AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_hpyl_reg_100.orf -o00530_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0643 164 glutamyl-tRNA synthetase (gltX) #4 HP0683 300 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #5 HP0869 58 hydrogenase expression/formation protein (hypA) #6 HP0870 207 flagellar hook (flgE) #7 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #8 HP1054 63 H. pylori predicted coding region HP1054 #9 HP1057 148 H. pylori predicted coding region HP1057 #10 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #11 HP1422 24 isoleucyl-tRNA synthetase (ileS) #12 HP1423 101 conserved hypothetical protein #13 HP1530 152 purine nucleoside phosphorylase (punB) #14 HP1531 42 H. pylori predicted coding region HP1531 Motif number 1 CAAACACCCATTACTCTTAAATCATGCCAAT 1 99 1 TTACCTTAAA 0.891669 -159 AAATAATAACACAACTTAAAAAAAACTACCC 1 156 1 ACAATTAAAA 0.53461 -102 TTAAAAAAAACTACCCTTAAAAAAATCAATC 1 171 1 CTACCTTAAA 0.736715 -87 CTTAAAAAAATCAATCTAAAATTCTTAAATT 1 186 1 TCAACTAAAA 0.852582 -72 TCTAAAATTCTTAAATTAAAATATAGCTATA 1 200 1 TTAATTAAAA 0.811442 -58 TATAGCTATAATACACTAAAACAATCTCAAG 1 221 1 ATACCTAAAA 0.853714 -37 AAACTCAAAATTAACCTAAAATCGCTTGACG 2 26 1 TTAACTAAAA 0.911857 -189 TTAAAAAATGTAAATTTTAAACAATAGCCCC 2 140 0 TAAATTTAAA 0.805571 -75 TAATCAAAAACTATTTTTAAATAAAGGGTTT 3 142 1 CTATTTTAAA 0.354702 -23 ATGACGGGGCTAAAACTAAAAGCGTGAGCAG 4 49 1 TAAACTAAAA 0.936668 -252 TAAAATCCTTAAACTCATTTTAG 4 288 0 AAATCTTAAA 0.726262 -13 ACTAAACCTTAATCTTTAAATTAGCCCCTA 5 39 0 TAATTTTAAA 0.698029 -20 GCTTGAGCGATAACCTTTAAAAAGCGTTATG 6 29 1 TAACTTTAAA 0.830371 -179 TTGATTAACAAAACTTTAAAATCCGCAACCA 6 109 1 AAACTTAAAA 0.776326 -99 CCGCAACCAATCATTCTAAAAAGCTATTTAG 6 131 1 TCATCTAAAA 0.763406 -77 AATAATATTTTAAAATTAAAAAGCG 7 5 0 TAAATTAAAA 0.86019 -127 TTTTACAATAATAAGTTTAAAATAGCCCTTA 7 76 0 ATAATTTAAA 0.580492 -56 TTAAAACGACTAACGCTAAAATTTTAAACCT 8 29 0 TAACCTAAAA 0.94587 -35 ATAACCCCCTAAAATTAAAACGACTAACGC 8 44 0 TAAATTAAAA 0.86019 -20 TTTCTTTCAATTATACTAAAATAATTAAAAT 9 95 0 TTATCTAAAA 0.852317 -54 TTAGCGTTGGTTATTCTAAAAAAATAACCGC 10 110 0 TTATCTAAAA 0.852326 -62 TTAGAATAACCAACGCTAAAAATAGCGCTTT 10 122 1 CAACCTAAAA 0.855917 -50 GCTAACATGCTAAAACTAAAACCCTTATAAG 12 42 1 TAAACTAAAA 0.936668 -60 AGTTATGGATAAAAACTTAAAGAATAGGGTA 12 71 1 AAAACTTAAA 0.826251 -31 CATTATAGACAAACCCTTAAAAGAAACACCT 13 90 0 AAACCTTAAA 0.848908 -63 **** ****** Masking