AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_bsub_mtub_100.orf -o060_bsub_mtub_100.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 asd 125 aspartate-semialdehyde dehydrogenase #2 dapG 91 aspartokinase I (alpha and beta subunits) #3 dapA 30 dihydrodipicolinate synthase #4 ypjD 300 alternate gene name: jojD #5 lysC 175 aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408) #6 dapA 68 dapA #7 Rv2754c 243 hypothetical protein Rv2754c #8 Rv2774c 152 hypothetical protein Rv2774c #9 ask 256 ask Motif number 1 ACAAACACGCGCGCTCGCGGCCGGGATAAAG 6 27 1 GCGCTCGCGC 0.994677 -42 GTCCGCGTTGGCGCTGGCTCCCAGAGTTGAA 7 47 0 GCGCTGGCTC 0.973585 -197 CGCCCGTCGAGCGTCCGCGTTGGCGCTGGCT 7 59 0 GCGTCCGCGT 0.984462 -185 TTGTGCCGCAGGGTCCACGCCCGTCGAGCGT 7 76 0 GGGTCCACGC 0.955979 -168 CCTCTACGTGGCACTGGCCAGTCACCTCGAC 7 125 1 GCACTGGCCG 0.915826 -119 GCGCAGACGCGGGTCCGCGGTCAGCAGGGGG 7 158 0 GGGTCCGCGT 0.93438 -86 CCGCGGACCCGCGTCTGCGCCGGGAGCCCGG 7 169 1 GCGTCTGCGC 0.950626 -75 CCGGGAGCCCGGGCTGACCTGCCACACCGAG 7 188 1 GGGCTGACCG 0.92024 -56 GCTCACCTTAGCGCCGGCCGCAACTAGACGA 7 220 0 GCGCCGGCCC 0.861876 -24 GGCGCTCACCTTAGCGCCGGCC 7 232 0 GCGCTCACCT 0.976389 -12 CGCCGCGACTGCGCCCACGACCTATCTAGGC 8 111 0 GCGCCCACGC 0.996438 -42 AAACAACTACGCGCTGACCGCCGCGACTGCG 8 129 0 GCGCTGACCC 0.964324 -24 CGTTCGCGATGCGCCGGTCTGAGGTTCCTTC 9 33 0 GCGCCGGTCG 0.943636 -224 CCGAGGAGGAGCACCCGCTGCACATGAAGCA 9 108 1 GCACCCGCTC 0.929525 -149 CGTTGACTCTGCGTCCACCGTGTGGGCTACT 9 146 1 GCGTCCACCT 0.975842 -111 CGCTGACTCTGCGTCCACCACGGGAATGTGC 9 178 0 GCGTCCACCC 0.992421 -79 AATAGGGGGCGCGCCGGCCTGCGCTGACTCT 9 199 0 GCGCCGGCCG 0.99702 -58 ********* * Masking position 1 Map Score: 37.072 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 1007 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 TAAAAAATTCGGTCATCACCCGCATATTCTATG 1 35 1 GGTCCCCCGC 0.944179 -91 CTGTAAAACTCCTTCCGCCAATCAGCTTCAT 1 105 0 CTCCCGCCAA 0.664855 -21 GAGAGTAAGGCGCTATCAGCCTGCTCTCTTCTG 2 40 1 CGCTCGCCTG 0.976021 -52 CCTGTAAAACCGCCCTCAGCCAGATTGTTCTGC 4 53 1 CGCCCGCCAG 0.996191 -248 CAAACACGCGCGCTCGCGGCCGGGATAAAGCGC 6 28 1 CGCTCGCCGG 0.990331 -41 TCCGCGTTGGCGCTGGCTCCCAGAGTTGAACCC 7 44 0 CGCTCCCCAG 0.971459 -200 TGTGCCGCAGGGTCCACGCCCGTCGAGCGTCCG 7 73 0 GGTCCCCCGT 0.723506 -171 CGTTTTACGACGCCCTCTACGTGGCACTGGCCA 7 112 1 CGCCCACGTG 0.957097 -132 CCAGTCACCTCGACATCCCCCTGCTGACCGCGG 7 142 1 CGACCCCCTG 0.883734 -102 CGCAGACGCGGGTCCGCGGTCAGCAGGGGGATG 7 155 0 GGTCCGTCAG 0.842733 -89 CGCGGACCCGCGTCTGCGCCGGGAGCCCGGGCT 7 170 1 CGTCCCCGGG 0.984364 -74 CTCACCTTAGCGCCGGCCGCAACTAGACGAACT 7 217 0 CGCCCGCAAC 0.888758 -27 CGCCGCCACCTTCGGGAAATCGATCG 8 4 1 CGCCCTCGGG 0.95693 -149 TGATCCGAGGCGTCAGCAGCGAAGGTGCTCATG 8 73 0 CGTCCGCGAA 0.911337 -80 GCCGCGACTGCGCCCACGACCTATCTAGGCTTT 8 108 0 CGCCCACCTA 0.872724 -45 AACAACTACGCGCTGACCGCCGCGACTGCGCCC 