AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -iphoB_mpneu_opreg_100.orf -g0.400 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ugpC 23 sn-glycerol-3-phosphate transport system permease protein; similar to Swiss-Prot Accession Number P10907, from E. coli #2 1673668 300 putative lipoprotein, MG186 homolog, from M. genitalium #3 potA 300 spermidine/putrescine transport ATP-binding prot; similar to Swiss-Prot Accession Number P23858, from E. coli #4 1673898 241 MG412 homolog, from M. genitalium #5 1674105 130 MG294 homolog, from M. genitalium #6 1674151 300 A19_orf229V Protein #7 rpsJ 93 ribosomal protein S10; similar to Swiss-Prot Accession Number P38518, from T. maritima #8 1674374 246 VXpSPT7_orf112 Protein Motif number 1 GACACCTTGGTTTTGATCAAGCATTTAATTGATG 2 38 0 TTTTGACAAT 0.917152 -263 AAACGGTTAATTTTTAGCAATTTAAGTAGTTTTA 2 115 0 TTTTTACATA 0.921102 -186 ATTGGCCTAATTTTGACCCTAAAACTAATTCAAA 2 148 0 TTTTGACCAA 0.939507 -153 AAATCTCTACTTTTTACCCCCTAAATAACCTAAC 2 203 1 TTTTTACCAA 0.959294 -98 AATTCCCCTTCTTTTAGCCTACAACTTCTCTTTT 3 17 1 CTTTTACCAA 0.956532 -284 GAAAGGGAATCTTTTAACAAGAAAAAAGAGAAGT 3 40 0 CTTTTACAAA 0.972631 -261 ATTCCCTTTCTTTTTATCAAGAAAATCTCTTTTT 3 64 1 TTTTTACAAA 0.974377 -237 ATAAAGACCACTTTTAAGACATAAAAAAAGAGAT 3 88 0 CTTTTAGAAA 0.666199 -213 TTGGACTAAATTTTGAACCAAAATAAAGACCACT 3 110 0 TTTTGACCAT 0.87269 -191 AACAGTCAAATTTTTAGCACAAATTTAACTGCAA 3 145 1 TTTTTACAAT 0.941478 -156 TTGTGAGATTTTTTGAACAGTTTTTGCAGTTAAA 3 168 0 TTTTGACATT 0.772517 -133 TTGCAATCATTTTTTTGCAAGAAAATTTATCCCA 3 204 1 TTTTTTCAAA 0.810911 -97 TTGTAGCAATTTTTGACCCCGCTTGCCCCCTAAA 3 240 0 TTTTGACCTT 0.677713 -61 GCTGCTTTTCTTTTAATCATTCAACCAATGGCCG 4 84 0 TTTTAACAAA 0.765062 -158 TTTCGGTACTTTTTAACCAACTTTTAATTAAGC 4 219 0 TTTTTACCTT 0.761207 -23 TTTCCTCTCACTTTTTGCAATAAATGTATGCCAA 5 18 1 CTTTTTCAAA 0.89083 -113 TAATGGATCACTGTTAGCACCTAAGAAAGTGGTT 6 19 0 CTGTTACAAA 0.764037 -282 TGAACCAAGCTTTTTTACACCGACAGCAATGGTC 6 140 1 TTTTTTCAAC 0.691064 -161 AGCGTAGTCATTTTGACCATCAAATTTCACCCTT 7 58 1 TTTTGACAAA 0.961683 -36 TAGTAAGTTTCTTTTAACAATTAAATGGGTCTTT 8 68 1 CTTTTACAAA 0.972632 -179 AATTCCTTATCTTTTTCCAAACTAGTTTGCCGCT 8 195 0 CTTTTTCATA 0.719578 -52 GCTTTTAGCAGTCACAATTGAACTG 8 232 0 CTTTTACAAC 0.898723 -15 ****** ** ** Masking position 4 Map Score: 29.8871 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 165 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 TTGTAATTTTTCGGCGGTCTTGCCA 2 6 1 ATTTTTCGGC 0.833135 -295 AAAAAAAGAGATTTTCTTGATAAAAAGAAA 3 70 0 ATTTTCTTGA 