position 7 Map Score: 28.0813 Number of sites scoring better than the average of aligned sites = 1591 Number in coding regions = 1246 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 2 TCTTAAAACAAACACCCATTACTCTTAAATCATGC 1 91 1 AAACATTATT 0.692577 -167 TTTTCTTATAAACAAAACCTAAATTGAGAAAAAAT 2 95 1 AAAACCTAAT 0.579212 -120 ATAGGTGGTAACTATCCCTTATTATATCTAATAGC 2 173 0 ACACCTTATT 0.931968 -42 TGAACGATCCTTATTTTATAGGTGGTA 2 198 0 AAGCCTTATT 0.851296 -17 AAAAACCCTTTATTTAAAAATAGTT 3 150 0 AAACCTTTTT 0.865574 -15 AACAGCTTGTAACCACCCTTAATGTCATCGCCCTG 4 77 0 AACCCTTATT 0.851296 -224 TTTGCCCTTTAATATGCCCTTTAATGAGCGCTGAT 4 161 0 AAACCCTTAT 0.805848 -140 AGGGAATTTTAACATGCCTTATCTTATAATTTGAC 4 255 0 AAACCTTACT 0.889502 -46 AAGGCATGTTAAAATTCCCTAAAATGAGTTTAAGG 4 270 1 AAACCCTAAT 0.9705 -31 TAAAATCCTTAAACTCATTTTAGGG 4 286 0 TAACCTTAAT 0.672788 -15 TAATCTTTAAATTAGCCCCTATTATATTGTATTAG 5 25 0 ATACCCTATT 0.956716 -34 ACTAAACCTTAATCTTTAAATTAGC 5 44 0 ACACCTTATT 0.93198 -15 GTGGTGTTGCAAAACCCCCTATTTTCTTATGAATT 6 62 1 AAACCCTATT 0.98227 -146 ATAAGTTTAAAATAGCCCTTACATTCAAAACGCTG 7 62 0 AAACCTTAAT 0.968059 -70 ATAACCCCCTAAAATTAAAACGACT 8 49 0 ATACCCTAAT 0.929205 -15 TAAAAATCCTAAGTGTTAAATATAGT 9 2 1 AAACCTAATT 0.77591 -147 ATTCTAAAAAAATAACCGCTATTATACCATAAGAA 10 94 0 AAACGCTATT 0.783756 -78 TGATTAATCCTTAGTCTTTTGTCT 11 8 0 ATACCTTATT 0.953188 -17 GCGTTTATTTTACCCTATTCTTTAAGTTTTT 12 81 0 ATTCCCTATT 0.625843 -21 TGAAATGTGAATGAAGCCTTAAAATTAAGGTGTTT 13 63 1 ATACCTTAAT 0.923614 -90 ** * ***** * * Masking position 15 Map Score: 22.8111 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 342 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 GTTTTTGCGTCAAGCGATTTTAGGTTAATT 2 34 0 CAAGCGATTT 0.913733 -181 AAACGCTGTTAGCTTTTTGATAACCAAC 3 9 1 TTAGCTTTTT 0.557936 -156 TGGCTAACGCCAAGCTTTTTATGGTTGGTT 3 32 0 CAAGCTTTTT 0.847405 -133 ATTTTTAAATAAAGGGTTTTT 3 154 1 AAAGGGTTTT 0.893611 -11 AGGGTGGTTACAAGCTGTTTAGGATCATTA 4 93 1 CAAGCTGTTT 0.870952 -208 AAACTCATTTTAGGGAATTTTAACATGCCT 4 271 0 TAGGGAATTT 0.699458 -30 AAAATGAGTTTAAGGATTTTA 4 290 1 TAAGGATTTT 0.940141 -11 CATAAGAAAATAGGGGGTTTTGCAACACCA 6 63 0 TAGGGGGTTT 0.871947 -145 ATCATTCTAAAAAGCTATTTAGGAACAACT 6 140 1 AAAGCTATTT 0.580166 -68 ATCAATGAGATTAGGAATTTA 7 121 1 TTAGGAATTT 0.707627 -11 TATTTAACACTTAGGATTTTTA 9 3 0 TTAGGATTTT 0.761189 -146 ACAAACAATTCAAGGGATTTGGCGATT 9 132 1 CAAGGGATTT 0.951138 -17 TGCATAAGCGGTTTCTATGCAAAG 