AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i010_ecoli_mtub_300.orf -o010_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ybaN 69 putative gene 58 #2 apt 152 adenine phosphoribosyltransferase #3 relA 47 (p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor #4 ygcA 56 putative enzyme #5 gmk 251 guanylate kinase #6 rpoZ 54 RNA polymerase, omega subunit #7 yihV 161 putative kinase #8 yihX 77 putative phosphatase #9 Rv1897c 57 hypothetical protein Rv1897c #10 relA 30 relA #11 apt 103 apt #12 secD 109 secD #13 Rv2588c 166 hypothetical protein Rv2588c Motif number 1 TCTCCTTTAGGGACCAGACCTGCCGAAATCGG 3 21 0 GGACCAGCCG 0.954692 -27 GAGTCTGCGAGGACGCTTCCTGAAAATCGTCT 5 74 1 GGACGCTCCG 0.812023 -178 TTATTATACACGGCGCGGCCATGTGACGTAGC 5 184 0 CGGCGCGCCT 0.966806 -68 AGCCTCGATGCTGCCAGGCCGGCTATGCAGTC 9 35 0 CTGCCAGCCG 0.965153 -23 GATAGGTCCGCTTCTCGTCGTGGAATTCTGTC 11 39 0 CTTCTCGCGG 0.808843 -65 CCGGCAACCGGCCGACCGGAACCGACGAG 12 8 1 CCGGCCGCCG 0.509747 -102 GTCGCGCAAGCGGCTCGTCGGTTCCGGTCGGC 12 21 0 CGGCTCGCGT 0.945159 -89 TGTCGCGCCGGGGCGCGTCGCGCAAGCGGCTC 12 37 0 GGGCGCGCGG 0.996074 -73 CGACGCGCCCCGGCGCGACACGTAGGCTCTGT 12 49 1 CGGCGCGCAG 0.913875 -61 CGATGTGAACCGGCGAGCCGGGTGAGGAGGAT 13 13 0 CGGCGAGCGG 0.993237 -154 CCCGTCCAGTCTGGCAGGCCGGAAACATCGGT 13 65 0 CTGGCAGCCG 0.583524 -102 ACAGTCCAGTGTGCCCGTCCAGTCTGGCAGGC 13 78 0 GTGCCCGCCG 0.993961 -89 CTGTTACCAGGTGCGCGGCCCGCGGGTAGGCC 13 106 1 GTGCGCGCCG 0.950668 -61 GCGCGGCCCGCGGGTAGGCCTGGCACCGTGAT 13 118 1 CGGGTAGCCG 0.776894 -49 ******* ** * Masking position 9 Map Score: 24.6944 Number of sites scoring better than the average of aligned sites = 2442 Number in coding regions = 2335 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 CGCAATAATTGCAACTGCGATTGTTGTGCT 2 11 0 GCAACTGCGA 0.979114 -142 GCGTTTTCGAGCACAGGCGCAGGCGGTCAA 2 59 1 GCACAGGCGC 0.875962 -94 CGTGATGAAAGCAAAGCCGAGTGGCAAAAA 5 42 1 GCAAAGCCGA 0.889433 -210 AAGCCGAGTGGCAAAAACGGAGTCTGCGAG 5 55 1 GCAAAAACGG 0.721172 -197 TGAATGACAGGCAAATGCGGAAGCAGCTAC 5 115 1 GCAAATGCGG 0.904961 -137 AAATGCGGAAGCAGCTACGCAAAACGCAAC 5 127 1 GCAGCTACGC 0.869978 -125 ATTTCGCTAATCACATACGAAAGATACTC 5 233 1 TCACATACGA 0.764894 -19 AGCCTACCCAGCCCCAGCGACTGCATAGCC 9 17 1 GCCCCAGCGA 0.97535 -41 AGCCGGCCTGGCAGCATCGAGGCTC 9 43 1 GCAGCATCGA 0.691417 -15 GTTCGTCACCTCCGACCTAGAGGAT 10 16 0 TCACCTCCGA 0.847548 -15 TTGACAGAATTCCACGACGAGAAGCGGACC 11 37 1 TCCACGACGA 0.672804 -67 ACAGCCCGGAGCACCTGCGACACTACGCTC 11 72 0 GCACCTGCGA 0.981048 -32 CGGCCGACCGGAACCGACGAGCCGCTTGCG 12 19 1 GAACCGACGA 0.899108 -91 GGGGCGCGTCGCGCAAGCGGCTCGTCGGTT 12 30 0 GCGCAAGCGG 0.741296 -80 TGCGCGACGCGCCCCGGCGCGACACGTAGG 12 45 1 GCCCCGGCGC 0.83514 -65 CCAGCGATGTGAACCGGCGAGCCGGGTGAG 13 19 0 GAACCGGCGA 0.956953 -148 ********** Masking position 8 Map Score: 16.6135 Number of sites scoring better than the average of aligned sites = 5734 Number in coding regions = 5501 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 3 AAACGTATCAAAAGTAACAGTTGTTTAACC 2 90 0 AAAGTAACAG 0.976482 -63 AGACTTTCTCAATTTAACAGTGTGACCTTA 4 32 0 AATTTAACAG 0.877118 -25 TAAATGACAAAAAGTGACATAACTGTATTC 7 