AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -irpoN_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 1673728 236 MG064 homolog, from M. genitalium #2 fruA 300 fructose-permease IIBC component; similar to Swiss-Prot Accession Number P20966, from E. coli #3 soj 300 protein (soj) homolog; similar to Swiss-Prot Accession Number P37522, from B. subtilis #4 cysA 67 sulfate transport ATP-binding protein; similar to Swiss-Prot Accession Number P14788, from Synechococcus sp #5 rpsJ 93 ribosomal protein S10; similar to Swiss-Prot Accession Number P38518, from T. maritima #6 1674374 246 VXpSPT7_orf112 Protein #7 1674375 121 putative lipoprotein, MG149 homolog, from M. genitalium #8 1674376 153 MG148 homolog, from M. genitalium #9 hlyC 25 hemolysin (hlyC) homolog protein; similar to GenBank Accession Number G64060, from H. influenzae #10 infB 280 protein synthesis initiation factor 2; similar to Swiss-Prot Accession Number P04766, from B. stearothermophilus Motif number 1 TAGCAAAACGGGTAACAAAATCGATTCCCT 1 63 0 GGTAACAAAA 0.792037 -174 TGTTCAATTGGGAAGCCAAACTTAATCTCG 1 195 1 GGAAGCCAAA 0.789158 -42 CCCAGGAACTGGAATCTAAATTTATTATAA 2 258 1 GGAATCTAAA 0.729755 -43 GCTATTAGTAGGTAAATAATATTAAGATAA 3 45 1 GGTAAATAAT 0.94831 -256 AATAGTAAACGGCAAACAAATTTGTTTTCC 3 125 1 GGCAAACAAA 0.92029 -176 ATAGGAAAATGGAAAACAAATTTGTTTGCC 3 135 0 GGAAAACAAA 0.944926 -166 TAATTTCGTCGGTAAATAATACCGGAATAA 3 237 1 GGTAAATAAT 0.94831 -64 AATGATTATGGGAAAATAATAAGGCCTGCA 6 165 1 GGAAAATAAT 0.948311 -82 AACCGTTTTTGGAAACTAATTTCTACCCTA 7 32 0 GGAAACTAAT 0.955061 -90 AAGGTAAATAATTTAGCTTTTT 8 3 1 GGTAAATAAT 0.94831 -151 TGTTTCACCTGGCAAACAATTTAAAGTTAA 8 128 1 GGCAAACAAT 0.92029 -26 AAGACTTTCTGGTAACTAAACATTGGCGCC 10 45 0 GGTAACTAAA 0.955061 -236 ********** Masking position 4 Map Score: 14.9587 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 108 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 CTAAAGAACTAGCCAAACAGCCAAAGGTCAA 1 25 1 AGCAAACAGC 0.958431 -212 GAAGAGCATACTGAAAACAGCTAGCAAAACG 1 83 0 CTAAAACAGC 0.857051 -154 TCTTTCTTGTTAACAAAAAGCGCAATAAAAA 2 94 1 TACAAAAAGC 0.916738 -207 CAAAAAGCGCAATAAAAAAGCAGACCACTGA 2 107 1 AAAAAAAAGC 0.942519 -194 GAAGTGGATACACCGAAAAGCGTAGTCATTT 5 40 1 CACGAAAAGC 0.943274 -54 AAAAAGCTCCAAGCTAAAAGCATTGGGACTT 6 31 0 AACTAAAAGC 0.925407 -216 ACTTACTAACAGCAAAAAAGCTCCAAGCTAA 6 45 0 AGAAAAAAGC 0.931153 -202 ACAATAAGATCGCCAAAAAGCGGGGTTACTA 6 111 1 CGCAAAAAGC 0.983251 -136 TCAATTGTGACTGCTAAAAGC 6 236 1 CTCTAAAAGC 0.87868 -11 ATTGCTGATTAAACAAAAAGCTAAATTATTT 8 16 0 AACAAAAAGC 0.978084 -138 