AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i068_bsub_mtub_300.orf -o068_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 proB 300 gamma-glutamyl kinase #2 proJ 76 glutamate 5-kinase #3 proH 146 alternate gene name: yoxE #4 rtp 299 replication terminator protein #5 yoxD 150 similar to 3-oxoacyl- acyl-carrier protein reductase #6 proA 300 proA #7 obg 85 obg #8 rplU 300 rplU Motif number 1 CCGCATGAAACCTGCCGAACCTGCCTTGGAG 1 122 1 CCGCCGAACC 0.905776 -179 GGAGCGTGCACAAGCGCGTTCAATCAAGGTG 1 199 1 CAGCGCGTTC 0.721324 -102 GTTCACACTTGGCGCCGGGTGTTTGTTTCTA 3 11 0 GGGCCGGGTG 0.850047 -136 AGTGTCACCCCCAGCCCGCCGGT 6 3 0 CCGCCCGCCG 0.993822 -298 TTCCGCAGACCGCGGCCGCCGTCGAGACCAC 6 36 1 CGGGCCGCCG 0.971537 -265 GAGACCACGCGAAGCCGGCTGGAACTCGCCC 6 59 1 GAGCCGGCTG 0.828627 -242 TCGCGCCGGGCAGGGGCGACGAATCGGGCGA 6 84 0 CAGGGCGACG 0.972981 -217 TCGCCCCTGCCCGGCGCGACGAATCGGTTTG 6 96 1 CCGCGCGACG 0.995262 -205 TAGGACTTCTCGCGGCCGCCGAAAGAGCTAA 6 131 0 CGGGCCGCCG 0.971537 -170 GCAAGCTGATCAGGGGCGACCGTCAAGTACG 6 185 1 CAGGGCGACC 0.956861 -116 TAGCAACCACCCAGCCGGATCGCTGCGCGGC 6 226 1 CCGCCGGATC 0.936273 -75 CAGCCGGATCGCTGCGCGGCCCGTCCGGAGC 6 237 1 GCGCGCGGCC 0.983484 -64 CGGCCCGTCCGGAGCGGGTCGTCTTACCTGG 6 253 1 GGGCGGGTCG 0.888055 -48 GGTCGTCTTACCTGGCCAGCGCAAGCCCGTT 6 269 1 CCGGCCAGCG 0.914102 -32 TGCCCCAGGGTAACGGGCTTGCGCT 6 286 0 CCGGGTAACG 0.713618 -15 AGTGGGCGCACACGCGCGACGC 7 2 0 CAGCGCGACG 0.986864 -84 CACTCCGGGGCCCGGGTGGTGACGTCATCCG 8 35 0 CCGGGTGGTG 0.788575 -266 CTCGACGCTACCGGCGCACTCCGGGGCCCGG 8 51 0 CCGCGCACTC 0.852189 -250 CGGGGTCAAACCAGCGGGGCCTCAGCGAGAT 8 119 0 CCGCGGGGCC 0.988646 -182 CCAGTTGTCGCCAGGCTGACGGCTGGAGACG 8 174 1 CCGGCTGACG 0.912051 -127 GGCTGGAGACGATGCGGGGTCCGTTGTAGGT 8 194 1 GAGCGGGGTC 0.789641 -107 GTCCGTTGTAGGTGCCCGCCCAAGACCCAGC 8 212 1 GGGCCCGCCC 0.958601 -89 GCGCGGGCCAGCGGCGGGACGCGTGCTGGGT 8 236 0 GCGCGGGACG 0.985896 -65 TTGCGCTTCGCGCGCGGGCCAGCGGCGGGAC 8 247 0 CGGCGGGCCA 0.817779 -54 GCCCGCGCGCGAAGCGCAACGCATGCAGCGG 8 259 1 GAGCGCAACG 0.856161 -42 ** ******** Masking position 4 Map Score: 40.3442 Number of sites scoring better than the average of aligned sites = 2957 Number in coding regions = 2750 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 AACGCGCTTGTGCACGCTCCGCTCTCCTGTAA 1 187 0 TGCAGCTCGC 