AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_hpyl_reg_100.orf -o00350_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 HP1067 290 chemotaxis protein (cheY) #4 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #5 HP1483 26 gerC2 protein (gerC2) #6 HP1490 103 hemolysin Motif number 1 AAGGTTTGGGTTTAGGGTTTGAATTATATTGATTT 1 21 0 TTTAGGTTTT 0.981081 -237 ATTCACACTCTTTAGACTTGAAATTTGAAAATAAT 1 128 1 TTTAGATTTT 0.937818 -130 GGGTAGTTTTTTTTAAGTTGTGTTATTATTTTCAA 1 152 0 TTTTAATTTA 0.824831 -106 GATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTG 1 167 0 TTTAAGGTTT 0.964526 -91 AATTTAAGAATTTTAGATTGATTTTTTTAAGGGTA 1 182 0 TTTTAGTTTT 0.974048 -76 CTTGAGATTGTTTTAGTGTATTATAGCTATATTTT 1 217 0 TTTTAGGTTA 0.892654 -41 ATTTTGAGTTTTTAGGAGCAGTTTTT 2 2 0 TTTAGGGCTT 0.760227 -213 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG 2 22 0 TTTTAGTTTT 0.974048 -193 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAAT 2 93 0 TTTAGGTTTA 0.957207 -122 GGGGCTATTGTTTAAAATTTACATTTTTTAAACGC 2 140 1 TTTAAATTTT 0.93901 -75 TGCTTCTCCTTTTAAGATTGCATTTAAATTAGGCT 3 264 0 TTTAAGTTTT 0.98146 -27 AAAGCGCTATTTTTAGCGTTGGTTATTCTAAAAAA 4 118 0 TTTTAGGTTA 0.892654 -54 AAACTCCTTGTTTTGGATTCAATTAAAGCGCTATT 4 142 0 TTTTGGTTTA 0.940686 -30 AGGCTTGATTTTTAAAGTTAGGCTTAATCTTTTAT 6 20 1 TTTAAATTTT 0.93901 -84 AGGCTTAATCTTTTATGTTAAAATTCTGAGATTTT 6 39 1 TTTTATTTTT 0.729223 -65 TTTTATATATTTTATATTTATCGTTAGGTTTTAGG 6 70 1 TTTATATTTT 0.661734 -34 ATCGTTAGGTTTTAGGTTTAAAGTT 6 89 1 TTTAGGTTTT 0.981081 -15 ****** ** ** Masking position 3 Map Score: 25.8376 Number of sites scoring better than the average of aligned sites = 886 Number in coding regions = 710 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 GTTTGGGTTTAGGGTTTGAATTATATTGATT 1 22 0 AGGGTTTAAT 0.941495 -236 AGATAGTCATAGCGTCTTAAAACAAACACCC 1 77 1 AGCGTCTAAA 0.975772 -181 AAACAATCTCAAGGTTTCAAAATTTAGCC 1 239 1 AAGGTTTAAA 0.834833 -19 CAAAGGGGCTATTGTTTAAAATTTACATTTT 2 136 1 ATTGTTTAAA 0.807158 -79 TATATCTAATAGCGTTTAAAAAATGTAAATT 2 155 0 AGCGTTTAAA 0.991468 -60 GGGTCATTGGATGGTTTGAAAAAAGAAAGAC 3 28 0 ATGGTTTAAA 0.943277 -263 TGCTATGATAATCGTTTAAAAGTAATAAAAT 3 79 0 ATCGTTTAAA 0.977114 -212 GCGTTCAATGAGCGTTCTTATTTGTAAAAAA 3 122 0 AGCGTTCTAT 0.838059 -169 ATAATAATAAATCGTTCCAAATAATAGCATG 3 200 0 ATCGTTCAAA 0.959788 -91 AAACAGCCAAAGCGTCTCTAACGCCTTATAA 3 227 0 AGCGTCTTAA 0.900236 -64 CGCTAAAAATAGCGCTTTAATTGAATCCAAA 4 135 1 AGCGCTTAAT 0.876431 -37 TTAAAAATCAAGCCTTCAAAAACC 6 4 0 AGCCTTCAAA 0.873558 -100 ******* *** Masking position 10 Map Score: 12.5389 Number of sites scoring better than the average of aligned sites = 1616 Number in coding regions = 1434 