; dna-pattern -v 1 -pl $RSAT/public_html/tmp/www-data/2026/04/21/dna-pattern_2026-04-21.100730_CVtlP3.pat -i $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.100730_ImxlNM.fasta -format fasta -return sites -origin -0 -N 4 -noov -2str -subst 2
; Citation: van Helden et al. (2000). Yeast 16(2), 177-187.
; Input file $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.100730_ImxlNM.fasta
; Input format fasta
; Pattern file $RSAT/public_html/tmp/www-data/2026/04/21/dna-pattern_2026-04-21.100730_CVtlP3.pat
; Search method IUPAC
; Threshold 0
; Allowed substitutions 2
; Return fields
; sites
; Patterns
; seq id score
; GCCGCC GCC-box 1
; GCCGCC DRE 1
; A/GCCGAC CRT 1
; GAAATTTC VWRE 1
; CACCG CEI 1
;
; Matching positions
; PatID Strand Pattern SeqID Start End matching_seq Score
GCC-box D GCCGCC pro-9590 -1189 -1184 GCCATC 0.67
GCC-box D GCCGCC pro-9590 -571 -566 TCCCCC 0.67
GCC-box D GCCGCC pro-9590 -401 -396 GCTGTC 0.67
GCC-box D GCCGCC pro-9590 -270 -265 GCAGCC 0.83
GCC-box R GCCGCC pro-9590 -1803 -1798 CCCACC 0.67
GCC-box R GCCGCC pro-9590 -1171 -1166 TCCTCC 0.67
GCC-box R GCCGCC pro-9590 -802 -797 GCTACC 0.67
GCC-box R GCCGCC pro-9590 -735 -730 ACAGCC 0.67
GCC-box R GCCGCC pro-9590 -271 -266 GCTGCA 0.67
DRE D GCCGCC pro-9590 -1189 -1184 GCCATC 0.67
DRE D GCCGCC pro-9590 -571 -566 TCCCCC 0.67
DRE D GCCGCC pro-9590 -401 -396 GCTGTC 0.67
DRE D GCCGCC pro-9590 -270 -265 GCAGCC 0.83
DRE R GCCGCC pro-9590 -1803 -1798 CCCACC 0.67
DRE R GCCGCC pro-9590 -1171 -1166 TCCTCC 0.67
DRE R GCCGCC pro-9590 -802 -797 GCTACC 0.67
DRE R GCCGCC pro-9590 -735 -730 ACAGCC 0.67
DRE R GCCGCC pro-9590 -271 -266 GCTGCA 0.67
CRT R A/GCCGAC pro-9590 -1802 -1795 ATGCCCAC 0.75
VWRE DR GAAATTTC pro-9590 -2074 -2067 GAGATTTT 0.75
VWRE DR GAAATTTC pro-9590 -1777 -1770 AAAATTTC 0.88
VWRE DR GAAATTTC pro-9590 -1763 -1756 GTAATTTG 0.75
VWRE DR GAAATTTC pro-9590 -1740 -1733 GAAACTTA 0.75
VWRE DR GAAATTTC pro-9590 -1715 -1708 ATAATTTC 0.75
VWRE DR GAAATTTC pro-9590 -1697 -1690 GATATTTT 0.75
VWRE DR GAAATTTC pro-9590 -1510 -1503 GCAATTTC 0.88
VWRE DR GAAATTTC pro-9590 -1447 -1440 AAAATTTC 0.88
VWRE DR GAAATTTC pro-9590 -1349 -1342 TATATTTC 0.75
VWRE DR GAAATTTC pro-9590 -1336 -1329 GATATTTG 0.75
VWRE DR GAAATTTC pro-9590 -1308 -1301 TAAATATC 0.75
VWRE DR GAAATTTC pro-9590 -1051 -1044 GAAATATG 0.75
VWRE DR GAAATTTC pro-9590 -948 -941 GAAAGTTA 0.75
VWRE DR GAAATTTC pro-9590 -934 -927 GAAAATTT 0.75
