AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_mgen_reg_100.orf -o02010_mgen_100.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MG042 197 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #2 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #3 MG109 59 serine/threonine protein kinase, putative #4 MG115 24 conserved hypothetical protein #5 MG142 258 translation initiation factor 2 (infB) #6 MG144 24 conserved hypothetical protein #7 MG148 38 conserved hypothetical protein #8 MG149 75 lipoprotein, putative #9 MG149.1 90 conserved hypothetical protein #10 MG150 89 ribosomal protein S10 (rpS10) #11 MG186 300 lipoprotein, putative #12 MG289 300 high affinity transport system protein P37 #13 MG304 176 ABC transporter, ATP binding protein #14 MG412 120 lipoprotein, putative Motif number 1 CTTAGCATATTTTAATCAATTAAATCTGT 1 9 1 ATTTTATCAA 0.909222 -189 AATCTGTTTATTTTTTAATAGTAAAAACACA 1 33 1 TTTTTAATAG 0.789196 -165 AATTAAGATATTTTTTATCAAAAATTAGCAT 1 126 1 TTTTTATCAA 0.9614 -72 TAAATACTTAATTTTCAATAAAAAACGTTAA 1 175 0 ATTTTAATAA 0.876193 -23 TAAAGCAGGATTTATAATCCAACTTCATTTG 2 97 0 TTTATATCCA 0.667439 -137 TTTGATACTTATTTTCAACAATATCACCTAT 3 13 0 ATTTTAACAA 0.944413 -47 CAAGACTTTGTTTATTAACAAGAAAACATTT 5 23 1 TTTATAACAA 0.91682 -236 GTAAAAGTTCTCTTTTAACAAAATGTTTTCT 5 43 0 TCTTTAACAA 0.744082 -216 TGCCCTTGAGATTTTGATTAAGATCAATTTC 5 100 0 ATTTTATTAA 0.806092 -159 CTTTGAGGTGTTTTTTATCTAGCTTTAAACC 5 154 0 TTTTTATCTA 0.938701 -105 CCTTAAGGTGTTTTTCAACTACAGCTTTGAG 5 178 0 TTTTTAACTA 0.963121 -81 CTTACACTGTTTTTTTATTTAATTGAGAAAA 9 63 1 TTTTTATTTA 0.863991 -28 CCGTAGTCAATTTATTAACTAACTAGTGAAC 10 60 1 TTTATAACTA 0.871569 -30 TGACAGTTGATTTTTGATCTTTTTTCACCGG 11 48 0 TTTTTATCTT 0.58297 -253 TATTTACTTATTTATTAACCATTGTTACCCA 11 159 1 TTTATAACCA 0.774073 -142 TGTTACCCAATTTTTCAACCACTTCCCCACT 11 181 1 TTTTTAACCA 0.929539 -120 TAAATTGTTATTTTTTAACAATTTGAACAAT 11 215 1 TTTTTAACAA 0.973188 -86 GTCTGTTTTAGTTTTAAACAAATTCAATTTC 12 22 0 GTTTTAACAA 0.799967 -279 CCGAATTACTTTTTTGAATTAAAGCTATTCT 12 100 0 TTTTTAATTA 0.915544 -201 TTAAAAAATATTTTTTAATAAAGATTAATTG 12 134 1 TTTTTAATAA 0.943543 -167 GTGAATATTTATTTTTATTAAAAACTTATAT 12 191 1 ATTTTATTAA 0.806092 -110 TTTGTAGTCTATTTTTAACTAATATAAAAAA 12 227 1 ATTTTAACTA 0.910692 -74 AAATTAATTGTTTTTAAATATTCAACTTTTT 12 253 0 TTTTTAATAT 0.623222 -48 TTAATCCTGGATTATTAATTATCAAAATTAA 12 277 0 ATTATAATTA 0.523332 -24 TGTGCTGCTCTTTTTTATTTGGAATATGTTC 13 23 0 TTTTTATTTG 0.566431 -154 TGCTTTTTTGTTTTTTATCTACCAAAAAACA 13 59 1 TTTTTATCTA 0.938701 -118 ATTTTTAAAATTTATAAATAAGCTTAGTTTG 