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 3 TAAAGATAGTCATAGCGTCTTAAAACAAAC 1 74 1 CATAGCGTCT 0.967088 -184 AAATTAACCTAAAATCGCTTGACGCAAAAA 2 33 1 AAAATCGCTT 0.717914 -182 AAATTCAATTCAAAGGGGCTATTGTTTAAA 2 126 1 CAAAGGGGCT 0.871631 -89 TATTATATCTAATAGCGTTTAAAAAATGTA 2 159 0 AATAGCGTTT 0.956249 -56 TTATCGCACTCAAAGAGTTATTTTATTACT 3 60 1 CAAAGAGTTA 0.663965 -231 TTTAAACAGCCAAAGCGTCTCTAACGCCTT 3 231 0 CAAAGCGTCT 0.982642 -60 TGGCTGTTTAAAAAGAGCCTAATTTAAATG 3 249 1 AAAAGAGCCT 0.878526 -42 TGCATAAGCGGTTTCTATGCAAA 4 4 1 ATAAGCGGTT 0.804316 -168 GGTTTCTATGCAAAGCGTTTCTTGAAGCTT 4 20 1 CAAAGCGTTT 0.985191 -152 CTTATGGTATAATAGCGGTTATTTTTTTAG 4 96 1 AATAGCGGTT 0.948442 -76 CAACGCTAAAAATAGCGCTTTAATTGAATC 4 132 1 AATAGCGCTT 0.948442 -40 GAATCCAAAACAAGGAGTTTATTTT 4 157 1 CAAGGAGTTT 0.745424 -15 ********** Masking position 7 Map Score: 11.8223 Number of sites scoring better than the average of aligned sites = 1500 Number in coding regions = 1385 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 AATTATATTGATTTAGCGTTACTT 1 4 0 ATTAGCGTTA 0.95181 -254 CCTATAAAATAAGGATCGTTCA 2 203 1 AAGATCGTTC 0.922537 -12 TGGAGCGTTCAATGAGCGTTCTTATTTGTAA 3 126 0 AAGAGCGTTC 0.976856 -165 CATTGGCTAAATGGAGCGTTCAATGAGCGTT 3 137 0 ATGAGCGTTC 0.989386 -154 CCTTATAATAATAAATCGTTCCAAATAATAG 3 204 0 ATAATCGTTC 0.943123 -87 ATTTATTATTATAAGGCGTTAGAGACGCTTT 3 219 1 ATAGGCGTTA 0.884864 -72 GGCTGTTTAAAAAGAGCCTAATTTAAATGCA 3 250 1 AAGAGCCTAA 0.76549 -41 AACTTTAAAAATCAAGCCTTCAAAAACC 6 8 0 ATAAGCCTTC 0.963064 -96 AACATAAAAGATTAAGCCTAACTTTAAAAAT 6 27 0 ATAAGCCTAA 0.819657 -77 TATATTTTATATTTATCGTTAGGTTTTAGGT 6 75 1 ATTATCGTTA 0.847861 -29 ** ******** Masking position 9 Map Score: 8.28621 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 559 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 TAAATCAATATAATTCAAACCCTAAACCCAA 1 20 1 TAATCAAACC 0.471703 -238 ATTCAAACCCTAAACCCAAACCTTTCTCTCA 1 32 1 TAAACCAAAC 0.849725 -226 ATAGCGTCTTAAAACAAACACCCATTACTCT 1 85 1 AAAAAAACAC 0.555547 -173 CCATTACTCTTAAATCATGCCAATTCACACT 1 106 1 TAAACATGCC 0.890301 -152 TTGAAATTTGAAAATAATAACACAACTTAAA 1 145 1 AAAAAATAAC 0.887955 -113 CACAACTTAAAAAAAACTACCCTTAAAAAAA 1 165 1 AAAAACTACC 0.88668 -93 GCTTGACGCAAAAACACTGCCTTAATTCTAC 2 49 1 AAAAACTGCC 0.843319 -166 ATTTTTCTTATAAACAAAACCTAAATTGAGA 2 93 1 TAAAAAAACC 0.91919 -122 ATGTAAATTTTAAACAATAGCCCCTTTGAAT 2 133 0 TAAAAATAGC 0.623031 -82 ATGGTTTGAAAAAAGAAAGACAAGGATTTTA 3 18 0 AAAAAAAGAC 0.844997 -273 GTTTAAAAGTAATAAAATAACTCTTTGAGTG 3 66 0 AATAAATAAC 0.374904 -225 CAAGGTAATTTTAATCAAAACATGCTATTAT 3 180 1 TTAACAAAAC 0.63992 -111 TTTGGCTGTTTAAAAAGAGCCTAATTTAAAT 3 247 1 TAAAAGAGCC 0.552395 -44 CTATTATACCATAAGAAAACCGCTCGCTTGT 4 80 0 