0.969888 -114 GCAGTTTTTTCGATATCTTCGCTGATTTCCTT 2 31 0 CGATTCTCGC 0.848906 -46 TTATCACTCCTGATAGCGGCGCTGCAGTTTTT 2 54 0 TGATGCGCGC 0.977419 -23 CGGCTTCGCGTGGTCTCGACGGCGGCCGCGGT 6 44 0 TGGTTCGCGG 0.922847 -257 TGGAACTCGCCCGATTCGTCGCCCCTGCCCGG 6 78 1 CCGATCGCGC 0.923253 -223 AAACACCAAACCGATTCGTCGCGCCGGGCAGG 6 101 0 CCGATCGCGC 0.923253 -200 TCCGGCTGGGTGGTTGCTATGCGATCAGGCGT 6 213 0 TGGTGCTTGC 0.886588 -88 CGACCCGCTCCGGACGGGCCGCGCAGCGATCC 6 242 0 CGGAGGGCGC 0.971416 -59 CGTGAATCTTCGCAGTGGGCGCACACGCGCGA 7 14 0 CGCATGGCGC 0.884088 -72 CCGCAGTAGCTGCACACTCCGCAGATGAAGGG 7 57 1 TGCAACTCGC 0.832282 -29 GTTGGACCGCTGATGGCTGCGGC 8 2 0 TGATGCTCGG 0.711325 -299 CGGAGTGCGCCGGTAGCGTCGAGATCGACGCT 8 59 1 CGGTGCGCGA 0.958606 -242 GAAAGTGCGCCGGTAGCGTCGATCTCGACGCT 8 73 0 CGGTGCGCGA 0.958606 -228 CACTTTCGTGTGCTGGCGTCGATCTCGCTGAG 8 98 1 TGCTGCGCGA 0.952546 -203 GGCTGACGGCTGGAGACGATGCGGGGTCCGTT 8 187 1 TGGAACGTGC 0.805493 -114 ATACTTCCGCTGCATGCGTTGCGCTTCGCGCG 8 264 0 TGCAGCGTGC 0.94455 -37 **** *** *** Masking position 11 Map Score: 17.6713 Number of sites scoring better than the average of aligned sites = 1733 Number in coding regions = 1651 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TTGGAGTCCTAGGGGGAAAACCTAGGCGCATA 1 147 1 AGGGGAAACC 0.979576 -154 GGGAAAACCTAGGCGCATAACCTGGCGTTACA 1 160 1 AGGCGAAACC 0.943339 -141 AATGGGTTTCCGTGGTACCACCTTGATTGAAC 1 216 0 CGTGGACACC 0.827641 -85 AGCATGCGGCTAAGCGTTCAAAGGA 2 4 1 ATGCGCAAGC 0.579858 -73 TTCTCGCGGCCGCCGAAAGAGCTAAACACCAA 6 124 0 CGCCGAGAGC 0.902632 -177 CGGATCGCTGCGCGGCCCGTCCGGAGCGGGTC 6 241 1 CGCGGCGTCC 0.872756 -60 AAGATTCACGAGGGGCAAAACCCGCAGTAGCT 7 36 1 AGGGGAAACC 0.979577 -50 CGCAGCCATCAGCGGTCCAACCCGGATGACGT 8 13 1 AGCGGCAACC 0.981118 -288 GTCAAACCAGCGGGGCCTCAGCGAGATCGACG 8 114 0 CGGGGCCAGC 0.977454 -187 CCTGCAACTACGGGGTCAAACCAGCGGGGCCT 8 128 0 CGGGGCAACC 0.991927 -173 GCCGCTGGCCCGCGCGCGAAGCGCAACGCATG 8 252 1 CGCGCCAAGC 0.864581 -49 GGAAGTATGAAGAGGCAGGAGCA 8 288 1 AGAGGAGAGC 0.761759 -13 ***** * **** Masking position 12 Map Score: 9.47136 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 502 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 AGAGCAAAATGAACCGCTGAAACATTTTGC 1 93 1 GAACCGCTGA 0.87805 -208 AATCAAGGTGGTACCACGGAAACCCATTTC 1 220 1 GTACCACGGA 0.955964 -81 