AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_ecoli_reg_300.orf -o00680_ecoli_300.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 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #2 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #3 yaiN 166 putative alpha helix chain #4 hyaA 300 hydrogenase-1 small subunit #5 torC 129 trimethylamine N-oxide reductase, cytochrome c-type subunit #6 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #7 katE 182 catalase; hydroperoxidase HPII(III) #8 glyA 300 serine hydroxymethyltransferase #9 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #10 hycA 211 transcriptional repression of hyc and hyp operons #11 pepP 25 proline aminopeptidase P II #12 ygfB 161 orf, hypothetical protein #13 b2997 188 putative hydrogenase subunit #14 b2998 118 orf, hypothetical protein #15 b3000 205 orf, hypothetical protein #16 fdoG 193 formate dehydrogenase-O, major subunit #17 metB 276 cystathionine gamma-synthase #18 BIME202 79 BIME #19 metF 234 5,10-methylenetetrahydrofolate reductase #20 katG 300 catalase; hydroperoxidase HPI(I) #21 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #22 yjcQ 140 putative enzyme #23 yjcR 300 putative membrane protein Motif number 1 GCTGTACTGTGCGCGCAACGACATTTTGTCCGAGTCG 1 38 1 GCCCCCATTT 0.97384 -39 CCGGCTAAACATCCCCACCGCCCGGCCAAAAGAAAAA 4 40 1 ATCCCCCGGC 0.873013 -261 CCGACCATAAGCGCCCGGTGTCCTGCCGGTGTCGCAA 4 256 1 GCCCTCCTGC 0.89724 -45 CGGTAGAAAAACGCACCACTGCCTGACAGGCCAGTTA 6 69 0 ACCCCCCTGC 0.981956 -163 GTCATTTTCGACACTCATCGACACGCCCATCCCCAAA 9 47 0 ACCCCCACGC 0.918486 -78 CTTCGTTTTAGCGCCCCGCCGCAGTATCATGATATCG 13 61 1 GCCCCCAGTT 0.968329 -128 AGATAAGAACACACACACCAACATTATGGTATTCTGT 16 23 1 ACCCCCATTT 0.958592 -171 TACGGTCAGTACCCACATCAACTGTGTGGTCTGGTCT 17 42 0 ACCCCCTGTT 0.82509 -235 TTTTCGGTTGACGCCCTTCGGCTTTTCCTTCATCTTT 19 137 1 ACCCCCTTTC 0.878607 -98 CAATGTGCTCCCCTCTACAGTGTTACCGTTACG 20 278 0 GCCCCCAGTT 0.968329 -23 TCACGTCAAAACTGACGACAGCCTGTTTTTCGTCAGA 21 53 1 ACGCCCCTGT 0.771875 -145 ACGCATACGCGCTCTCGACTACAGTATGCATCTTTTA 21 146 0 GCCCCCAGTT 0.968329 -52 TGAGCGCGCTCAACTCCCTGCCATTACCGGTG 22 6 1 GCCCCCCTGC 0.988702 -135 TATGCCAACAGTTCTCTCTCGCATGGCGATGCAACTC 23 16 1 GTCCTCATGC 0.596204 -285 AGCCTGGATAATTCCCGTCTTCATGGTTTCGGGATGC 23 61 1 ATCCCCATGT 0.879569 -240 CGCCCTTTTTGCTCTCTACGCCATGCTGTTCTGGCTG 23 244 1 GCCCCCATGT 0.987073 -57 ** * * * **** * Masking position 6 Map Score: 15.8047 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 1046 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 GGCAGGGAAGGCCGCCCCGGATAGCGGGCGGCAGAAGGAA 3 9 0 GCGGAGCGGC 0.74538 -158 