0.65341 -231 AATTGCAATCATTTTTTTGCAAGAAAATTT 3 202 1 ATTTTTTTGC 0.972493 -99 AAAAACAACGATTTTCTGGCGTTTATTCTT 4 156 0 ATTTTCTGGC 0.91778 -86 TTTCTAATTTATTTTTTGGCAAGCTAACCG 5 59 1 ATTTTTTGGC 0.96676 -72 CTTGAACCAAGCTTTTTTACACCGACAGCA 6 138 1 GCTTTTTTAC 0.758046 -163 AAAACAGCTGACTTTATTGCTAACGCTAAG 6 188 1 ACTTTATTGC 0.916598 -113 AAGCATTGGGACTTGTTTGCGCTAGTTAAG 8 15 0 ACTTGTTTGC 0.964374 -232 TTAGCTTGGAGCTTTTTTGCTGTTAGTAAG 8 45 1 GCTTTTTTGC 0.97761 -202 TAGTAACCCCGCTTTTTGGCGATCTTATTG 8 112 0 GCTTTTTGGC 0.972915 -135 CGGGGTTACTACTTTTTTGAAGTTGTTTAA 8 131 1 ACTTTTTTGA 0.915626 -116 CTTTTTCCAAACTAGTTTGCCGCTTGCAGG 8 189 0 ACTAGTTTGC 0.75818 -58 ********** Masking position 3 Map Score: 10.5565 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 212 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 ATTGCTGGTTTAAACTGCTTTCA 1 4 0 TAAACTGCTT 0.941545 -20 ATATTTAGAGTAAAACTACTTAAATTGCTAA 2 105 1 TAAACTACTT 0.985702 -196 ATTTTGACCCTAAAACTAATTCAAAAACGGT 2 142 0 TAAACTAATT 0.871108 -159 TTTAACTACTTAATTTTTAAA 3 290 0 TTAACTACTT 0.973092 -11 AATCGTTGTTTTTAACTACTTAAAGCACAAC 4 173 1 TTAACTACTT 0.973092 -69 TCGGTACTTTTTAACCAACTTTTAATTAAGC 4 219 0 TAACCAACTT 0.888464 -23 AACTTTGAAACCACTTTCTTAGGTGC 6 6 1 TAAACCACTT 0.978899 -295 CGCTTTTCGGTGTATCCACTTCGACCAAAGC 7 31 0 TTATCCACTT 0.813465 -63 ATCATTGAAATTAAACAACTTCAAAAAAGTA 8 140 0 TAAACAACTT 0.967732 -107 * ********* Masking position 4 Map Score: 9.50901 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 52 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 ATTTAGTGCACAATTGCTAAGAGCGCCTGTAT 2 75 1 CAATGCTAAA 0.978818 -226 AAAACTACTTAAATTGCTAAAAATTAACCGTT 2 116 1 AAATGCTAAA 0.801468 -185 GACCCTAAAACTAATTCAAAAACGGTTAATTT 2 136 0 CTATTCAAAA 0.718531 -165 AGCACAAATTTAACTGCAAAAACTGTTCAAAA 3 160 1 TAATGCAAAA 0.91684 -141 ACTAGTGCTAAAACTAACCAGAT 4 2 1 CTATGCTAAA 0.972291 -240 AACACTCCAGCAATCGCTGATAAAGATCAGGT 4 38 0 CAACGCTGAA 0.821555 -204 GCCGTGGCACCTAAAGCTAACACTCCAGCAAT 4 56 0 CTAAGCTAAA 0.896975 -186 TGGCATACATTTATTGCAAAAAGTGAGAGGAA 5 19 0 TTATGCAAAA 0.890591 -112 ACCACTTTCTTAGGTGCTAACAGTGATCCATT 6 20 1 TAGTGCTAAA 0.689477 -281 TGGTCAGCAGCAATCGATAAAAACAGCTGACT 6 169 1 CAACGATAAA 0.657534 -132 GACTTTATTGCTAACGCTAAGAGTACACAGGC 6 197 1 CTACGCTAAA 0.962639 -104 ACGGCTTAACTAGCGCAAACAAGTCCCAATG 8 10 1 CTACGCAAAA 0.945839 -237 AGAAACTTACTAACAGCAAAAAAGCTCCAAGC 8 48 0 TAAAGCAAAA 0.73294 -199 TGAAATTAAACAACTTCAAAAAAGTAGTAACC 8 134 0 CAATTCAAAA 0.770743 -113 AGTTCAATTGTGACTGCTAAAAGC 8 233 1 TGATGCTAAA 0.792588 -14 *** ****** * Masking position 10 Map Score: 12.7204 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 159 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 AATTTCCCGCTTTCTTTTTTTAAAAAATCT 2 179 1 TTTCTTTTTT 0.964501 -122 TTTTAAAAAATCTCTACTTTTTACCCCCTA 2 196 1 TCTCTACTTT 0.849807 -105 GCCTACAACTTCTCTTTTTTCTTGTTAAAA 3 33 1 TCTCTTTTTT 0.957177 -268 AAAGATTCCCTTTCTTTTTATCAAGAAAAT 3 60 1 TTTCTTTTTA 0.858908 -241 ATCAAGAAAATCTCTTTTTTTATGTCTTAA 3 79 1 TCTCTTTTTT 0.957177 -222 TTAAAAGTGGTCTTTATTTTGGTTCAAAAT 3 105 1 TCTTTATTTT 0.550415 -196 ATAAATACCGTTTTTTCTTTAAAAATTAAG 3 273 1 TTTTTTCTTT 0.748763 -28 CCTTTGCTAATTTCTTTTTACGAGAGGCTG 4 114 0 TTTCTTTTTA 0.858908 -128 TTTTCTGGCGTTTATTCTTTGCCAATTGTT 4 145 0 TTTATTCTTT 0.628271 -97 GCAAGTTGCATTTCTTAGTTGTGCTTTAAG 4 191 0 TTTCTTAGTT 0.748468 -51 CAAAAACGTTTTTCTAATTTATTTTTTGGC 5 49 1 TTTCTAATTT 0.753242 -82 ACGGCATTACTTTCTTTGTTAAGTTAGATC 6 108 1 TTTCTTTGTT 0.903997 -193 ********** Masking position 5 Map Score: 9.65429 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 158 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 GGTCAAAATTAGGCCAATTTCCCGCTTTCT 2 164 1 AGGCCAATTT 0.886168 -137 TGAACAATTTAGATAAATTTACATTAATTG 2 255 0 AGATAAATTT 0.847256 -46 CACCGTAGTTAGTTCAATTTAGGTAAAG 2 283 1 AGTTCAATTT 0.964354 -18 ACCAAAATAAAGACCACTTTTAAGACATAA 3 98 0 AGACCACTTT 0.892616 -203 GTCCAAAAACAGTCAAATTTTTAGCACAAA 3 138 1 AGTCAAATTT 0.908169 -163 CAGTTTTTGCAGTTAAATTTGTGCTAAAAA 3 155 0 AGTTAAATTT 0.913606 -146 TAATTAAGCAAGTTGCATTTCTTAGTTGTG 4 198 0 AGTTGCATTT 0.864496 -44 CGATAAAAACAGCTGACTTTATTGCTAACG 6 183 1 AGCTGACTTT 0.762163 -118 GTATGCTTTAAGTTGACTTTCAGCTGCACT 6 239 0 AGTTGACTTT 0.912393 -62 TCACTTTAAAAGACCCATTTAATTGTTAAA 8 80 0 AGACCCATTT 0.83589 -167 GGAATTAGTCAGTTCAATTGTGACTGCTAA 8 223 1 AGTTCAATTG 0.835923 -24 ********** Masking position 1 Map Score: 6.07541 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 84 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TTAGAGTAAAACTACTTAAATTGCTAAAAAT 2 109 1 ACTACTAAAT 0.942871 -192 TCTACTTTTTACCCCCTAAATAACCTAACAA 2 208 1 ACCCCTAAAT 0.930282 -93 TAACCTAACAACTACACAATTAATTCCCAAT 2 228 1 ACTACCAATT 0.804762 -73 TTTAACTACTTAATTTTTAAAGAAA 3 286 0 ACTACTAATT 0.918521 -15 GTTGTTTTTAACTACTTAAAGCACAACTAAG 4 177 1 ACTACTAAAG 0.921575 -65 AACCGGATTAACCCCATAATTACCACTAAAA 5 84 1 ACCCCTAATT 0.901129 -47 CCCCATAATTACCACTAAAATAATGGCGTAA 5 95 1 ACCACAAAAT 0.929231 -36 TGTGACACAACGAAATTACGCCATTAT 5 114 0 ACAACAAATT 0.799219 -17 CGAAGTGGATACACCGAAAAGCGTAGTCATT 7 39 1 