AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -imalT_mpneu_opreg_300.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 rpsJ 93 ribosomal protein S10; similar to Swiss-Prot Accession Number P38518, from T. maritima #5 1674374 246 VXpSPT7_orf112 Protein #6 1674375 121 putative lipoprotein, MG149 homolog, from M. genitalium #7 1674376 153 MG148 homolog, from M. genitalium #8 hlyC 25 hemolysin (hlyC) homolog protein; similar to GenBank Accession Number G64060, from H. influenzae #9 infB 280 protein synthesis initiation factor 2; similar to Swiss-Prot Accession Number P04766, from B. stearothermophilus Motif number 1 TGAAAGCAGTTTAAACCAGCAAT 1 10 1 TTTAACCAAA 0.909168 -14 AACGGTTAATTTTTAGCAATTTAAGTAGTTTTA 2 115 0 TTTTGCAATA 0.835417 -186 ATTGGCCTAATTTTGACCCTAAAACTAATTCAA 2 149 0 TTTTACCCAA 0.932403 -152 GTAGAGATTTTTTAAAAAAAGAAAGCGGGAAAT 2 180 0 TTTAAAAAAA 0.602682 -121 AAATCTCTACTTTTTACCCCCTAAATAACCTAA 2 203 1 TTTTACCCTA 0.819573 -98 ATTCCCCTTCTTTTAGCCTACAACTTCTCTTTT 3 18 1 TTTTGCCTAA 0.620437 -283 AAAGGGAATCTTTTAACAAGAAAAAAGAGAAGT 3 40 0 TTTTACAAAA 0.97115 -261 TTCCCTTTCTTTTTATCAAGAAAATCTCTTTTT 3 65 1 TTTTTCAAAA 0.70876 -236 TAAAGACCACTTTTAAGACATAAAAAAAGAGAT 3 88 0 TTTTAGACAA 0.8744 -213 TTGGACTAAATTTTGAACCAAAATAAAGACCAC 3 111 0 TTTTAACCAA 0.780334 -190 AATTTGACTGTTTTTGGACTAAATTTTGAACCA 3 124 0 TTTTGGACAA 0.60221 -177 AACAGTCAAATTTTTAGCACAAATTTAACTGCA 3 145 1 TTTTAGCAAA 0.905273 -156 TTTTGAACAGTTTTTGCAGTTAAATTTGTGCTA 3 159 0 TTTTGCAGAA 0.744479 -142 TGCAATCATTTTTTTGCAAGAAAATTTATCCCA 3 205 1 TTTTGCAAAA 0.814573 -96 GGGTCAAAAATTGCTACAATAAATACCGTTTTT 3 255 1 TTGCACAAAA 0.584646 -46 CTACTTAATTTTTAAAGAAAAAACGGTATTTAT 3 273 0 TTTAAGAAAA 0.746007 -28 AGCCTTAAGATTGTAGCAAATAA 4 1 0 TTGTGCAAAA 0.793717 -93 AGCGTAGTCATTTTGACCATCAAATTTCACCCT 4 58 1 TTTTACCAAA 0.967789 -36 TGACCATCAAATTTCACCCTTAAGAACTGAGAT 4 71 1 ATTTACCCAA 0.548944 -23 AGTAAGTTTCTTTTAACAATTAAATGGGTCTTT 5 69 1 TTTTACAAAA 0.971455 -178 TGGAAACTAATTTCTACCCTAAAAAGACTACTT 6 20 0 TTTCACCCAA 0.835089 -102 TTAAAACCGTTTTTGGAAACTAATTTCTACCCT 6 33 0 TTTTGAAAAA 0.801495 -89 TTATTTTGAATTTTTAAAAATAAGCCTCTAATT 6 65 0 TTTTAAAAAA 0.839494 -57 GTTTAGCTGTTTTCTGCAAATTAACTCCCCTAG 7 92 0 TTTCGCAATA 0.590579 -62 CCGCTCCAGTTTTAAAGCAGCTACACTTAAATA 9 161 0 TTTAAGCATA 0.369829 -120 TTCCCTTTCCTTTAAACAAGCAATAATGTGATC 9 254 0 TTTAACAAAA 0.907969 -27 **** **** ** Masking position 2 Map Score: 27.5942 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 324 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 TGAAAGCAGTTTAAACCAGCAAT 1 5 1 AGCAGTTTAA 0.615684 -19 TTTAGAGTAAAACTACTTAAATTGCTAAAA 2 108 1 AACTACTTAA 0.909932 -193 