; dna-pattern -v 1 -pl $RSAT/public_html/tmp/www-data/2026/05/11/dna-pattern_2026-05-11.160400_cpvqjh.pat -i $RSAT/public_html/tmp/www-data/2026/05/11/tmp_sequence_2026-05-11.160400_SX1YnS.fasta -format fasta -return sites -origin -0 -N 4 -return limits -noov -2str -subst 0
; Citation: van Helden et al. (2000). Yeast 16(2), 177-187.
; Input file $RSAT/public_html/tmp/www-data/2026/05/11/tmp_sequence_2026-05-11.160400_SX1YnS.fasta
; Input format fasta
; Pattern file $RSAT/public_html/tmp/www-data/2026/05/11/dna-pattern_2026-05-11.160400_cpvqjh.pat
; Search method regexp
; Threshold 0
; Allowed substitutions 0
; Return fields
; limits
; sites
; Patterns
; seq id score
; CGCG CGCG 1
;
; Matching positions
; PatID Strand Pattern SeqID Start End matching_seq Score
START_END DR - transcript:Os02t0306401-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os02t0306401-01 -1949 -1946 tggcCGCGccgc 1.00
CGCG DR CGCG transcript:Os02t0306401-01 -1914 -1911 cggcCGCGtagg 1.00
CGCG DR CGCG transcript:Os02t0306401-01 -1838 -1835 cggcCGCGccgc 1.00
CGCG DR CGCG transcript:Os02t0306401-01 -1815 -1812 tcgcCGCGccaa 1.00
CGCG DR CGCG transcript:Os02t0306401-01 -1796 -1793 aaggCGCGaggg 1.00
CGCG DR CGCG transcript:Os02t0306401-01 -5 -2 caggCGCGc 1.00
START_END DR - transcript:Os02t0650300-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os02t0650300-01 -1508 -1505 actcCGCGgact 1.00
CGCG DR CGCG transcript:Os02t0650300-01 -493 -490 gaacCGCGatta 1.00
START_END DR - transcript:Os02t0649900-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os02t0649900-01 -1586 -1583 gcggCGCGccgt 1.00
CGCG DR CGCG transcript:Os02t0649900-01 -1230 -1227 cgtgCGCGggtt 1.00
CGCG DR CGCG transcript:Os02t0649900-01 -1208 -1205 tgggCGCGagcg 1.00
CGCG DR CGCG transcript:Os02t0649900-01 -1192 -1189 caagCGCGgcgt 1.00
CGCG DR CGCG transcript:Os02t0649900-01 -1166 -1163 ttggCGCGaggc 1.00
CGCG DR CGCG transcript:Os02t0649900-01 -496 -493 gggcCGCGtccc 1.00
START_END DR - transcript:Os06t0569500-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os06t0569500-01 -673 -670 tgacCGCGcgat 1.00
START_END DR - transcript:Os06t0568600-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os06t0568600-01 -1642 -1639 cagcCGCGtgct 1.00
CGCG DR CGCG transcript:Os06t0568600-01 -1295 -1292 tcttCGCGgatc 1.00
START_END DR - transcript:Os01t0626400-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os01t0626400-01 -584 -581 aaaaCGCGgtgg 1.00
START_END DR - transcript:Os01t0826400-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os01t0826400-01 -1555 -1552 cagaCGCGttga 1.00
CGCG DR CGCG transcript:Os01t0826400-01 -246 -243 gcttCGCGcaag 1.00
CGCG DR CGCG transcript:Os01t0826400-01 -34 -31 gagaCGCGgcgg 1.00
CGCG DR CGCG transcript:Os01t0826400-01 -19 -16 tggtCGCGacct 1.00
START_END DR - transcript:Os05t0474800-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os05t0474800-01 -346 -343 gattCGCGaccg 1.00
CGCG DR CGCG transcript:Os05t0474800-01 -315 -312 ccccCGCGacca 1.00
START_END DR - transcript:Os01t0881300-02 -2000 -1 - 0.00
START_END DR - transcript:Os03t0347500-01 -2000 -1 - 0.00
START_END DR - transcript:Os01t0952800-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os01t0952800-01 -1507 -1504 atcaCGCGtcgt 1.00
CGCG DR CGCG transcript:Os01t0952800-01 -1449 -1446 acgcCGCGcgcg 1.00
CGCG DR CGCG transcript:Os01t0952800-01 -1445 -1442 cgcgCGCGcacg 1.00
CGCG DR CGCG transcript:Os01t0952800-01 -1417 -1414 ggcaCGCGcggc 1.00
CGCG DR CGCG transcript:Os01t0952800-01 -1377 -1374 ccggCGCGtgtc 1.00
CGCG DR CGCG transcript:Os01t0952800-01 -1361 -1358 cccaCGCGctac 1.00