AAAGAGGAAAGGGGGGGGGGCTAATCGGCAGGGAAGGCCGCC 3 35 0 GGGGCGCAGG 0.985794 -132 CTTTTGGCCGGGCGGTGGGGATGTTTAGCCGGTTGCTAAACG 4 30 0 GGGGAGCCGG 0.966744 -271 TTATGGTCGGCAAGCGACGTCCCTGTAGCAAGGCAAACCATC 4 224 0 CAGGCGCAAG 0.747358 -77 ATAAGCGCCCGGTGTCCTGCCGGTGTCGCAAGGAGGAGAGAC 4 262 1 GGGGCGCAAG 0.873924 -39 GCTCGCTGTTTTGTCTCTCTTGCCGTTAAAAATTAA 6 5 1 GCGGCGCCGT 0.902943 -227 AACACCGTTTCCAGAATAGTCTCCGAAGCGGGATCTGGCTGG 7 80 1 CCGGCGCGGG 0.967075 -103 GCTGAGGCTTTGCCCGTTTTGCAGGCGTTACGCCT 9 4 1 GAGGCGCAGG 0.967313 -121 TATGGTTATCGATATCATGATACTGCGGCGGGGCGCTAAAAC 13 65 0 GAAGTGCGGG 0.621908 -124 CACGGTAACGCCTGTACGGTAAACTATGCGGGTTTACGGTCA 17 71 0 CCGGAGCGGG 0.871465 -206 AGCACAAAATGCTGCCTCGAAATGAGGGCGGGAAAATAAGGT 20 32 1 GCGGAGCGGG 0.946604 -269 AATGTCTGCCGCGTGATGGCTGTCACGCGGTATTTCGTTTC 21 10 1 CGGGCGCGGT 0.975031 -188 GGCGTTCTTTCATGAAGAGTTAAGCGAGCGGCGACCAGGTCG 22 54 1 CAGGTGCGGC 0.837665 -87 GGCAGCCTACCCAGAGTTGCACGGTCTGCGGCACGCGACCTG 22 89 0 CCGGAGCGGC 0.97452 -52 CGAGATCAGAATCACCAGCAGGCAGCCTACCC 22 119 0 CGGGAGCAGG 0.977418 -22 AACAGCATGGCGTAGAGAGCAAAAAGGGCGGTATAAATAATT 23 232 0 CGAGAGCGGT 0.70831 -69 ** * * * ***** Masking position 9 Map Score: 16.1353 Number of sites scoring better than the average of aligned sites = 1455 Number in coding regions = 1381 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 3 CTCTCGCTCTTCCTCAATATGGTAATA 2 18 0 TCTTCCTCAA 0.818056 -17 TTCCTTCTGCCGCCCGCTATCCGGG 3 6 1 TCTGCCGCCC 0.794718 -161 TCCTCTTTGTTTTCCGACCACATTCACCGG 3 69 1 TTTCCGACCA 0.621626 -98 GTAGTGAAACTTTTGCACAAAACAATACAA 4 116 0 TTTTGCACAA 0.535992 -185 AGAACATCTGTTTGCCACAAAATAATCCGC 6 132 0 TTTGCCACAA 0.766266 -100 TTCTTTTTGATTTCGCGCAAAAAGATTCAG 6 158 1 TTTCGCGCAA 0.762548 -74 AGGGCCGCTGTTTTGGTCAAAAAACTCTCT 7 134 0 TTTTGGTCAA 0.609846 -49 TGAAATGTCATTTTCGACACTCATCGACAC 9 60 0 TTTTCGACAC 0.703447 -65 CATCGGCATGTTTTCGTCAAAAATGACAAT 9 88 1 TTTTCGTCAA 0.803468 -37 TGGCATATATTTTGCCTCAATCGCAAAATC 13 144 0 TTTGCCTCAA 0.864231 -45 AAAGAACGACTTTTGCGCACGCTATTTTTT 14 51 0 TTTTGCGCAC 0.741983 -68 TATCCCGTAGTCTGGCTCACAGAGTGACGA 15 74 1 TCTGGCTCAC 0.677502 -132 TTTGCCCAGTTTTTCGTCACTCTGTGAGCC 15 87 0 TTTTCGTCAC 0.821611 -119 CCGCCAAAGATTTCCCACAAGAGTTGCTGG 15 180 1 TTTCCCACAA 0.791849 -26 ATTGGCTCAATTTCCCTCCATCCAGGAAGG 16 67 0 TTTCCCTCCA 0.820737 -127 ATTCTGGACCTTTGCGGCCCCTTCCGCAAA 16 95 1 TTTGCGGCCC 0.778772 -99 TACTTAATCCTCTTCGTCAATAAATTGAGA 17 15 1 TCTTCGTCAA 0.758026 -262 CTTCCCTGATTTTTCCTCACCATCATTGGT 19 104 1 TTTTCCTCAC 0.868601 -131 ATAACCTTATTTTCCCGCCCTCATTTCGAG 20 47 0 TTTCCCGCCC 0.854411 -254 CGGTCTCGCTCCAGTTAATCAAA 21 185 0 TCTCGCTCCA 0.572884 -13 AGTTGCACGGTCTGCGGCACGCGACCTGGT 22 