AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_hpyl_reg_100.orf -o00650_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 HP0193_HP0194 214 HP0193: fumarate reductase, cytochrome b subunit (frdC), HP0194: triosephosphate isomerase (tpi) #3 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #4 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) Motif number 1 ATTATATTGATTTAGCGTTACTT 1 1 0 TTTAGCTATT 0.900366 -257 GGGTTTAGGGTTTGAATTATATTGATTTAGCGT 1 16 0 TTTGAATTTT 0.828463 -242 GAGAGAAAGGTTTGGGTTTAGGGTTTGAATTAT 1 29 0 TTTGGGTAGG 0.74355 -229 ATTGGCATGATTTAAGAGTAATGGGTGTTTGTT 1 97 0 TTTAAGGATG 0.837156 -161 GGTAGTTTTTTTTAAGTTGTGTTATTATTTTCA 1 153 0 TTTAAGTTTT 0.948716 -105 GATTGATTTTTTTAAGGGTAGTTTTTTTTAAGT 1 169 0 TTTAAGGATT 0.956573 -89 ATTTAAGAATTTTAGATTGATTTTTTTAAGGGT 1 183 0 TTTAGATATT 0.967071 -75 ATTTACATTTTTTAAACGCTATTAGATATAATA 2 47 0 TTTAAAGTTT 0.782898 -168 CAATAGCCCCTTTGAATTGAATTTTTTCTCAAT 2 86 1 TTTGAATATT 0.918009 -129 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAA 2 108 1 TTTAGGTTTT 0.970912 -107 TTCTACTACATTTGAAATAATTTTTCTTATAAA 2 129 0 TTTGAATATT 0.918009 -86 GTCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 2 180 1 TTTAGGTATT 0.987242 -35 ATTTTGAGTTTTTAGGAGCAGTTTTT 2 199 1 TTTAGGGATT 0.975457 -16 AGATATGCACTTTAGGCTCATGTTTCTCTAACG 3 68 0 TTTAGGTAGT 0.947534 -214 TGGATTTTATTTTAGGTTTTGTTTTGGATTGAG 3 193 0 TTTAGGTTTT 0.970912 -89 GTCTTTGCCTTTAAGTTGATTTATTATTCATA 3 260 0 TTTAAGTATT 0.977214 -22 AACTCCTTGTTTTGGATTCAATTAAAGCGCTAT 4 143 0 TTTGGATATT 0.952835 -29 ****** * * ** Masking position 3 Map Score: 27.7324 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 578 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 TGGGTTTAGGGTTTGAATTATATTGATTTA 1 20 0 GTTTGAATTA 0.494903 -238 AGTAATGGGTGTTTGTTTTAAGACGCTATG 1 84 0 GTTTGTTTTA 0.833777 -174 TTTAAGTTGTGTTATTATTTTCAAATTTCA 1 146 0 GTTATTATTT 0.669658 -112 TTTTTTTAAGGGTAGTTTTTTTTAAGTTGT 1 166 0 GGTAGTTTTT 0.943733 -92 AAGAATTTTAGATTGATTTTTTTAAGGGTA 1 182 0 GATTGATTTT 0.867656 -76 GTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 GCTATATTTT 0.864673 -51 GAAACCTTGAGATTGTTTTAGTGTATTATA 1 227 0 GATTGTTTTA 0.793909 -31 GGCTAAATTTTGAAACCTTGA 1 247 0 GCTAAATTTT 0.790236 -11 ATTCAAAGGGGCTATTGTTTAAAATTTACA 2 73 0 GCTATTGTTT 0.85155 -142 TCTCAATTTAGGTTTTGTTTATAAGAAAAA 2 112 1 GGTTTTGTTT 0.903688 -103 AGCGATTTTAGGTTAATTTTGAGTTTTTAG 2 184 1 GGTTAATTTT 0.860377 -31 GTGCATATCTGCTTGATTTTAGATCCCCAC 3 91 1 GCTTGATTTT 0.95239 -191 AGGGCGATCCGTTTATTTTTTTCACAAAAA 3 165 0 GTTTATTTTT 0.859526 -117 TTTTATTTTAGGTTTTGTTTTGGATTGAGG 3 192 0 GGTTTTGTTT 0.903688 -90 TAACAGGTTGGATTTTATTTTAGGTTTTGT 3 204 0 GATTTTATTT 0.752301 -78 AAAACCGCTCGCTTGTATTTGCAAAAACAC 4 66 0 GCTTGTATTT 0.936994 -106 GTATAATAGCGGTTATTTTTTTAGAATAAC 4 102 1 GGTTATTTTT 0.923204 -70 CAATTAAAGCGCTATTTTTAGCGTTGGTTA 4 128 0 GCTATTTTTA 0.789666 -44 ********** Masking position 3 Map Score: 17.9054 Number of sites scoring better than the average of aligned sites = 2006 Number in coding regions = 1696 