AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i205_bsub_mtub_300.orf -o205_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 pgsA 300 phosphatidylglycerophosphate synthase #2 recA 172 multifunctional SOS repair regulator #3 pbpX 167 penicillin-binding protein #4 ymdA 276 similar to hypothetical proteins #5 ymdB 68 similar to hypothetical proteins #6 spoVS 199 spoVS #7 tdh 265 threonine 3-dehydrogenase #8 ymcB 147 similar to hypothetical proteins #9 cotE 261 morphogenic protein #10 mutS 132 mutS Motif number 1 TGGCAGCTCTTTAAAAGAAGGAACGCTGAAAAAA 1 51 1 TAAAAGAAAC 0.795248 -250 AGGAACGCTGAAAAAAGACGAAACCTATAAAAAA 1 69 1 AAAAAGAAAC 0.943793 -232 CGAAACCTATAAAAAAGACATAACTGATCAGAAA 1 87 1 AAAAAGAAAC 0.943793 -214 GATTGTAAATAAAAAGGAAGAAAAGTCATCTTAA 1 228 1 AAAAGGAAAA 0.982008 -73 TAGTGGTAACATAAAGGAGGAAAAAATAGA 2 153 1 AAAAGGAAAA 0.982008 -20 AAAATAAGTTTCAAATGATACAAAAGGCTGAGTG 3 15 1 TAAATGAAAA 0.925312 -153 TATTTTGCAAAAAAATGATAAAAATATTGCTTTT 3 67 1 AAAATGAAAA 0.981672 -101 TGTTAAAAAAACAAATGTTACAACTTCATTGTAA 4 109 0 AAAATGTAAC 0.722247 -168 ATTTTCAAGAAGAAAGGATTTACAAA 5 53 1 AAAAGGAACA 0.931639 -16 AAATATCACAATAAATGAAAAACAACCTGTTTGC 7 46 0 AAAATGAACA 0.93043 -220 TTTTTAGCACATAAATGAGCGAATATACAAAATC 7 93 1 AAAATGAAAT 0.916245 -173 ATACAAAATCAGAAATGAGCTAAAACGTTTCAAA 7 117 1 AAAATGAAAA 0.981672 -149 AATAATAATCAATAAGGAATCAAAAGAGGAAGAG 8 27 0 ATAAGGAAAA 0.814254 -121 AAGTTTGGTTTGAAAGGAGAAAATATGAC 8 129 1 TAAAGGAAAT 0.720551 -19 TTTTAACCGCACAAATGATAAAAAAACACGGGCC 9 27 0 AAAATGAAAA 0.981672 -235 TTGTGCGGTTAAAAATGAACTAAATAATCTATGT 9 47 1 AAAATGAAAA 0.981672 -215 ACAAAAAGTGATAAAAGAATGATATATCAATATA 10 51 0 AAAAAGAATA 0.717759 -82 * ****** *** Masking position 5 Map Score: 23.4943 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 461 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 2 AAAGAAGGAACGCTGAAAAAAGACGAAACCT 1 64 1 CGCGAAAAAA 0.685974 -237 GCACCTAATCTGAAAATAAAAATCAACGGTA 1 145 1 TGAAATAAAA 0.790795 -156 CCATAAAGATTGTAAATAAAAAGGAAGAAAA 1 221 1 TGTAATAAAA 0.847954 -80 CATACTCGGACGTGAAGAAAAGTCATCTGGT 1 264 0 CGTAAGAAAA 0.877039 -37 GAGGATAATGTGCTGAAAATA 2 1 0 TGCGAAAATA 0.727628 -172 ATAGGAATCACGCCAAGAAAAAATCCGAATA 2 72 1 CGCAAGAAAA 0.866444 -101 TGAAGGGATTTGCCAAGAAAAAAGCGAACGC 2 104 0 TGCAAGAAAA 0.939312 -69 TGCAAAAAAATGATAAAAATATTGCTTTTTT 3 72 1 TGAAAAAATA 0.868777 -96 CTAAAAAAGTTGTCAAAAAAAGCAATATTTT 3 87 0 TGTAAAAAAA 0.950141 -81 ATTCGGCACGTGAAAAGAAGACTGGCCTGCA 4 38 1 TGAAAGAAGA 0.769998 -239 TTAACAATCATGTTAAAAAAACAAATGTTAC 4 122 0 TGTAAAAAAA 0.950135 -155 GGTTCTAGTATGTTGAGAAAACTAGACAATG 4 200 1 TGTGAGAAAA 0.836511 -77 AATTCCTTGCCGTCAAAAAAATAAAGTGATG 