22 limit START_END D -500 -1 . 0 0 0 0 AT4G26480 limit START_END D -500 -1 . 0 0 0 0 AT5G03905 limit START_END D -500 -1 . 0 0 0 0 AT1G22660 limit START_END D -500 -1 . 0 0 0 0 FRS6 limit START_END D -500 -1 . 0 0 0 0 RPS2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -236 -229 TTGCCCGC 8.1 2.3e-05 -10.680 4.638 PAP11 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -454 -447 ATACCGGC 5.0 7.4e-04 -7.209 3.131 ATPAP15 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -180 -173 ATTCCCAC 6.5 2.7e-04 -8.217 3.569 VHA-A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -400 -393 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 VHA-A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -352 -345 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 VHA-A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -266 -259 CGTCCCGC 6.5 2.7e-04 -8.217 3.569 VHA-A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -167 -160 TTCCCCGA 4.8 8.8e-04 -7.036 3.056 VHA-A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -131 -124 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT5G45480 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -475 -468 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 RRF site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -494 -487 GTTCTCGC 5.7 3.4e-04 -7.987 3.469 RRF site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -446 -439 GTTCGCGC 6.0 3.1e-04 -8.079 3.509 RRF site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -428 -421 TTACCGGC 5.3 5.1e-04 -7.581 3.292 RRF site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -417 -410 GCTCCCGC 6.4 2.7e-04 -8.217 3.569 PGK3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -437 -430 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 PGK3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -281 -274 TTTCCCGA 7.1 1.4e-04 -8.874 3.854 PGK3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -205 -198 TCTCCGGC 5.2 5.9e-04 -7.435 3.229 CRRSP48 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -278 -271 TTCGCCGC 5.4 4.2e-04 -7.775 3.377 RPL10B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -342 -335 AGTCCCGT 4.7 9.5e-04 -6.959 3.022 RPL10B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -157 -150 ATTCCGGC 6.8 2.1e-04 -8.468 3.678 AT2G37435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -398 -391 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT2G37435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -217 -210 TTACCCGT 5.3 5.1e-04 -7.581 3.292 AT2G37435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -164 -157 TTACCCGT 5.3 5.1e-04 -7.581 3.292 AT2G37435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -139 -132 TTACCCGA 5.2 5.9e-04 -7.435 3.229 AT2G37435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -92 -85 TTACCCGA 5.2 5.9e-04 -7.435 3.229 EMB1687 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -430 -423 TATCCGGC 5.5 4.2e-04 -7.775 3.377 EMB1687 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -424 -417 ATGCCCGC 7.7 3.5e-05 -10.260 4.456 EMB1687 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -371 -364 TATGCCGC 5.6 3.5e-04 -7.958 3.456 AT4G14360 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -466 -459 CTTCCAGC 5.3 5.1e-04 -7.581 3.292 WRKY22 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -457 -450 TATCTCGC 5.7 3.4e-04 -7.987 3.469 WRKY22 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -423 -416 TTGTCCGC 5.1 6.7e-04 -7.308 3.174 AT1G22660 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -203 -196 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT1G22660 