87 0 TCTGCGGCAC 0.813294 -54 ATGCTCATTATCTCCGGCAATCCCGGTGAT 23 94 1 TCTCCGGCAA 0.817886 -207 ********** Masking position 3 Map Score: 18.1545 Number of sites scoring better than the average of aligned sites = 1687 Number in coding regions = 1516 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 4 TAAATCCACACAGTTTGTATTGTTTTGTGCAAAA 4 102 1 CAGGTTTGTT 0.959873 -199 CGCACGTCGCCAGAAAGTATTGTTAATAAAGCGT 4 144 0 CAGGTTTGTT 0.959873 -157 CAGAGGGTTTTACTCATTCTGTTC 5 1 1 CAGGTTTACT 0.889864 -129 TTGTGGCAAACAGATGTTCTTTTTGATTTCGCGC 6 142 1 CAGTTTTTTT 0.841434 -90 AGCAAAGCATAAGCACGTATTTTTGCCCAGTTTT 15 104 0 AAGGTTTTTT 0.732648 -102 TTGCACTCCTCAGTTGGTGTTTTTTTAAGCAAAG 15 131 0 CAGGTTTTTT 0.974485 -75 TCCCTCCATCCAGGAAGGGTTTGTAACAGAATAC 16 51 0 CAGGGTTTGT 0.867897 -143 TTTATATTTGCAGTCCGGTTTGCTTTGCATACCG 19 34 1 CAGGGTTGCT 0.947219 -201 ATAAGGTTATCAGCCTTGTTTTCTCCCTCATTAC 20 67 1 CAGTGTTTCT 0.799242 -234 AAACTGACGACAGCCTGTTTTTCGTCAGAGTTTT 21 61 1 CAGGTTTTCG 0.897946 -137 GGGAATTATCCAGGCTGTTTTTTTGAGTTGCATC 23 43 0 CAGGTTTTTT 0.974485 -258 CTTATTATCCCAGCTGGTTTTTCTGCGCCATTGC 23 129 1 CAGGTTTTCT 0.980863 -172 *** ** ***** Masking position 2 Map Score: 9.23689 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 233 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TTCCTTCTGCCGCCCGCTATCCGGGGCGGCC 3 10 1 CCGCCCCTTC 0.867772 -157 CGATTAGCCCCCCCCCCTTTCCTCTTTGTTTT 3 50 1 CCCCCCTTCC 0.925027 -117 ATCGCACGTCTCTCCTCCTTGCGACACC 4 283 0 CGTCTCCCCC 0.643822 -18 AGCCCCTGTACGTCCCGCTTTGCGTGTATTTC 7 46 1 CGTCCCCTTG 0.723368 -137 ACCAAAACAGCGGCCCTTTCAGTAATAAATTA 7 147 1 CGGCCCTTAG 0.866557 -36 ACTCATCGACACGCCCATCCCCAAACAGGCGT 9 40 0 ACGCCCTCCC 0.823786 -85 ATCGCCTCCCATTAACTATTGCCAGC 10 5 1 CCTCCCTTAC 0.944396 -207 GCCGTGTCGACGTGTCATTTCGACATCATCGA 10 85 0 CGTGTCTTCG 0.496049 -127 AACACTCTCCTTACGTTTTTTGTTT 11 11 0 ACTCTCTTCG 0.711965 -15 CATGAATATTCCTCCCTTTGACGACGA 12 145 1 CCTCCCTTAC 0.944396 -17 GACCTCTCCTTTCCACCGTTCAAT 15 3 1 CCTCTCTTCC 0.945922 -203 TGGACCTTTGCGGCCCCTTCCGCAAAGAAAAA 16 99 1 CGGCCCTTCG 0.961612 -95 AAGAAAAATAACTCCCACTCCCTGCACACGCA 16 123 1 ACTCCCCTCC 0.870791 -71 GACATTGTCACGTCCCATTTACATTCGCTTGC 16 155 0 CGTCCCTTAC 0.903802 -39 CGCTCAACTCCCTGCCATTACCGGTGGTCAGG 22 17 1 CCTGCCTTCC 0.904268 -124 CCTTATTTTGACGCTCATCACGAGGCGAGTTA 23 166 1 ACGCTCTCCG 0.468274 -135 ATTATTTATACCGCCCTTTTTGCTCTCTACGC 23 233 1 CCGCCCTTTG 0.900155 -68 ****** ** ** Masking position 6 Map Score: 9.88965 Number of sites scoring better than the average of aligned sites = 1346 Number in coding regions = 1203 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 6 CTTTCTGGCGACGTGCGCCAGTGCAGAAGGA 