AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_ecoli_reg_100.orf -o00640_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 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #2 dnaE 36 DNA polymerase III, alpha subunit #3 sdhC 300 succinate dehydrogenase, cytochrome b556 #4 BIME45 63 BIME #5 sucC 85 succinyl-CoA synthetase, beta subunit #6 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #7 goaG 37 4-aminobutyrate aminotransferase #8 ydbO 284 orf, hypothetical protein #9 fliY 87 putative periplasmic binding transport protein #10 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #11 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #12 atoB 30 acetyl-CoA acetyltransferase #13 ackA 300 acetate kinase #14 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #15 b2659 230 orf, hypothetical protein #16 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #17 yqeF 251 putative acyltransferase #18 sbm 203 methylmalonyl-CoA mutase (MCM) #19 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #20 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #21 acs 300 acetyl-CoA synthetase Motif number 1 TGCATTAATGTTTTCCGCAGTTGCTATACA 8 108 0 TTTTCCGCAG 0.891252 -177 GGCGGGGTTTTTTTCTGCCTGGAATTTACC 10 53 1 TTTTCTGCCT 0.947368 -126 ATGATTATCCGTTTCTGCAGGGTTTTTAAT 10 126 0 GTTTCTGCAG 0.851833 -53 CACTGTGCAAATTTCTGCATAGCAAGTTTT 11 15 0 ATTTCTGCAT 0.824217 -181 CAGTGCGCAATTTTCTGCATAGCCGCTCAT 11 40 1 TTTTCTGCAT 0.918141 -156 ACTGCAAATTTTTTTTGCATGATGGAAGAA 13 187 0 TTTTTTGCAT 0.825178 -114 GCATAATGCCATTTTTGCCCCCAACAGACC 14 84 0 ATTTTTGCCC 0.83396 -72 TTTAATGTTATATCTGCCCCGATAAAACG 15 10 1 ATATCTGCCC 0.762426 -221 ACTAAACATATTATCTGCCCCGTTTTATCG 15 30 0 TTATCTGCCC 0.88475 -201 TCAGACGTCGTTTTTTGCCGCCTGAGATTT 18 94 0 TTTTTTGCCG 0.953741 -110 TGAATGCATTTTTTTTGCTGGCGACAAACC 18 121 1 TTTTTTGCTG 0.697182 -83 CAATGTCACCTTTTCCGCAGCGCAAAAACT 19 64 0 TTTTCCGCAG 0.891252 -237 GTATATTTTGTTTTTTGCCGGAGGATAGCA 19 105 1 TTTTTTGCCG 0.953741 -196 CCAGAGCGTGATTTCTGCCGAGCGTGATCA 20 67 1 ATTTCTGCCG 0.953446 -123 ACCCTGCCGTTTATTTGCACAATTCTACTT 21 181 1 TTATTTGCAC 0.668116 -120 ********** Masking position 4 Map Score: 13.9157 Number of sites scoring better than the average of aligned sites = 956 Number in coding regions = 847 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 2 AATAATAACACGGCCTGCCGCAATCGTAAGAATGAGAC 1 45 0 CGCCTGCGAA 0.98254 -60 ATGCAAAACACTGCTTCCAGATGCGAAAACGACACGTT 3 132 0 