AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifruR_hpyl_opreg_100.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0027 198 isocitrate dehydrogenase (icd) #2 HP0088 223 RNA polymerase sigma-70 factor (rpoD) #3 HP0121 186 phosphoenolpyruvate synthase (ppsA) #4 HP0921 143 glyceraldehyde-3-phosphate dehydrogenase (gap) #5 HP1100 65 6-phosphogluconate dehydratase #6 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #7 HP1350 209 protease Motif number 1 TGTTTATCCTTTTTCTAAAGTTTGAGTAACTATA 1 175 0 TTTTTGTTTG 0.798773 -24 TAAAAAAGCTTTTTAGTATTTTTTACATTTTGTG 2 51 1 TTTTGTTTTT 0.975313 -173 TCTAATTATATTATTGGAATTTTTCCCCGCTTTA 2 97 0 TTATGTTTTT 0.783394 -127 ATAATTAGAATTTAAGCTATTTTTTAGTAGAATA 2 122 1 TTTAGTTTTT 0.983134 -102 TGGGCGGTTAGTTAGGTATTTTTGAATAGAAAGG 3 17 0 GTTAGTTTTG 0.956693 -170 TTCTTTTTGGTTTATGATTTTATTGTATAATGGG 3 47 0 TTTAGTTATT 0.940025 -140 AGAGCTTTAGTTTTAGCTAGTTTGTATTACTAAG 3 101 0 TTTTGGTTTG 0.973671 -86 TAATGATCATTTTAAGGGAGTTTT 3 173 1 TTTAGGTTTT 0.97478 -14 TGTTTGGTATTTTACTACATTTTGCGCTATTATA 4 71 0 TTTATTTTTG 0.898299 -73 CAATTTCAATTTTAGGGGGTTTTGTTTGGTATTT 4 93 0 TTTAGTTTTG 0.987993 -51 CAATAACCCTTTTAGAGTGTTTTTGAGTTATTA 5 10 1 TTTTGGTTTT 0.963231 -56 AATGCCTTTATTTAAGAGCATTTGTGATAGAATG 6 41 1 TTTAGATTTG 0.912706 -48 GGATCGGGGAGTTACGCGTTTTTGTTGTATCGTT 7 78 1 GTTAGTTTTG 0.956693 -132 TTTTATTCAATTTTTGCGTTTATTCTATCTAAAA 7 152 0 TTTTGTTATT 0.913964 -58 AAGAATCACCTTTAAGGTTTTATTCAATTTTTGC 7 169 0 TTTAGTTATT 0.940025 -41 **** * ***** Masking position 11 Map Score: 21.9988 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 870 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 GAATGCGTGTTTAAAAGTAGCGGTTGGAAATAA 1 101 0 TTAAAAACGG 0.76659 -98 GGTTTGTTTTTATAGAGGGGTGGAATGGAG 2 8 1 TTTTATAGGG 0.917594 -216 TATAGAGGGGTGGAATGGAGGGGTGGAATGTAA 2 21 1 TGGAATAGGG 0.969125 -203 GTGATGAATATTTAATAAAGCGGGGAAAAATTC 2 82 1 TTTAATACGG 0.973988 -142 TAGCTTTTGATTGAAAGCATGGGTTCTTACTTT 2 189 1 TTGAAAAGGG 0.98485 -35 TTAGGTATTTTTGAATAGAAAGGGTGGTT 3 7 0 TTGAATAAGG 0.94716 -180 TACTAAGCTTTTTAATAAGAGGGTGTATTCTTT 3 75 0 TTTAATGGGG 0.942868 -112 ATTTATTGAGTTGAATTCAAGGAGTAAAAC 4 8 0 TTGAATAGGA 0.929176 -136 TATATTAAATCTTAATTAAAGGGGTATTC 5 47 1 CTTAATAGGG 0.952491 -19 AATGGTGATTTTTAAATAAAGGGAAAAC 6 71 1 TTTAAAAGGG 0.971574 -18 CGATTTGCATGTGAATGGATCGGGGAGTTACGC 7 62 1 GTGAATACGG 0.964706 -148 CTCAAAATGAGTGAATGAATGGGCATGTTATCT 7 116 1 GTGAATAGGG 0.98595 -94 ****** * *** Masking position 5 Map Score: 14.8063 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 240 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 AAAAAAGATTTTTAAGGGTTATATAGTATT 1 135 1 TTTAAGGGTT 