AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02060_ecoli_reg_100.orf -o02060_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #2 hrsA 108 protein modification enzyme, induction of ompC #3 ptsG 294 PTS system, glucose-specific IIBC component #4 malX 174 PTS system, maltose and glucose-specific II ABC #5 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #6 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #7 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #8 manX 300 PTS enzyme IIAB, mannose-specific #9 manY 62 PTS enzyme IIC, mannose-specific #10 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #11 gatZ 28 putative tagatose 6-phosphate kinase 1 #12 gatY 197 tagatose-bisphosphate aldolase 1 #13 fruB 300 PTS system, fructose-specific IIA/fpr component #14 b2383 24 putative PTS system enzyme IIA component, enzyme I #15 b2386 21 putative transport protein #16 b2387 218 putative PTS system enzyme IIB component #17 ptsH 300 PTS system protein HPr #18 ptsI 44 PEP-protein phosphotransferase system enzyme I #19 crr 40 PTS system, glucose-specific IIA component #20 yfeU 163 putative regulator #21 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #22 ascF 256 PTS system enzyme II ABC (asc), cryptic, transports specific beta-glucosides #23 ygdP 300 putative invasion protein #24 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #25 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #26 agaZ 248 putative tagatose 6-phosphate kinase 2 #27 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #28 agaC 38 PTS system N-acetylgalactosamine-specific IIC component 1 #29 ptsN 117 phosphotransferase system enzyme IIA, regulates N metabolism #30 yhbJ 45 orf, hypothetical protein #31 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #32 glvB 24 PTS system, arbutin-like IIB component #33 glvC 34 PTS system, arbutin-like IIC component #34 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #35 frvA 300 PTS system, fructose-specific IIA component #36 frwC 300 PTS system, fructose-like enzyme II component #37 pflD 50 formate acetyltransferase 2 #38 sgaT 291 orf, hypothetical protein #39 treB 118 PTS system enzyme II, trehalose specific #40 sgcA 130 putative PTS system enzyme II A component #41 sgcC 286 putative PTS system enzyme IIC component Motif number 1 ACGCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGT 1 129 0 TTGTGATCAC 0.983715 -172 TATGTGATCAATTTCACTTGATTGAAA 2 92 0 TTGTGATCAC 0.983715 -17 AGTGCCAATTTGTTTGACGGCTATCACGTTTCAACTT 3 145 0 TTTTGATCAC 0.749731 -150 ACTCCCTGATTATGTGACAGATAAAACGTTTTACCTT 4 22 1 TTGTGAAAAC 0.747303 -153 ATCAGAGGCGTCTCTGATATGTTTAACTCCCGTTTAA 8 27 0 TTCTGATAAC 0.586946 -274 GTGTGAAAACTGAGTGATAATCAACACAATACG 9 7 0 TAGTGAACAC 0.54887 -56 TATTGTCGTTTTTGTGATCGTTATCTCGATATTTAAA 12 124 1 TTGTGATCTC 0.889639 -74 CTCTTCACACTCTGCGAGTGTAGACTCAATGATTCCT 20 62 1 TTGCGAACTC 0.503308 -102 TATCTTTCATTTTGCGATCAAAATAACACTTTTAAAT 21 164 1 TTGCGATAAC 0.824276 -92 ATTTTTTATATTTGTGAAACCGGTCACCTGAATATTT 22 84 0 TTGTGATCAC 0.983715 -173 CATATAAATATTTGTGATCTACAACACGCCTTATCTA 25 71 0 TTGTGAACAC 0.944461 -230 AAATATCAATTATGTAATATGCATCACGATATGCGGT 25 112 1 TTGTAATCAC 0.832641 -189 AGATAATGGTTTTCTGATCTGATTCACAAAAGAAACA 26 134 0 TTCTGATCAC 0.890962 -115 ATGGCATTTAAATGTGAGTAGTGTCACATTTTTGTTT 31 26 0 ATGTGATCAC 0.812094 -275 ACACAAGCGTTTTGTGATGAACGTCACGTCAATTACC 31 96 1 TTGTGATCAC 0.983715 -205 CCCCTATATTTATGTGATTGATATCACACAAAAGGCC 31 140 1 TTGTGATCAC 0.983715 -161 TAACCGTCAATTTGCGACGCGTCTCACAAGACGCTGT 36 100 1 TTGCGATCAC 0.964251 -201 TTTAATGGAATGTGTAATTCAATTAACTAAATGAATT 38 147 1 TTGTAATAAC 0.463867 -145 TGTGGAATTATTTGCGGGTCGCGTCACATTTAATCAT 38 226 1 TTGCGGTCAC 0.740946 -66 * ***** **** Masking position 17 Map Score: 24.8969 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 107 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 2 TTCAATCAAGTGAAATTGATCACATA 2 93 1 TGATGTCACA 0.908726 -16 CCTGTGGTTATGACCCTCTTCACATTTCGGGCAA 7 101 0 TGACCTCACA 0.980236 -198 GTTAAATTACGGATCTTCATCACATAAAATAATT 8 140 1 GGATCTCACA 0.838524 -161 AGCAAAAGTTTGATGTGCTGCACAATTTTTTGCC 13 126 0 TGATCGCACA 0.893444 -175 AATTTTTCTTTGTGTCCCCTCACAAGGTCGACCT 16 73 1 TGTCCTCACA 0.953006 -146 CTCACAAGGTCGACCTGCGTCACACTTCCGTACA 16 91 1 CGATCTCACA 0.932964 -128 TAAGTTCTTATGACGCTCTTCACACTCTGCGAGT 20 47 1 TGACCTCACA 0.980239 -117 GTAGTAATTCCGTAGTTCTTCACAACTCTATCCA 23 104 1 CGTTCTCACA 0.857239 -197 AGATAAGGCGTGTTGTAGATCACAAATATTTATA 25 72 1 TGTTGTCACA 0.812002 -229 AATGGTTTTCTGATCTGATTCACAAAAGAAACAT 26 133 0 TGATATCACA 0.864289 -116 CATGGCGGTCTGTTGTGCGGCACAACGGGCCATT 29 33 1 TGTTCGCACA 0.780107 -85 GTACTGTTTCTCCTCACAACGTCTAAAA 30 28 0 TGTCCTCACA 0.955337 -18 AACAAAAATGTGACACTACTCACATTTAAATGCC 31 27 1 TGACATCACA 0.891943 -274 GTAATTGACGTGACGTTCATCACAAAACGCTTGT 31 98 0 TGATCTCACA 0.974527 -203 GCCTTTTGTGTGATATCAATCACATAAATATAGG 31 142 0 TGATATCACA 0.863568 -159 CAGCGTCTTGTGAGACGCGTCGCAAATTGACGGT 36 102 0 TGACCTCGCA 0.895022 -199 TCGCAAGTTATGAGGCGGATCGCATTTTTGTACT 36 159 1 TGACGTCGCA 0.739591 -142 GAATTATTTGCGGGTCGCGTCACATTTAATCATA 38 230 1 CGGCCTCACA 0.739872 -62 *** * * ***** Masking