8 126 0 CGCTCGCCGC 0.979384 -27 GATCCAGACCGGCTTCCCGTCGCGGGACGTTCG 9 58 0 GGCTCGTCGC 0.72591 -199 GTTGACTCTGCGTCCACCGTGTGGGCTACTCGC 9 147 1 CGTCCGTGTG 0.87046 -110 GCTGACTCTGCGTCCACCACGGGAATGTGCGAG 9 175 0 CGTCCACGGG 0.953775 -82 GGGGCGCGCCGGCCTGCGCTGACTCTGCGTCCA 9 192 0 GGCCCCTGAC 0.707846 -65 **** * ***** Masking position 7 Map Score: 26.3193 Number of sites scoring better than the average of aligned sites = 2751 Number in coding regions = 2564 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 ATGAAAAAATTGCCGCTCCGATTAAAATAA 4 108 1 TGCCGCTCCG 0.962757 -193 GTTTGTCCAGCGACACGCCGCC 6 3 0 CGACACGCCG 0.788409 -66 CCGGCGCAGACGCGGGTCCGCGGTCAGCAG 7 162 0 CGCGGGTCCG 0.933851 -82 TGCGCCGGGAGCCCGGGCTGACCTGCCACA 7 184 1 GCCCGGGCTG 0.867277 -60 CGCCGCCACCTTCGGGAAAT 8 1 1 CGCCGCCACC 0.852844 -152 ACGCGCTGACCGCCGCGACTGCGCCCACGA 8 122 0 CGCCGCGACT 0.914614 -31 ACCAAACAACTACGCGCTGACCGCCGCGA 8 134 0 CTACGCGCTG 0.827344 -19 GGTAGTTGCTCCGGGATGGTGAGAAGGA 9 9 1 CTCCGGGATG 0.928386 -248 GTTCGCGATGCGCCGGTCTGAGGTTCCTTC 9 33 0 CGCCGGTCTG 0.987309 -224 ATCGCGAACGTCCCGCGACGGGAAGCCGGT 9 54 1 TCCCGCGACG 0.869575 -203 CGCGACGGGAAGCCGGTCTGGATCAGACCC 9 67 1 AGCCGGTCTG 0.871751 -190 CCTCCTCGGACGCCGCGACGGGGTCTGATC 9 87 0 CGCCGCGACG 0.862924 -170 ATAGGGGGCGCGCCGGCCTGCGCTGACTCT 9 199 0 CGCCGGCCTG 0.984727 -58 ********** Masking position 5 Map Score: 14.0963 Number of sites scoring better than the average of aligned sites = 1491 Number in coding regions = 1411 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 AAACTCCTTCCGCCAATCAGCTTCATTGAAT 1 100 0 CGCCAATCAC 0.990217 -26 AATCTAATTTCTCCAAGCATCACACAAAACC 4 152 1 CTCCAAGCAC 0.990217 -149 TGAACGAAACCTCCTATCATCCTCTTACATG 4 280 0 CTCCTATCAC 0.945656 -21 CGGGATAAAGCGCCAGGTAACCTTGGGAGCC 6 48 1 CGCCAGGTAC 0.950362 -21 AGATCGGCTTCTTCAGGCAACAGATTTGGTG 7 13 1 CTTCAGGCAC 0.940669 -231 ACGTGGCACTGGCCAGTCACCTCGACATCCC 7 130 1 GGCCAGTCAC 0.959174 -114 CTGGACCTGTCTCCAATCTTCCCCGGAAAGG 9 230 1 CTCCAATCTC 0.945656 -27 ********* * Masking position 4 Map Score: 4.54144 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 261 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 GATGACCGAATTTTTTAGTTTGGGAAAGATT 1 21 0 TTTTTTATTT 0.957988 -105 TATGATTTTACGTTTTATTTTACCATAGAAT 1 60 0 CGTTTTATTT 0.855836 -66 GGAGCGGCAATTTTTTCATTTGGCTTGGTTC 4 96 0 TTTTTTCTTT 0.957175 -205 AAAAAACATATTTTTTATTTTAATCGGAGCG 4 121 0 TTTTTTATTT 0.957988 -180 AAAAAATATGTTTTTTAATCTAATTTCTCCA 4 136 1 TTTTTTATCT 0.875256 -165 GCACGTTTGCTGTTTTCTTTTTCATCCACTA 4 215 0 TGTTTTCTTT 0.956347 -86 TCTCATTGCTTTTTTTATTGTGGACAAAGCG 5 108 1 TTTTTTATGT 0.875256 -68 TGTTTCCCTTTCCGGGGAAGA 9 246 0 TGTTTCCTTT 0.853348 -11 ******* *** Masking position 5 Map Score: 4.12136 Number of sites scoring better than the average of aligned sites = 666 Number in