0.908592 -64 TTTGTTTTTATAGAGGGGTGGAATGGAGGG 2 13 1 TAGAGGGGTG 0.975609 -211 AGGGGTGGAATGGAGGGGTGGAATGTAAAA 2 26 1 TGGAGGGGTG 0.964178 -198 GAATATTTAATAAAGCGGGGAAAAATTCCA 2 87 1 TAAAGCGGGG 0.780072 -137 ATTTTTGAATAGAAAGGGTGGTT 3 4 0 AGAAAGGGTG 0.765413 -183 AGCTTTTTAATAAGAGGGTGTATTCTTTTT 3 73 0 TAAGAGGGTG 0.877848 -114 TAATGATCATTTTAAGGGAGTTTT 3 173 1 TTTAAGGGAG 0.775873 -14 CAATTTCAATTTTAGGGGGTTTTGTTTGGT 4 97 0 TTTAGGGGGT 0.878223 -47 AAAAACACTCTAAAAGGGTTATTG 5 5 0 TAAAAGGGTT 0.949872 -61 TAAATCTTAATTAAAGGGGTATTC 5 52 1 TTAAAGGGGT 0.922289 -14 AAAGGCATTCTTAAGGGGTTCTGTCTCATT 6 20 0 TTAAGGGGTT 0.956428 -69 GCATTTGTGATAGAATGGTGATTTTTAAAT 6 58 1 TAGAATGGTG 0.731235 -31 ********** Masking position 7 Map Score: 8.87869 Number of sites scoring better than the average of aligned sites = 1242 Number in coding regions = 1069 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 4 TAGGAGTTGAATGCTATCAAAACTTAAGGAAG 1 15 0 ATCTATCAAA 0.956195 -184 TCAACTCCTAATTATAAGCCAAAAAATTAAAT 1 37 1 ATATAAGCAA 0.77153 -162 TTGAGTAACTATACTAGCGCAAAAATACTATA 1 156 0 ATCTAGCCAA 0.98313 -43 ATACAATAAAATCATAAACCAAAAAGAATACA 3 53 1 ATATAAACAA 0.800706 -134 TTAGTAATACAAACTAGCTAAAACTAAAGCTC 3 102 1 AACTAGCAAA 0.841589 -85 TCTTAAAACAAAAATATAACAATGATAGCATG 3 137 0 AAATATACAA 0.615269 -50 TAGGTCCAATATAATAGCGCAAAATGTAGTAA 4 62 1 ATATAGCCAA 0.973365 -82 TTAATATATAATAATAACTCAAAAACACTCTA 5 23 0 ATATAACCAA 0.958748 -43 AAAAATCACCATTCTATCACAAATGCTCTTAA 6 52 0 ATCTATCCAA 0.983448 -37 ATGAATGGGCATGTTATCTAAATTTTAGATAG 7 130 1 ATTTATCAAA 0.771558 -80 TTTTGCGTTTATTCTATCTAAAATTTAGATAA 7 143 0 ATCTATCAAA 0.95618 -67 ** ***** *** Masking position 6 Map Score: 9.22324 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 134 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 AATTATAAGCCAAAAAATTAAATGATTTCT 1 46 1 CAAAAAATTA 0.936344 -153 AACACGCATTCAAAAAAAGATTTTTAAGGG 1 123 1 CAAAAAAAGA 0.939786 -76 AAATATTCATCACAAAATGTAAAAAATACT 2 65 0 CACAAAATGT 0.703327 -159 TGTTATTCTACTAAAAAATAGCTTAAATTC 2 129 0 CTAAAAAATA 0.869461 -95 TTTCTTAAAACAAAAATATAACAATGATAG 3 141 0 CAAAAATATA 0.819801 -46 AAAACTCCCTTAAAATGATCATTAAGTT 3 169 0 CTTAAAATGA 0.860666 -18 ACAAAACCCCCTAAAATTGAAATTGAAGTC 4 102 1 CTAAAATTGA 0.959256 -42 ATCGTTTAGGCTCAAAATGAGTGAATGAAT 7 106 1 CTCAAAATGA 0.943972 -104 TTTATTCTATCTAAAATTTAGATAACATGC 7 138 0 CTAAAATTTA 0.90948 -72 AGAATAAACGCAAAAATTGAATAAAACCTT 7 160 1 CAAAAATTGA 0.959256 -50 ********** Masking position 5 Map Score: 10.0255 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 377 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 AACTTTAGAAAAAGGATAAACA 1 187 1 AAAGATAAAC 0.971537 -12 GACACTCCATAAAGTAAGAACCCATGCTTTC 2 201 0 AAAGAAGAAC 0.95057 -23 TTATACAATAAAATCATAAACCAAAAAGAAT 3 51 1 AAATATAAAC 0.769917 -136 CATAAACCAAAAAGAATACACCCTCTTATTA 3 65 1 AAAGATACAC 0.973671 -122 GTAAAATACCAAACAAAACCCCCTAAAATTG 4 90 1 AAACAAACCC 0.799047 -54 ATTTTTAAATAAAGGGAAAAC 6 78 1 AAAGGAAAAC 0.829416 -11 AGGCTCTAAAGTAAGCCCCATTTCTAAT 7 8 1 AAAGAAGCCC 0.957578 -202 TGCAAATCGCAAAGCATGCCCGTTACAAAAA 7 40 0 AAAGATGCCC 0.970629 -170 TAAATTTTAGATAGAATAAACGCAAAAATTG 7 148 1 ATAGATAAAC 0.827672 -62 TTGAGATTAGAAAGAATCACCTTTAAGGTTT 7 183 0 AAAGATCACC 0.919217 -27 **** ****** Masking position 3 Map Score: 7.35226 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 229 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AGCCAAAAAATTAAATGATTTCTTTTAAAA 1 53 1 TTAAATGATT 0.464858 -146 TGATTTCTTTTAAAAACATTGCGTTTTTTC 1 68 1 TAAAAACATT 0.934362 -131 ATATAACCCTTAAAAATCTTTTTTTGAATG 1 129 0 TAAAAATCTT 0.819186 -70 TATACTAGCGCAAAAATACTATATAACCCT 1 149 0 CAAAAATACT 0.760159 -50 TAAAAAATACTAAAAAGCTTTTTTACATTC 2 46 0 TAAAAAGCTT 0.899003 -178 CATTATACAATAAAATCATAAACCAAAAAG 3 49 1 TAAAATCATA 0.596198 -138 AATCATAAACCAAAAAGAATACACCCTCTT 3 62 1 CAAAAAGAAT 0.695397 -125 ACCCTCTTATTAAAAAGCTTAGTAATACAA 3 84 1 TAAAAAGCTT 0.899003 -103 TTTCTTAAAACAAAAATATAACAATGATAG 3 141 0 CAAAAATATA 0.672022 -46 AAAACTCCCTTAAAATGATCATTAAGTTTC 3 167 0 TAAAATGATC 0.605867 -20 TAGGGTTAATTAAAATTATTTATTGAGTTG 4 28 0 TAAAATTATT 0.805983 -116 AATAATAACTCAAAAACACTCTAAAAGGGT 5 16 0 CAAAAACACT 0.834085 -50 ATGCCCGTTACAAAAACATTAGAAATGGGG 7 26 0 CAAAAACATT 0.935507 -184 ********** Masking position 5 Map Score: 6.4111 Number of sites scoring better than the average of aligned sites = 1223 Number in coding regions = 1000 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 8 TTGACTTCCTTAAGTTTTGATAGCATT 1 8 1 CCTTAAGTTT 0.963432 -191 ACTATATAACCCTTAAAAATCTTTTTTTGA 1 132 0 CCTTAAAAAT 0.78994 -67 TTAAAATGATCATTAAGTTTCTTAAAACAA 3 158 0 CATTAAGTTT 0.943678 -29 ATACCCCTTTAATTAAGATTTAATATATAA 5 44 0 AATTAAGATT 0.75691 -22 GGTTCTGTCTCATTAAGCATCAA 6 4 0 CATTAAGCAT 0.915364 -85 AGACAGAACCCCTTAAGAATGCCTTTATTT 6 24 1 CCTTAAGAAT 0.966658 -65 AAAGAATCACCTTTAAGGTTTTATTCAATT 7 174 0 CTTTAAGGTT 0.847875 -36 ********** Masking position 5 Map Score: 1.58204 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 228 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 ********** No masking Map Score: 3.44146e-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: 3.44146e-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 11 ********** No masking Map Score: 3.44146e-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