4 161 1 AGTGCGCCAG 0.83452 -140 CTTGCCGACCATAAGCGCCCGGTGTCCTGCC 4 252 1 AAAGCGCCCG 0.906521 -49 CAATCACCTGAGGAATGCCTG 9 114 1 AGAATGCCTG 0.764522 -11 CCTCCCATTAACTATTGCCAGCTACAAGCAA 10 15 1 ATATTGCCAG 0.843491 -197 TACAAGCAATAATTGTGCCAGTGTTGATTAT 10 37 1 ATTGTGCCAG 0.892152 -175 CCCGTTTAACAGAGATGCCAGCTTTAAGCAT 10 181 0 AAGATGCCAG 0.853669 -31 TTGAGGCAAAATATATGCCAGGTCTTCGCAA 13 154 1 AATATGCCAG 0.928316 -35 TCAGAAATTTAATAATGCCCGGTACTCATGT 18 13 1 ATAATGCCCG 0.933468 -67 GTTTTGAATAAATAGTGCCCGTAATATCAGG 21 90 1 ATAGTGCCCG 0.929184 -108 CTCTTCATGAAAGAACGCCAGCAGCCTGACC 22 42 0 AGAACGCCAG 0.912258 -99 TGCCAGATTGATATTTGCCCGCTGAATAACT 23 193 0 AATTTGCCCG 0.770989 -108 AATAATTCCGACAAATGCCAGATTGATATTT 23 208 0 AAAATGCCAG 0.961492 -93 AATAGATTAGAAAAATGCCAGCCAGAACAGC 23 268 0 AAAATGCCAG 0.961492 -33 * ********* Masking position 1 Map Score: 10.8673 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 322 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 CTGCCGTAAGCCGTTCATCCTGACCAGTGCCGCTGTTCA 5 50 1 CCCCCTGCAG 0.975296 -80 GCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAA 8 152 0 ACCGCTACAG 0.769521 -149 GCCTTTATAGGCGGTCCTGTTGGACAACGGCGAACAGTA 8 236 0 GCCGTTGCAG 0.945706 -65 CCCCAAACAGGCGTAACGCCTGCAAAACGGGCAAAGCCT 9 15 0 GCACCTGAAG 0.790872 -110 GCCACCTTCCTGCTGATTGACTGCGCTGC 12 1 1 GCCCCTGGAG 0.987883 -161 CGACACTATAGCTACCCTGATGAGAAGAGACAAGCCCTT 12 72 1 GCCGATGAAG 0.750692 -90 ATTTACATTCGCTTGCTGCGTGTGCAGGGAGTGGGAGTT 16 132 0 GCCCGTGCAG 0.992655 -62 ATGAAAGAACGCCAGCAGCCTGACCACCGGTAATGGCAG 22 28 0 GCCCCTGCAG 0.996731 -113 ACGGTCTGCGGCACGCGACCTGGTCGCCGCTCGCTTAAC 22 72 0 GCCCCTGCGG 0.990625 -69 AGAATCACCAGCAGGCAGCCTACCCAGAGTTGCACGGTC 22 105 0 GCCCCTACAG 0.976938 -36 ATTATCTCCGGCAATCCCGGTGATCGGCGCTTATTATCC 23 100 1 GCCGGTGCGG 0.959975 -201 CCGCTGAATAACTCGCCTCGTGATGAGCGTCAAAATAAG 23 167 0 ACCCGTGGAG 0.847851 -134 ** * **** ** * Masking position 11 Map Score: 8.28018 Number of sites scoring better than the average of aligned sites = 608 Number in coding regions = 559 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 CAGCATCTCACGTGAAGCGATGGTTTGCCT 4 206 1 CGTGAAGCGA 0.963633 -95 CGCTTATGGTCGGCAAGCGACGTCCCTGTA 4 239 0 CGGCAAGCGA 0.991652 -62 ATTATGGTTTAGTGAAGCGATCTTAATGAG 5 95 0 AGTGAAGCGA 0.839168 -35 TAATTTTTAACGGCAAGAGAGACAAAACAG 6 16 0 CGGCAAGAGA 0.920923 -216 CCTGCACACGCAGCAAGCGAATGTAAATGG 16 143 1 CAGCAAGCGA 0.920922 -51 AGCCGAAGGGCGTCAACCGAAAAATGACCA 19 130 0 CGTCAACCGA 0.915839 -105 TTTCATGAAGAGTTAAGCGAGCGGCGACCA 22 61 1 AGTTAAGCGA 0.656701 -80 GCACGGTCTGCGGCACGCGACCTGGTCGCC 22 83 0 CGGCACGCGA 0.96928 -58 TGAGTTGCATCGCCATGCGAGAGAGAACTG 23 24 