10 5 1 TAAGCGGTTT 0.950027 -167 CAAATACAAGCGAGCGGTTTTCTTATGGTA 10 75 1 CGAGCGGTTT 0.66908 -97 GAATCCAAAACAAGGAGTTTATTTT 10 157 1 CAAGGAGTTT 0.944583 -15 CCACTCTTTTTAAGGAATTTGT 12 3 0 TAAGGAATTT 0.922636 -99 CCATAACTTATAAGGGTTTTAGTTTTAGCA 12 49 0 TAAGGGTTTT 0.966341 -53 GCCTTAAAATTAAGGTGTTTCTTTTAAGGG 13 78 1 TAAGGTGTTT 0.932731 -75 GTGTTTCTTTTAAGGGTTTGTCTATAATGC 13 92 1 TAAGGGTTTG 0.742715 -61 GGATGCGAAAAAAGGATTTTC 13 142 1 AAAGGATTTT 0.821317 -11 ********** Masking position 8 Map Score: 20.526 Number of sites scoring better than the average of aligned sites = 1689 Number in coding regions = 1452 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 4 GTTTGTTTTAAGACGCTATGACTATCTTTA 1 74 0 AGACGCTATG 0.890145 -184 TTCAATTCAAAGGGGCTATTGTTTAAAATT 2 129 1 AGGGGCTATT 0.890701 -86 TACATTTTTTAAACGCTATTAGATATAATA 2 159 1 AAACGCTATT 0.977273 -56 AAACGCTGTTAGCTTTTTGA 3 1 1 AAACGCTGTT 0.934532 -164 TTTTTAAATAAAGGGTTTTT 3 155 1 AAGGGTTTTT 0.532789 -10 ACGCTAGGCAAAGCGCTATCAGCGCTCATT 4 144 1 AAGCGCTATC 0.974725 -157 AACGCTTTTTAAAGGTTATCGCTCAAGCTT 6 27 0 AAAGGTTATC 0.697654 -181 AACCTTTAAAAAGCGTTATGGGGTGGTGTT 6 40 1 AAGCGTTATG 0.874879 -168 AATCATTCTAAAAAGCTATTTAGGAACAAC 6 139 1 AAAAGCTATT 0.768498 -69 CTTACATTCAAAACGCTGTCTTTGATTGAA 7 50 0 AAACGCTGTC 0.906223 -82 TTTTGAATGTAAGGGCTATTTTAAACTTAT 7 67 1 AAGGGCTATT 0.965503 -65 AAGCTTCAAGAAACGCTTTGCATAGAAACC 10 20 0 AAACGCTTTG 0.861804 -152 CTAAAAAAATAACCGCTATTATACCATAAG 10 96 0 AACCGCTATT 0.920968 -76 GATTCAATTAAAGCGCTATTTTTAGCGTTG 10 132 0 AAGCGCTATT 0.983914 -40 ********** Masking position 1 Map Score: 15.9241 Number of sites scoring better than the average of aligned sites = 873 Number in coding regions = 776 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 AAGAATTTTAGATTGATTTTTTTAAGGGTA 1 182 0 GATTGATTTT 0.806622 -76 GTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 GCTATATTTT 0.778407 -51 GGCTAAATTTTGAAACCTTGA 1 247 0 GCTAAATTTT 0.583194 -11 AGCCCCTTTGAATTGAATTTTTTCTCAATT 2 116 0 AATTGAATTT 0.26664 -99 AAAAACCCTTTATTTAAAAATAGTTT 3 149 0 CCTTTATTTA 0.438658 -16 TTAGCCCCGTCATTGATTTTAGTGATGACG 4 32 0 CATTGATTTT 0.753264 -269 CCTCATTTGCCCTTTAATATGCCCTTTAAT 4 171 0 CCTTTAATAT 0.445009 -130 AAGATTTAAGGCTAGAATTTTGCGTTTTTT 4 213 0 GCTAGAATTT 0.885057 -88 AACAACTTTTGCTTTATTTTGCATAGATTG 6 163 1 GCTTTATTTT 0.930036 -45 ATTTTGCATAGATTGAATTTCTTTAAATTA 6 178 1 GATTGAATTT 0.835181 -30 