AGTTAATTTGCAGAAAACAGCTAAACCATTG 8 99 1 CAAAAACAGC 0.942454 -55 ** ******** Masking position 6 Map Score: 11.5942 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 139 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GCAAACAATTTATAAAAATTTTTGCGTTTTCTTTTATT 2 9 0 TAAATTTTTT 0.906274 -292 CGAGCTCTTCTAAAAATTCCGTTTCTTTCTTGTTAACAAA 2 71 1 TAATCGTTTT 0.864347 -230 AATCTAAATTTATTATAAATATTGGATTTTCTGACTTTAG 2 270 1 TAAATATTTT 0.663856 -31 TTAATATTATTAGTATTTATTTAGTATTATGCTA 3 5 0 TAATTTTTTT 0.958558 -296 ATTATTTACCTACTAATAGCTTAATATTATTAGTATTTAT 3 25 0 TAATCTTTTT 0.973767 -276 TTCTTTAACATAATATTATCTTAATATTATTTACCTACTA 3 50 0 TAATCTTTTT 0.973767 -251 GCTTAAATTCTAATATTTATTTAGTATTATTCCGGTATTA 3 253 0 TAATTTTTTT 0.958558 -48 TATCCACTTCGACCAAAGCCTTAAGATTGTAGCAAATAA 5 10 0 GAAACTTTTT 0.877164 -84 TGTGTCACTTTAAAAGACCCATTTAATTGTTAAAAGAAAC 6 74 0 TAAACATTTT 0.760153 -173 AAAGCGGGGTTACTACTTTTTTGAAGTTGTTTAATTTCAA 6 127 1 TAATTTTTTT 0.958558 -120 CAATTGAACTGACTAATTCCTTATCTTTTTCCAAACTAGT 6 203 0 GAATCTTTTT 0.944696 -44 AAGGTAAATAATTTAGCTTTTTGTTTAATCAG 8 3 1 GGATTTTTTT 0.755481 -151 ATGGCATTAACTTTAAATTGTTTGCCAGGTG 8 133 0 TGATCTTTTT 0.91507 -21 AGCGTTTTTGTAACAGTGCTTTAAAGTTTTTCCGCTCCAG 10 185 0 TAATTTTTTT 0.958558 -96 ** * * *** ** * Masking position 5 Map Score: 13.9747 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 32 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TAACAGTAGCATAAAGAAGAGCATACTGAA 1 99 0 ATAAAGAAGA 0.832886 -138 AATAAAAGAAAACGCAAAAAT 2 2 1 ATAAAAGAAA 0.894252 -299 TAATATTATGTTAAAGAAAAAGTTTCTCTA 3 72 1 TTAAAGAAAA 0.934982 -229 TCTCTATACTATATAGAAGATTAGTATTTA 3 96 1 ATATAGAAGA 0.639242 -205 AGAAAGTGGTATATAGGAAAATGGAAAACA 3 147 0 ATATAGGAAA 0.891106 -154 CATTTAATTGTTAAAAGAAACTTACTAACA 6 65 0 TTAAAAGAAA 0.894252 -182 TTTTGAATTTTTAAAAATAAGCCTCTAATT 7 65 0 TTAAAAATAA 0.542058 -57 AAATTGCTGATTAAACAAAAAGCTAAATTA 8 19 0 TTAAACAAAA 0.70415 -135 TTTTTTATATATAAAGGAAATTGCTGATTA 8 36 0 ATAAAGGAAA 0.958363 -118 TTTCCTTTATATATAAAAAAGGTAATACAA 8 46 1 ATATAAAAAA 0.652589 -108 ACAAAAACGCTTAAAGGTAAGCTGTTCTGA 10 214 1 TTAAAGGTAA 0.837581 -67 TATTGCTTGTTTAAAGGAAAGGGAAAGCG 10 262 1 TTAAAGGAAA 0.958363 -19 ********** Masking position 5 Map Score: 8.17022 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 150 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TTTATAAAAATTTTTGCGTTTTCTTTTATT 2 11 0 TTTTTGCGTT 0.934765 -290 GTCTGCTTTTTTATTGCGCTTTTTGTTAAC 2 102 0 TTATTGCGCT 0.959399 -199 AAAACAAATTTGTTTGCCGTTTACTATTAA 3 123 0 TGTTTGCCGT 0.910781 -178 ACCACTTTCTTTTTCGCGGTTGGGCACATT 3 167 1 TTTTCGCGGT 