0 CGCCATGCGA 0.858078 -277 ********** Masking position 5 Map Score: 5.72417 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 357 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 ATAAATTTTATTCTCCAGTGTTATATACTA 3 99 1 TTCTCCAGTG 0.879744 -68 TCTGGCGACGTGCGCCAGTGCAGAAGGATG 4 164 1 TGCGCCAGTG 0.990468 -137 GGTTATACTGTTCGCCGTTGTCCAACAGGA 8 231 1 TTCGCCGTTG 0.916458 -70 AAGCAATAATTGTGCCAGTGTTGATTATCC 10 40 1 TGTGCCAGTG 0.920658 -172 ATGCGATCGATGCGCCATTTACCACACATT 13 110 0 TGCGCCATTT 0.879744 -79 AGTTTAGCGATTCGCCAGCGCGTATCCCGT 15 52 1 TTCGCCAGCG 0.945653 -154 TGCTCCTTGTTTCGACATTGTCACGTCCCA 16 170 0 TTCGACATTG 0.821816 -24 CTGGTTTTTCTGCGCCATTGCCAGCCTTAT 23 142 1 TGCGCCATTG 0.984965 -159 ********** Masking position 1 Map Score: 5.45604 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 943 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 CCCATTAACTATTGCCAGCTACAAGCAATA 10 18 1 ATTGCCAGCT 0.955469 -194 GTTTAACAGAGATGCCAGCTTTAAGCATTT 10 179 0 GATGCCAGCT 0.935816 -33 AGGCAAAATATATGCCAGGTCTTCGCAACG 13 157 1 TATGCCAGGT 0.927587 -32 TTGTCGGTGAAATGTCAGGCACCAGAGTAA 17 237 0 AATGTCAGGC 0.603023 -40 GAAATTTAATAATGCCCGGTACTCATGTTT 18 16 1 AATGCCCGGT 0.913044 -64 CGGCGCTTATTATCCCAGCTGGTTTTTCTG 23 124 1 TATCCCAGCT 0.762956 -177 TTTCTGCGCCATTGCCAGCCTTATTTTGAC 23 148 1 ATTGCCAGCC 0.938563 -153 CAGATTGATATTTGCCCGCTGAATAACTCG 23 191 0 TTTGCCCGCT 0.828752 -110 AATTCCGACAAATGCCAGATTGATATTTGC 23 206 0 AATGCCAGAT 0.860067 -95 AGATTAGAAAAATGCCAGCCAGAACAGCAT 23 266 0 AATGCCAGCC 0.971213 -35 ********** Masking position 3 Map Score: 5.56987 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 717 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 11 TAAAAATGGACCTATTTTTCTTTTGGCCGG 4 61 0 CCTATTTTTC 0.826318 -240 GCTCGCTGTTTTGTCTCTCTTGCC 6 5 1 GCTGTTTTGT 0.847386 -227 TGCTTTCCTCTTTTTTCAGGGGTATT 6 216 0 CCTCTTTTTT 0.77233 -16 ACATTGCAGGGCTATTTTTTATAAGATGCA 8 25 0 GCTATTTTTT 0.889035 -276 ATGGTTCTTTGGTGTTTTTCAGAAAGAATG 8 57 1 GGTGTTTTTC 0.851159 -244 TTTTGCGCACGCTATTTTTTCATGCTTGTT 14 41 0 GCTATTTTTT 0.889035 -78 GTATTTTTGCCCAGTTTTTCGTCACTCTGT 15 92 0 CCAGTTTTTC 0.68989 -114 CTCCTCAGTTGGTGTTTTTTTAAGCAAAGC 15 130 0 GGTGTTTTTT 0.874234 -76 TTTCATCTTCCCTGATTTTTCCTCACCATC 19 98 1 CCTGATTTTT 0.74789 -137 CTGACGACAGCCTGTTTTTCGTCAGAGTTT 21 64 1 CCTGTTTTTC 0.950512 -134 AATTATCCAGGCTGTTTTTTTGAGTTGCAT 23 44 0 GCTGTTTTTT 0.97001 -257 TATTATCCCAGCTGGTTTTTCTGCGCCATT 23 131 1 GCTGGTTTTT 0.858977 -170 ********** Masking position 6 Map Score: 6.35619 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 511 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 12 CGTGAAGCGATGGTTTGCCTTGCTACAGGGA 