position 14 Map Score: 22.9667 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 77 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 TGAACTTTACTCGTTTTAGCCATTAATTAC 3 30 0 TCGTTTTAGC 0.780728 -265 TACCGTATACTCCTTTCAGCCACAAAAAAA 7 185 1 TCCTTTCAGC 0.861502 -114 CACAATCGAATCGATTCAGATAAGGGCTAC 8 219 0 TCGATTCAGA 0.777756 -82 ATCAGCAATTTCATTTCAGCAGCGTCAGCA 13 64 0 TCATTTCAGC 0.880962 -237 CATAATACTTCTGTTTCAGCACGCAAGGAA 13 175 0 CTGTTTCAGC 0.855666 -126 CTTTCTTGAAACGTTTCAGCGCGATCTTGT 13 205 1 ACGTTTCAGC 0.935538 -96 CTGAATTGAAACGATTCAGCCTCTATGAGA 13 266 0 ACGATTCAGC 0.916806 -35 CTGAATCGTTTCAATTCAGCAAGAGAGGAG 13 277 1 TCAATTCAGC 0.848932 -24 TTGATTCAGCCTGTCGGAAC 17 1 1 TTGATTCAGC 0.88953 -300 AATCATAAAATCGATTCAGCTTTGGCTTTT 17 82 0 TCGATTCAGC 0.977981 -219 TTTCTTAATTCCGTTTCAGCATCGGCATTT 22 178 1 CCGTTTCAGC 0.970326 -79 CAAGCTACTCTCGTTTCAGTGACTTTCATT 26 103 1 TCGTTTCAGT 0.920918 -146 ATCTTTCGTTTTGTTTCAGTTGATACTGCG 26 197 0 TTGTTTCAGT 0.678582 -52 GGACAGTTAACCGATTCAGTGCCAGATTTC 31 184 1 CCGATTCAGT 0.831744 -117 ********** Masking position 8 Map Score: 14.2224 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 231 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 CGCACTTTGCTACGGCTTCCCTATCGGGAGG 12 57 1 TACGGCTCCC 0.985578 -141 AAGGCAAAAAAACGGCCTCCCGATAGGGAAG 12 72 0 AACGGCTCCC 0.981093 -126 CTCATAACTTTACGGCTTTCCTTGCGTGCTG 13 158 1 TACGGCTTCC 0.9566 -143 GGGCAGTGACTACCGCTTCCTTGTGCGGGGC 21 62 0 TACCGCTCCT 0.873402 -194 TTTATTACCAAACGGCAACCTAATCTAATCA 21 210 0 AACGGCACCT 0.884819 -46 TATTTGTGAAACCGGTCACCTGAATATTTTT 22 82 0 ACCGGTACCT 0.478199 -175 GGTGAATAAAAACGGCTATCCACCCCTTCCT 23 145 1 AACGGCATCC 0.874947 -156 GAGAGTGGTTTACCGTCTTCCTGGAGTATGA 23 239 1 TACCGTTTCC 0.619614 -62 TTTTCAAAACACCGGTTTCCCTGCTCAATTG 25 208 1 ACCGGTTCCC 0.860925 -93 ATCTACAAGGTCCGGCTACCTCTGCCGCCAC 31 219 1 TCCGGCACCT 0.823186 -82 TCCCGGTACGGTTTTCTGTTTACAGGA 36 7 1 TACGGTTTCT 0.669259 -294 AGCGCACGGCAACGGCCTGCCATGTGACAAA 36 42 1 AACGGCTGCC 0.932775 -259 GACATGCCGGTACCGCATGCCACAAGGATCT 41 14 0 TACCGCTGCC 0.83895 -273 CAACAGTGATTACGGCATCCCTACGCTTAAT 41 183 1 TACGGCTCCC 0.985578 -104 ****** **** Masking position 3 Map Score: 11.0368 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 488 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 GTACAATTTGCAGCAAAATAAAAATACGGCTTGAA 1 242 1 CGAAAAAAAT 0.82511 -59 AACTCTTTGACGGGAAAATTTAAAATAAA 6 5 0 CGAAATAAAA 0.971484 -80 TAAATCAATACCGCAATATTTAAATTGCGGTTTTT 6 46 1 CGAAATAAAT 0.94608 -39 ATCCCTCTGTAACAATAAAAAGGACTATTT 10 7 1 CGAAATAAAA 0.971484 -24 