CGCG DR CGCG transcript:Os01t0952800-01 -1348 -1345 tggcCGCGcgcg 1.00
CGCG DR CGCG transcript:Os01t0952800-01 -1344 -1341 cgcgCGCGtctc 1.00
START_END DR - transcript:Os03t0741100-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os03t0741100-01 -444 -441 aatcCGCGaaaa 1.00
CGCG DR CGCG transcript:Os03t0741100-01 -334 -331 aaacCGCGtagc 1.00
CGCG DR CGCG transcript:Os03t0741100-01 -97 -94 atccCGCGttcg 1.00
START_END DR - transcript:Os07t0580900-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os07t0580900-01 -1412 -1409 cagtCGCGgcac 1.00
START_END DR - transcript:Os09t0368500-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os09t0368500-01 -1665 -1662 tcgtCGCGggga 1.00
CGCG DR CGCG transcript:Os09t0368500-01 -1606 -1603 tccaCGCGgggg 1.00
CGCG DR CGCG transcript:Os09t0368500-01 -1529 -1526 tcctCGCGagga 1.00
CGCG DR CGCG transcript:Os09t0368500-01 -1467 -1464 ccatCGCGccgc 1.00
CGCG DR CGCG transcript:Os09t0368500-01 -548 -545 atgcCGCGttct 1.00
START_END DR - transcript:Os06t0498800-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os06t0498800-01 -32 -29 tcacCGCGagag 1.00
START_END DR - transcript:Os08t0140300-01 -2000 -1 - 0.00
START_END DR - transcript:Os12t0268000-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os12t0268000-01 -488 -485 ttttCGCGaact 1.00
START_END DR - transcript:Os06t0604200-02 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os06t0604200-02 -995 -992 aattCGCGagac 1.00
CGCG DR CGCG transcript:Os06t0604200-02 -293 -290 cttaCGCGcctt 1.00
CGCG DR CGCG transcript:Os06t0604200-02 -122 -119 agcaCGCGgtcg 1.00
START_END DR - transcript:Os02t0776900-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os02t0776900-01 -118 -115 catcCGCGtgat 1.00
CGCG DR CGCG transcript:Os02t0776900-01 -93 -90 agagCGCGcgcc 1.00
CGCG DR CGCG transcript:Os02t0776900-01 -85 -82 cgccCGCGgcgc 1.00
START_END DR - transcript:Os03t0325600-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os03t0325600-01 -1741 -1738 agacCGCGgcat 1.00
CGCG DR CGCG transcript:Os03t0325600-01 -116 -113 gtagCGCGtgct 1.00
START_END DR - transcript:Os07t0143200-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os07t0143200-01 -772 -769 cagcCGCGcggg 1.00
START_END DR - transcript:Os10t0477600-01 -2000 -1 - 0.00
START_END DR - transcript:Os06t0104900-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os06t0104900-01 -993 -990 cgtgCGCGctct 1.00
CGCG DR CGCG transcript:Os06t0104900-01 -656 -653 cagcCGCGacct 1.00
START_END DR - transcript:Os01t0819200-00 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os01t0819200-00 -1602 -1599 gatcCGCGatgg 1.00
START_END DR - transcript:Os05t0473401-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os05t0473401-01 -1963 -1960 ccgcCGCGtcca 1.00
CGCG DR CGCG transcript:Os05t0473401-01 -1944 -1941 tcccCGCGcggt 1.00
CGCG DR CGCG transcript:Os05t0473401-01 -1894 -1891 tcgcCGCGccgg 1.00
CGCG DR CGCG transcript:Os05t0473401-01 -1657 -1654 gggaCGCGtctt 1.00
CGCG DR CGCG transcript:Os05t0473401-01 -102 -99 gggcCGCGgggg 1.00
CGCG DR CGCG transcript:Os05t0473401-01 -77 -74 gcggCGCGgcga 1.00
CGCG DR CGCG transcript:Os05t0473401-01 -68 -65 cgacCGCGccat 1.00
CGCG DR CGCG transcript:Os05t0473401-01 -54 -51 ccggCGCGcgca 1.00
CGCG DR CGCG transcript:Os05t0473401-01 -40 -37 ggggCGCGgatg 1.00