TATTGTAGAAGAGCCGCGGAGGAGAATAA 1 282 1 GAGCCGCGGA 0.977301 -19 CGGGCTGGGGGTGACACTGATTCCGCAGAC 6 16 1 GTGACACTGA 0.497749 -285 GTCTCGACGGCGGCCGCGGTCTGCGGAATC 6 34 0 CGGCCGCGGT 0.832505 -267 CGCCGGGCAGGGGCGACGAATCGGGCGAGT 6 82 0 GGGCGACGAA 0.684633 -219 CGACCGTCAAGTACGCCTGATCGCATAGCA 6 201 1 GTACGCCTGA 0.906062 -100 CGCTCCGGACGGGCCGCGCAGCGATCCGGC 6 239 0 GGGCCGCGCA 0.973574 -62 CATCCGGGTTGGACCGCTGATGGCTGCGGC 8 11 0 GGACCGCTGA 0.969211 -290 GTCACCACCCGGGCCCCGGAGTGCGCCGGT 8 43 1 GGGCCCCGGA 0.995566 -258 GGGCCCCGGAGTGCGCCGGTAGCGTCGAGA 8 53 1 GTGCGCCGGT 0.944072 -248 GCACACGAAAGTGCGCCGGTAGCGTCGATC 8 81 0 GTGCGCCGGT 0.944072 -220 TGCAGGTCACGTACCCTTGACCAGTTGTCG 8 154 1 GTACCCTTGA 0.588121 -147 CACCTACAACGGACCCCGCATCGTCTCCAG 8 196 0 GGACCCCGCA 0.95402 -105 ********** Masking position 4 Map Score: 16.2952 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 688 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 ATCATTGAGCGTTGAAGAGGATTAGTAAGCAGA 1 46 1 GTGAAGGGTT 0.928139 -255 GATTCATAAGGACGAAATGGGTTTCCGTGGTAC 1 230 0 GAGAAAGGTT 0.972011 -71 TATGAATCAGGATGAAATGGGTTTTTTTATTGT 1 255 1 GAGAAAGGTT 0.972011 -46 TTTTTTTATTGTAGAAGAGCCGCGGAGGAGAAT 1 276 1 GTGAAGGCGC 0.822651 -25 ATACATATTTGTCGAAAAGAAACAATACAAATC 3 64 1 GTGAAAGAAC 0.573422 -83 GTTACCACGTGAGGAAATGATGTCAAGTTTGAA 3 107 0 GAGAAAGAGT 0.954269 -40 GTCAGTGACAGAAGAAGGAGTGCATATG 4 282 1 GAGAAGAGGC 0.880229 -18 GGTAATGACATAAGAAAAGGAGTGAACAT 5 7 0 TAGAAAGGGT 0.871506 -144 TTTTTAATCAGAAGAAATGATATTTACACAGTT 5 51 1 GAGAAAGAAT 0.804265 -100 ATATGTAAACAAAGAAAGGGTGCTTCAA 5 133 1 AAGAAAGGGC 0.873599 -18 TGCCCGGCGCGACGAATCGGTTTGGTGTTTAGC 6 103 1 GAGAATGGTT 0.861566 -198 ACACTCCGCAGATGAAGGGGAGCTCG 7 70 1 GAGAAGGGGC 0.991117 -16 GACGGCTGGAGACGATGCGGGGTCCGTTGTAGG 8 191 1 GAGATGGGGT 0.920965 -110 ** **** ** ** Masking position 5 Map Score: 9.74645 Number of sites scoring better than the average of aligned sites = 1002 Number in coding regions = 866 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 6 GGAAATCAGCGAAGATATCGAAAAAACTGC 2 33 1 GAAGATATCG 0.792469 -44 AAACTGCAGCGCCGCTATCAGGAGTGATAA 2 56 1 GCCGCTATCA 0.968624 -21 CGTTTAAATTGAAGATAGCAGTAAATGCAG 4 93 1 GAAGATAGCA 0.665008 -207 GCAGACCGCGGCCGCCGTCGAGACCACGCG 6 40 1 GCCGCCGTCG 0.917515 -261 TGCGGAGTGTGCAGCTACTGCGGGTTTTGC 7 50 