CGCTTCCGTA 0.769392 -169 TTCCTCCGGTCTGCTTGCGGGTCAGACAGCGTCCTTTC 3 184 0 CGCTTGCGTA 0.975481 -117 TGCGCTTACCCGGCTTACAGAACAAAAAGA 6 3 0 CGCTTACGAA 0.664451 -272 GCTCACTTGCCGCCTTGATGCAACTTGAATGATTTTGT 6 61 0 CCCTTGAGAA 0.937415 -214 AAGGCAGAGGCGGCTTGAAGGATGAAGTGTATATAAAG 6 150 1 CGCTTGAGAT 0.870181 -125 GGGATCTCTGCGCCCTGACGTTCACAAACTGCATATAT 6 221 1 CCCCTGAGTA 0.964764 -54 TTCTGGCACTCCCCTTGCTATTGCCTGACTGTACCCAC 11 142 1 CCCTTGCATA 0.75643 -54 TATCCTTTAGCAGCCTGAAGGCCTAAGTAGTACATATT 13 76 1 CGCCTGAGCT 0.741124 -225 CGCTCTATGGCTCCCTGACGTTTTTTTAGCCACGTATC 13 257 1 CCCCTGAGTA 0.964764 -44 AGTTATGTCTCTGACTGCTGCTCAGGCATATTTCCTTT 17 140 1 CGACTGCGTA 0.771766 -112 TCGTTTTTTGCCGCCTGAGATTTGTCTATTTTGTGATG 18 79 0 CGCCTGAATA 0.777371 -125 CGACCTCGTCCTCCCTGACGCAGTTTTTGCGCTGCGGA 19 43 1 CCCCTGAGAT 0.893988 -258 ACCGGCGTCCCGGCCTGCTGGAATTTATCGCTATGCAT 19 191 1 CGCCTGCGAT 0.951698 -110 ACGACCAGATCACCTTGCGGATTCAGGAGACTGAC 20 165 1 CCCTTGCGTA 0.968873 -25 GCTTTTGTTCTCCTTGTAGGATGTTAATAATATGTGG 21 274 0 CCCTTGTGAA 0.728572 -27 * ****** * * * Masking position 6 Map Score: 13.322 Number of sites scoring better than the average of aligned sites = 1588 Number in coding regions = 1497 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 CTTCAGATTCCGGTTTACTTAATC 2 23 0 TCAGTTCGGT 0.89879 -14 GAACAGCCTATACTGCCGCCAGGTCTCCGGAAC 3 69 1 TCTGCGCAGG 0.785019 -232 GCTGGGTGGCTCGGGATTGCAGGGTGTTCCGGA 3 94 0 TGGGTTCAGG 0.869008 -207 TTCTGTTACCTGGAGACGTCGGGATTTCCTTCC 3 218 0 TGAGCGCGGG 0.976039 -83 TATTATTCCCTGGGGACTACGGGCACAGAGGTT 3 255 0 TGGGCTCGGG 0.983633 -46 TAATGCCTTATCCGGTCTACAGTGCAGGTGAAA 4 20 0 TCGGCTCAGT 0.92675 -44 ATACGAAATATTCGGTCTACGGTTTAAAAGATA 5 36 1 TCGGCTCGGT 0.977528 -50 CCTTTACGATTCCAGTTTTCGTGAATTAATTAA 8 255 0 TCAGTTCGTG 0.645069 -30 AAAAAAACCCCGCCGGTGGCGGGGAAGCACGTT 10 34 0 CCCGTGCGGG 0.764449 -145 AGGGGTTATTTGGGGGTTACAGGTAAATTCCAG 10 71 0 TGGGTTCAGG 0.869008 -108 TATGTACTACTTAGGCCTTCAGGCTGCTAAAGG 13 79 0 TAGGCTCAGG 0.693935 -222 AAAAAATGCATTCAGACGTCGTTTTTTGCCGCC 18 102 0 TCAGCGCGTT 0.746302 -102 ATGAGGGTATTTGCGCCTACGGTGAGCTTTTTA 18 155 0 TGCGCTCGGT 0.89924 -49 TTCCAGCAGGCCGGGACGCCGGTCTATTTTGCC 19 181 0 CGGGCGCGGT 0.901589 -120 TCGCTATGCATACAGCTGTCGGGGCATACGCTT 19 218 1 TCAGTGCGGG 0.95825 -83 GCATACGCTTTACAGACGGCGGTGAAACGCCTG 19 241 1 TCAGCGCGGT 0.967195 -60 * *** ** **** Masking position 5 Map Score: 12.3815 Number of sites scoring better than the average of aligned sites = 1597 Number in