13 108 1 TTTATAATAA 0.823134 -69 AATGAAATGCATTTTTATTAATTGCAAAT 14 9 0 ATTTTATTAA 0.806092 -112 TTTAGTCTAGTTTTTTCACAAGCCAATTAAT 14 43 0 TTTTTCACAA 0.744109 -78 TTTTTAAACAGATTAAATCTT 14 110 0 TTTTTAACAG 0.900226 -11 ***** ***** Masking position 5 Map Score: 37.0485 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 818 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 ACCTTGTTTCTATTTAACAAAATTGGTTTGAAAA 1 69 1 TATTAAAATT 0.390388 -129 GTATAACAATTTTTTATGCTAATTTTTGATAAAA 1 138 0 TTTTCTAATT 0.977496 -60 GCATAAAAAATTGTTATACTAATTAACGTTTTTT 1 153 1 TTTTCTAATT 0.977496 -45 AAAAAACAGGTTCTTTTTTTATTTCTATTTAGTA 2 209 1 TTTTTTATTT 0.943667 -25 CAATTTCAAGTTGGTTGTCTAATTTTACAAGACG 5 73 0 TTGTCTAATT 0.938942 -186 TCTAAACTTTTTGCAACTAATTAATTAGTTAA 7 9 1 TTTGCTAATT 0.790801 -30 TATTAGTTAACTAATTAATTAGTTGC 7 23 0 TTGTCTAATT 0.938942 -16 GGTTTAATTTGTTAGCTTATTTAGAAAAATTC 8 9 1 TTTTTTATTT 0.943667 -67 CACCTAATTATAATTTGCTTATTTTGAATTTTTC 8 34 0 TATTTTATTT 0.788983 -42 AAAAAGATAGTTATTAACTTAATTTAGAATTAAC 9 14 1 TTTTTTAATT 0.956803 -77 CTTACACTGTTTTTTTATTTAATTGAGAAAATAT 9 63 1 TTTTTTAATT 0.956803 -28 AGTTCACTAGTTAGTTAATAAATTGACTACGGAT 10 58 0 TTGTTAAATT 0.740831 -32 ATGGGTCCAGTTGTTCCACTATTT 11 1 0 TTTTCTATTT 0.970459 -300 TGACAGTTGATTTTTGATCTTTTTTCACCGGATA 11 45 0 TTTTCTTTTT 0.658578 -256 TTTACCCAAATTATTTACTTATTTATTAACCATT 11 148 1 TTTTTTATTT 0.943667 -153 TTATTAACCATTGTTACCCAATTTTTCAACCACT 11 170 1 TTTTCAATTT 0.922929 -131 TAAATTGTTATTTTTTAACAATTTGAACAATTAA 11 215 1 TTTTCAATTT 0.922928 -86 CCAGTTAAGCTTGTTAGCTAAATTTACATTAATA 11 266 0 TTTTTAAATT 0.889797 -35 TATATTCAAATTTGTAGTCTATTTTTAACTAATA 12 217 1 TTGTCTATTT 0.920824 -84 ATATTCAACTTTTTTATATTAGTTAAAAATAGAC 12 233 0 TTTTTTAGTT 0.865396 -68 TAAAAACAATTAATTTTGATAATTAATAATCCAG 12 268 1 TATTATAATT 0.637375 -33 TAGCTCTGACTTATTTTTAAAATTTATAAATAAG 13 96 1 TTTTAAAATT 0.741642 -81 CTCAGGTTATTATTTAGTCTAGTTTTTTCACAAG 14 52 0 TATTCTAGTT 0.737813 -69 ** ** ****** Masking position 13 Map Score: 28.5664 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 254 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 ATTTTAATCAATTAAATCTGTTTATTTTTTAAT 1 19 1 ATTAAACTTT 0.911131 -179 TAAAAACACAATTTAACCTTGTTTCTATTTAAC 1 54 1 ATTTAACTTT 0.858035 -144 TGTTATACTAATTAACGTTTTTTATTGAAAATT 1 164 1 ATTAACTTTT 0.744372 -34 AGGATTTATAATCCAACTTCATTTGAAACCAAA 2 89 0 ATCCAATTTT 0.882749 -145 TTTAAAAGCTTTTCAATTTGATACTTATTTTCA 3 27 0 TTTCAATTTA 0.632363 -33 TTAAGATCAATTTCAAGTTGGTTGTCTAATTTT 5 81 0 TTTCAATTTT 0.881165 -178 TAGGATTAATTTTACTTCAAGCTG 6 8 0 ATTAATTTTT 