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -70 -63 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 FRS6 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -233 -226 TTACCCAC 5.0 7.4e-04 -7.209 3.131 FRS6 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -71 -64 ATTCCCTC 6.6 2.6e-04 -8.255 3.585 RPS2 site 5015_E2Fb_Athamap_20091028_ R -236 -229 TTGCCCGC 8.3 2.3e-05 -10.680 4.638 PAP11 site 5015_E2Fb_Athamap_20091028_ R -454 -447 ATACCGGC 4.6 9.4e-04 -6.970 3.027 PAP11 site 5015_E2Fb_Athamap_20091028_ R -340 -333 TTTTACGC 4.5 9.4e-04 -6.970 3.027 ATPAP15 site 5015_E2Fb_Athamap_20091028_ D -180 -173 ATTCCCAC 6.3 2.7e-04 -8.217 3.569 VHA-A site 5015_E2Fb_Athamap_20091028_ R -400 -393 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 VHA-A site 5015_E2Fb_Athamap_20091028_ R -352 -345 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 VHA-A site 5015_E2Fb_Athamap_20091028_ D -266 -259 CGTCCCGC 6.4 2.7e-04 -8.217 3.569 VHA-A site 5015_E2Fb_Athamap_20091028_ D -167 -160 TTCCCCGA 4.8 7.9e-04 -7.143 3.102 VHA-A site 5015_E2Fb_Athamap_20091028_ D -131 -124 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT5G45480 site 5015_E2Fb_Athamap_20091028_ D -475 -468 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 RRF site 5015_E2Fb_Athamap_20091028_ D -494 -487 GTTCTCGC 5.5 3.6e-04 -7.929 3.444 RRF site 5015_E2Fb_Athamap_20091028_ R -446 -439 GTTCGCGC 5.8 3.1e-04 -8.079 3.509 RRF site 5015_E2Fb_Athamap_20091028_ D -428 -421 TTACCGGC 5.3 5.1e-04 -7.581 3.292 RRF site 5015_E2Fb_Athamap_20091028_ D -417 -410 GCTCCCGC 6.2 2.8e-04 -8.181 3.553 PGK3 site 5015_E2Fb_Athamap_20091028_ R -437 -430 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 PGK3 site 5015_E2Fb_Athamap_20091028_ D -281 -274 TTTCCCGA 7.3 1.3e-04 -8.948 3.886 PGK3 site 5015_E2Fb_Athamap_20091028_ D -205 -198 TCTCCGGC 5.1 5.8e-04 -7.452 3.237 CRRSP48 site 5015_E2Fb_Athamap_20091028_ D -278 -271 TTCGCCGC 5.4 4.4e-04 -7.729 3.357 RPL10B site 5015_E2Fb_Athamap_20091028_ R -157 -150 ATTCCGGC 6.7 2.1e-04 -8.468 3.678 AT2G37435 site 5015_E2Fb_Athamap_20091028_ D -398 -391 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT2G37435 site 5015_E2Fb_Athamap_20091028_ R -217 -210 TTACCCGT 5.2 5.1e-04 -7.581 3.292 AT2G37435 site 5015_E2Fb_Athamap_20091028_ R -164 -157 TTACCCGT 5.2 5.1e-04 -7.581 3.292 AT2G37435 site 5015_E2Fb_Athamap_20091028_ D -139 -132 TTACCCGA 5.2 5.8e-04 -7.452 3.237 AT2G37435 site 5015_E2Fb_Athamap_20091028_ R -92 -85 TTACCCGA 5.2 5.8e-04 -7.452 3.237 EMB1687 site 5015_E2Fb_Athamap_20091028_ D -430 -423 TATCCGGC 5.4 3.9e-04 -7.849 3.409 EMB1687 site 5015_E2Fb_Athamap_20091028_ R -424 -417 ATGCCCGC 7.6 5.8e-05 -9.755 4.237 EMB1687 site 5015_E2Fb_Athamap_20091028_ R -371 -364 TATGCCGC 5.5 3.6e-04 -7.929 3.444 AT4G14360 site 5015_E2Fb_Athamap_20091028_ R -466 -459 CTTCCAGC 5.2 5.1e-04 -7.581 3.292 WRKY22 site 5015_E2Fb_Athamap_20091028_ R -457 -450 TATCTCGC 5.6 3.3e-04 -8.016 3.481 WRKY22 site 5015_E2Fb_Athamap_20091028_ R -423 -416 TTGTCCGC 5.1 6.5e-04 -7.339 3.187 AT1G22660 site 5015_E2Fb_Athamap_20091028_ R -203 -196 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT1G22660 site 5015_E2Fb_Athamap_20091028_ D -70 -63 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 FRS6 site 5015_E2Fb_Athamap_20091028_ R -233 -226 TTACCCAC 4.9 6.9e-04 -7.279 3.161 FRS6 site 5015_E2Fb_Athamap_20091028_ D -71 -64 ATTCCCTC 6.4 2.6e-04 -8.255 3.585 PAP11 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -346 -336 TACGCGTTCAT 5.5 3.9e-04 -7.849 3.409 ATPAP15 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -179 -169 