coding regions = 1476 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 4 ATTGCGGCAGGCCGTGTTATTATTGTCGTTTC 1 59 1 GCGTGTTTTA 0.812802 -46 ATAAGATGTAGCGGAGTTGTTTTTGTGTTTAC 9 17 1 GCGAGTTTTT 0.965239 -71 CCCGCCACCGGCGGGGTTTTTTTCTGCCTGGA 10 44 1 GCGGGTTTTT 0.989941 -135 TGGGTGAAATGAGGGGTTATTTGGGGGTTACA 10 83 0 GAGGGTTTTT 0.895813 -96 ATCCGTTTCTGCAGGGTTTTTAATCGGACGAT 10 118 0 GCGGGTTTTA 0.956616 -61 CTCATATAACGCAGGGCTGTTTATC 10 164 1 GCGGGCTTTT 0.987799 -15 TGGTCGAACCGCGGAGTTACTTT 14 2 0 GCGAGTTCTT 0.826597 -154 TAAACAAAATGGAGGGCAATTTACCATAAACC 17 35 1 GGGGGCATTT 0.812126 -217 TTGCGCCTACGGTGAGCTTTTTACGTGGGTTT 18 146 0 GGGAGCTTTT 0.84481 -58 AGGCCGGGACGCCGGTCTATTTTGCCCCAGAG 19 175 0 GCGGTCTTTT 0.918359 -126 CAAATAAACGGCAGGGTAATTTTTGAAGGTCA 21 166 0 GCGGGTATTT 0.956616 -135 AGGGGTATTGGCAGTTTTGTTTAGTATTTGGG 21 226 0 GCGTTTTTTT 0.729182 -75 ** ***** *** Masking position 11 Map Score: 10.3728 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 553 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 ATTGCGGCAGGCCGTGTTATTATTGTCGTT 1 59 1 GCCGTGTTAT 0.818473 -46 CATATAGTTTGTCGGGTTTTATCCTGAACA 3 16 0 GTCGGGTTTT 0.954921 -285 GCTCGGGATTGCAGGGTGTTCCGGAGACCT 3 89 0 GCAGGGTGTT 0.933601 -212 GCATCTGGAAGCAGTGTTTTGCATGACGCG 3 146 1 GCAGTGTTTT 0.90264 -155 ACCTGGAGACGTCGGGATTTCCTTCCTCCG 3 214 0 GTCGGGATTT 0.748787 -87 CCCGCCACCGGCGGGGTTTTTTTCTGCCTG 10 44 1 GCGGGGTTTT 0.971492 -135 TGGGTGAAATGAGGGGTTATTTGGGGGTTA 10 85 0 GAGGGGTTAT 0.722697 -94 ATCCGTTTCTGCAGGGTTTTTAATCGGACG 10 120 0 GCAGGGTTTT 0.983655 -59 AACATTTAACGTAGGGTATTAAGGCAAAGT 15 174 0 GTAGGGTATT 0.877134 -57 CAAATAAACGGCAGGGTAATTTTTGAAGGT 21 168 0 GCAGGGTAAT 0.907946 -133 AGCGTTAAATGTAGGGGTATTGGCAGTTTT 21 240 0 GTAGGGGTAT 0.75949 -61 ********** Masking position 10 Map Score: 6.30676 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 518 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 AAGTTTCACCTGCACTGTAGACCGGATAAGG 4 17 1 TGCACTGAGA 0.949127 -47 CTTTTGACTCTTCACGGTTAATCGGAAA 7 8 0 TTCACGGTAA 0.827265 -30 AAAACATTAATGCACTGATAAATAATGATTT 8 124 1 TGCACTGTAA 0.978977 -161 ACAATGGCTCTACACTGCAAACAGACATAAC 9 51 1 TACACTGAAA 0.920767 -37 ATTAACATCATGCACTGCAAATTTTTTTTGC 13 199 0 TGCACTGAAA 0.983775 -102 AGTAAATGGCTTCACTGCAAAATGACCGTTA 15 64 0 TTCACTGAAA 0.953396 -167 CATTTACTATTGCACTGTTAATTGGTGCGAG 17 228 1 TGCACTGTAA 0.978889 -24 ******* *** Masking position 4 Map Score: 4.93244 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TCCGGTCTGCTTGCGGGTCAGACAGCGTCCT 