START_END DR - transcript:Os09t0454600-00 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os09t0454600-00 -1948 -1945 ccgtCGCGtcgt 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -1524 -1521 tgtgCGCGagcg 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -804 -801 gaggCGCGggcc 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -783 -780 gaggCGCGagca 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -772 -769 atggCGCGgtgg 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -269 -266 accaCGCGgtca 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -249 -246 caagCGCGaagg 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -230 -227 caccCGCGcgcg 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -226 -223 cgcgCGCGcgcg 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -222 -219 cgcgCGCGcgag 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -151 -148 cggcCGCGcgcg 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -147 -144 cgcgCGCGggca 1.00
CGCG DR CGCG transcript:Os09t0454600-00 -62 -59 acgaCGCGgcga 1.00
START_END DR - transcript:Os03t0853200-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os03t0853200-01 -1824 -1821 tcgtCGCGcact 1.00
CGCG DR CGCG transcript:Os03t0853200-01 -1798 -1795 cagaCGCGtgag 1.00
CGCG DR CGCG transcript:Os03t0853200-01 -799 -796 tagtCGCGcctt 1.00
CGCG DR CGCG transcript:Os03t0853200-01 -740 -737 gcaaCGCGtggt 1.00
CGCG DR CGCG transcript:Os03t0853200-01 -711 -708 ccaaCGCGtgtg 1.00
CGCG DR CGCG transcript:Os03t0853200-01 -628 -625 ttctCGCGggag 1.00
START_END DR - transcript:Os11t0707300-00 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os11t0707300-00 -574 -571 tgtaCGCGcaca 1.00
START_END DR - transcript:Os02t0574000-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os02t0574000-01 -504 -501 ccagCGCGaagc 1.00
CGCG DR CGCG transcript:Os02t0574000-01 -492 -489 aggaCGCGtact 1.00
START_END DR - transcript:Os07t0131250-00 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os07t0131250-00 -1246 -1243 agtgCGCGcgtt 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -751 -748 cggcCGCGtcac 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -595 -592 acgaCGCGatac 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -496 -493 cgagCGCGtcag 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -385 -382 caggCGCGgccg 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -376 -373 ccggCGCGcgtc 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -317 -314 cctcCGCGgcgg 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -286 -283 cgggCGCGtcct 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -210 -207 ccgtCGCGgcgc 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -205 -202 gcggCGCGgcgc 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -200 -197 gcggCGCGttca 1.00
CGCG DR CGCG transcript:Os07t0131250-00 -15 -12 gaggCGCGggct 1.00
START_END DR - transcript:Os03t0197200-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os03t0197200-01 -867 -864 agggCGCGcagc 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -792 -789 ctccCGCGccgc 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -535 -532 gcggCGCGcaga 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -496 -493 cggaCGCGaagg 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -439 -436 cgctCGCGgcgg 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -388 -385 tgctCGCGtcgg 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -364 -361 ccggCGCGctca 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -334 -331 gctaCGCGatcg 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -286 -283 gctaCGCGctca 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -274 -271 tgatCGCGccgg 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -234 -231 cgccCGCGgctt 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -129 -126 ctggCGCGtcat 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -56 -53 tcgcCGCGgtgg 1.00