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 3 GAATTATATTGATTTAGCGTTACTT 1 6 0 GATTTAGCGT 0.930325 -252 GAAAGGTTTGGGTTTAGGGTTTGAATTATA 1 28 0 GGTTTAGGGT 0.910108 -230 CATAAAGATAGTCATAGCGTCTTAAAACAA 1 72 1 GTCATAGCGT 0.959988 -186 AGATTGATTTTTTTAAGGGTAGTTTTTTTT 1 173 0 TTTTAAGGGT 0.840023 -85 CCTTGAGATTGTTTTAGTGTATTATAGCTA 1 223 0 GTTTTAGTGT 0.918708 -35 TTAAGGCAGTGTTTTTGCGTCAAGCGATTT 2 162 1 GTTTTTGCGT 0.973691 -53 TCTTTGCCTAGTTTCAGGGTTTTAATAGAA 3 13 0 GTTTCAGGGT 0.917399 -269 TTTCTAAGCAGTCTTTGCCTAGTTTCAGGG 3 24 0 GTCTTTGCCT 0.88068 -258 AAAGAAATTTTTTAAAGCGTTAGAGAAACA 3 51 1 TTTAAAGCGT 0.677034 -231 AAAAATATTATTCTTATCGTTCAATGATTA 3 140 0 TTCTTATCGT 0.8552 -142 GTCTTTGCCTTTAAGTTGAT 3 272 0 GTCTTTGCCT 0.88068 -10 GCGAGCGGTTTTCTTATGGTATAATAGCGG 4 84 1 TTCTTATGGT 0.75134 -88 TAAAGCGCTATTTTTAGCGTTGGTTATTCT 4 124 0 TTTTTAGCGT 0.978637 -48 ********** Masking position 10 Map Score: 12.2866 Number of sites scoring better than the average of aligned sites = 1166 Number in coding regions = 1057 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TTTAAGAGTAATGGGTGTTTGTTTTAAGAC 1 90 0 ATGGGTGTTT 0.803307 -168 TTTTTTTAAGGGTAGTTTTTTTTAAGTTGT 1 166 0 GGTAGTTTTT 0.780314 -92 GTAGAATTAAGGCAGTGTTTTTGCGTCAAG 2 156 1 GGCAGTGTTT 0.968922 -59 AGTTTTTAGGAGCAGTTTTT 2 205 1 AGCAGTTTTT 0.984865 -10 TTTCTTTCTAAGCAGTCTTTGCCTAGTTTC 3 28 0 AGCAGTCTTT 0.959666 -254 TGCATAAGCGGTTTCTATGCAAAGCG 4 7 1 AGCGGTTTCT 0.967603 -165 GGCGCAATGCATCGGTGTTTTTGCAAATAC 4 52 1 ATCGGTGTTT 0.961053 -120 AATACAAGCGAGCGGTTTTCTTATGGTATA 4 77 1 AGCGGTTTTC 0.967607 -95 ATGGTATAATAGCGGTTATTTTTTTAGAAT 4 99 1 AGCGGTTATT 0.952728 -73 ********** Masking position 6 Map Score: 8.35775 Number of sites scoring better than the average of aligned sites = 732 Number in coding regions = 661 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 ACAAACACCCATTACTCTTAAATCATGCCA 1 98 1 ATTACTCTTA 0.726353 -160 AAGTTGTGTTATTATTTTCAAATTTCAAGT 1 143 0 ATTATTTTCA 0.904479 -115 TTTAAGGGTAGTTTTTTTTAAGTTGTGTTA 1 162 0 GTTTTTTTTA 0.836176 -96 TTTTAGATTGATTTTTTTAAGGGTAGTTTT 1 177 0 ATTTTTTTAA 0.915214 -81 TAAAATTTACATTTTTTAAACGCTATTAGA 2 54 0 ATTTTTTAAA 0.793293 -161 TTGAATTGAATTTTTTCTCAATTTAGGTTT 2 97 1 TTTTTTCTCA 0.745916 -118 ATTTGAAATAATTTTTCTTATAAACAAAAC 2 123 0 ATTTTTCTTA 0.955128 -92 TTAGAAAGAAATTTTTTAAAGCGTTAGAGA 3 47 1 ATTTTTTAAA 0.793293 -235 TCACAAAAATATTATTCTTATCGTTCAATG 3 144 0 ATTATTCTTA 0.939254 -138 CGATCCGTTTATTTTTTTCACAAAAATATT 3 161 0 ATTTTTTTCA 0.928751 -121 AAGTTGATTTATTATTCATAGTATCACTTT 3 250 0 ATTATTCATA 0.846088 -32 TTTAGCGTTGGTTATTCTAAAAAAATAACC 4 112 0 GTTATTCTAA 0.828081 -60 ********** Masking position 10 Map Score: 10.8333 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 640 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 6 ********** No masking Map Score: 1.58751e-13 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 7 ********** No masking Map Score: 1.58751e-13 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 8 ********** No masking Map Score: 1.58751e-13 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