GGTTATCCTTTAATTTAAAGAAATTC 6 192 0 CCTTTAATTT 0.921993 -16 GGCTTGATCTTGGAGTTAAGG 8 2 1 GCTTGATCTT 0.706891 -62 AACGACTAACGCTAAAATTTTAAACCTTAA 8 26 0 GCTAAAATTT 0.629599 -38 AGCGTTAGTCGTTTTAATTTTAGGGGGTTA 8 43 1 GTTTTAATTT 0.460505 -21 TCGCCAAATCCCTTGAATTGTTTGTTAAAA 9 127 0 CCTTGAATTG 0.871886 -22 AAAACCGCTCGCTTGTATTTGCAAAAACAC 10 66 0 GCTTGTATTT 0.786147 -106 TAAAAATAGCGCTTTAATTGAATCCAAAAC 10 138 1 GCTTTAATTG 0.837486 -34 AAAATAAACTCCTTGTTTTGGATTCAATTA 10 152 0 CCTTGTTTTG 0.414095 -20 AAAAGAAACACCTTAATTTTAAGGCTTCAT 13 73 0 CCTTAATTTT 0.794886 -80 GTGATCGCCTTTAATTTAGAATGCTCC 14 26 0 CCTTTAATTT 0.921993 -17 ********** Masking position 3 Map Score: 11.2538 Number of sites scoring better than the average of aligned sites = 1488 Number in coding regions = 1266 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 6 TCAATATAATTCAAACCCTAAACCCAAACCTT 1 24 1 TCAACCTAAA 0.871236 -234 ACTTAAAAAAAACTACCCTTAAAAAAATCAAT 1 169 1 AATACCTTAA 0.532371 -89 TGACGCAAAAACACTGCCTTAATTCTACTACA 2 52 1 ACCTCCTTAA 0.76518 -163 TTTCTTATAAACAAAACCTAAATTGAGAAAAA 2 96 1 ACAACCTAAA 0.964508 -119 ATAGGTGGTAACTATCCCTTATTATATCTAAT 2 176 0 ACATCCTTAT 0.75314 -39 CTTTTTGATAACCAACCATAAAAAGCTTGGCG 3 23 1 ACAACATAAA 0.532053 -142 ATAGTTTTTGATTATACCTAAAGAATACTTAA 3 124 0 ATATCCTAAA 0.614984 -41 AACAGCTTGTAACCACCCTTAATGTCATCGCC 4 80 0 AACACCTTAA 0.818944 -221 AGGGAATTTTAACATGCCTTATCTTATAATTT 4 258 0 AAATCCTTAT 0.513248 -43 TAAAATCCTTAAACTCATTTTA 4 289 0 TAAACCTTAA 0.789277 -12 ACTAAACCTTAATCTTTAAATT 5 47 0 ACAACCTTAA 0.977541 -12 TTTTTGATTAACAAAACTTTAAAATCCGCAAC 6 106 1 ACAACTTTAA 0.645526 -102 ACGCTAAAATTTTAAACCTTAACTCCAAGATC 8 16 0 TTAACCTTAA 0.718965 -48 AATTAAAACGACTAACGCTAAAATTTTAAACC 8 30 0 ACAAGCTAAA 0.756172 -34 TAAAAATCCTAAGTGTTAAATAT 9 2 1 AAAACCTAAG 0.686716 -147 TAAAATTTTTACCCACCCTAATAAAGTCATGC 9 46 0 ACCACCTAAT 0.696992 -103 TTTTAGAATAACCAACGCTAAAAATAGCGCTT 10 120 1 ACAAGCTAAA 0.756173 -52 TGATTAATCCTTAGTCTTTTGTCT 11 11 0 ATAACCTTAG 0.705716 -14 ATGCTAAAACTAAAACCCTTATAAGTTATGGA 12 48 1 TAAACCTTAT 0.513242 -54 TGAAATGTGAATGAAGCCTTAAAATTAAGGTG 13 63 1 ATAACCTTAA 0.911298 -90 AGCATTATAGACAAACCCTTAAAAGAAACACC 13 91 0 ACAACCTTAA 0.97754 -62 ** ** ****** Masking position 9 Map Score: 20.739 Number of sites scoring better than the average of aligned sites = 865 Number in coding regions = 733 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 7 TAGACTTGAAATTTGAAAATAATAACACAACTT 