0 GCAGCTACTG 0.74434 -36 GCCGCAGCCATCAGCGGTCCAAC 8 4 1 GCAGCCATCA 0.934527 -297 CAACCCGGATGACGTCACCACCCGGGCCCC 8 30 1 GACGTCACCA 0.845395 -271 CGTCGATCTCGACGCTACCGGCGCACTCCG 8 59 0 GACGCTACCG 0.986316 -242 CGTCGAGATCGACGCTACCGGCGCACTTTC 8 75 1 GACGCTACCG 0.986316 -226 CAGCGAGATCGACGCCAGCACACGAAAGTG 8 98 0 GACGCCAGCA 0.962397 -203 ********** Masking position 4 Map Score: 6.75383 Number of sites scoring better than the average of aligned sites = 917 Number in coding regions = 845 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 ACGCTCAATGATTTTTTTATATTATGCAAA 1 28 0 ATTTTTTTAT 0.787149 -273 GATGAAATGGGTTTTTTTATTGTAGAAGAG 1 265 1 GTTTTTTTAT 0.937224 -36 CGAAAGACAGGTTTTCATTT 4 1 0 GTTTTCATTT 0.806544 -299 CTTTCGACAGGTTTTTTTATTTGAATGAAA 4 25 1 GTTTTTTTAT 0.937224 -275 GATTGCCAGGGTTTACATATCTCATTTTAC 4 64 0 GTTTACATAT 0.858795 -236 TTGGTACATAGTTTTCTTAGTTCTATTATA 4 125 0 GTTTTCTTAG 0.86133 -175 TTCAGTCGAAATTTATTTTTTCCGCTACAC 4 158 1 ATTTATTTTT 0.405443 -142 GTTATTTCATGTTTACTGATTATAGGTGTA 4 183 0 GTTTACTGAT 0.745979 -117 TAAATATTCAATTTTCTTTTATTGTTTTCC 4 240 0 ATTTTCTTTT 0.743899 -60 ATGTTCACTCCTTTTCTTATGTCATTACCC 5 11 1 CTTTTCTTAT 0.82736 -140 CCCTGTATCCGTTTTTTTAATCAGAAGAAA 5 38 1 GTTTTTTTAA 0.654811 -113 CCCTTTCTTTGTTTACATATGTACGATATC 5 123 0 GTTTACATAT 0.858795 -28 ********** Masking position 4 Map Score: 5.02482 Number of sites scoring better than the average of aligned sites = 1103 Number in coding regions = 836 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 8 ACCGCTGAAACATTTTGCCGCATGAAACCT 1 105 1 CATTTTGCCG 0.945034 -196 TTCCTTTGAACGCTTAGCCGCATGCT 2 7 0 CGCTTAGCCG 0.459661 -70 TTACATATCTCATTTTACCGGTACGGATTT 4 52 0 CATTTTACCG 0.748461 -248 GTGTCACCCCCAGCCCGCCGGT 6 3 0 CAGCCCGCCG 0.949184 -298 GAGTTCCAGCCGGCTTCGCGTGGTCTCGAC 6 56 0 CGGCTTCGCG 0.82629 -245 CAAACCGATTCGTCGCGCCGGGCAGGGGCG 6 97 0 CGTCGCGCCG 0.710225 -204 GTCCTACCAGCGTCTTGCCGGGATTATCGG 6 156 1 CGTCTTGCCG 0.971126 -145 CGCCCCTGATCAGCTTGCCGATAATCCCGG 6 173 0 CAGCTTGCCG 0.96931 -128 CGGAGCGGGTCGTCTTACCTGGCCAGCGCA 6 262 1 CGTCTTACCT 0.642837 -39 CTCCAGCCGTCAGCCTGGCGACAACTGGTC 8 172 0 CAGCCTGGCG 0.926252 -129 ACCCAGCACGCGTCCCGCCGCTGGCCCGCG 8 236 1 CGTCCCGCCG 0.954507 -65 ********** Masking position 9 Map Score: 10.7359 Number of sites scoring