5 25 0 CGTAAAAAAA 0.888735 -44 GGCAAGGAATTTTCAAGAAGAAAGGATTTAC 5 45 1 TTTAAGAAGA 0.44627 -24 TATGGTTATTTTATAAAAATATTAAAAAGAA 6 18 1 TTAAAAAATA 0.519286 -182 CCACAATGCTTTTCAAAAATAGCGGGCTACC 6 94 0 TTTAAAAATA 0.614469 -106 CTCATTTATGTGCTAAAAATACTATCGGGAG 7 81 0 TGCAAAAATA 0.898834 -185 AGCTAAAACGTTTCAAAAAAAATTTCCGCCC 7 134 1 TTTAAAAAAA 0.75665 -132 GTACACTCATTGAGAATAATAATCAATAAGG 8 44 0 TGAAATAATA 0.659586 -104 ACCGCACAAATGATAAAAAAACACGGGCCTG 9 25 0 TGAAAAAAAA 0.92814 -237 *** ******* Masking position 6 Map Score: 18.5776 Number of sites scoring better than the average of aligned sites = 1537 Number in coding regions = 1222 Number in noncoding regions = 315 Number of orfs with sites within 600 bp upstream = 317 Fraction of orfs with sites within 600 bp upstream = 0.0509155 Motif number 3 GAAAGAACCTTACCGTTGATTTTTATTTTCAGAT 1 152 0 TACCTTTTTT 0.762396 -149 TTATGGTTTGTGCCATCACTTTTTTCGGATCGAG 1 193 0 TGCCCTTTTT 0.989388 -108 AATCCGAATATGCGTTCGCTTTTTTCTTGGCAAA 2 93 1 TGCGCTTTTT 0.931255 -80 AATTCCATTTTGCACACGTTTTGTTAGACGAATA 3 123 0 TGCACTTTGT 0.912448 -45 TCTTAACGTTTGCAGGCCAGTCTTCTTTTCACGT 4 45 0 TGCACGTCTT 0.827466 -232 ACAATGTACATGCCGACACTTTTTAAGCAACAAC 4 225 1 TGCCCTTTTT 0.989388 -52 AGTTGCTATATTCCTGCTTTTCTTTTTAATATTT 6 34 0 TTCCCTTCTT 0.879461 -166 AATAGCGGGCTACCTTCCATTTTTACTATATTCA 6 74 0 TACCCTTTTT 0.941578 -126 GTTTGCGTAATGCAAACAGGTTGTTTTTCATTTA 7 35 1 TGCACGTTGT 0.840285 -231 CAAAAAAAATTTCCGCCCATTTTTCAAGACAGAT 7 147 1 TTCCCTTTTT 0.958496 -119 TGCCTTTACAGGCCCGTGTTTTTTTATCATTTGT 9 17 1 GGCCTTTTTT 0.745388 -245 GTACCAAATGTTCAATTGGTTTTTCTGTGCTCAG 9 79 1 TTCATTTTTT 0.597254 -183 TCCGGCATGCCTCCTTGTTCTTCTTCGTGTT 9 241 0 TGCCCGTTCT 0.898615 -21 **** * ***** Masking position 11 Map Score: 8.48517 Number of sites scoring better than the average of aligned sites = 1078 Number in coding regions = 894 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 4 TTACCGTTGATTTTTATTTTCAGATTAGGT 1 147 0 TTTTTATTTT 0.862165 -154 CTCTGATACATTATGATATTTTGATAGGAA 2 49 1 TTATGATATT 0.680896 -124 ACTCAGCTTTTTTGTATTTTGCAAAAAAAT 3 53 1 TTTGTATTTT 0.753542 -115 CTGCTTTTCTTTTTAATATTTTTATAAAAT 6 25 0 TTTTAATATT 0.712276 -175 CACTAAGGAGTTGCTATATTCCTGCTTTTC 6 46 0 TTGCTATATT 0.899183 -154 CCTTCCATTTTTACTATATTCACTAAGGAG 6 66 0 TTACTATATT 0.798325 -134 TTTTCATTTATTGTGATATTTTCTCCCGAT 7 59 1 TTGTGATATT 0.827814 -207 CATTTCTGATTTTGTATATTCGCTCATTTA 7 104 0 TTTGTATATT 0.895831 -162 TGAAAAATTCTTGTTATATTCGGATTGTAC 7 233 0 TTGTTATATT 0.926071 -33 AAACTTTGTATTTTTATATTTTATTTATAA 9 178 1 TTTTTATATT 0.946218 -84 CCAAGTCTCTTTTTTATATTGATATATCAT 10 37 1 TTTTTATATT 0.946218 -96 