AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iada_ecoli_bsub_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 #15 alkA_adaA 270 alkA: DNA-3-methyladenine glycosylase, adaA: methylphosphotriester-DNA alkyltransferase and transcriptional regulator (AraC/XylS family) Motif number 1 ATTGATATCGAACAAAGGGCCTGCGGGCCCTT 3 16 1 AACAAAGCCT 0.95453 -96 GAAAACAATGAAAAAAGGGCCCGCAGGCCCTT 3 30 0 AAAAAAGCCC 0.981634 -82 AGAGTACACCAAAAAACTGAGTTTGTACGCTG 3 61 0 AAAAAAGAGT 0.936252 -51 TTCGATTCTGAAAAAATTGCGCACGATACGTC 5 25 0 AAAAAAGCGC 0.984556 -61 TCCCCGTGTAAAAAAACAGCCCGAAACC 6 7 0 AAAAAAGCCC 0.981634 -69 ACAAAAAACAGACTGATCGAGGTC 9 3 1 AAAAAAGACT 0.924892 -101 TCGGGGAAGGAAAAAAGCGAGGATTTAACACT 10 98 0 AAAAAAGAGG 0.843018 -107 TTAGATTGCTGACAAAATGCGCTTTGTTCATG 11 37 1 GACAAAGCGC 0.903182 -143 GCCCAAGATATAAAAAACGCGTGTCGAAAATT 15 67 0 TAAAAAGCGT 0.917438 -204 CGGGAGTAGATAAAAATGGCCCAAGATATAAA 15 85 0 TAAAAAGCCC 0.93694 -186 ATAGCAAGATAACAAAATGAGTAAAGATGATT 15 182 1 AACAAAGAGT 0.901948 -89 ****** **** Masking position 6 Map Score: 12.1236 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 315 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 2 ATTGTTGGTTTTTGCGTGATGGTGACCGGGC 2 19 1 TTTGCGGATG 0.912139 -55 GGTTTCGGGCTGTTTTTTTACA 6 2 1 GTTTCGGCTG 0.883078 -74 GCGATCCTGCGTTCCCCGCTGATCTATTTAG 6 43 1 GTTCCCGCTG 0.89728 -33 TGGCAGATATTTTGCCTGCCGGGCGAACAGT 10 23 1 TTTGCCGCCG 0.989833 -182 TAAATGTATTTTTTCCCGATTTCCCTTTTGA 10 177 1 TTTTCCGATT 0.89447 -28 CGTGAACGCCTTATCCGGCCTACATAATCAC 11 79 1 TTATCCGCCT 0.884816 -101 ATATATTGAATTTGCGTGATTATGTAGGCCG 11 94 0 TTTGCGGATT 0.885532 -86 TGCACTACGTTTATCCGGCCTACATGATCTC 11 129 0 TTATCCGCCT 0.884816 -51 TTGTTTACGTTTTGCCTGATGCACTACGTTT 11 148 0 TTTGCCGATG 0.963839 -32 TTTTTTTGCCAGCCTCGCTAAAAGG 13 5 1 TTTGCCGCCT 0.986403 -46 CCTTAAAATAGTTGCCAGCCTTTTAGCGAGG 13 23 0 GTTGCCGCCT 0.978466 -28 ****** **** Masking position 2 Map Score: 11.0357 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 AAGCGGATGAATAAGGAGATGCG 1 58 1 ATAAGGAGAT 0.896844 -13 AGCTCCCTGGTTAAGGATAGCCTTTAGGCT 2 50 0 TTAAGGATAG 0.937814 -24 GACCGTTCGCATGAGGATAATCACGT 3 96 1 ATGAGGATAA 0.908944 -16 TGTCAAATACTTAAGAATAAGTTATTGATT 4 25 1 TTAAGAATAA 0.723049 -276 AAATAAGCATATAAGGAAAAGAGAGA 5 70 1 ATAAGGAAAA 0.913347 -16 TTCTTTTTCTATAAGGATAATGA 8 69 1 ATAAGGATAA 0.977127 -13 GGCAACTATTTTAAGGATAAAAT 13 38 1 TTAAGGATAA 0.963797 -13 GATGAGCATTGTAAGGAGAGGTGAGATAA 15 10 0 GTAAGGAGAG 0.896597 -261 ATTATTTAAGATAAGGAGAATGAAAAA 15 254 1 ATAAGGAGAA 0.976678 -17 ********** Masking position 4 Map Score: 7.63538 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 55 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 GTCTGAATAACGTTTATGCTGAAAGCGGATGAA 1 36 1 CTTTAGCTGA 0.924879 -35 TTAAGGATAGCCTTTAGGCTGCCCGGTCACCAT 2 37 0 CTTTAGCTGC 0.719699 -37 AAAAACTGAGTTTGTACGCTGAAAACAATGAAA 3 49 0 TTGTAGCTGA 0.947619 -63 AGGCAAAATATCTGCCAGGCGTACCAGAA 10 7 0 TTGCCGGCGA 0.928581 -198 AGATATTTTGCCTGCCGGGCGAACAGTGTGATA 10 27 1 CTGCCGGCGA 0.95872 -178 AAATGCGCTTTGTTCATGCCGGATGCGGCGTGA 11 51 1 TTTCAGCCGA 0.966499 -129 CCGGATAAGGCGTTCACGCCGCATCCGGCATGA 11 64 0 CTTCAGCCGA 0.978727 -116 TTTGCGTGATTATGTAGGCCGGATAAGGCGTTC 11 82 0 TTGTAGCCGA 0.976952 -98 TTGCAGAGATCATGTAGGCCGGATAAACGTAGT 11 124 1 CTGTAGCCGA 0.985423 -56 TTGTTTACGTTTTGCCTGATGCACTACGTTTAT 11 146 0 TTGCCGATGA 0.696291 -34 * **** **** * Masking position 3 Map Score: 6.11573 Number of sites scoring better than the average of aligned sites = 1173 Number in coding regions = 807 Number in noncoding regions = 366 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 5 TACATTTTGAAACATCTATAGCGATAAATG 4 134 1 AACATCTATA 0.902455 -167 CGATAAATGAAACATCTTAAAAGTTTTAGT 4 155 1 AACATCTTAA 0.867579 -146 ATACTGATTAACCCTCATTAATCAGTCGGC 4 232 0 ACCCTCATTA 0.933427 -69 GCGTATAACCCTCTAAATAGATCAGCG 6 59 0 ACCCTCTAAA 0.953547 -17 TGGCTGGTTTATCATCAATATAAATGTATT 10 157 1 ATCATCAATA 0.772049 -48 ATCAACCTCAAAAGGGAAATCGG 10 192 0 AACCTCAAAA 0.877096 -13 TCAATACCCTCTTTAAAAGAAGAGG 11 6 1 ACCCTCTTTA 0.953547 -174 ACAAAAAAAAACCATCCAAATCTGGATGGC 12 30 0 ACCATCCAAA 0.824765 -97 TAATTATCTTACCAGCTATAGACAAAAAAA 12 51 0 ACCAGCTATA 0.773913 -76 ACTACACTATAACCTCATAAATAGAAAAAA 15 133 1 AACCTCATAA 0.857254 -138 TTATCACATAATCATCTTTACTCATTTTGT 15 193 0 ATCATCTTTA 0.806679 -78 ********** Masking position 1 Map Score: 6.55381 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 183 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 TGAAAGCAAAGCGCAGCGTCTGAATAACGTTTA 1 19 1 GCGAGGTCTA 0.994624 -52 TTATCCTCATGCGAACGGTCGCAAGAGTACACC 3 83 0 GCGACGTCGA 0.990594 -29 TAAGATTATTGCGGAATGGCGAAATAAGCACCT 4 84 0 GCGAAGGCGA 0.978641 -217 CGGCGTAGCGTCTGAAGCGTGGAGT 7 3 1 GCGAGGTCTA 0.994625 -83 AGCGTCTGAAGCGTGGAGTCATATCCTCTGGCG 7 17 1 GCGGGGTCAA 0.945374 -69 TGCCTGCCGGGCGAACAGTGTGATACATTGCTG 10 35 1 GCGACGTGTA 0.960657 -170 GTGTCGGATAGCGTAATGGCTTACCCGACACAG 10 65 0 GCGAAGGCTA 0.982227 -140 *** ** **** * Masking position 13 Map Score: 5.19123 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 142 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 CTGCGCTTTGCTTTCATATTCCGG 1 4 0 CTTTCATATC 0.905107 -67 GCGGGCCCTTTTTTCATTGTTTTCAGCGTAC 3 38 1 TTTTCATTTT 0.897437 -74 GTGCGCAATTTTTTCAGAATCGAAAGGTTCA 5 33 1 TTTTCAGATC 0.960253 -53 ATGTCGGTGGTTTTCTTTTTCTATAAGGATA 8 57 1 TTTTCTTTTC 0.800462 -25 TACCATCGCTTTTTCAGAGTTACAGCACTTT 9 49 0 TTTTCAGATT 0.904267 -55 TTTTCAAAATCACCGTTTGCT 9 93 0 TTTTCAAATC 0.898574 -11 TCTGGATGGCTTTTCATAATTCTGAGAAA 12 9 0 TTTTCATATT 0.933498 -118 TTTTTCATTCTCCTTATCTTAA 15 259 0 TTTTCATTTC 0.957238 -12 ******** ** Masking position 4 Map Score: 4.35738 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 175 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 AATCAGCTCCCTGGTTAAGGATAGCC 2 58 0 CTCCCTGGTT 0.869087 -16 GGAACGCAGGATCGCTGGCTCCCCGTGTAA 6 28 0 ATCGCTGGCT 0.968716 -48 CCTCAGGGATGTCGGTGGTTTTCTTTTTCT 8 49 1 GTCGGTGGTT 0.821809 -33 GACACAGCTTGTGGCTGGTTTATCATCAAT 10 146 1 GTGGCTGGTT 0.965357 -59 CCATCCAAATCTGGATGGCTTTTCATAATT 12 19 0 CTGGATGGCT 0.913429 -108 CCATCCAGATTTGGATGGTTTTTTTTTGTC 12 31 1 TTGGATGGTT 0.664306 -96 TTTTTTGTCTATAGCTGGTAAGATAATTAC 