AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iada_ecoli_opreg_300.orf -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 alkA 70 3-methyl-adenine DNA glycosylase II, inducible #2 ada 73 O6-methylguanine-DNA methyltransferase; transcription activator/repressor #3 yojL 111 orf, hypothetical protein #4 ompC 300 outer membrane protein 1b (Ib;c) #5 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #6 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #7 hflK 85 protease specific for phage lambda cII repressor #8 yjeT 81 orf, hypothetical protein #9 purA 103 adenylosuccinate synthetase #10 yjeB 204 orf, hypothetical protein #11 yjfH 179 orf, hypothetical protein #12 yjfI 126 orf, hypothetical protein #13 yjfK 50 orf, hypothetical protein #14 aidB 68 putative acyl coenzyme A dehydrogenase Motif number 1 GATTGATATCGAACAAAGGGCCTGCGGGCCC 3 15 1 GAACAAAGGC 0.983967 -97 TGAAAACAATGAAAAAAGGGCCCGCAGGCCC 3 32 0 GAAAAAAGGC 0.993043 -80 AAGAGTACACCAAAAAACTGAGTTTGTACGC 3 63 0 CAAAAAACGA 0.905315 -49 TTTCGATTCTGAAAAAATTGCGCACGATACG 5 27 0 GAAAAAATGC 0.948752 -59 AGCATATAAGGAAAAGAGAGA 5 75 1 GAAAAGAGGA 0.927023 -11 CTCCCCGTGTAAAAAAACAGCCCGAAACC 6 9 0 AAAAAAACGC 0.89147 -67 ACAAAAAACAGACTGATCGAGG 9 2 1 CAAAAAACGA 0.905315 -102 ATTTTTGAGTGCAAAAAGTGCTGTAACTCTG 9 35 1 GCAAAAAGGC 0.967449 -69 TTCGGGGAAGGAAAAAAGCGAGGATTTAACA 10 100 0 GAAAAAAGGA 0.983848 -105 CATCCGGCATGAACAAAGCGCATTTTGTCAG 11 45 0 GAACAAAGGC 0.983967 -135 ******** ** Masking position 5 Map Score: 13.1802 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 438 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 ATTGTTGGTTTTTGCGTGATGGTGACCGGGC 2 19 1 TTTGCGGATG 0.930581 -55 GGTTTCGGGCTGTTTTTTTACA 6 2 1 GTTTCGGCTG 0.906997 -74 GCGATCCTGCGTTCCCCGCTGATCTATTTAG 6 43 1 GTTCCCGCTG 0.918562 -33 TGGCAGATATTTTGCCTGCCGGGCGAACAGT 10 23 1 TTTGCCGCCG 0.992108 -182 TAAATGTATTTTTTCCCGATTTCCCTTTTGA 10 177 1 TTTTCCGATT 0.91628 -28 CGTGAACGCCTTATCCGGCCTACATAATCAC 11 79 1 TTATCCGCCT 0.908416 -101 ATATATTGAATTTGCGTGATTATGTAGGCCG 11 94 0 TTTGCGGATT 0.909001 -86 TGCACTACGTTTATCCGGCCTACATGATCTC 11 129 0 TTATCCGCCT 0.908416 -51 TTGTTTACGTTTTGCCTGATGCACTACGTTT 11 148 0 TTTGCCGATG 0.971765 -32 TTTTTTTGCCAGCCTCGCTAAAAGG 13 5 1 TTTGCCGCCT 0.989438 -46 CCTTAAAATAGTTGCCAGCCTTTTAGCGAGG 13 23 0 GTTGCCGCCT 0.983241 -28 ****** **** Masking position 2 Map Score: 12.8376 Number of sites scoring better than the average of aligned sites = 1642 Number in coding regions = 1509 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 GCATAAACGTTATTCAGACGCTGCGCTTTGCTTTCA 1 19 0 TTAGACTCGC 0.993716 -52 TTTGGTGTACTCTTGCGACCGTTCGCATGAGGATAA 3 80 1 TTCGACTCGC 0.99069 -32 GTTAGGTGCTTATTTCGCCATTCCGCAATAATCTTA 4 81 1 TTCGCCTCGC 0.986227 -220 ATGACTCCACGCTTCAGACGCTACGCCG 7 3 0 GTAGACTCGC 0.994781 -83 ACACAGCAATGTATCACACTGTTCGCCCGGCAGGCA 10 35 0 GTACACTCGC 0.987742 -170 TTGCTGTGTCGGGTAAGCCATTACGCTATCCGACAC 10 62 1 GTAGCCTCGC 0.99195 -143 AGGGTTAGATTGCTGACAAAATGCGCTTTGTTCATG 11 33 1 TTACAATCGC 0.896431 -147 * * **** * *** Masking position 12 Map Score: 6.88758 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 91 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 GACCGTTCGCATGAGGATAATCACGT 3 96 1 ATGAGGATAA 0.86129 -16 CGACTGATTAATGAGGGTTAATCAGTATGC 4 234 1 ATGAGGGTTA 0.967361 -67 