coding regions = 473 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 6 GGGGCTGATGTGGAAAAGGGCATAAAGCAAA 4 13 1 TGGAAAGGGC 0.731119 -288 AAGGGCATAAAGCAAAAGTGTAATACCTGTA 4 28 1 AGCAAAGTGT 0.845754 -273 ATCTAATGGAAGGAAAAGGGGTTTTGTGTGA 4 171 0 AGGAAAGGGG 0.731535 -130 AAAAGAAAACAGCAAACGTGCTTAAACATTT 4 225 1 AGCAAAGTGC 0.965333 -76 TTATCCCGGCCGCGAGCGCGCGTGTTTGTCC 6 25 0 CGCGAGGCGC 0.959179 -44 CGATCGATTTCCCGAAGGTGGCGGCG 8 6 0 CCCGAAGTGG 0.863336 -147 AGGCGTCAGCAGCGAAGGTGCTCATGTGAAA 8 68 0 AGCGAAGTGC 0.986978 -85 CGCTGACCGCCGCGACTGCGCCCACGACCTA 8 118 0 CGCGACGCGC 0.977397 -35 ACCGGCGCATCGCGAACGTCCCGCGACGGGA 9 46 1 CGCGAAGTCC 0.954002 -211 CCTCGGACGCCGCGACGGGGTCTGATCCAGA 9 83 0 CGCGACGGGT 0.92539 -174 GCGTCCACCACGGGAATGTGCGAGTAGCCCA 9 168 0 CGGGAAGTGC 0.98575 -89 ****** **** Masking position 5 Map Score: 8.11686 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 509 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 TGTTTTTTAATCTAATTTCTCCAAGCATCA 4 144 1 TCTAATTTCT 0.872477 -157 TGGAGGGCTATCTCGTTGTTCATAATCATT 5 43 1 TCTCGTTGTT 0.943314 -133 AGAGGAATACTCTCATTGCTTATCAATTAA 5 81 0 TCTCATTGCT 0.987722 -95 AGAGTATTCCTCTCATTGCTTTTTTTATTG 5 98 1 TCTCATTGCT 0.987722 -78 ACCGAGTTCGTCTAGTTGCGGCCGGCGCTA 7 213 1 TCTAGTTGCG 0.945542 -31 ********** Masking position 6 Map Score: 1.73846 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 55 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TTTATTCACCTCATCATGATTCAAT 3 16 0 TTCACCTCAC 0.989914 -15 TATGCCCTTTTCCACATCAGCCCCTC 4 6 0 TCCACATCAC 0.97 -295 AAAGCGCTCTTTCTCCTCACCCGCACGAACC 5 133 1 TTCTCCTCAC 0.986907 -43 GCACTGGCCAGTCACCTCGACATCCCCCTGC 7 135 1 GTCACCTCGC 0.9531 -109 ATTGCTGGGTTTCACATGAGCACCTTCGCTG 8 59 1 TTCACATGAC 0.837331 -94 GGTCTGAGGTTCCTTCTCACCATCCCGGAGC 9 18 0 TCCTTCTCAC 0.921918 -239 CAGCGGGTGCTCCTCCTCGGACGCCGCGACG 9 97 0 TCCTCCTCGA 0.888206 -160 ********* * Masking position 7 Map Score: 1.56265 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 315 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 9 CAGGCTGATAGCGCCTTACTCTCTTCTATTC 2 32 0 GCGCCTTACC 0.989511 -60 AGGAGAAAGAGCGCTTTGTCCACAATAAAAA 5 119 0 GCGCTTTGTC 0.963538 -57 AGGTTACCTGGCGCTTTATCCCGGCCGCGAG 6 40 0 GCGCTTTATC 0.98638 -29 GTTTTACGACGCCCTCTACGTGGCACTGGCC 7 113 1 GCCCTCTACT 0.909325 -131 TGCACATGAAGCACTTTACACGTTGACTCTG 9 126 1 GCACTTTACC 0.966286 -131 AGGCCGGCGCGCCCCCTATTCTGGACCTGTC 9 210 1 GCCCCCTATC 0.971573 -47 ********* * Masking position 7 Map Score: 1.22227 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 98 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ********** No masking Map Score: -1.93024e-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: -1.93024e-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: -1.93024e-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