VWRE DR GAAATTTC pro-9590 -862 -855 GAAAATTT 0.75
VWRE DR GAAATTTC pro-9590 -791 -784 GAAATGTA 0.75
VWRE DR GAAATTTC pro-9590 -552 -545 ACAATTTC 0.75
VWRE DR GAAATTTC pro-9590 -509 -502 AAAGTTTC 0.75
VWRE DR GAAATTTC pro-9590 -475 -468 GAAATTTA 0.88
VWRE DR GAAATTTC pro-9590 -233 -226 GAAATGTT 0.75
VWRE DR GAAATTTC pro-9590 -209 -202 AAAAGTTC 0.75
VWRE DR GAAATTTC pro-9590 -134 -127 TAAAATTC 0.75
VWRE DR GAAATTTC pro-9590 -76 -69 GAAATTGT 0.75
CEI D CACCG pro-9590 -2010 -2006 CTCTG 0.60
CEI D CACCG pro-9590 -1914 -1910 CAACT 0.60
CEI D CACCG pro-9590 -1896 -1892 AACCC 0.60
CEI D CACCG pro-9590 -1885 -1881 CAAGG 0.60
CEI D CACCG pro-9590 -1868 -1864 CATAG 0.60
CEI D CACCG pro-9590 -1849 -1845 AACAG 0.60
CEI D CACCG pro-9590 -1797 -1793 CATAG 0.60
CEI D CACCG pro-9590 -1657 -1653 AATCG 0.60
CEI D CACCG pro-9590 -1647 -1643 CACAA 0.60
CEI D CACCG pro-9590 -1635 -1631 CACTT 0.60
CEI D CACCG pro-9590 -1600 -1596 GACCT 0.60
CEI D CACCG pro-9590 -1578 -1574 CATCT 0.60
CEI D CACCG pro-9590 -1557 -1553 CACTT 0.60
CEI D CACCG pro-9590 -1550 -1546 CACAA 0.60
CEI D CACCG pro-9590 -1463 -1459 CAAAG 0.60
CEI D CACCG pro-9590 -1457 -1453 TACAG 0.60
CEI D CACCG pro-9590 -1269 -1265 TACCA 0.60
CEI D CACCG pro-9590 -1211 -1207 AATCG 0.60
CEI D CACCG pro-9590 -1205 -1201 TACCT 0.60
CEI D CACCG pro-9590 -1187 -1183 CATCC 0.60
CEI D CACCG pro-9590 -1167 -1163 GACCA 0.60
CEI D CACCG pro-9590 -1133 -1129 CAACT 0.60
CEI D CACCG pro-9590 -1117 -1113 CTCCA 0.60
CEI D CACCG pro-9590 -1029 -1025 CACTT 0.60
CEI D CACCG pro-9590 -891 -887 AAACG 0.60
CEI D CACCG pro-9590 -690 -686 CAAGG 0.60
CEI D CACCG pro-9590 -680 -676 GACCG 0.80
CEI D CACCG pro-9590 -655 -651 CACAT 0.60
CEI D CACCG pro-9590 -615 -611 CATCA 0.60
CEI D CACCG pro-9590 -586 -582 CACAA 0.60
CEI D CACCG pro-9590 -572 -568 CTCCC 0.60
CEI D CACCG pro-9590 -530 -526 TAGCG 0.60
CEI D CACCG pro-9590 -519 -515 GACTG 0.60
CEI D CACCG pro-9590 -512 -508 CACAA 0.60
CEI D CACCG pro-9590 -453 -449 CACCC 0.80
CEI D CACCG pro-9590 -442 -438 GTCCG 0.60
CEI D CACCG pro-9590 -352 -348 CATTG 0.60
CEI D CACCG pro-9590 -329 -325 CTCCA 0.60
CEI D CACCG pro-9590 -304 -300 CAACT 0.60
CEI D CACCG pro-9590 -269 -265 CAGCC 0.60
CEI D CACCG pro-9590 -259 -255 CACTT 0.60
CEI D CACCG pro-9590 -248 -244 CAACT 0.60
CEI D CACCG pro-9590 -239 -235 CACTA 0.60
CEI D CACCG pro-9590 -224 -220 GAACG 0.60
CEI D CACCG pro-9590 -202 -198 CAACG 0.80
CEI D CACCG pro-9590 -190 -186 CACTT 0.60