0.945862 -134 TTATTTAGTATTATTCCGGTATTATTTACC 3 247 0 TTATTCCGGT 0.878011 -54 CATTGGGACTTGTTTGCGCTAGTTAAGCCG 6 12 0 TGTTTGCGCT 0.984046 -235 GCTTGGAGCTTTTTTGCTGTTAGTAAGTTT 6 48 1 TTTTTGCTGT 0.893052 -199 GACCTGGTAGTGTTTGCGCTAAATCCACCC 10 123 0 TGTTTGCGCT 0.984046 -158 TGCTTTAAAGTTTTTCCGCTCCAGTTTTAA 10 179 0 TTTTTCCGCT 0.957942 -102 ********** Masking position 4 Map Score: 9.90232 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 72 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 TGTCAACTAAAGAACTAGCCAAACAGCCAA 1 19 1 AGAACTAGCC 0.940936 -218 GTTAATAACTTGAACTAGCCACAGGTTTAA 1 162 1 TGAACTAGCC 0.987136 -75 GCACTTTTAATGAACTAGTTTTT 1 224 1 TGAACTAGTT 0.945458 -13 AGTGTTTAATTGAACTGGCCTGTCCCGTTG 4 29 1 TGAACTGGCC 0.989324 -39 CAGTCACAATTGAACTGACTAATTCCTTAT 6 219 0 TGAACTGACT 0.908704 -28 TTGCATAGTGTGAAATGGTTAGATTAACGA 10 11 0 TGAAATGGTT 0.730838 -270 AGCAATAATGTGATCTAGCTCTGCGTCAGA 10 239 0 TGATCTAGCT 0.929538 -42 ********** Masking position 3 Map Score: 4.64839 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 35 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ATTCCAGGTAAAGTTAATAACTTGAACTAGC 1 150 1 AATTAATAAC 0.92806 -87 GGTTGGGCACATTTTAATACCACGTTGGTAG 3 184 1 ATTTAATACC 0.953805 -117 CGTTGGTAGCATCTTAATACCCTGATGGTAT 3 206 1 ATTTAATACC 0.953806 -95 TTTACCGACGAAATTAATACCATCAGGGTAT 3 222 0 AATTAATACC 0.982579 -79 TGTTAAAAGAAACTTACTAACAGCAAAAAAG 6 56 0 AATTACTAAC 0.774084 -191 ATAAGCCTCTAATTTAAAACCGTTTTTGGAA 7 48 0 AATTAAAACC 0.953801 -74 AAACAATTTAAAGTTAATGCCAT 8 141 1 AATTAATGCC 0.937424 -13 ATAAAATTTAAACCTAATTTAACT 9 4 1 AATTTAAACC 0.787243 -22 ** ******** Masking position 1 Map Score: 5.81758 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 41 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CAATTGAACACAGTTAAACCTGTGGCTAGT 1 175 0 CAGTTAAACC 0.973499 -62 CAGGCCAGTTCAATTAAACACTTAAAGAAT 4 21 0 CAATTAAACA 0.766585 -47 GCCTGTCCCGTTGTTAAACCTGACATGTTT 4 46 1 TTGTTAAACC 0.932063 -22 TTGTTTGCGCTAGTTAAGCCGT 6 3 0 TAGTTAAGCC 0.954999 -244 TAAGCAAATATAATTAAACCGTCTTTTATC 7 95 1 TAATTAAACC 0.936099 -27 TTGCAGAAAACAGCTAAACCATTGTTTCAC 8 106 1 CAGCTAAACC 0.972977 -48 GACTTTCTGGTAACTAAACATTGGCGCCAA 10 43 0 TAACTAAACA 0.766586 -238 AGAAAGTCTTTTGCTAAGCCGCTACTTTTG 10 65 1 TTGCTAAGCC 0.883925 -216 ********** Masking position 6 Map Score: 4.55129 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 106 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 TAGCATAATACTAAATAAATACTAA 3 6 1 TAATACTAAA 0.939854 -295 TAAATACTAATAATATTAAGCTATTAGTAG 3 26 1 TAATATTAAG 0.957915 -275 