ATAAAAAACC 0.710916 -92 TGGTTATTCTAAAAAAATAACCGCTATTATA 4 103 0 AAAAAATAAC 0.887955 -69 CCTAACTTTAAAAATCAAGCCTTCAAAAACC 6 11 0 AAAACAAGCC 0.890301 -93 ACATAAAAGATTAAGCCTAACTTTAAAAATC 6 26 0 TTAACCTAAC 0.550053 -78 ACTTTAAACCTAAAACCTAACGATAAATATA 6 82 0 TAAACCTAAC 0.849725 -22 **** ****** Masking position 11 Map Score: 11.521 Number of sites scoring better than the average of aligned sites = 1703 Number in coding regions = 1440 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 6 GTAATGGGTGTTTGTTTTAAGACGCTATGA 1 83 0 TTTGTTTTAA 0.617101 -175 AGACTTGAAATTTGAAAATAATAACACAAC 1 141 1 TTTGAAAATA 0.852316 -117 TTCTACTACATTTGAAATAATTTTTCTTAT 2 74 1 TTTGAAATAA 0.891006 -141 CAATTTAGGTTTTGTTTATAAGAAAAATTA 2 91 0 TTTGTTTATA 0.532321 -124 CAATAGCCCCTTTGAATTGAATTTTTTCTC 2 120 0 TTTGAATTGA 0.86555 -95 CATTGGATGGTTTGAAAAAAGAAAGACAAG 3 25 0 TTTGAAAAAA 0.937493 -266 ATTCAGTTTGTTTGCTATGATAATCGTTTA 3 92 0 TTTGCTATGA 0.791303 -199 AGCGTTCTTATTTGTAAAAAAATTCAGTTT 3 113 0 TTTGTAAAAA 0.886922 -178 AATAGCATGTTTTGATTAAAATTACCTTGA 3 179 0 TTTGATTAAA 0.835743 -112 GCTTTGGCTGTTTAAAAAGAGCCTAATTTA 3 245 1 TTTAAAAAGA 0.550059 -46 CAAGAAACGCTTTGCATAGAAACCGCTTAT 4 14 0 TTTGCATAGA 0.911001 -158 CTCGCTTGTATTTGCAAAAACACCGATGCA 4 59 0 TTTGCAAAAA 0.928417 -113 ********** Masking position 10 Map Score: 9.16549 Number of sites scoring better than the average of aligned sites = 1011 Number in coding regions = 839 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 7 ACAACTTAAAAAAAACTACCCTTAAAAAAA 1 166 1 AAAAACTACC 0.832113 -92 TACCCTTAAAAAAATCAATCTAAAATTCTT 1 182 1 AAAATCAATC 0.960345 -76 TATAATACACTAAAACAATCTCAAGGTTTC 1 227 1 TAAAACAATC 0.677608 -31 TCAAGGTTTCAAAATTTAGCC 1 247 1 AAAATTTAGC 0.777863 -11 CTAAAAACTCAAAATTAACCTAAAATCGCT 2 22 1 AAAATTAACC 0.914855 -193 AATTGAGAAAAAATTCAATTCAAAGGGGCT 2 116 1 AAATTCAATT 0.431836 -99 AGCCTAATTTAAATGCAATCTTAAAAGGAG 3 264 1 AAATGCAATC 0.747989 -27 GTGTTTTTGCAAATACAAGCGAGCGGTTTT 4 66 1 AAATACAAGC 0.912671 -106 GTTATTCTAAAAAAATAACCGCTATTATAC 4 102 0 AAAAATAACC 0.880083 -70 CCTAACTTTAAAAATCAAGCCTTCAAAAAC 6 12 0 AAAATCAAGC 0.974628 -92 TTTAACATAAAAGATTAAGCCTAACTTTAA 6 31 0 AAGATTAAGC 0.726608 -73 ********** Masking position 8 Map Score: 5.2648 Number of sites scoring better than the average of aligned sites = 1217 Number in coding regions = 1071 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 8 ********** No masking Map Score: 1.46615e-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 9 ********** No masking Map Score: 1.46615e-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 10 ********** No masking Map Score: 1.46615e-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