CEI D CACCG pro-9590 -175 -171 TACCT 0.60
CEI D CACCG pro-9590 -166 -162 AACCC 0.60
CEI D CACCG pro-9590 -127 -123 CAACT 0.60
CEI D CACCG pro-9590 -93 -89 CACTC 0.60
CEI R CACCG pro-9590 -2010 -2006 CAGAG 0.60
CEI R CACCG pro-9590 -1985 -1981 CACAT 0.60
CEI R CACCG pro-9590 -1965 -1961 GACCA 0.60
CEI R CACCG pro-9590 -1911 -1907 CATAG 0.60
CEI R CACCG pro-9590 -1883 -1879 TACCT 0.60
CEI R CACCG pro-9590 -1876 -1872 CATCA 0.60
CEI R CACCG pro-9590 -1858 -1854 TACCT 0.60
CEI R CACCG pro-9590 -1831 -1827 CACTA 0.60
CEI R CACCG pro-9590 -1804 -1800 CACCC 0.80
CEI R CACCG pro-9590 -1757 -1753 TACCA 0.60
CEI R CACCG pro-9590 -1708 -1704 TACCG 0.80
CEI R CACCG pro-9590 -1654 -1650 TATCG 0.60
CEI R CACCG pro-9590 -1455 -1451 TACTG 0.60
CEI R CACCG pro-9590 -1342 -1338 TATCG 0.60
CEI R CACCG pro-9590 -1330 -1326 TACCA 0.60
CEI R CACCG pro-9590 -1245 -1241 TATCG 0.60
CEI R CACCG pro-9590 -1208 -1204 TACCG 0.80
CEI R CACCG pro-9590 -1199 -1195 TACGG 0.60
CEI R CACCG pro-9590 -1175 -1171 CATCT 0.60
CEI R CACCG pro-9590 -1165 -1161 CATGG 0.60
CEI R CACCG pro-9590 -1137 -1133 GACTG 0.60
CEI R CACCG pro-9590 -1103 -1099 CACAT 0.60
CEI R CACCG pro-9590 -1045 -1041 AACCA 0.60
CEI R CACCG pro-9590 -845 -841 CATAG 0.60
CEI R CACCG pro-9590 -806 -802 CACTT 0.60
CEI R CACCG pro-9590 -799 -795 CAGCT 0.60
CEI R CACCG pro-9590 -784 -780 AACCT 0.60
CEI R CACCG pro-9590 -759 -755 CATAG 0.60
CEI R CACCG pro-9590 -748 -744 AACCA 0.60
CEI R CACCG pro-9590 -735 -731 CAGCC 0.60
CEI R CACCG pro-9590 -727 -723 CACAA 0.60
CEI R CACCG pro-9590 -719 -715 CATAG 0.60
CEI R CACCG pro-9590 -708 -704 AACCA 0.60
CEI R CACCG pro-9590 -686 -682 CATCC 0.60
CEI R CACCG pro-9590 -677 -673 AATCG 0.60
CEI R CACCG pro-9590 -667 -663 ATCCG 0.60
CEI R CACCG pro-9590 -527 -523 CATCG 0.80
CEI R CACCG pro-9590 -467 -463 GATCG 0.60
CEI R CACCG pro-9590 -440 -436 CCCGG 0.60
CEI R CACCG pro-9590 -402 -398 CAGCT 0.60
CEI R CACCG pro-9590 -370 -366 TACTG 0.60
CEI R CACCG pro-9590 -352 -348 CAATG 0.60
CEI R CACCG pro-9590 -282 -278 TACTG 0.60
CEI R CACCG pro-9590 -237 -233 CATAG 0.60
CEI R CACCG pro-9590 -221 -217 TACCG 0.80
CEI R CACCG pro-9590 -200 -196 CACGT 0.60
CEI R CACCG pro-9590 -161 -157 CATAG 0.60
CEI R CACCG pro-9590 -72 -68 CACAA 0.60
CEI R CACCG pro-9590 -14 -10 CAAAG 0.60
; Host name rsat
; Job started 2026-04-21.100730
; Job done 2026-04-21.100730
; Seconds 0.12
; user 0.12
; system 0
; cuser 0
; csystem 0