better than the average of aligned sites = 1338 Number in coding regions = 1260 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 9 ATGCGCCTAGGTTTTCCCCCTAGGACTCCAA 1 147 0 GTTTTCCCCT 0.981089 -154 GTAACGCCAGGTTATGCGCCTAGGTTTTCCC 1 160 0 GTTATGCCCT 0.937988 -141 TGAACCGGGTGTTTTCTGCTTTTCATTATAC 3 37 1 GTTTTCTCTT 0.887977 -110 TTATTGATTTGTATTGTTTCTTTTCGACAAA 3 71 0 GTATTGTTCT 0.734224 -76 TTCTTTTATTGTTTTCCTTCTTTATATTAAA 4 226 0 GTTTTCCTCT 0.922275 -74 CGTATTGGATGTATTGTACTTATAATGTGAT 5 95 1 GTATTGTCTT 0.825212 -56 TCGGTTTGGTGTTTAGCTCTTTCGGCGGCCG 6 119 1 GTTTAGCCTT 0.855335 -182 GCTACTGCGGGTTTTGCCCCTCGTGAATCTT 7 36 0 GTTTTGCCCT 0.988291 -50 ******* *** Masking position 2 Map Score: 3.78436 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 327 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 GAGAGCGGAGCGTGCACAAGCGCGTTCAAT 1 193 1 CGTGCACAAG 0.484014 -108 AGTGTCACCCCCAGCCCGCCGGT 6 4 0 CCAGCCCGCC 0.956525 -297 CACTGATTCCGCAGACCGCGGCCGCCGTCG 6 30 1 GCAGACCGCG 0.731604 -271 CGGCCGCCGTCGAGACCACGCGAAGCCGGC 6 48 1 CGAGACCACG 0.715132 -253 CGGGCGAGTTCCAGCCGGCTTCGCGTGGTC 6 61 0 CCAGCCGGCT 0.83202 -240 TCGCCCCTGCCCGGCGCGACGAATCGGTTT 6 96 1 CCGGCGCGAC 0.862218 -205 TCTTACCTGGCCAGCGCAAGCCCGTTACCC 6 274 1 CCAGCGCAAG 0.978502 -27 CTTCGCAGTGGGCGCACACGCGCGACGC 7 9 0 GGCGCACACG 0.748676 -77 AGGGGCAAAACCCGCAGTAGCTGCACACTC 7 46 1 CCCGCAGTAG 0.409616 -40 CTCGACGCTACCGGCGCACTCCGGGGCCCG 8 52 0 CCGGCGCACT 0.933747 -249 ATCGACGCTACCGGCGCACTTTCGTGTGCT 8 82 1 CCGGCGCACT 0.933747 -219 GAGATCGACGCCAGCACACGAAAGTGCGCC 8 94 0 CCAGCACACG 0.984753 -207 GTTGTAGGTGCCCGCCCAAGACCCAGCACG 8 216 1 CCCGCCCAAG 0.970087 -85 CGCCCAAGACCCAGCACGCGTCCCGCCGCT 8 228 1 CCAGCACGCG 0.985225 -73 CCGCCGCTGGCCCGCGCGCGAAGCGCAACG 8 250 1 CCCGCGCGCG 0.743897 -51 CGCAACGCATGCAGCGGAAGTATGAAGAGG 8 273 1 GCAGCGGAAG 0.733837 -28 ********** Masking position 4 Map Score: 17.6145 Number of sites scoring better than the average of aligned sites = 1339 Number in coding regions = 1239 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 ********** No masking Map Score: -1.25466e-13 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: -1.25466e-13 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: -1.25466e-13 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