AGTAGGTAAATAATATTAAGATAATATTAT 3 51 1 TAATATTAAG 0.957915 -250 AATATTAAGATAATATTATGTTAAAGAAAA 3 62 1 TAATATTATG 0.848836 -239 GATTAGTATTTAATAGTAAACGGCAAACAA 3 114 1 TAATAGTAAA 0.894636 -187 AATACCGGAATAATACTAAATAAATATTAG 3 254 1 TAATACTAAA 0.939854 -47 ********** Masking position 5 Map Score: 2.83239 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 12 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 AAGAGCTCGCTTAATTCCGGAATTTGCTGT 2 50 0 TTAATTCCGG 0.849841 -251 TGGGCACATTTTAATACCACGTTGGTAGCA 3 187 1 TTAATACCAC 0.945465 -114 TGGTAGCATCTTAATACCCTGATGGTATTA 3 209 1 TTAATACCCT 0.957582 -92 ACCGACGAAATTAATACCATCAGGGTATTA 3 220 0 TTAATACCAT 0.954363 -81 TCGTCGGTAAATAATACCGGAATAATACTA 3 242 1 ATAATACCGG 0.908924 -59 AGCCTCTAATTTAAAACCGTTTTTGGAAAC 7 46 0 TTAAAACCGT 0.854921 -76 CAATTTAAAGTTAATGCCAT 8 144 1 TTAATGCCAT 0.865494 -10 CTACACTTAAATAATACCCCCGACCTGGTA 10 144 0 ATAATACCCC 0.872634 -137 ********** Masking position 4 Map Score: 2.64569 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 = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 CGATTTTGTTACCCGTTTTGCTAGCTGTTT 1 70 1 ACCCGTTTTG 0.933803 -167 AACTGGCCTGTCCCGTTGTTAAACCTGACA 4 41 1 TCCCGTTGTT 0.919958 -27 TCTAATTTAAAACCGTTTTTGGAAACTAAT 7 42 0 AACCGTTTTT 0.974323 -80 AATATAATTAAACCGTCTTTTATCTGAATA 7 101 1 AACCGTCTTT 0.93279 -21 AAAACAGCTAAACCATTGTTTCACCTGGCA 8 112 1 AACCATTGTT 0.848343 -42 CGCTAAATCCACCCGTAGTTGATGCTCTAA 10 107 0 ACCCGTAGTT 0.931763 -174 GCTTACCTTTAAGCGTTTTTGTAACAGTGC 10 206 0 AAGCGTTTTT 0.879493 -75 ********** Masking position 6 Map Score: 1.46357 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 101 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 12 ********** No masking Map Score: -4.59478e-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: -4.59478e-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 GCTGTTTTCAGTATGCTCTTCTTTATGCTAC 1 93 1 GTAGCTCTTC 0.989568 -144 TAGTGTTGTTGTACGCTATTCCAGGTAAAGT 1 133 1 GTAGCTATTC 0.936212 -104 CCGGAATTAAGCGAGCTCTTCTAAAAATTCC 2 60 1 GCGGCTCTTC 0.951561 -241 CCTTAGCAGGGTGTCCTCTTAACCACTTGAG 2 221 1 GTGCCTCTTA 0.929872 -80 TACCACGTTGGTAGCATCTTAATACCCTGAT 3 201 1 GTACATCTTA 0.718777 -100 GCTTTTCGGTGTATCCACTTCGACCAAAGCC 5 30 0 GTACCACTTC 0.937483 -64 ACGCTTAAAGGTAAGCTGTTCTGACGCAGAG 10 220 1 GTAGCTGTTC 0.956051 -61 *** ******* Masking position 9 Map Score: 0.654253 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 23 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 ********** No masking Map Score: -4.59478e-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