TAAATAACCTAACAACTACACAATTAATTC 2 224 1 AACAACTACA 0.904106 -77 GCACAAATTTAACTGCAAAAACTGTTCAAA 3 161 1 AACTGCAAAA 0.78465 -140 TTTAACTACTTAATTTTTAAAGA 3 288 0 AACTACTTAA 0.909932 -13 GAAACTTACTAACAGCAAAAAAGCTCCAAG 5 49 0 AACAGCAAAA 0.876153 -198 AGTTTCTTTTAACAATTAAATGGGTCTTTT 5 73 1 AACAATTAAA 0.787736 -174 ATTGAAATTAAACAACTTCAAAAAAGTAGT 5 138 0 AACAACTTCA 0.892399 -109 GTTCAATTGTGACTGCTAAAAGC 5 234 1 GACTGCTAAA 0.849307 -13 ACCCTAAAAAGACTACTTAAAAGAACC 6 8 0 GACTACTTAA 0.730614 -114 TGATTAAACAAAAAGCTAAATTATTTACCT 7 12 0 AAAAGCTAAA 0.69756 -142 ATTTGCAGAAAACAGCTAAACCATTGTTTC 7 104 1 AACAGCTAAA 0.976055 -50 TCACCTGGCAAACAATTTAAAGTTAATGCC 7 132 1 AACAATTTAA 0.765507 -22 CCAGTTTTAAAGCAGCTACACTTAAATAAT 9 159 0 AGCAGCTACA 0.822277 -122 TCTGCGTCAGAACAGCTTACCTTTAAGCGT 9 220 0 AACAGCTTAC 0.8295 -61 ********** Masking position 10 Map Score: 13.3023 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 382 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 GATGTATGGCAAGACCGCCGAAAAATTACAA 2 5 0 AAAGCAAATT 0.981835 -296 CGCTCTTAGCAATTGTGCACTAAATTTTGACACCTTG 2 63 0 AATGCAAATT 0.969864 -238 CACAATTGCTAAGAGCGCCTGTATATTTAGAGTAAAA 2 83 1 AAAGCTATTT 0.734652 -218 TTTTTAAAAAAAGAAAGCGGGAAATTGGCCTAATTTT 2 168 0 AAAGCAAATG 0.978283 -133 TTGCAGTTAAATTTGTGCTAAAAATTTGACTGTTTTT 3 142 0 ATTGCAAATT 0.762444 -159 AACTGTTCAAAAAATCTCACAAAATTGCAATCATTTT 3 180 1 AAATCAAATG 0.718259 -121 CTTGCCCCCTAAAACTGGGATAAATTTTCTTGCAAAA 3 216 0 AAAGGAAATT 0.934855 -85 TTTAGGGGGCAAGCGGGGTCAAAAATTGCTACAATAA 3 240 1 AACGGAAATT 0.860576 -61 GTGACACAATAAGATCGCCAAAAAGCGGGGTTACTAC 5 106 1 AAAGCAAACG 0.923656 -141 ATGGGAAAATAATAAGGCCTGCAAGCGGCAAACTAGT 5 172 1 AAAGCCAACG 0.656149 -75 GAATTTTTAAAAATAAGCCTCTAATTTAAAACCGTTT 6 54 0 AATGCTAATT 0.86627 -68 AAGTTAAATTAGGTTTAAATTTTAT 8 4 0 AATGGAAATT 0.900489 -22 ACACTATGCAAAGTTGGCGCCAATGTTTAGTTACCAG 9 30 1 AATGCAATTT 0.54922 -251 GCGTTTTTGTAACAGTGCTTTAAAGTTTTTCCGCTCC 9 187 0 AAAGCAAATT 0.982063 -94 CCTTTCCTTTAAACAAGCAATAATGTGATCTAGCTCT 9 247 0 AACGCAATTG 0.838983 -34 ** * ** *** ** Masking position 13 Map Score: 12.6066 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 158 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 ATTTCCCGCTTTCTTTTTTTAAAAAATCTC 2 180 1 TTCTTTTTTT 0.778201 -121 TTTGTTAATTCCCCTTCTTTTAGCCTAC 3 9 1 TTCCCCTTCT 0.916249 -292 AGCCTACAACTTCTCTTTTTTCTTGTTAAA 3 32 1 TTCTCTTTTT 0.972818 -269 TGTTAAAAGATTCCCTTTCTTTTTATCAAG 3 55 1 TTCCCTTTCT 0.97909 -246 TATCAAGAAAATCTCTTTTTTTATGTCTTA 3 78 1 ATCTCTTTTT 0.84944 -223 GACTAATTCCTTATCTTTTTCCAAACTAGT 5 203 0 TTATCTTTTT 0.921443 -44 GGTAAATAATTTAGCTTTTTGTTTAATCAG 7 13 1 TTAGCTTTTT 0.840865 -141 TATCGTTGTATTACCTTTTTTATATATAAA 