3 187 0 TTCGGGTCAG 0.904505 -114 TTCAATTGCCGGAGAAGGCGATAATGC 4 47 0 TGCGGAGAAG 0.957606 -17 TTGTTCTGTAAGCCGGGTAAGCGCAATGCGC 6 16 1 AGCGGGTAAG 0.790476 -259 CAGGTAAGTGATTCGGGGGAGCGAACGCAGC 6 118 1 ATCGGGGGAG 0.896523 -157 ACCCCGCCGGTGGCGGGGAAGCACGTTGCTG 10 30 0 TGCGGGGAAG 0.983995 -149 TGCCCCGTTTTATCGGGGCAGATATAACATT 15 14 0 TACGGGGCAG 0.977224 -217 TGCCCCGATAAAACGGGGCAGATAATATGTT 15 25 1 AACGGGGCAG 0.944722 -206 AAAGGAAATATGCCTGAGCAGCAGTCAGAGA 17 147 0 TGCTGAGCAG 0.84449 -105 TGATTGCGTTTTACGGAGCAAATA 18 190 1 TTCGGAGCAA 0.688897 -14 TTTTGTTTTTTGCCGGAGGATAGCAGCAGAT 19 110 1 TGCGGAGGAT 0.808254 -191 TGCATACAGCTGTCGGGGCATACGCTTTACA 19 224 1 TGCGGGGCAT 0.970086 -77 ** ******** Masking position 10 Map Score: 6.64404 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 626 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 8 AAAGTTACACAATAGTTAAGTAAAATCACAAATTTTGTATG 8 190 0 ATATACACAA 0.874976 -95 TGCAGTGTAGAGCCATTGTTTGTAAACACAAAAACAACTCC 9 29 0 ATGTACACAA 0.986185 -59 ACAGTGCGCAATTTTCTGCATAGCCGCTCATTCTCCTTATA 11 39 1 ATGTCCTCAT 0.74262 -157 TCCCCTTGCTATTGCCTGACTGTACCCACAACGGTGTATGC 11 151 1 ATGTCCACAA 0.972141 -45 AATGTTACTAATTTGTTGCTTTTGATCACAATAAGAAAACA 15 198 1 ATGTACACAA 0.986166 -33 AATTGTTTAAAAAAAGTGATTTTTATCACAAAGGAAATATG 17 166 0 ATGTACACAA 0.986185 -86 TCCATCAAATAATGCCTGATAGCACATATCAGGCGTT 18 7 1 ATGTACACAT 0.973989 -197 TTCTTTTTGTATTCCTTGAATCACATCACAAAATAGACAAA 18 56 1 ATGTACACAA 0.986185 -148 TTTGACCTTAAGTCTCCGCATCTTAGCACATCGTTCATCCA 20 29 1 ACGTACACAT 0.897429 -161 * ** * * ***** Masking position 11 Map Score: 5.13313 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 14 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 TCTTATATTTTGACAGGAAGAGTATC 1 89 1 TGACAGGAAG 0.867118 -16 GAGATTAAGTAAACCGGAATCTGAAG 2 21 1 AAACCGGAAT 0.708421 -16 ACCCGCAAGCAGACCGGAGGAAGGAAATCC 3 200 1 AGACCGGAGG 0.946352 -101 CGTCTCCAGGTAACAGAAAGTTAACCTCTG 3 233 1 TAACAGAAAG 0.645005 -68 CCTGCACTGTAGACCGGATAAGGCATTATC 4 25 1 AGACCGGATA 0.507481 -39 GATAGACGTGAAACAGGAGTCATA 6 261 1 AAACAGGAGT 0.824833 -14 GCACCCCTACAAACAGAAGGAATATAAA 12 13 1 AAACAGAAGG 0.897811 -18 AACCAGGTTCAGACAGAAAGGTCCCTA 14 139 1 AGACAGAAAG 0.90379 -17 AGGCAAAGTGAGACAGGAAATGAATAACTA 15 153 0 AGACAGGAAA 0.834294 -78 CCTTTGAAAACAGGATGTAGCG 16 8 1 AAACAGGATG 0.902001 -15 AAGGTCAAAAAAACAGAAGGGTAAAAA 20 8 0 AAACAGAAGG 0.897811 -182 TGCTGTTGAAAAAGAGGAAGATACTGACTA 21 92 0 AAAGAGGAAG 