AGGCATATAACAGAGGGTTAATAAC 4 286 1 CAGAGGGTTA 0.982603 -15 CTGATCTATTTAGAGGGTTATACGC 6 61 1 TAGAGGGTTA 0.953933 -15 CTTTCGACGCCAGAGGATATGACTCCACGC 7 27 0 CAGAGGATAT 0.837339 -59 TCTTCTTTTAAAGAGGGTATTGA 11 4 0 AAGAGGGTAT 0.957916 -176 TCTTTAAAAGAAGAGGGTTAGATTGCTGAC 11 20 1 AAGAGGGTTA 0.985534 -160 ********** Masking position 4 Map Score: 6.62595 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 68 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TCATCCGCTTTCAGCATAAACGTTATTCAG 1 38 0 TCAGCATAAA 0.842129 -33 TGGTGACCGGGCAGCCTAAAGGCTATCCTT 2 38 1 GCAGCCTAAA 0.935542 -36 TTCATTGTTTTCAGCGTACAAACTCAGTTT 3 50 1 TCAGCGTACA 0.850601 -62 TCAGTATGCAGTGGCATAAAAAAGCAAATA 4 255 1 GTGGCATAAA 0.782378 -46 CACTGTTCGCCCGGCAGGCAAAATATCTGC 10 25 0 CCGGCAGGCA 0.922786 -180 CACGCCGCATCCGGCATGAACAAAGCGCAT 11 53 0 CCGGCATGAA 0.975448 -127 CATGCCGGATGCGGCGTGAACGCCTTATCC 11 65 1 GCGGCGTGAA 0.961652 -115 AACGCCTTATCCGGCCTACATAATCACGCA 11 83 1 CCGGCCTACA 0.986822 -97 CTACGTTTATCCGGCCTACATGATCTCTGC 11 126 0 CCGGCCTACA 0.986822 -54 ********** Masking position 10 Map Score: 6.29307 Number of sites scoring better than the average of aligned sites = 1130 Number in coding regions = 747 Number in noncoding regions = 383 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 6 ATGAAAAAAGGGCCCGCAGGCCCTTTGTTCG 3 24 0 GCCCGCAGGC 0.991037 -88 GGGGAACGCAGGATCGCTGGCTCCCCGTGTA 6 29 0 GATCGCTGGC 0.97197 -47 TTATTGACCTGTACCGCAGTCGTTATA 8 7 0 GACCGCAGTC 0.947807 -75 TTCTGGTACGCCTGGCAGATATTTTG 10 6 1 GACGCCTGGC 0.974942 -199 CACACTGTTCGCCCGGCAGGCAAAATATCTG 10 26 0 GCCGGCAGGC 0.739225 -179 CAGCCTTTTAGCGAGGCTGGCAAAAAAA 13 8 0 GGAGGCTGGC 0.777127 -43 CAGCCTCGCTAAAAGGCTGGCAACTATTTTA 13 20 1 AAAGGCTGGC 0.911956 -31 * ********* Masking position 7 Map Score: 4.89415 Number of sites scoring better than the average of aligned sites = 1329 Number in coding regions = 1282 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 AGCGCAAGATTGTTGGTTTTTGCGTGATGG 2 11 1 TGTTGGTTTT 0.816493 -63 GGTTTCGGGCTGTTTTTTTACACGGGG 6 8 1 GGCTGTTTTT 0.891481 -68 CCTGAGGATGCGGTGGCTTTATTGACCTGT 8 26 0 CGGTGGCTTT 0.975473 -56 TCAGGGATGTCGGTGGTTTTCTTTTTCTAT 8 51 1 CGGTGGTTTT 0.985962 -31 TTTAAGCAAACGGTGATTTTGAAAA 9 89 1 CGGTGATTTT 0.90109 -15 CACAGCTTGTGGCTGGTTTATCATCAATAT 10 148 1 GGCTGGTTTA 0.919027 -57 ATCCAAATCTGGATGGCTTTTCATAATTCT 12 17 0 GGATGGCTTT 0.958653 -110 ATCCAGATTTGGATGGTTTTTTTTTGTCTA 12 33 1 GGATGGTTTT 0.976159 -94 ********** Masking position 4 Map Score: 6.37183 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 416 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 GTATCATATTCGTGTTGGATTATTCTGCAT 4 183 1 CGTGTTGGAT 0.897368 -118 GATACATTGCTGTGTCGGGTAAGCCATTAC 10 56 1 TGTGTCGGGT 0.961431 -149 GATTTAACACTGTGTCGGATAGCGTAATGG 10 79 0 TGTGTCGGAT 0.985544 -126 GCGCTTTGTTCATGCCGGATGCGGCGTGAA 11 55 1 CATGCCGGAT 0.982614 -125 CGTGATTATGTAGGCCGGATAAGGCGTTCA 11 81 0 TAGGCCGGAT 0.982614 -99 AGAGATCATGTAGGCCGGATAAACGTAGTG 11 128 1 TAGGCCGGAT 0.982614 -52 ********** Masking position 10 Map Score: 4.46312 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 242 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 9 CTTAAGTATTTGACAGCACTGAATGTCAA 4 10 0 TGACAGCACT 0.965977 -291 TTTTTCAGAGTTACAGCACTTTTTGCACTC 9 41 0 TTACAGCACT 0.877241 -63 GGCTTACCCGACACAGCAATGTATCACACT 