4 216 1 TGGTTTGCTT 0.807126 -85 CTGAAGGTAATCGTTTGCGTAAATTCCTTTG 8 173 1 TCGTTTGCTA 0.882621 -128 GCAAAAGTCGTTCTTTGCCTAAAATATCGCT 14 65 1 TTCTTTGCTA 0.968132 -54 TACGTGCTTATGCTTTGCTTAAAAAAACACC 15 119 1 TGCTTTGCTA 0.979495 -87 GGAGTTATTTTTCTTTGCGGAAGGGGCCGCA 16 107 0 TTCTTTGCGA 0.90336 -87 ACATCTAAACTTCTTTGCGTATAGATTGAGC 17 175 0 TTCTTTGCTA 0.968132 -102 CAGTCCGGTTTGCTTTGCATACCGGATTTTC 19 44 1 TGCTTTGCTA 0.979495 -191 ******** ** Masking position 6 Map Score: 3.19448 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 15 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 AATTGACCTACCTCAATAGCGGTAGAAAAA 6 95 0 CCTCAATAGC 0.935416 -137 CGACGAAATTCATCTTTAGCTTAAAAATCT 10 116 1 CATCTTTAGC 0.736604 -96 GTAAATGGCGCATCGATCGCATTATTGATT 13 118 1 CATCGATCGC 0.951939 -71 ATATATTTTGCCTCAATCGCAAAATCAATA 13 140 0 CCTCAATCGC 0.981514 -49 CGTTCACCTCATTCGCTATATATTGT 14 103 0 CCTCATTCGC 0.958503 -16 ACCTTACCTCATCAATCGCTTGTAGTTAT 19 216 0 CATCAATCGC 0.977762 -19 TGTAAGATCTCAACTATCGCATCCGTGGAT 20 213 1 CAACTATCGC 0.830287 -88 ********** Masking position 7 Map Score: 4.24224 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 101 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 TCAATGCATACCCCCCTATAGTATATAACA 3 117 0 CCCCCCTATA 0.937442 -50 ATATAGAATACCCCCCTATAGTATATTGC 3 148 1 CCCCCCTATA 0.937442 -19 CGGCAAGCGACGTCCCTGTAGCAAGGCAAA 4 229 0 CGTCCCTGTA 0.746128 -72 AATAACCCCTGTAGAATTATGGT 5 117 0 AACCCCTGTA 0.96135 -13 TAGCCGATTTAGCCCCTGTACGTCCCGCTT 7 36 1 AGCCCCTGTA 0.964095 -147 GTCCAACAGGACCGCCTATAAAGGCCAAAA 8 250 1 ACCGCCTATA 0.903817 -51 AAACAGGCGTAACGCCTGCAAAACGGGCAA 9 20 0 AACGCCTGCA 0.802398 -105 ATGTCACGGTAACGCCTGTACGGTAAACTA 17 87 0 AACGCCTGTA 0.938606 -190 ********** Masking position 10 Map Score: 2.85375 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 110 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 AAAGAAAAATAGGTCCATTTTTATCGCTAA 4 68 1 AGGTCCATTT 0.917858 -233 TTAAAAATTAAGCTGAATTTTATAGCATTT 6 36 1 AGCTGAATTT 0.724384 -196 CTATTGAGGTAGGTCAATTTGCGAAGGCGG 6 106 1 AGGTCAATTT 0.850482 -126 ATTTTTTATAAGATGCATTTGAGATACATC 8 12 0 AGATGCATTT 0.924974 -289 AAAACACCAAAGAACCATTTACATTGCAGG 8 45 0 AGAACCATTT 0.78274 -256 TTTAAGCTAAAGATGAATTTCGTCGCCGTG 10 111 0 AGATGAATTT 0.877561 -101 AACGAAGGGAAGAAGCATTAGTGTAATTAA 13 38 0 AGAAGCATTA 0.585107 -151 TCACGCCGACAGGTGCATTACACGATGTCA 17 111 0 AGGTGCATTA 0.813924 -166 AGCTTAATTAAGATCAATTTGATCTACATC 20 167 1 AGATCAATTT 0.853 -134 ********** Masking position 7 Map Score: 1.91724 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 100 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727