TCAAAAGCGCCACGAATAGTCAAAATGCCATTTCA 13 14 1 CCAAATAAAA 0.927306 -287 AGCAGCCAATCAGCAACAGTGAAATGGCATTTTGA 13 33 0 CGAAATAAAT 0.94608 -268 ACGATTCAGCCTCTATGAGAAAAAAAGCGCCAACC 13 251 0 CCATAAAAAA 0.479786 -50 ATTGAATAAACTGTATGATTTAAAAGATTATCGGG 16 41 0 CGATATAAAA 0.901578 -178 TCTAATCAGATTGAAAGATTTAAAAGTGTTATTTT 21 183 0 TGAAATAAAA 0.658426 -73 TGACCGGTTTCACAAATATAAAAAATGAACAATTC 22 95 1 CCAAAAAAAA 0.774267 -162 TACCGTCCGGCGGTAAAAATAAAATACTCGTGCGG 25 250 0 CGAAATAAAT 0.94608 -51 CCGGACGGTACCCTAAAAATAAAATAAGGATAATT 25 275 1 CCAAATAAAT 0.867899 -26 TACCGCTTTGCGGCAAAACTCCAAAAAAAAACCTG 34 98 0 CGAAATCAAA 0.822137 -36 AAAATAGTGTCAGGATTAATCAAAACCAATCACAT 38 42 0 CGATATAAAA 0.901578 -250 ATATATTGCGCGGAAAAATTTAAAAACGGGAACGT 39 55 0 CGAAATAAAA 0.971484 -64 * * ** * * **** Masking position 8 Map Score: 11.3814 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 141 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 AGATAAAACGTTTTATCAAATTTTAGTGAGGCAT 4 102 0 TTTATCATTT 0.778094 -73 AATCATACAGTTTATTCAATTTTTCTTTGTGTCC 16 56 1 TTTTTCATTT 0.96503 -163 TCGCTATCCTTTTATTCAAACTTTCAAATTAAAA 21 126 1 TTTTTCATTT 0.96503 -130 AAGAGAGTGAATTGTTCATTTTTTATATTTGTGA 22 104 0 ATTTTCATTT 0.795209 -153 GATAGCCGTTTTTATTCACCTTTTCTGTGGATAG 23 131 0 TTTTTCATTT 0.96503 -170 ATCAAGCAATTTTTTTCAGGTTTTGCCCGCTTAG 34 44 0 TTTTTCATTT 0.96503 -90 GTCAGGCCGTTTTTTTCAGGTTTTTTTTTGGAGT 34 82 1 TTTTTCATTT 0.96503 -52 TCATTAATGGGTTATTCATTATTTTTGTGATTTA 35 119 0 GTTTTCATTT 0.851964 -182 TTACATTACATTTGTCCAGCTTTTGGCAGATTTG 36 69 0 TTTTCCATTT 0.913729 -232 AAATGGCCTTTTTATCCACTGTTTGCTCCGCCTG 36 212 1 TTTTCCATTT 0.913729 -89 GCAATGACCATTTTTTGACTTTTTGCCAGGGAAG 38 86 1 TTTTTGATTT 0.763186 -206 *** **** *** Masking position 8 Map Score: 8.55447 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 44 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TTACAGAACATCGGCAGTACAATTTGCAGC 1 226 1 TCGGCAGTAC 0.564679 -75 CGCCCAATTTTCGGCGGTGAACTTTACTCG 3 47 0 TCGGCGGTGA 0.875447 -248 CGCCGAAAATTGGGCGGTGAATAACCACGT 3 61 1 TGGGCGGTGA 0.860577 -234 AGCCTCGCCGTGTACAGGGCATCTAAGCGC 3 213 0 TGTACAGGGC 0.829172 -82 TATTCGACAGGGATAATTGTT 15 4 1 TCGACAGGGA 0.923912 -18 ACCGCTTCCTTGTGCGGGGCGTGATGCTTT 21 52 0 TGTGCGGGGC 0.944095 -204 CCTTGCACAATCGGCGGGAAAAATATTCAG 22 64 1 TCGGCGGGAA 0.819324 -193 TAAACCACTCTCTGCAGGGCATTACACACT 23 221 0 TCTGCAGGGC 0.959051 -80 TGAAAGCAATTGAGCAGGGAAACCGGTGTT 25 215 0 TGAGCAGGGA 0.917936 -86 GCAATTAGCATGTGCATGGCGGTCTGTTGT 29 19 1 TGTGCATGGC 0.688184 -99 TTTGACGAAGGCGGCAGGGATCGCAGAAGG 40 55 0 GCGGCAGGGA 0.874672 -76 GTCAAAAGTATCGACGGGGATCGCTACCAG 