12 52 1 ATAGCTGGTA 0.677913 -75 GCCTTTTAGCGAGGCTGGCAAAAAAA 13 7 0 GAGGCTGGCA 0.897773 -44 GCCTCGCTAAAAGGCTGGCAACTATTTTAA 13 22 1 AAGGCTGGCA 0.879116 -29 TCTGTCATGAATCCATGGCAGTGACCATAC 14 31 1 ATCCATGGCA 0.550619 -38 TAAGAAAACTCACGCTGGTTGAAATTAGTT 15 222 0 CACGCTGGTT 0.917339 -49 ********** Masking position 6 Map Score: 3.14669 Number of sites scoring better than the average of aligned sites = 3803 Number in coding regions = 3660 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 9 GGGTTAATCAGTATGCAGTGGCATAAAAAA 4 248 1 GTATGCAGTG 0.970892 -53 TCCATATTTGTTATGCGGTGATCCCTGTTG 7 58 0 TTATGCGGTG 0.970895 -28 ACATCCCTGAGGATGCGGTGGCTTTATTGA 8 31 0 GGATGCGGTG 0.995144 -51 TGTTCATGCCGGATGCGGCGTGAACGCCTT 11 61 1 GGATGCGGCG 0.991734 -119 ********** Masking position 4 Map Score: 2.16451 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 83 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 10 TGATGTTAGGTGCTTATTTCGCCATTCCGC 4 77 1 TGCTTATTTC 0.83922 -224 TGGATTATTCTGCATTTTTGGGGAGAATGG 4 198 1 TGCATTTTTG 0.957921 -103 TGCCTTTATTTGCTTTTTTATGCCACTGCA 4 261 0 TGCTTTTTTA 0.794708 -40 TTTCCTTATATGCTTATTTGTACTTTGAAC 5 59 0 TGCTTATTTG 0.957921 -27 GTTTGTGCTCCATATTTGTTATGCGGTG 7 68 0 TCCATATTTG 0.957348 -18 GATGGTAGAATCCATTTTTAAGCAAACGGT 9 73 1 TCCATTTTTA 0.792401 -31 TGAAAAGCCATCCAGATTTGGATGGTTTTT 12 24 1 TCCAGATTTG 0.856363 -103 ATTAATAAAATGAATATTTGCAATACGTAA 12 78 0 TGAATATTTG 0.803033 -49 ********** Masking position 7 Map Score: 2.62712 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 11 AAACGTTATTCAGACGCTGCGCTTTGCTTT 1 21 0 CAGACGCTGC 0.981556 -50 CTCCACGCTTCAGACGCTACGCCG 7 5 0 CAGACGCTAC 0.910701 -81 AATGGCTTACCCGACACAGCAATGTATCAC 10 54 0 CCGACACAGC 0.993756 -151 ATTACGCTATCCGACACAGTGTTAAATCCT 10 81 1 CCGACACAGT 0.968254 -124 AAATAAATTAGCGACACAGCTTGTGGCTGG 10 134 1 GCGACACAGC 0.978345 -71 ********** Masking position 4 Map Score: 1.69187 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 359 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 GTACTCTTGCGACCGTTCGCATGAGGATAA 3 86 1 GACCGTTCGC 0.979825 -26 AGAGTTACAGCACTTTTTGCACTCAAAAAT 9 35 0 CACTTTTTGC 0.93195 -69 TTTTCAAAATCACCGTTTGCTTAAAAATGG 9 84 0 CACCGTTTGC 0.988258 -20 CAATGTATCACACTGTTCGCCCGGCAGGCA 10 35 0 CACTGTTCGC 0.988258 -170 ********** Masking position 6 Map Score: 0.708471 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 70 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 TTTTGCGTGATGGTGACCGGGCAGCCTAAA 2 28 1 TGGTGACCGG 0.935839 -46 GGGGAACGCAGGATCGCTGGCTCCCCGTGT 6 30 0 GGATCGCTGG 0.888823 -46 AAGACAACAGGGATCACCGCATAACAAATA 7 54 1 GGATCACCGC 0.965693 -32 CCGGCCTACATGATCTCTGCAATATATTGA 11 116 0 TGATCTCTGC 0.925642 -64 ACCATTAGTATGGTCACTGCCATGGATTCA 14 38 0 TGGTCACTGC 0.98471 -31 ACCATACTAATGGTGACTGCCATTG 14 54 1 TGGTGACTGC 0.971149 -15 ********** Masking position 4 Map Score: 0.80068 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 ********** No masking Map Score: 1.35957e-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: 1.35957e-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