TGTATCAACGTTTCTATTTTCCAACCTTCA 10 96 0 TTTCTATTTT 0.816635 -37 ********** Masking position 6 Map Score: 10.847 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 154 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 TTTTCAGCACATTATCCTCCTAAGAAAACA 2 13 1 ATTATCCTCC 0.808141 -160 TCTATTTTTTCCTCCTTTATGTTAC 2 158 0 TTTTTCCTCC 0.979009 -15 TCATTTTTTCCTCCCAAAATAAAT 3 154 0 TTTTTCCTCC 0.979009 -14 GCTTGACAAGTATTTCCGACACATTTACAA 4 85 1 TATTTCCGAC 0.841285 -192 TTTATTGTGATATTTTCTCCCGATAGTATT 7 65 1 TATTTTCTCC 0.943074 -201 TTTCAAAAAAAATTTCCGCCCATTTTTCAA 7 144 1 AATTTCCGCC 0.946745 -122 GTCATATTTTCTCCTTTCAAACCA 8 134 0 TATTTTCTCC 0.943074 -14 ********** Masking position 5 Map Score: 5.44616 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 224 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 6 TTTTTATAGGTTTCGTCTTTTTTCAGCGTTCCT 1 69 0 TTTCCTTTTT 0.79742 -232 CCGGTGCGGATATCAACTTGTTTCTGATCAGTT 1 108 0 TATCCTTTTT 0.797399 -193 TAAGATGACTTTTCTTCCTTTTTATTTACAATC 1 228 0 TTTCCCTTTT 0.933114 -73 TGAGTTTTTCACTCAGCCTTTTGTATCATTTGA 3 25 0 ACTCCCTTTG 0.977492 -143 TGAGTGAAAAACTCAGCTTTTTTGTATTTTGCA 3 43 1 ACTCCTTTTT 0.945084 -125 ACTTTCACCTCCTCTTGCTATGAACTT 4 260 0 TCACCCTTTG 0.923501 -17 AATAAAGCATTCTCAACCTGTTTGCGTAATGCA 7 16 1 TCTCCCTTTT 0.983869 -250 AATAAATGAAAAACAACCTGTTTGCATTACGCA 7 38 0 AAACCCTTTT 0.779493 -228 GGAAGAGTAAACTCTTCCTCTTG 8 1 0 ACTCCCTTTG 0.977492 -147 GGAAGAGTTTACTCTTCCTCTTTTGATTCCTTA 8 16 1 ACTCCCTTTT 0.983869 -132 **** *** *** Masking position 9 Map Score: 10.611 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 190 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 TAAAAAGGAAGAAAAGTCATCTTAATTACCA 1 237 1 GAAAATCATC 0.955712 -64 CGGACGTGAAGAAAAGTCATCTGGTAATTAA 1 258 0 GAAAATCATC 0.955712 -43 CTTTCTTCTTGAAAATTCCTTGCCGTCAAAA 5 38 0 GAAAATCCTT 0.943872 -31 GTGTTCATTAGAACAATCATTATTAGATGTT 6 144 0 GAACATCATT 0.956698 -56 TTGTTCTAATGAACACTCACTTATCCATTGT 6 159 1 GAACATCACT 0.837733 -41 AATCCTCCTTGAAAAATTCTTGTTATATTCG 7 241 0 GAAAATTCTT 0.622301 -25 GTACAATCCTCCTTGAAAAAT 7 255 0 GTACATCCTC 0.935999 -11 AAGAGGAAGAGTAAACTCTTCCTCTTG 8 7 0 GTAAATCTTC 0.740042 -141 ACCTATCATTGTACACTCATTGAGAATAATA 8 54 0 GTACATCATT 0.920578 -94 ***** ***** Masking position 5 Map Score: 4.79283 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 207 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 TCGGAAATACTTGTCAAGCTTGCCATCTTAA 4 73 0 TTGTCAGCTT 0.978974 -204 TTCATCGCCCTTGTCAAGTTTAAATGGTTTA 4 150 0 TTGTCAGTTT 0.987558 -127 GGCATGTACATTGTCTAGTTTTCTCAACATA 4 208 0 TTGTCAGTTT 0.987558 -69 TGCTGGGCATTTGTCTAGTGTGCATTTTTAT 9 204 0 TTGTCAGTGT 0.978974 -58 ***** ***** Masking position 7 Map Score: 1.62124 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 8 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 9 ATAAAAAGGAAGAAAAGTCATCTTAATTAC 1 236 1 AGAAAAGTCA 0.869291 -65 TCGGACGTGAAGAAAAGTCATCTGGTAATT 1 260 0 AGAAAAGTCA 0.869291 -41 TCAACATACTAGAACCTTCACAGGGAATGA 4 186 0 AGAACCTTCA 0.943739 -91 CAGAGCTTCAATAACCTTTATACTGAAGGG 8 96 1 ATAACCTTTA 0.796747 -52 TCAGCCGCGTATAAACTTTATCGCACTTAT 9 109 1 ATAAACTTTA 0.873777 -153 AGGGGTGCCTAGAAACTTTACTTATAAGTG 9 132 0 AGAAACTTTA 0.968013 -130 ACAATGGAACAGAAACTTTGTATTTTTATA 9 166 1 AGAAACTTTG 0.944866 -96 GTTGGAAAATAGAAACGTTGATACATAGTG 10 101 1 AGAAACGTTG 0.943816 -32 ********** Masking position 4 Map Score: 2.35395 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 205 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 TCCGACACATTTACAATGAAGTTGTAACAT 4 99 1 TTACAATGAA 0.962791 -178 ATAATGATTGTTCTAATGAACACTCACTTA 6 152 1 TTCTAATGAA 0.857426 -48 CCCCTTAGTTTTACAATGGATAAGTGAGTG 6 172 0 TTACAATGGA 0.955462 -28 TCAATAACCTTTATACTGAAGGGTGGAAGT 8 103 1 TTATACTGAA 0.857492 -45 GCACCCCTGCATACAATGGAACAGAAACTT 9 154 1 ATACAATGGA 0.841081 -108 TTTGTTTATGTTATAATGAAGGTTGGAAAA 10 80 1 TTATAATGAA 0.942713 -53 ********** Masking position 5 Map Score: 1.17717 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 51 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 11 TTTAAAGAGCTGCCACTTCATCGCGCACTCA 1 35 0 TCCACTTCAT 0.986114 -266 AAAGCCCCTCCAATTTCATACTCGGACGT 1 282 0 TCAATTTCAT 0.933282 -19 TCCTTTATGTTACCACTACATATACTATACC 2 140 0 TCCACTACAT 0.955722 -33 AAACAAATGTTACAACTTCATTGTAAATGTG 4 104 0 TCAACTTCAT 0.969247 -173 TTTACGCTTATTCCATATCATGGTACAATCC 7 211 1 TCCATATCAT 0.90548 -55 * ********* Masking position 5 Map Score: 0.138473 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 96 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 GCCATCACTTTTTTCGGATCGAGTTCATATG 1 185 0 TTTTCGGATG 0.980892 -116 TACATTATGATATTTTGATAGGAATCACGCC 2 55 1 TATTTTGATG 0.862196 -118 AGCGAACGCATATTCGGATTTTTTCTTGGCG 2 82 0 TATTCGGATT 0.933734 -91 TGGGGATGGCTTTTTGGATAGCAACATCTAA 6 122 1 TTTTTGGATG 0.957959 -78 ATTCTTGTTATATTCGGATTGTACCATGATA 7 226 0 TATTCGGATG 0.98656 -40 ********* * Masking position 4 Map Score: 0.129783 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 64 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 ********** No masking Map Score: -4.23951e-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: -4.23951e-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 15 ********** No masking Map Score: -4.23951e-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