22 0 AAAGTGACAT 0.917513 -140 TATCGTCAAAAAATTGACAGCCGTCACTTT 7 93 1 AAATTGACAG 0.986113 -69 AATTGTTTAAAAAGTGACGGCTGTCAATTT 7 103 0 AAAGTGACGG 0.969093 -59 AAGAAATTAACTGTAGCGGGAAA 8 65 0 AAATTAACTG 0.894478 -13 CATCTGCAGGTAATTGACAGAATTCCACGA 11 24 1 TAATTGACAG 0.936478 -80 ********** Masking position 7 Map Score: 5.21211 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 155 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 CGTCCTCTCCTTTAGGGACCA 3 37 0 GTCCTCTCCT 0.981208 -11 GCCCAGTCATTTCTTCACCTGTGGAGCTTT 6 29 1 TTCTTCACCT 0.88068 -26 AACCCTCTCCTGAATACAGTT 7 2 1 ACCCTCTCCT 0.964777 -160 AGCCAAACCCATCCTTTCCCGCTACAGTTA 8 51 1 ATCCTTTCCC 0.933081 -27 GTTCGTCACCTCCGACCTAGA 10 20 0 TTCGTCACCT 0.916242 -11 ATCCTCTCCCAGACAGCCCG 11 94 0 ATCCTCTCCC 0.990783 -10 AGATCCTCCTCACCCGGCTCGCCGG 13 6 1 CTCCTCACCC 0.979767 -161 ********** Masking position 5 Map Score: 4.6349 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 133 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 CGCTGTAGATAGTCAGGCAGATATACAACG 5 14 1 AGTCAGGCAG 0.975096 -238 GCAAAAACGGAGTCTGCGAGGACGCTTCCT 5 65 1 AGTCTGCGAG 0.954639 -187 GTGGCAAGGTATGAAGCCAGGTTAACGGTC 8 19 0 ATGAAGCCAG 0.724907 -59 GAGCCTCGATGCTGCCAGGCCGGCTATG 9 40 0 ATGCTGCCAG 0.970116 -18 ATCGGAGCGTAGTGTCGCAGGTGCTCCGGG 11 68 1 AGTGTCGCAG 0.869557 -36 ATCCTCTCCCAGACAGCCCGGAGCACCTGC 11 84 0 AGACAGCCCG 0.901596 -20 GTGCCCGTCCAGTCTGGCAGGCCGGAAACA 13 70 0 AGTCTGGCAG 0.98678 -97 GTAACAGTCCAGTGTGCCCGTCCAGTCTGG 13 83 0 AGTGTGCCCG 0.977535 -84 TATTGCGATCACGGTGCCAGGCCTACCCGC 13 127 0 ACGGTGCCAG 0.943742 -40 ********** Masking position 1 Map Score: 4.8577 Number of sites scoring better than the average of aligned sites = 1436 Number in coding regions = 1338 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 6 ACCGCCTGCGCCTGTGCTCGAAAACGCCAGA 2 55 0 CCTGTGCCGA 0.904458 -98 GGTATGAAGCCAGGTTAACGGTCACAAAAAT 8 11 0 CAGGTTACGG 0.919395 -67 TCCGATAGGTCCGCTTCTCGTCGTGGAATTC 11 43 0 CCGCTTCCGT 0.946225 -61 CGTAGTGTCGCAGGTGCTCCGGGCTGTCTGG 11 75 1 CAGGTGCCCG 0.971311 -29 TTCCGGTCGGCCGGTTGCCGG 12 1 0 CCGGTTGCGG 0.902965 -109 ACGTGTCGCGCCGGGGCGCGTCGCGCAAGCG 12 41 0 CCGGGGCCGT 0.91795 -69 ACCCGGCTCGCCGGTTCACATCGCTGGTAAA 13 22 1 CCGGTTCCAT 0.932722 -145 GGACTGTTACCAGGTGCGCGGCCCGCGGGTA 13 103 1 CAGGTGCCGG 0.992869 -64 TATTGCGATCACGGTGCCAGGCCTACCCGCG 13 126 0 ACGGTGCAGG 0.838497 -41 ******* *** Masking position 5 Map Score: 6.0946 Number of sites scoring better than the average of aligned sites = 1139 Number in coding regions = 1087 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 ATTGAGTGTTGTCAGCTTACAGAGTG 1 54 0 TGTTGTCAGC 0.902739 -16 GGCATGATACTGAAATCAGGT 6 2 0 TGAAATCAGG 0.897369 -53 GTGACATAACTGTATTCAGGAGAGGGTT 7 9 0 TGTATTCAGG 0.876621 -153 TGGCAAGGTATGAAGCCAGGTTAACGGTCA 8 18 0 TGAAGCCAGG 0.981632 -60 GAGCCTCGATGCTGCCAGGCCGGCTATGC 9 39 0 TGCTGCCAGG 0.983191 -19 CACACTGGACTGTTACCAGGTGCGCGGCCC 13 97 1 TGTTACCAGG 0.971176 -70 ATTGCGATCACGGTGCCAGGCCTACCCGCG 13 126 0 CGGTGCCAGG 0.94736 -41 ********** Masking position 8 Map Score: 3.43529 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 527 