ACACCAAAAG 0.773884 -55 TTCAATTGTGACTGCTAAAAGC 8 235 1 ACTGCAAAAG 0.74586 -12 ***** ***** Masking position 8 Map Score: 3.86447 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 69 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 GCCATACATCAATTAAATGCTTGATCAAAACC 2 32 1 AATTATGCTT 0.942086 -269 AATTGCTAAAAATTAACCGTTTTTGAATTAGT 2 127 1 AATTCCGTTT 0.776776 -174 AAATTAGGCCAATTTCCCGCTTTCTTTTTTTA 2 169 1 AATTCCGCTT 0.968908 -132 ATTCTTTGCCAATTGTTTCCTTTGCTAATTTC 4 130 0 AATTTTCCTT 0.831755 -112 TTCTTTGTTAAGTTAGATCCTTGAACCAAGCT 6 119 1 AGTTATCCTT 0.940991 -182 CAACATTTAGAGTTTCATCCTTGCGTACGTAT 6 265 0 AGTTATCCTT 0.940992 -36 TTGACCATCAAATTTCACCCTTAAGAACTGAG 7 70 1 AATTACCCTT 0.962694 -24 TTTCCAAACTAGTTTGCCGCTTGCAGGCCTTA 8 184 0 AGTTCCGCTT 0.968299 -63 **** ****** Masking position 1 Map Score: 2.99773 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 67 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 ATTGCTGGTTTAAACTGCTT 1 14 0 ATTGCTGGTT 0.772576 -10 AACGGTATTTATTGTAGCAATTTTTGACCC 3 255 0 ATTGTAGCAA 0.872991 -46 TTTATCAGCGATTGCTGGAGTGTTAGCTTT 4 46 1 ATTGCTGGAG 0.958478 -196 GGAATAATGAATTGTTGCAGGGTAATCTAA 6 50 0 ATTGTTGCAG 0.963619 -251 GTTTTTATCGATTGCTGCTGACCATTGCTG 6 163 0 ATTGCTGCTG 0.976751 -138 CAACTATCAAAGTGCAGCTGAAAGTCAACT 6 229 1 AGTGCAGCTG 0.908491 -72 AAGCCTTAAGATTGTAGCAAATAA 7 5 0 ATTGTAGCAA 0.872991 -89 ********** Masking position 1 Map Score: 1.89304 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 57 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 TTAGCAATTGTGCACTAAATTTTGACACCTTG 2 63 0 TGCCTAAATT 0.985211 -238 TAAGTAGTTTTACTCTAAATATACAGGCGCTC 2 95 0 TACCTAAATT 0.938414 -206 AGCGGGAAATTGGCCTAATTTTGACCCTAAAA 2 158 0 TGGCTAATTT 0.880066 -143 TGACTGTTTTTGGACTAAATTTTGAACCAAAA 3 121 0 TGGCTAAATT 0.97616 -180 GTTAAATTTGTGCTAAAAATTTGACTGTTTTT 3 142 0 TGCAAAAATT 0.823528 -159 CCCCTAAAACTGGGATAAATTTTCTTGCAAAA 3 216 0 TGGATAAATT 0.941196 -85 TCTCACTTTTTGCAATAAATGTATGCCAAAAA 5 23 1 TGCATAAATT 0.963018 -108 GCAAGGATGAAACTCTAAATGTTGGGTTAGGT 6 273 1 AACCTAAATT 0.731948 -28 *** ****** * Masking position 7 Map Score: 4.5745 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 33 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 ********** No masking Map Score: -2.16472e-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 12 ********** No masking Map Score: -2.16472e-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 13 ********** No masking Map Score: -2.16472e-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