1 140 1 ATTTGAATAT 0.645489 -118 GCTATATTTTAATTTAAGAATTTTAGATTGATT 1 194 0 AATTTAAATT 0.602834 -64 GGCTAAATTTTGAAACCTTGAGATTGTTT 1 239 0 ATTTTGACTT 0.803669 -19 TTTTAGGTTAATTTTGAGTTTTTAGGAGCAGTT 2 14 0 ATTTTGATTT 0.879839 -201 ATTCTACTACATTTGAAATAATTTTTCTTATAA 2 73 1 ATTTGAAATT 0.77219 -142 AGCCCCTTTGAATTGAATTTTTTCTCAATTTAG 2 113 0 AATTGAATTT 0.645504 -102 TATTGTTTAAAATTTACATTTTTTAAACGCTAT 2 145 1 AATTTACTTT 0.805127 -70 TAAGGCTAGAATTTTGCGTTTTTTCATTTTTTT 4 204 0 ATTTTGCTTT 0.902213 -97 TTATCTTATAATTTGACTTCGTTTCATCAAAGA 4 239 0 ATTTGACCTT 0.837607 -62 TTGGTTGCGGATTTTAAAGTTTTGTTAATCAAA 6 108 0 ATTTTAATTT 0.929502 -100 CTTTTGCTTTATTTTGCATAGATTGAATTTCTT 6 168 1 ATTTTGCAAT 0.515079 -40 CGCTTTTTAATTTTAAAATATTATTTAATATG 7 10 1 ATTTTAATTT 0.929497 -122 AAAACTCACCATTTTACAATAATAAGTTTAAAA 7 85 0 ATTTTACTAT 0.805107 -47 GTGGGTAAAAATTTTACTCCATTTTAACCGGTC 9 62 1 ATTTTACCTT 0.902677 -87 TTAACCGGTCATTTTAATTATTTTAGTATAATT 9 85 1 ATTTTAAATT 0.859226 -64 GCGTTTATTTTACCCTATTCTTTAAGTTT 12 83 0 ATTTTACTTT 0.943156 -19 ******* * ** Masking position 4 Map Score: 11.5108 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 393 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 AAGTAACGCTAAATCAATATAATTCA 1 4 1 TAGCTAATCA 0.921177 -254 TACTCTTAAATCATGCCAATTCACACTCTTTAG 1 110 1 TAGCCAATCA 0.933837 -148 TAAAATCGCTTGACGCAAAAACACTGCCTTAAT 2 42 1 TAGCAAAACA 0.966945 -173 AACACTGCCTTAATTCTACTACATTTGAAATAA 2 61 1 TATCTACACA 0.804607 -154 ATCTCTTAAATGATGCCTATTCATGTTTGATAA 3 69 1 TAGCCTATCA 0.641997 -96 GCTAAAAGATTACTCTAATACAATATAATAGG 5 10 1 TATCTAAACA 0.956224 -49 TAAAGTTTTGTTAATCAAAAAGATCGACCAAAT 6 94 0 TATCAAAAGA 0.738981 -114 TGTATATGTTTCAATCAAAGACAGCGTTTTGAA 7 41 1 TATCAAAACA 0.956201 -91 GCATCGGTGTTTTTGCAAATACAAGCGAGCGGT 10 60 1 TTGCAAAACA 0.788512 -112 TTAGCGTTGGTTATTCTAAAAAAATAACCGCTA 10 108 0 TATCTAAAAA 0.656391 -64 GCGCTTTAATTGAATCCAAAACAAGGAGTTTAT 10 146 1 TATCCAAACA 0.963475 -26 * * ***** *** Masking position 13 Map Score: 3.95501 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 112 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 ATAGATTGAATTTCTTTAAATTAAAGGATA 6 185 1 TTTCTTTAAA 0.670299 -23 TATGTATATGTTTCAATCAAAGACAGCGTT 7 39 1 TTTCAATCAA 0.916582 -93 AAAATAGCCCTTACATTCAAAACGCTGTCT 7 59 0 TTACATTCAA 0.916533 -73 ATGGTGAGTTTTACAATCAATGAGATTAGG 7 106 1 TTACAATCAA 0.776475 -26 TTGTTAAAAGTTTCTTTCAATTATACTAAA 9 106 0 TTTCTTTCAA 