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 AAGTGTATGCCTGCTTGTTACGGTGGTAC 2 134 0 CCTGCTTGTT 0.714407 -19 ACGTTGTATATCTGCCTGACTATCTACAGC 5 15 0 TCTGCCTGAC 0.981533 -237 AGACTCCGTTTTTGCCACTCGGCTTTGCTT 5 50 0 TTTGCCACTC 0.933071 -202 TGCTTCCGCATTTGCCTGTCATTCACTGCA 5 110 0 TTTGCCTGTC 0.956441 -142 TATGACATGCTTTGCTTGTCTGTTTTTGAT 7 50 1 TTTGCTTGTC 0.833949 -112 GGCTTCATACCTTGCCACATAGCCAAACCC 8 31 1 CTTGCCACAT 0.813235 -47 GCCCGGAGCACCTGCGACACTACGCTCCGA 11 69 0 CCTGCGACAC 0.893073 -35 ATCCTCTCCCAGACAGCCCGGAGC 11 90 0 TCTCCCAGAC 0.904892 -14 ATGTTTCCGGCCTGCCAGACTGGACGGGCA 13 69 1 CCTGCCAGAC 0.988277 -98 ********** Masking position 3 Map Score: 4.68105 Number of sites scoring better than the average of aligned sites = 2373 Number in coding regions = 2218 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 9 AAAATGATAATTGTTATGCTAAAGTAGCCA 1 26 1 TTGTTATGCT 0.917219 -44 GCAACTGCGATTGTTGTGCT 2 1 0 TTGTTGTGCT 0.958132 -152 GCAGTTGCAATTATTGCGTACAGCCAGTAC 2 23 1 TTATTGCGTA 0.828703 -130 ACTGTTACTTTTGATACGTTTAAAACGCGC 2 99 1 TTGATACGTT 0.807814 -54 GTATGCCTGCTTGTTACGGTGGTACTCACG 2 129 0 TTGTTACGGT 0.932241 -24 TTGCGCAAAGTTGTTGCGTTTTGCGTAGCT 5 139 0 TTGTTGCGTT 0.979775 -113 TTGCTCACACTTTTTGCGCAAAGTTGTTGC 5 152 0 TTTTTGCGCA 0.849993 -100 TATGTAGGCTTTATTTCGCTAATCACATAC 5 221 1 TTATTTCGCT 0.839489 -31 ********** Masking position 5 Map Score: 2.21172 Number of sites scoring better than the average of aligned sites = 802 Number in coding regions = 714 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 10 CCAGTACATTCTGGCGTTTTCGAGCACAGGCGCAG 2 46 1 CTGCTCGAGC 0.978454 -107 GTATATCTGCCTGACTATCTACAGCGGAG 5 5 0 CTACTACAGC 0.76332 -247 TTGACGATAAATTACAAATACGATCAAAAACAGAC 7 67 0 ATACACGATC 0.87857 -95 ACCTTGCCACATAGCCAAACCCATCCTTTCCCGCT 8 39 1 ATGCACCATC 0.96786 -39 ACAATGAGCCTACCCAGCCCCAGCGACT 9 4 1 ATAGTCCAGC 0.969086 -54 TTACCTGCAGATGGCACTGGCCATCG 11 2 0 ATGCTCCATC 0.987989 -102 CGGTCAGCAGATAGGCTTTACCAGCGATGTGAACC 13 34 0 ATGGTCCAGC 0.987682 -133 CGTCTTTCGTATTGGTATTGCGATCACGGTGCCAG 13 137 0 ATGGTCGATC 0.968823 -30 ** ** * ***** Masking position 13 Map Score: 1.66674 Number of sites scoring better than the average of aligned sites = 1189 Number in coding regions = 1143 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 CAGCTTACAGAGTGGCTACTTTAGCATAACA 1 37 0 AGTGGCTACT 0.916629 -33 AAGTGTGAGCAAGGGCTACGTCACATGGCCG 5 170 1 AAGGGCTACT 0.96129 -82 TTAGCGAAATAAAGCCTACATACGAGCTTAT 5 212 0 AAAGCCTACT 0.986109 -40 ACAATGAGCCTACCCAGCCCCAGCG 9 5 1 TGAGCCTACC 0.934345 -53 TACCCCCGACAGAGCCTACGTGTCGCGCCGG 12 58 0 AGAGCCTACT 0.988469 -52 CATCGCTGGTAAAGCCTATCTGCTGACCGAT 13 40 1 AAAGCCTATT 0.902035 -127 ATCACGGTGCCAGGCCTACCCGCGGGCCGCG 13 119 0 CAGGCCTACC 0.935402 -48 ********* * Masking position 8 Map Score: 2.60556 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 49 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 ********** No masking Map Score: 2.52486e-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: 2.52486e-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: 2.52486e-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