0.727798 -209 ********** Masking position 3 Map Score: 4.89596 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 435 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 10 GTGTTCTGTCCATCCTTCAGTAATCGTT 5 68 0 TGTCATCCTC 0.945005 -18 CCCGGCAATCTATACACAAAATCATTCAAGTTGCATC 6 46 1 TATAATCATC 0.811804 -229 ACATTCTTTATATACACTTCATCCTTCAAGCCGCCTC 6 156 0 TATCATCCTC 0.972341 -119 TATGCCCGTTTATTTCTGGCGACATTCTTTATATACA 6 177 0 TATCGACATC 0.823396 -98 AGACTCAAGATATTTCTTCCATCATGCAAAAAAAATT 13 174 1 TATCATCATC 0.980148 -127 CACCGACATTTATGATTAACATCATGCACTGCAAATT 13 207 0 TATCATCATC 0.980148 -94 TAATCATAAATGTCGGTGTCATCATGCGCTACGCTCT 13 226 1 TGTCATCATC 0.960213 -75 GCTGTTATGTTTTAATGTGCAACATTCATGGTCTGTT 14 55 1 TTTCAACATC 0.800257 -101 ACTTACAATTGATTAAAGACAACATTCACAGTGTGGT 21 31 0 GATCAACATC 0.823392 -270 TTATGCCACATATTATTAACATCCTACAAGGAGAACA 21 269 1 TATCATCCTC 0.972341 -32 *** ****** * Masking position 3 Map Score: 4.27155 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 82 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 TCAAATTCATATACATTATGCCATTGGCTGA 13 124 1 ATCATTATGC 0.736224 -177 CTTGAGTCTATGCCATTTTGCGTAATTTTCA 13 152 0 TGCATTTTGC 0.947484 -149 AAGATATTTCTTCCATCATGCAAAAAAAATT 13 180 1 TTCATCATGC 0.917282 -121 CATTTATGATTAACATCATGCACTGCAAATT 13 207 0 TACATCATGC 0.862802 -94 TAAATGTCGGTGTCATCATGCGCTACGCTCT 13 232 1 TGCATCATGC 0.975991 -69 GGGGCAAAAATGGCATTATGCGTCCCCAAAG 14 93 1 TGCATTATGC 0.976455 -63 GTTTACTAACGGTCATTTTGCAGTGAAGCCA 15 58 1 GGCATTTTGC 0.923899 -173 TAGACTTGACGGACATTGTGCAGCGATCTGC 19 135 0 GGCATTGTGC 0.910454 -166 ** ******** Masking position 5 Map Score: 2.77732 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 142 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CGTTCCATCTTTTGTTCGCCAAACTTT 1 8 1 TCTTTTGTTC 0.745105 -97 TAATTGTAATGATTTTGTGAACAGCCTATA 3 51 1 GATTTTGTGA 0.82468 -250 CAACTTGAATGATTTTGTGTATAGATTGCC 6 49 0 GATTTTGTGT 0.927793 -226 TAGCGGAGTTGTTTTTGTGTTTACAAACAA 9 25 1 GTTTTTGTGT 0.727339 -63 AATTGCCCTCCATTTTGTTTAATTTGTAGA 17 26 0 CATTTTGTTT 0.695897 -226 GAGATTTGTCTATTTTGTGATGTGATTCAA 18 71 0 TATTTTGTGA 0.785115 -133 AACGAAGGTATATTTTGTTTTTTGCCGGAG 19 98 1 TATTTTGTTT 0.862229 -203 ATTTCTTTAATCTTTTGTTTGCATATTTTT 20 104 1 TCTTTTGTTT 0.83772 -86 TCGAAGTGTGTATTTTGTGTTAAAAATATG 20 125 0 TATTTTGTGT 0.908928 -65 GCTTTTGTTCTCCTTGTAGG 21 291 0 GCTTTTGTTC 0.790067 -10 ********** Masking position 5 Map Score: 2.77429 