0.832334 -17 AACTGGACCCATTAAAACTGCTTATCCGGTGAA 11 23 1 ATTAAACTTT 0.911131 -278 TTTTAAACAAATTCAATTTCGTTTGTAACTT 12 9 0 ATTCAATTTT 0.971729 -292 GTTGCTGGCAATTAATCTTTATTAAAAAATATT 12 140 0 ATTAATTTTT 0.832225 -161 TATTACTTAGATTCAAGTTGCTGGCAATTAATC 12 156 0 ATTCAATTTG 0.823726 -145 TAAAGTGAATATTTATTTTTATTAAAAACTTAT 12 187 1 ATTTATTTTT 0.745251 -114 AAAAACTTATATTCAAATTTGTAGTCTATTTTT 12 210 1 ATTCAATTTA 0.888217 -91 GTTTTTAAATATTCAACTTTTTTATATTAGTTA 12 242 0 ATTCAATTTT 0.971671 -59 ATTATTAATTATCAAAATTAATTGTTTTTAAAT 12 265 0 ATCAAATTTT 0.821651 -36 CTGACTTATTTTTAAAATTTATAAATAAGCTTA 13 101 1 TTTAAATTTA 0.517512 -76 AATGCATTTCATTTAAATTAATTGGCTTGTGAA 14 27 1 ATTTAATTTT 0.923425 -94 TTTAGAAAAGATTTAATCTGTTTAAAAA 14 103 1 ATTTAACTTT 0.858056 -18 ****** ** ** Masking position 9 Map Score: 15.8663 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 182 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TTTTACTATTAAAAAATAAACAGATTTAAT 1 29 0 AAAAAATAAA 0.790097 -169 AAAAAAATGATACTAATAACGATTACTAG 2 10 0 TACTAATAAC 0.473107 -224 TTTTTTTATAAAATAATCAAGAACATCAGC 2 33 1 AAATAATCAA 0.896482 -201 TACTAAATAGAAATAAAAAAAGAACCTGTT 2 213 0 AAATAAAAAA 0.742823 -21 TGCAACTAATAACAAGACTTTGT 5 4 1 AACTAATAAC 0.935924 -255 AAAAACACTCAAATAATAACCCCTGCCCTT 5 124 0 AAATAATAAC 0.943093 -135 AACTTTTTGCAACTAATTAATTAGTTAACT 7 15 1 AACTAATTAA 0.497499 -24 GCTTATTTAGAAAAATTCAAAATAAGCAAA 8 25 1 AAAAATTCAA 0.449014 -51 ATTTAGAATTAACTAATGACAGTGTACACT 9 35 1 AACTAATGAC 0.664634 -56 TTTCTCAATTAAATAAAAAAACAGTGTAAG 9 63 0 AAATAAAAAA 0.742823 -28 TTGGTGTATCAACTAAAAACTAAAGCGTTA 10 27 0 AACTAAAAAC 0.774686 -63 AAATCCCCATAACTATTCAACGGCGTAGCG 11 98 0 AACTATTCAA 0.700727 -203 ATGGGGATTTAAATAATCACACCAAGTTAA 11 118 1 AAATAATCAC 0.921237 -183 TCAAATTGTTAAAAAATAACAATTTATAGA 11 211 0 AAAAAATAAC 0.835629 -90 TAACAATTTGAACAATTAAATTGCAAAAAA 11 230 1 AACAATTAAA 0.504386 -71 ATTAAATTGCAAAAAATAACTATATTAATG 11 244 1 AAAAAATAAC 0.835629 -57 ACTTGAATCTAAGTAATAAAGTGAATATTT 12 171 1 AAGTAATAAA 0.641571 -130 TAATAAAAATAAATATTCACTTTATTACTT 12 181 0 AAATATTCAC 0.782038 -120 AATTGTTTTTAAATATTCAACTTTTTTATA 12 249 0 AAATATTCAA 0.72652 -52 AACATATTCCAAATAAAAAAGAGCAGCACA 13 24 1 AAATAAAAAA 0.742823 -153 ATTTGCAATTAATAAAAATGCATTTC 14 7 1 AATTAATAAA 0.54704 -114 AAACTAGACTAAATAATAACCTGAGTGTCA 14 61 1 AAATAATAAC 0.943093 -60 ********** Masking position 5 Map Score: 22.0009 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 210 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TTTACTATTAAAAAATAAACAGATTTAATTG 1 27 0 AAAATAAACA 0.65768 -171 