7 51 0 TTACCTTTTT 0.948992 -103 CGCTTTCCCTTTCCTTTAAACAAG 9 267 0 TTCCCTTTCC 0.916249 -14 ********** Masking position 7 Map Score: 6.72776 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 85 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AAGTAGTTTTACTCTAAATATACAGGCGCT 2 96 0 ACTCTAAATA 0.7766 -205 CCTAATTTTGACCCTAAAACTAATTCAAAA 2 147 0 ACCCTAAAAC 0.985058 -154 TACTTTTTACCCCCTAAATAACCTAACAAC 2 210 1 CCCCTAAATA 0.972477 -91 CCCCGCTTGCCCCCTAAAACTGGGATAAAT 3 228 0 CCCCTAAAAC 0.990446 -73 ACTAATTTCTACCCTAAAAAGACTACTTAA 6 18 0 ACCCTAAAAA 0.976704 -104 CAAATTAACTCCCCTAGAACCCCTATACTA 7 79 0 CCCCTAGAAC 0.974294 -75 ********** Masking position 5 Map Score: 5.59597 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 29 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 AACTACACAATTAATTCCCAATTAATGTAA 2 237 1 TTAATTCCCA 0.969852 -64 TTTGTTAATTCCCCTTCTTTTAGC 3 5 1 TTAATTCCCC 0.974904 -296 TTGAAGTTGTTTAATTTCAATGATTATGGG 5 147 1 TTAATTTCAA 0.726297 -100 GCAGGCCTTATTATTTTCCCATAATCATTG 5 164 0 TTATTTTCCC 0.882479 -83 AGGGTAGAAATTAGTTTCCAAAAACGGTTT 6 33 1 TTAGTTTCCA 0.944323 -89 TTTCTGCAAATTAACTCCCCTAGAACCCCT 7 85 0 TTAACTCCCC 0.9228 -69 GCGCCAATGTTTAGTTACCAGAAAGTCTTT 9 46 1 TTAGTTACCA 0.870342 -235 ********** Masking position 3 Map Score: 3.31283 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 70 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 AAACTAATTCAAAAACGGTTAATTTTTAGC 2 131 0 AAAAACGGTT 0.989671 -170 AATTTAGTCCAAAAACAGTCAAATTTTTAG 3 132 1 AAAAACAGTC 0.803698 -169 ATTTAACTGCAAAAACTGTTCAAAAAATCT 3 167 1 AAAAACTGTT 0.893168 -134 TTTCTTGCAAAAAAATGATTGCAATTTTGT 3 198 0 AAAAATGATT 0.649189 -103 TTTTTAAAGAAAAAACGGTATTTATTGTAG 3 268 0 AAAAACGGTA 0.968047 -33 TACTAACAGCAAAAAAGCTCCAAGCTAAAA 5 43 0 AAAAAAGCTC 0.711607 -204 ATTAGTTTCCAAAAACGGTTTTAAATTAGA 6 42 1 AAAAACGGTT 0.989671 -80 TATTCAGATAAAAGACGGTTTAATTATATT 6 101 0 AAAGACGGTT 0.947517 -21 CTTTATATATAAAAAAGGTAATACAACGAT 7 50 1 AAAAAAGGTA 0.856438 -104 TGCCAGGTGAAACAATGGTTTAGCTGTTTT 7 112 0 AACAATGGTT 0.773331 -42 GCACTGTTACAAAAACGCTTAAAGGTAAGC 9 206 1 AAAAACGCTT 0.962456 -75 ********** Masking position 5 Map Score: 12.2711 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 173 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 AAAAAAAGAAAGCGGGAAATTGGCCTAATT 2 170 0 AGCGGGAAAT 0.670312 -131 GGCTAAAAGAAGGGGAATTAACAAA 3 6 0 AGGGGAATTA 0.893705 -295 TTAGGGGGCAAGCGGGGTCAAAAATTGCTA 3 241 1 AGCGGGGTCA 0.983751 -60 TACACCGAAAAGCGTAGTCATTTTGACCAT 4 48 1 AGCGTAGTCA 0.904948 -46 CGGCTTAACTAGCGCAAACAAGTCCCAATG 5 12 1 AGCGCAAACA 0.942436 -235 ATCGCCAAAAAGCGGGGTTACTACTTTTTT 5 119 1 AGCGGGGTTA 0.967011 -128 