40 79 1 TCGACGGGGA 0.908844 -52 TTAACCCGAATCGGCATGGAGTCAACGACG 40 110 1 TCGGCATGGA 0.846655 -21 AGTTCCTGACTGAACAGGGCATTTCAGCCA 41 77 1 TGAACAGGGC 0.788479 -210 TTGATCCCTGTGAGCAGGGCGGCGCCATTA 41 210 0 TGAGCAGGGC 0.940443 -77 ********** Masking position 5 Map Score: 8.84097 Number of sites scoring better than the average of aligned sites = 1061 Number in coding regions = 973 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 8 AAACTTATTTTATCATTCAAAAAATCAGGTCGGA 1 63 0 TTCTCAAAAA 0.593067 -238 GCAGTACAATTTGCAGCAAAATAAAAATACGGCT 1 239 1 TGCGAAAAAA 0.741159 -62 TGAAACGTGATAGCCGTCAAACAAATTGGCACTG 3 149 1 TGCGCAAAAA 0.977514 -146 TAAAACGTTTTATCTGTCACATAATCAGGGAGTA 4 21 0 TTCGCACAAA 0.884641 -154 ATTTTAAATTTTCCCGTCAAAGAGTTATTTCATA 6 14 1 TCCGCAAAAG 0.946574 -71 CCTCTTCACATTTCGGGCAAATAATTCGCGAAGA 7 87 0 TTCGCAAAAA 0.956759 -212 CGTATACTCCTTTCAGCCACAAAAAAAGTCATGT 7 188 1 TTCGCACAAA 0.884641 -111 GCGGAGTGTCTGGCTGACAGATAATCGTCGATGA 7 265 1 TGCGCAGAAA 0.891149 -34 AAATCGCCGTTACCAGACAAATAATGCATTTACT 16 141 0 TCCGCAAAAA 0.972297 -78 ATATGTCCGTTTGCGGACAAGCAATAGATAAGGC 25 47 1 TGCGCAAGAA 0.872671 -254 TACCCGGGCTTGCAGGCAAAAAAGAGATCTAGA 33 12 0 TGCGCAAAAA 0.977512 -23 AACAACAACTTCCCTGGCAAAAAGTCAAAAAATG 38 94 0 TCCGCAAAAG 0.946574 -198 AGAGCGCTTATCCCCGGCAAAGAGCAATAACCCT 40 24 1 TCCGCAAAAG 0.946575 -107 * ** * **** ** Masking position 9 Map Score: 10.2614 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 119 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 TCAGGCCAAAAAAAACCGGCGCAATGGCCGGT 7 44 0 AAAAACGGGC 0.987434 -255 GGCTACAACCAAAAACCCCTGCGTTTCGCGAT 8 193 0 AAAAACCCGC 0.950796 -108 CATCCGGCATAAAAACACGCGCACTTTGCTAC 12 38 1 AAAAACCGGC 0.984482 -160 TGAAAGGCAAAAAAACGGCCTCCCGATAGGGA 12 74 0 AAAAACGCTC 0.72773 -124 CGCGTCTGTTAAAAACTGGCGCTAACAATACA 17 211 1 AAAAACGGGC 0.987434 -90 TTACTACGGGAAAACCCGGAGCATTCTGAATA 23 79 0 AAAACCGGGC 0.974626 -222 GGTAAAAATAAAATACTCGTGCGGTTTAATGA 25 242 0 AAATACCGGC 0.909098 -59 ACATTAACAAAAAACCTCGGGCTTCCAGCCTG 31 248 1 AAAACCCGGC 0.96876 -53 GGAAAAATTTAAAAACGGGAACGTTCCCGAAA 39 47 0 AAAAACGGAC 0.8977 -72 ****** ** ** Masking position 3 Map Score: 6.73071 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 98 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 AGAATTAATCCCGCTGTACGGAAGTGTGACGCA 16 106 0 CGTGTACGGA 0.974366 -113 CAAATAATTGCAGATGTATGGAATCATATATCC 20 116 0 CGTGTATGGA 0.831378 -48 GCATGGCGGTCTGTTGTGCGGCACAACGGGCCA 29 32 1 CGTGTGCGGA 0.992874 -86 CGGGATCCAGTTTTGCGGTAAAAC 32 5 0 CGTTTGCGGA 0.991408 -20 TTGCCCTCTACCGCTTTGCGGCAAAACTCCAAA 34 