0.948025 -43 GTTATTCCTTTTTCATTCACCACTTATTCA 13 26 0 TTTCATTCAC 0.966327 -127 TTCATTCACATTTCATTCACATGTTATTCC 13 48 0 TTTCATTCAC 0.966327 -105 AATTTTAAGGCTTCATTCACATTTCATTCA 13 59 0 CTTCATTCAC 0.870228 -94 AATTAAGGTGTTTCTTTTAAGGGTTTGTCT 13 85 1 TTTCTTTTAA 0.670686 -68 ********** Masking position 7 Map Score: 6.49728 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 308 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 TAAATTTTAAACAATAGCCCCTTTGAATTG 2 131 0 ACAATAGCCC 0.980701 -84 CTTAATCTTTAAATTAGCCCCTATTATATT 5 32 0 AAATTAGCCC 0.971661 -27 TAATAAGTTTAAAATAGCCCTTACATTCAA 7 69 0 AAAATAGCCC 0.988589 -63 ACCAACGCTAAAAATAGCGCTTTAATTGAA 10 130 1 AAAATAGCGC 0.969986 -42 ********** Masking position 5 Map Score: 2.23976 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 23 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 TAAGAGTAATGGGTGTTTGTTTTAAGACGC 1 88 0 GGGTGTTTGT 0.926354 -170 ATTTTTTTAAGGGTAGTTTTTTTTAAGTTG 1 167 0 GGGTAGTTTT 0.942325 -91 AGCTTTTTATGGTTGGTTATCAAAAAGCTA 3 20 0 GGTTGGTTAT 0.955444 -145 ATGACATTAAGGGTGGTTACAAGCTGTTTA 4 84 1 GGGTGGTTAC 0.935778 -217 AAGCGTTATGGGGTGGTGTTGCAAAACCCC 6 50 1 GGGTGGTGTT 0.949933 -158 CGCAATGCATCGGTGTTTTTGCAAATACAA 10 54 1 CGGTGTTTTT 0.908078 -118 GTATAATAGCGGTTATTTTTTTAGAATAAC 10 102 1 GGTTATTTTT 0.713993 -70 CTATTTTTAGCGTTGGTTATTCTAAAAAAA 10 117 0 CGTTGGTTAT 0.883542 -55 ********** Masking position 4 Map Score: 1.85115 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 477 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 12 ATAAAGATAGTCATAGCGTCTTAAAACAAA 1 73 1 TCATAGCGTC 0.901748 -185 TTATTATATCTAATAGCGTTTAAAAAATGT 2 160 0 TAATAGCGTT 0.968184 -55 ATCAAAAAGCTAACAGCGTTT 3 2 0 TAACAGCGTT 0.889899 -163 TAATGAGCGCTGATAGCGCTTTGCCTAGCG 4 145 0 TGATAGCGCT 0.936401 -156 TAATACAATATAATAGGGGCTAATTTAAAG 5 26 1 TAATAGGGGC 0.842002 -33 TCTTATGGTATAATAGCGGTTATTTTTTTA 10 95 1 TAATAGCGGT 0.970458 -77 CCAACGCTAAAAATAGCGCTTTAATTGAAT 10 131 1 AAATAGCGCT 0.895562 -41 ATTCACGCTATAATAACGCC 13 1 0 TAATAACGCC 0.839679 -152 ********** Masking position 5 Map Score: 2.57241 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 222 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 ********** No masking Map Score: 3.98858e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 3.98858e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 3.98858e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0