CTTAATTTTCAATAAAAAACGTTAATTAGTA 1 169 0 AATAAAAACG 0.621332 -29 TTTATAAAATAATCAAGAACATCAGCACATG 2 37 1 AATCAGAACA 0.689717 -197 AAGCATGATTACAATAAAGCAGGATTTATAA 2 111 0 ACAAAAAGCA 0.947548 -123 CCAGCTTCTAAATCTAAAGCATGATTACAAT 2 127 0 AATCAAAGCA 0.890244 -107 TGGTTACCTGAAACAAAAGTAACCAGCTTCT 2 149 0 AAACAAAGTA 0.59431 -85 TTGTTTATTAACAAGAAAACATTTTGTTAAA 5 30 1 ACAAAAAACA 0.948564 -229 TCTAGCTTTAAACCAAAAACACTCAAATAAT 5 137 0 AACCAAAACA 0.899381 -122 TCTCAATTAAATAAAAAAACAGTGTAAGTGT 9 60 0 ATAAAAAACA 0.740461 -31 TATCAACTAAAAACTAAAGCGTTATGATTGT 10 20 0 AAACAAAGCG 0.873742 -70 TCAAATTGTTAAAAAATAACAATTTATAGAG 11 210 0 AAAAATAACA 0.688467 -91 AATTTGTTTAAAACTAAAACAGACAGGGAAA 12 29 1 AAACAAAACA 0.965862 -272 TATTCCAAATAAAAAAGAGCAGCACAACAGC 13 28 1 AAAAAGAGCA 0.855172 -149 TAGATAAAAAACAAAAAAGCAGCTGTTGTGC 13 49 0 ACAAAAAGCA 0.947548 -128 TTTTTTATCTACCAAAAAACAGATTTTTAGC 13 69 1 ACCAAAAACA 0.853508 -108 AATACCCAAAACACCAAAACAAT 13 164 1 ACACAAAACA 0.958742 -13 **** ****** Masking position 8 Map Score: 11.2213 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 282 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TTATCAAAAATTAGCATAAAAAATTGTTATA 1 140 1 TTAGCATAAA 0.557077 -58 TGTTTTCTTGTTAATAAACAAAGTCTTGTTA 5 20 0 TTAATAAAAA 0.677152 -239 TATTAGTTAACTAATTAATTAGT 7 26 0 TTAGTTAATA 0.713077 -13 TTTTTCTAAATAAGCTAACAAATTAAACC 8 9 0 TAAGCTAAAA 0.900615 -67 AAATTCAAAATAAGCAAATTATAATTAGGTG 8 37 1 TAAGCAAATA 0.650694 -39 ATTTTTAGTAAAGAAAGACACCTAA 8 61 0 TTAGTAAAAA 0.95119 -15 AATTCTAAATTAAGTTAATAACTATCTTTTT 9 14 0 TAAGTTAAAA 0.920106 -77 TTTTCTCAATTAAATAAAAAAACAGTGTAAG 9 63 0 TAAATAAAAA 0.623148 -28 AGTTCACTAGTTAGTTAATAAATTGACTACG 10 61 0 TTAGTTAAAA 0.917438 -29 GGTTAATAAATAAGTAAATAATTTGGGTAAA 11 148 0 TAAGTAAAAA 0.936218 -153 TAATGTAAATTTAGCTAACAAGCTTAACTGG 11 269 1 TTAGCTAAAA 0.920256 -32 CTAACTCTGAATAGCAAAAAATATAAGAATA 12 75 1 ATAGCAAAAA 0.573673 -226 CAATTAATCTTTATTAAAAAATATTTTTTAA 12 134 0 TTATTAAAAA 0.535193 -167 AACTTGAATCTAAGTAATAAAGTGAATATTT 12 170 1 TAAGTAATAA 0.568719 -131 CTTTTTTATATTAGTTAAAAATAGACTACAA 12 228 0 TTAGTTAAAA 0.938649 -73 TAGTTTGCTACAAGTTAAAAACCTCAGTTTT 13 132 1 CAAGTTAAAA 0.621528 -45 ******** ** Masking position 3 Map Score: 13.451 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 209 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TCAATTTTGCTGTAAAAAATTAAGATATTTTTTAT 1 109 1 TAAAAATAGA 0.96723 -89 AAAATTAGCATAAAAAATTGTTATACTAATTAACG 1 146 1 TAAAATTATA 0.6571 -52 TTTAAATACTTAATTTTCAATAAAA 1 183 0 TAAATATATT 0.576189 -15 TTGATTATTTTATAAAAAAATGATACTAATAACGA 