CGCG DR CGCG transcript:Os03t0197200-01 -22 -19 gcgaCGCGcgac 1.00
START_END DR - transcript:Os11t0687100-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os11t0687100-01 -1614 -1611 tcacCGCGttcg 1.00
START_END DR - transcript:Os11t0687200-01 -2000 -1 - 0.00
START_END DR - transcript:Os09t0569800-00 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os09t0569800-00 -1712 -1709 tatcCGCGcagg 1.00
START_END DR - transcript:Os09t0361200-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os09t0361200-01 -1240 -1237 tatcCGCGacta 1.00
CGCG DR CGCG transcript:Os09t0361200-01 -1165 -1162 ccatCGCGgtaa 1.00
CGCG DR CGCG transcript:Os09t0361200-01 -1120 -1117 cggcCGCGtctg 1.00
START_END DR - transcript:Os04t0178300-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os04t0178300-01 -1832 -1829 tatgCGCGtgat 1.00
CGCG DR CGCG transcript:Os04t0178300-01 -1162 -1159 cgtgCGCGaccg 1.00
CGCG DR CGCG transcript:Os04t0178300-01 -1120 -1117 cggtCGCGccct 1.00
CGCG DR CGCG transcript:Os04t0178300-01 -1111 -1108 cctcCGCGccgg 1.00
CGCG DR CGCG transcript:Os04t0178300-01 -1082 -1079 cctcCGCGctgg 1.00
CGCG DR CGCG transcript:Os04t0178300-01 -1048 -1045 cctcCGCGccga 1.00
CGCG DR CGCG transcript:Os04t0178300-01 -1036 -1033 ccacCGCGaccg 1.00
CGCG DR CGCG transcript:Os04t0178300-01 -463 -460 ttttCGCGgtat 1.00
START_END DR - transcript:Os02t0570400-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os02t0570400-01 -719 -716 caggCGCGgcga 1.00
CGCG DR CGCG transcript:Os02t0570400-01 -95 -92 cgttCGCGgctc 1.00
CGCG DR CGCG transcript:Os02t0570400-01 -5 -2 tcgtCGCGa 1.00
START_END DR - transcript:Os01t0757200-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os01t0757200-01 -1924 -1921 ccctCGCGgccc 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -1904 -1901 agacCGCGagac 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -560 -557 tgttCGCGtaca 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -428 -425 acgtCGCGgccc 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -339 -336 gcagCGCGcgcg 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -335 -332 cgcgCGCGcgcg 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -331 -328 cgcgCGCGcgcg 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -327 -324 cgcgCGCGagcg 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -273 -270 ttctCGCGtctc 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -245 -242 tgccCGCGggga 1.00
CGCG DR CGCG transcript:Os01t0757200-01 -235 -232 gaccCGCGctgc 1.00
START_END DR - transcript:Os04t0178400-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os04t0178400-01 -1834 -1831 ttaaCGCGtgat 1.00
START_END DR - transcript:Os02t0569900-01 -2000 -1 - 0.00
START_END DR - transcript:Os10t0498000-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os10t0498000-01 -502 -499 agctCGCGagct 1.00
START_END DR - transcript:Os03t0856700-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os03t0856700-01 -1006 -1003 tgaaCGCGcaat 1.00
CGCG DR CGCG transcript:Os03t0856700-01 -461 -458 tggcCGCGgccg 1.00
CGCG DR CGCG transcript:Os03t0856700-01 -175 -172 tagcCGCGgtcg 1.00
START_END DR - transcript:Os03t0115800-01 -2000 -1 - 0.00
CGCG DR CGCG transcript:Os03t0115800-01 -1941 -1938 tgccCGCGcgaa 1.00
CGCG DR CGCG transcript:Os03t0115800-01 -1931 -1928 aatgCGCGggct 1.00
CGCG DR CGCG transcript:Os03t0115800-01 -1119 -1116 atgcCGCGcaaa 1.00
CGCG DR CGCG transcript:Os03t0115800-01 -269 -266 ttgaCGCGtcaa 1.00
; Host name rsat
; Job started 2026-05-11.160400
; Job done 2026-05-11.160400
; Seconds 0.13
; user 0.13
; system 0.01
; cuser 0
; csystem 0