TTCCCACTATC 4.6 8.3e-04 -7.094 3.081 U2.4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -500 -490 ATCCCACCAAG 5.0 6.0e-04 -7.419 3.222 VHA-A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -404 -394 TTCCCTCACAT 5.6 3.9e-04 -7.849 3.409 VHA-A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -356 -346 CTCTCGCCATT 6.0 2.7e-04 -8.217 3.569 VHA-A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -265 -255 GTCCCGCTAAT 8.2 3.4e-05 -10.289 4.469 VHA-A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -166 -156 TCCCCGAGAAA 5.0 6.0e-04 -7.419 3.222 VHA-A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -60 -50 TTACGGCCCAA 5.7 3.3e-04 -8.016 3.481 AT5G45480 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -213 -203 TTCCCTTCATA 4.8 7.2e-04 -7.236 3.143 RRF site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -450 -440 TTCGCGCTTAC 5.6 3.6e-04 -7.929 3.444 RRF site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -416 -406 CTCCCGCTAAT 8.2 3.4e-05 -10.289 4.469 RRF site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -31 -21 TTACGGCCCAT 5.6 3.9e-04 -7.849 3.409 PGK3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -466 -456 TACCCGGAAAA 4.5 9.1e-04 -7.002 3.041 PGK3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -441 -431 TTCCCGCCAAG 9.8 6.5e-06 -11.944 5.187 PGK3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -280 -270 TTCCCGATTAA 4.9 6.5e-04 -7.339 3.187 RPL10B site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -496 -486 CTCCGGCTCAT 4.9 6.5e-04 -7.339 3.187 RPL10B site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -161 -151 TTCCGGCGACT 5.5 3.9e-04 -7.849 3.409 AT2G37435 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -494 -484 AACCAGCCCTT 5.8 3.1e-04 -8.079 3.509 AT2G37435 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -397 -387 TTCCCACTCAT 6.9 1.3e-04 -8.948 3.886 AT2G37435 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -138 -128 TACCCGACTAA 5.9 2.9e-04 -8.146 3.538 EMB1687 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -428 -418 TGCCCGCCGGA 5.4 4.2e-04 -7.775 3.377 EMB1687 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -356 -346 CACTCGCCATT 4.8 7.2e-04 -7.236 3.143 EMB1687 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -296 -286 TTCTCGACCAA 5.8 3.1e-04 -8.079 3.509 AT5G38640 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -408 -398 CACCAGCCCTA 5.2 5.0e-04 -7.601 3.301 AT4G14360 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -470 -460 TTCCAGCCATA 8.5 2.4e-05 -10.637 4.620 AT4G14360 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -240 -230 TTACAGCGCAT 5.0 6.5e-04 -7.339 3.187 AT4G10700 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -90 -80 TACGCTCCAAA 6.6 1.6e-04 -8.740 3.796 AT3G08715 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -57 -47 TTGCCTCGCAT 4.5 9.1e-04 -7.002 3.041 WRKY22 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -461 -451 ATCTCGCAAAA 4.9 6.5e-04 -7.339 3.187 AT4G26480 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -488 -478 GTCGCACGCAA 4.9 7.2e-04 -7.236 3.143 AT1G22660 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -69 -59 TTCCCGCTTAA 8.5 2.4e-05 -10.637 4.620 FRS6 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -70 -60 TTCCCTCCGTT 5.6 3.6e-04 -7.929 3.444 ; ; 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_ 34 0 ; 2 5015_E2Fb_Athamap_20091028_ 34 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 32 0 ; TOTAL 100 0 ; Host name rsat ; Job started 2026-08-17.132448 ; Job done 2026-08-17.132449 ; Seconds 0.48 ; user 0.48 ; system 0.05 ; cuser 0.82 ; csystem 0.09