2 18 0 TAAAAATATA 0.944369 -216 CAGTACCATTTCCAAAAAACTGAGAACCTGAAAAA 2 178 1 TAAAAATAGA 0.970104 -56 ATTAATTAGTTGCAAAAAGTTTAGA 7 1 0 TAAAAATAGA 0.970033 -38 GCTTATCCGGTGAAAAAAGATCAAAAATCAACTGT 11 42 1 TAAAAATAAA 0.8081 -259 ACTCTGAATAGCAAAAAATATAAGAATAGCTTTAA 12 78 1 GAAAAATAGA 0.918369 -223 ATAGCTTTAATTCAAAAAAGTAATTCGGATCTTAA 12 103 1 TAAAAATATT 0.85853 -198 TATTTATTTTTATTAAAAACTTATATTCAAATTTG 12 196 1 TTAAAATATA 0.656893 -105 TTATAAATTTTAAAAATAAGTCAGAGCTAAAAATC 13 90 0 TAAATATAGA 0.879132 -87 TTTGCTACAAGTTAAAAACCTCAGTTTTAAATACC 13 135 1 GAAAAATAGT 0.800011 -42 * ***** * *** Masking position 6 Map Score: 7.72079 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 74 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TATTAAAAAATAAACAGATTTAATTGATTA 1 23 0 TAAACAGATT 0.839928 -175 GAAACAAAAGTAACCAGCTTCTAAATCTAA 2 141 0 TAACCAGCTT 0.971675 -93 TGCAACTAATAACAAGACTTTGTTTATTA 5 10 1 TAACAAGACT 0.734274 -249 AGGTGTTTTTTATCTAGCTTTAAACCAAAA 5 150 0 TATCTAGCTT 0.816634 -109 ATTAAGTTAATAACTATCTTTTTTAG 9 7 0 TAACTATCTT 0.848342 -84 ACTAACTAGTGAACTAGATTTTG 10 77 1 GAACTAGATT 0.837338 -13 TTGCAAAAAATAACTATATTAATGTAAATT 11 250 1 TAACTATATT 0.812876 -51 TAAATTTAGCTAACAAGCTTAACTGGTTGT 11 274 1 TAACAAGCTT 0.93837 -27 TTTTTAAACAGATTAAATCTTTTC 14 107 0 TAAACAGATT 0.839928 -14 ********** Masking position 6 Map Score: 2.43456 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 90 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ACAAGGTTAAATTGTGTTTTTACTATTAAA 1 46 0 ATTGTGTTTT 0.60948 -152 GGTTATTATTTGAGTGTTTTTGGTTTAAAG 5 133 1 TGAGTGTTTT 0.823152 -126 CTACAGCTTTGAGGTGTTTTTTATCTAGCT 5 161 0 GAGGTGTTTT 0.891391 -98 AACTAACCTTAAGGTGTTTTTCAACTACAG 5 185 0 AAGGTGTTTT 0.907103 -74 AAATTATAATTAGGTGTCTTTCTTTACTAA 8 52 1 TAGGTGTCTT 0.868684 -24 ACTCTATAAATTGTTATTTTTTAACAATTT 11 209 1 TTGTTATTTT 0.697838 -92 TACATTAATATAGTTATTTTTTGCAATTTA 11 246 0 TAGTTATTTT 0.739943 -55 CAAGCTTAACTGGTTGTTTTTGAG 11 287 1 TGGTTGTTTT 0.925529 -14 TTATCAAAATTAATTGTTTTTAAATATTCA 12 260 0 TAATTGTTTT 0.784334 -41 AACAGCTGCTTTTTTGTTTTTTATCTACCA 13 53 1 TTTTTGTTTT 0.746957 -124 ATTGTTTTGGTGTTTTGGGTATTTAA 13 161 0 TTGGTGTTTT 0.966116 -16 ********** Masking position 5 Map Score: 3.82247 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 348 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 ********** No masking Map Score: 1.98485e-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: 1.98485e-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: 1.98485e-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