108 0 CGTTTGCGGA 0.991408 -26 AGTGAAAGGTCAGATTTGCGGAGTAATGCACAT 35 180 0 CGTTTGCGGG 0.972606 -121 TCACAAGACGCTGTTTTGCGGCATGCTTCCGGT 36 123 1 CGTTTGCGGA 0.991408 -178 * * ******* * Masking position 7 Map Score: 6.58231 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 39 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 GCCTGTCTGCGCAAATCCAGGTTACGCTTAA 1 27 0 GCAATCCAGG 0.924553 -274 AAAAACCGGCGCAATGGCCGGTTTCCGTTGT 7 35 0 GCAAGGCCGG 0.973011 -264 ACATTCGTTTGCAAAGGAAGGTAAATCTTTG 8 68 0 GCAAGGAAGG 0.823969 -233 AATTTATGCTGCCAGCCCAGGAGAGTGGAAG 20 11 0 GCCACCCAGG 0.88322 -153 TTTCTATTAAGCAAATGCAAGCCCACCTTGC 26 63 1 GCAATGCAAG 0.63961 -186 TTTTTTGCCTGCAAGCCCGGGTA 33 22 1 GCAACCCGGG 0.972638 -13 AGAGCGCACGGCAACGGCCTGCCATGTGACA 36 40 1 GCAAGGCCTG 0.779462 -261 GAAACAATAGGCAATCGCAGGCGGAGCAAAC 36 232 0 GCAACGCAGG 0.981677 -69 ATGGGCTTTCGCAAGCCCGGGAGCAGCTT 36 282 1 GCAACCCGGG 0.972638 -19 TCTCCCGCTCGCAAGGGCGGGTTCGCTTTCC 37 16 1 GCAAGGCGGG 0.981313 -35 **** ****** Masking position 4 Map Score: 6.5576 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 448 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TGCCCGAAATGTGAAGAGGGTCATAACCACAG 7 102 1 GTGAGAGGTC 0.968363 -197 AGGTTAAGGCTTGCGGAGTGTCTGGCTGACAG 7 253 1 TTGCGAGGTC 0.610682 -46 ATTATTTTATGTGATGAAGATCCGTAATTTAA 8 141 0 GTGAGAAATC 0.881774 -160 GCAAAAAATTGTGCAGCACATCAAACTTTTGC 13 127 1 GTGCGCAATC 0.846118 -174 GTACGGAAGTGTGACGCAGGTCGACCTTGTGA 16 92 0 GTGAGCAGTC 0.960529 -127 TGCGCTCTTCGTGCGTCGCGTCTGTTAAAAAC 17 195 1 GTGCTCGGTC 0.867773 -106 CTCGCAGAGTGTGAAGAGCGTCATAAGAACTT 20 48 0 GTGAGAGGTC 0.968363 -116 CACAGAAAAGGTGAATAAAAACGGCTATCCAC 23 136 1 GTGATAAAAC 0.350423 -165 TGTTTCTTTTGTGAATCAGATCAGAAAACCAT 26 134 1 GTGATCAATC 0.756901 -115 ATGGCCCGTTGTGCCGCACAACAGACCGCCAT 29 34 0 GTGCGCAAAC 0.577564 -84 TTTAGACGTTGTGAGGAGAAACAGTAC 30 29 1 GTGAGAGAAC 0.769945 -17 GCATTTAAATGTGAGTAGTGTCACATTTTTGT 31 28 0 GTGATAGGTC 0.899013 -273 CAAGCGTTTTGTGATGAACGTCACGTCAATTA 31 99 1 GTGAGAAGTC 0.944332 -202 AAAAAATTGCTTGATTCACGTCAGGCCGTTTT 34 63 1 TTGATCAGTC 0.414022 -71 GAGCGATTAAGTGATGAGAGGCGATATGTCGG 35 236 0 GTGAGAGGGC 0.817017 -65 ACAGCGTCTTGTGAGACGCGTCGCAAATTGAC 36 105 0 GTGAACGGTC 0.759166 -196 ATCGCAAGTTATGAGGCGGATCGCATTTTTGT 36 158 1 ATGAGCGATC 0.522207 -143 **** *** *** Masking position 2 Map Score: 9.97653 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 576 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 13 GTTTTCTGGTTTAGCCAGTAAAAGGGAGTG 1 93 1 TTAGCCAGTA 0.82412 -208 CCCGATAAATTCATCCTGTAAATAATACAA 2 47 1 TCATCCTGTA 0.876354 -62 TGTACTTCTCCTGTTTACGTAAGAC 9 48 0 TTCTCCTGTT 0.844438 -15 GCGGGATTAATTCTCCAGTAAATGCATTAT 16 125 1 TTCTCCAGTA 0.844435 -94 CAGCTTTGGCTTTTCCTGTAACGATTAATT 17 66 0 TTTTCCTGTA 0.862972 -235 CGGTTCGACTTTAGCCTGTATTGTTAGCGC 17 229 0 TTAGCCTGTA 0.936821 -72 CGGATTTTATCCTGTTATCAGTAGGG 22 241 0 TTATCCTGTT 0.905536 -16 AATATTATCCTGTAGAGGAGAGAG 24 14 0 TTATCCTGTA 0.968087 -14 CCGTGCGCTCTTATCCTGTAAACAGAAAAC 36 21 0 TTATCCTGTA 0.968087 -280 ********** Masking position 9 Map Score: 5.56773 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 28 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 GACAAAACTCACAAAAGACACGCGTTTAAT 1 141 1 ACAAAAGACA 0.673896 -160 TTCAGCCACAAAAAAAGTCATGTTGGTTTC 7 199 1 AAAAAAGTCA 0.598603 -100 TGAAAGGCAAAAAAACGGCCTCCCGATAGG 12 76 0 AAAAACGGCC 0.904901 -122 TAACGATCACAAAAACGACAATATGAAAAT 12 117 0 AAAAACGACA 0.716731 -81 GAAATCGAAAACAAACGACAGGAT 12 184 1 ACAAACGACA 0.820319 -14 AGCAATTAGGAAAAATGGCAAAAAATTGTG 13 110 1 AAAAATGGCA 0.85191 -191 TGTTTTATTACCAAACGGCAACCTAATCTA 21 214 0 CCAAACGGCA 0.731891 -42 TTGTGCAAGGACAATCGGCAAACGGTGCAG 22 44 0 ACAATCGGCA 0.775783 -213 AAAGGTGAATAAAAACGGCTATCCACCCCT 23 142 1 AAAAACGGCT 0.595476 -159 AGATATAACAACAAATGTCAATACCGCATA 25 141 0 ACAAATGTCA 0.729058 -160 CATTAACCGTACAAATGGCCCGTTGTGCCG 29 50 0 ACAAATGGCC 0.885994 -68 GATTTTCGCTAAAAATGGCATTTAAATGTG 31 47 0 AAAAATGGCA 0.85191 -254 TTGATATCACACAAAAGGCCGTCGACTGGA 31 157 1 ACAAAAGGCC 0.885994 -144 AAAACCTGAAAAAAACGGCCTGACGTGAAT 34 76 0 AAAAACGGCC 0.904901 -58 TACTGATATTACAAAAGTCCAGTAAATGGC 36 189 1 ACAAAAGTCC 0.668287 -112 GATGGAGGAAACAATAGGCAATCGCAGGCG 36 240 0 ACAATAGGCA 0.610309 -61 GCAGCCAACCAAAAATGTCATCTGCCATGG 39 93 1 AAAAATGTCA 0.598603 -26 ********** Masking position 4 Map Score: 12.4066 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 387 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 15 GACACGCGTTTAATTTGCGATACGAATTAAA 1 157 1 TAATTGCGAT 0.968302 -144 CCGCAATATTTAAATTGCGGTTTTTAAGGGT 6 56 1 TAATTGCGGT 0.877109 -29 TTCGGGCAAATAATTCGCGAAGATAATTAAG 7 79 0 TAATCGCGAA 0.886785 -220 ATGCTCTGGGTAACTTGCGAAACCAACATGA 7 216 0 TAATTGCGAA 0.94126 -83 ATCCGTAATTTAACTTTCGATTAGCAGAAAT 8 123 0 TAATTTCGAT 0.857454 -178 ATATCTAAAATAAATCGCGAAACGCAGGGGT 8 180 1 TAATCGCGAA 0.886785 -121 CACAATATTTTAAATTTCGATTTGAAAAATT 35 39 1 TAATTTCGAT 0.857454 -262 ATCCGCCTCATAACTTGCGATAAACCGGAAG 36 148 0 TAATTGCGAT 0.968302 -153 TCCTGAACGATAAATTGTGATCTTCGCTGCG 39 16 1 TAATTGTGAT 0.749671 -103 *** ******* Masking position 5 Map Score: 5.33975 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555