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 118 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 13 TGGCGGCAGTATAGGCTGTTCACAAAATCA 3 60 0 ATAGGCTGTT 0.789925 -241 AATAACGCCCACATGCTGTTCTTATTATTC 3 280 0 ACATGCTGTT 0.984099 -21 TCTATCAGATATATGCAGTTTGTGAACGTC 6 237 0 ATATGCAGTT 0.898178 -38 AATTTGCAGTGCATGATGTTAATCATAAAT 13 207 1 GCATGATGTT 0.796499 -94 CGCTACATCCTGTTTTCAAAGG 16 9 0 ACATCCTGTT 0.911066 -14 GTGGTATTTTACATGCACTTACAATTGATT 21 54 0 ACATGCACTT 0.864567 -247 ATGCAGTTATGCATGCTGTTGAAAAAGAGG 21 105 0 GCATGCTGTT 0.97226 -196 TCTTTGAGGAACATGCAGTTATGCATGCTG 21 117 0 ACATGCAGTT 0.974694 -184 ********** Masking position 3 Map Score: 3.75653 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 190 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 ATCATTACAATTAACCTACATATAGTTTGTCG 3 32 0 TTACCTCATA 0.562585 -269 AACCCCCAAATAACCCCTCATTTCACCCACTA 10 86 1 TACCCCCATT 0.962897 -93 GATAAACAGCCCTGCGTTATATGAGTTA 10 161 0 CACCCTCGTT 0.917756 -18 ATTTTCTGCATAGCCGCTCATTCTCCTTATAA 11 49 1 TACCGCCATT 0.734035 -147 CCATCCAATTTATCCCTTCATATTCAATTAGT 11 85 1 TACCCTCATA 0.918139 -111 CTTTGCCTTAATACCCTACGTTAAATGTTACT 15 175 1 ATCCCTCGTT 0.719484 -56 TTATGGTAAATTGCCCTCCATTTTGTTTAATT 17 32 0 TTCCCTCATT 0.918139 -220 ACGCCCTATCTACCCCTCTATTGGTGGGTTAG 17 87 1 TACCCTTATT 0.693583 -165 TTGCTGGCGACAAACCCACGTAAAAAGCTCAC 18 135 1 CAACCCCGTA 0.51284 -69 CGTAGGCGCAAATACCCTCATTTTGATTGCGT 18 167 1 AAACCCCATT 0.699416 -37 AAAAACAAAATATACCTTCGTTGCGCCAATGT 19 88 0 TAACCTCGTT 0.893284 -213 AAACTGCCAATACCCCTACATTTAACGCTTAT 21 241 1 TACCCTCATT 0.969275 -60 ** **** **** Masking position 11 Map Score: 2.03941 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 237 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 15 TAGTTTAAGTTTCACCTGCACTGTAG 4 7 1 AAGTTTCACC 0.822737 -57 AAAATCATTCAAGTTGCATCAAGGCGGCAA 6 63 1 AAGTTGCATC 0.625181 -212 TACTCTCCAGATGTTTCACATTTCTGTTGC 8 14 1 ATGTTTCACA 0.8328 -271 TGTTTTATGAAAGTTACACAATAGTTAAGT 8 210 0 AAGTTACACA 0.904719 -75 GCTATGCAGAAATTTGCACAGTGCGCAATT 11 22 1 AATTTGCACA 0.919405 -174 CTGAGTTGTGAATTTGCACA 13 1 0 AATTTGCACA 0.919405 -300 CAGACCATGAATGTTGCACATTAAAACATA 14 60 0 ATGTTGCACA 0.948075 -96 GTGTGGTTATTTGTTACACATAGGGGC 21 8 0 TTGTTACACA 0.611497 -293 CCCTGCCGTTTATTTGCACAATTCTACTTT 21 182 1 TATTTGCACA 0.78284 -119 ********** Masking position 5 Map Score: 2.19886 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 181 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529