10 51 0 ACACAGCAAT 0.897535 -154 AAGCGCATTTTGTCAGCAATCTAACCCTCT 11 31 0 TGTCAGCAAT 0.948333 -149 GCCTACATGATCTCTGCAATATATTGAATT 11 113 0 TCTCTGCAAT 0.933758 -67 ATTAGTATGGTCACTGCCATGGATTCATGA 14 35 0 TCACTGCCAT 0.956149 -34 ATACTAATGGTGACTGCCATTG 14 57 1 TGACTGCCAT 0.956149 -12 ********** Masking position 10 Map Score: 3.56215 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 127 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 GAATAACGTTTATGCTGAAAGCGGATGAAT 1 40 1 TATGCTGAAA 0.947886 -31 GCCTAAAGGCTATCCTTAACCAGGGAGCTG 2 51 1 TATCCTTAAC 0.916782 -23 ACTGAGTTTGTACGCTGAAAACAATGAAAA 3 48 0 TACGCTGAAA 0.849486 -64 TCTCTCTTTTCCTTATATGCTTATTTG 5 69 0 TTTCCTTATA 0.870344 -17 TCATTATCCTTATAGAAAAAGAAA 8 68 0 TATCCTTATA 0.939177 -14 AAAATCACCGTTTGCTTAAAAATGGATTCT 9 79 0 TTTGCTTAAA 0.922194 -25 ATTTTATCCTTAAAATAGTTGCCA 13 37 0 TATCCTTAAA 0.972606 -14 ********** Masking position 8 Map Score: 2.65139 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 55 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 GTGATACATTGCTGTGTCGGGTAAGCCATT 10 54 1 GCTGTGTCGG 0.996876 -151 AGGATTTAACACTGTGTCGGATAGCGTAAT 10 81 0 ACTGTGTCGG 0.991532 -124 CCAGCCACAAGCTGTGTCGCTAATTTATTT 10 134 0 GCTGTGTCGC 0.994241 -71 ********** Masking position 5 Map Score: 1.91863 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 8 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 GCGGAATGGCGAAATAAGCACCTAACATCA 4 77 0 GAAATAAGCA 0.856579 -224 CCATTCTCCCCAAAAATGCAGAATAATCCA 4 198 0 CAAAAATGCA 0.963029 -103 TGCAGTGGCATAAAAAAGCAAATAAAGGCA 4 261 1 TAAAAAAGCA 0.815817 -40 GTTCAAAGTACAAATAAGCATATAAGGAAA 5 59 1 CAAATAAGCA 0.963029 -27 CACCGCATAACAAATATGGAGCACAAAC 7 68 1 CAAATATGGA 0.962522 -18 ACCGTTTGCTTAAAAATGGATTCTACCATC 9 73 0 TAAAAATGGA 0.813692 -31 AAAAACCATCCAAATCTGGATGGCTTTTCA 12 24 0 CAAATCTGGA 0.872153 -103 TTACGTATTGCAAATATTCATTTTATTAAT 12 78 1 CAAATATTCA 0.823466 -49 ********** Masking position 4 Map Score: 3.93045 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 201 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 13 TTTAGGCTGCCCGGTCACCATCACGCAAAA 2 28 0 CCGGTCACCA 0.952515 -46 ACACGGGGAGCCAGCGATCCTGCGTTCCCC 6 30 1 CCAGCGATCC 0.91663 -46 TATTTGTTATGCGGTGATCCCTGTTGTCTT 7 54 0 GCGGTGATCC 0.974818 -32 TCAATATATTGCAGAGATCATGTAGGCCGG 11 116 1 GCAGAGATCA 0.944813 -64 TGAATCCATGGCAGTGACCATACTAATGGT 14 38 1 GCAGTGACCA 0.988835 -31 CAATGGCAGTCACCATTAGTATGGT 14 54 0 GCAGTCACCA 0.978855 -15 ********** Masking position 7 Map Score: 1.77805 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 373 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 CCGGAATATGAAAGCAAAGCGCA 1 4 1 GAATATGAAA 0.925941 -67 CTTGCATTTACATTTTGAAACATCTATAGC 4 126 1 CATTTTGAAA 0.822179 -175 AATCCAACACGAATATGATACTAAAACTTT 4 174 0 GAATATGATA 0.721885 -127 TGAACCTTTCGATTCTGAAAAAATTGCGCA 5 34 0 GATTCTGAAA 0.961806 -52 AAAGTGCTGTAACTCTGAAAAAGCGATGGT 9 49 1 AACTCTGAAA 0.793097 -55 AGCAAACGGTGATTTTGAAAA 9 93 1 GATTTTGAAA 0.942129 -11 TTTCTCAGAATTATGAAAAGCCATCCAG 12 9 1 AATTATGAAA 0.887417 -118 ********** Masking position 8 Map Score: 1.04832 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 130 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 15 ********** No masking Map Score: 7.91135e-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