TAGGGGTTCTAGGGGAGTTAATTTGCAGAA 7 84 1 AGGGGAGTTA 0.91543 -70 GGGTGGATTTAGCGCAAACACTACCAGGTC 9 123 1 AGCGCAAACA 0.942436 -158 TTAAAACTGGAGCGGAAAAACTTTAAAGCA 9 179 1 AGCGGAAAAA 0.939891 -102 ********** Masking position 1 Map Score: 4.53324 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 107 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 GAGTAAAACTACTTAAATTGCTAAAAATTA 2 112 1 ACTTAAATTG 0.831178 -189 TGAACAATTTAGATAAATTTACATTAATTG 2 255 0 AGATAAATTT 0.834115 -46 CACCGTAGTTAGTTCAATTTAGGTAAAG 2 283 1 AGTTCAATTT 0.932045 -18 GTCCAAAAACAGTCAAATTTTTAGCACAAA 3 138 1 AGTCAAATTT 0.867653 -163 CAGTTTTTGCAGTTAAATTTGTGCTAAAAA 3 155 0 AGTTAAATTT 0.965588 -146 GGAATTAGTCAGTTCAATTGTGACTGCTAA 5 223 1 AGTTCAATTG 0.943062 -24 TTAAACAAAAAGCTAAATTATTTACCTT 7 9 0 AGCTAAATTA 0.799776 -145 GTTCTAGGGGAGTTAATTTGCAGAAAACAG 7 89 1 AGTTAATTTG 0.842311 -65 AAGTTAAATTAGGTTTAAATT 8 15 0 AGTTAAATTA 0.937651 -11 ********** Masking position 6 Map Score: 6.55893 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 50 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 ATTTAGAGTAAAACTACTTAAATTGCTAAA 2 107 1 AAACTACTTA 0.907869 -194 TTTGACCCTAAAACTAATTCAAAAACGGTT 2 141 0 AAACTAATTC 0.84299 -160 CTAAATAACCTAACAACTACACAATTAATT 2 223 1 TAACAACTAC 0.696278 -78 ACCAAAATAAAGACCACTTTTAAGACATAA 3 98 0 AGACCACTTT 0.644519 -203 TTTAACTACTTAATTTTTAAAG 3 289 0 TAACTACTTA 0.893337 -12 CTTTTCGGTGTATCCACTTCGACCAAAGCC 4 30 0 TATCCACTTC 0.590571 -64 AAGTTTCTTTTAACAATTAAATGGGTCTTT 5 72 1 TAACAATTAA 0.253781 -175 CATTGAAATTAAACAACTTCAAAAAAGTAG 5 139 0 AAACAACTTC 0.928586 -108 ACAATTGAACTGACTAATTCCTTATCTTTT 5 214 0 TGACTAATTC 0.700656 -33 TACCCTAAAAAGACTACTTAAAAGAACC 6 9 0 AGACTACTTA 0.834755 -113 CCGTTTTTGGAAACTAATTTCTACCCTAAA 6 30 0 AAACTAATTT 0.550374 -92 TTCACCTGGCAAACAATTTAAAGTTAATGC 7 131 1 AAACAATTTA 0.658565 -23 TCGTTAATCTAACCATTTCACACTATGCA 9 10 1 TAACCATTTC 0.79272 -271 ********** Masking position 6 Map Score: 2.05455 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 307 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 11 GTAATTTTTCGGCGGTCTTGCCATACATCA 2 13 1 GGCGGTCTTG 0.988007 -288 TAAATATACAGGCGCTCTTAGCAATTGTGC 2 82 0 GGCGCTCTTA 0.987066 -219 CCCGCTTTTTGGCGATCTTATTGTGTCACT 5 105 0 GGCGATCTTA 0.980947 -142 CTACCAGGTCGGGGGTATTATTTAAGTGTA 9 143 1 GGGGGTATTA 0.929515 -138 ********** Masking position 6 Map Score: 0.158103 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 ********** No masking Map Score: 2.06301e-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: 2.06301e-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: 2.06301e-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