AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iada_ecoli_hinf_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 0.984837 -97 TGAAAACAATGAAAAAAGGGCCCGCAGGCCC 3 32 0 GAAAAAAGGC 0.993423 -80 AAGAGTACACCAAAAAACTGAGTTTGTACGC 3 63 0 CAAAAAACGA 0.910063 -49 TTTCGATTCTGAAAAAATTGCGCACGATACG 5 27 0 GAAAAAATGC 0.951439 -59 AGCATATAAGGAAAAGAGAGA 5 75 1 GAAAAGAGGA 0.930766 -11 CTCCCCGTGTAAAAAAACAGCCCGAAACC 6 9 0 AAAAAAACGC 0.896834 -67 ACAAAAAACAGACTGATCGAGG 9 2 1 CAAAAAACGA 0.910063 -102 ATTTTTGAGTGCAAAAAGTGCTGTAACTCTG 9 35 1 GCAAAAAGGC 0.969182 -69 TTCGGGGAAGGAAAAAAGCGAGGATTTAACA 10 100 0 GAAAAAAGGA 0.984724 -105 CATCCGGCATGAACAAAGCGCATTTTGTCAG 11 45 0 GAACAAAGGC 0.984837 -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 GATTGTTGGTTTTTGCGTGATGGTGACCGG 2 18 1 TTTTGCGTGA 0.953713 -56 ATTCTTAAGTATTTGACAGCACTGAATGTC 4 13 0 ATTTGACAGC 0.922363 -288 TCGAGGTCATTTTTGAGTGCAAAAAGTGCT 9 27 1 TTTTGAGTGC 0.93498 -77 CTGGCAGATATTTTGCCTGCCGGGCGAACA 10 22 1 TTTTGCCTGC 0.991869 -183 ACAAAGCGCATTTTGTCAGCAATCTAACCC 11 34 0 TTTTGTCAGC 0.927766 -146 AATATATTGAATTTGCGTGATTATGTAGGC 11 96 0 ATTTGCGTGA 0.915315 -84 GTTGTTTACGTTTTGCCTGATGCACTACGT 11 150 0 TTTTGCCTGA 0.975598 -30 TTTTTTTGCCAGCCTCGCTAAAA 13 4 1 TTTTGCCAGC 0.990001 -47 TCCTTAAAATAGTTGCCAGCCTTTTAGCGA 13 25 0 AGTTGCCAGC 0.923873 -26 ********** Masking position 4 Map Score: 12.2862 Number of sites scoring better than the average of aligned sites = 732 Number in coding regions = 662 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 3 TAAACGTTATTCAGACGCTGCGCTTTGCTTTC 1 20 0 TCGAGCTGCG 0.99156 -51 ACTCCACGCTTCAGACGCTACGCCG 7 4 0 TCGAGCTACG 0.953075 -82 TCTTTCGACGCCAGAGGATATGACTCCACGCT 7 26 0 CCGAGATATG 0.851429 -60 CACCGACATCCCTGAGGATGCGGTGGCTTTAT 8 34 0 CCGAGATGCG 0.99156 -48 GTGCTGTAACTCTGAAAAAGCGATGGTAGAAT 9 52 1 TCGAAAAGCG 0.930255 -52 TAATGGCTTACCCGACACAGCAATGTATCACA 10 53 0 CCGAACAGCA 0.864839 -152 CATTACGCTATCCGACACAGTGTTAAATCCTC 10 80 1 TCGAACAGTG 0.898154 -125 GATAAACCAGCCACAAGCTGTGTCGCTAATTT 10 138 0 CCCAGCTGTG 0.909574 -67 TTTGTTCATGCCGGATGCGGCGTGAACGCCTT 11 59 1 CCGAGCGGCG 0.994631 -121 ATTATGTAGGCCGGATAAGGCGTTCACGCCGC 11 75 0 CCGAAAGGCG 0.971214 -105 ** ** ****** Masking position 5 Map Score: 9.58028 Number of sites scoring better than the average of aligned sites = 2442 Number in coding regions = 1843 Number in noncoding regions = 599 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 CATCCGCTTTCAGCATAAACGTTATTCAGACGCTG 1 32 0 CGCTAAAGTT 0.97582 -39 GGTGACCGGGCAGCCTAAAGGCTATCCTTAACCAG 2 39 1 CGCTAAAGTT 0.97582 -35 TCATTGTTTTCAGCGTACAAACTCAGTTTTTTGGT 3 51 1 CGCTACAATA 0.970947 -61 ATAAATGAAACATCTTAAAAGTTTTAGTATCATAT 4 157 1 CTCTAAAGTT 0.760755 -144 TTTTATGCCACTGCATACTGATTAACCCTCATTAA 4 241 0 CGCTACTATA 0.902819 -60 CAGTATGCAGTGGCATAAAAAAGCAAATAAAGGCA 4 256 1 TGCTAAAAGA 0.772591 -45 ACAGGGATCACCGCATAACAAATATGGAGCACAAA 7 60 1 CGCTAACATT 0.875408 -26 AAATCACCGTTTGCTTAAAAATGGATTCTACCATC 9 73 0 TGCTAAAAGA 0.772591 -31 CTGTGTCGGATAGCGTAATGGCTTACCCGACACAG 10 65 0 TGCTAATGTA 0.767558 -140 ACGCCTTATCCGGCCTACATAATCACGCAAATTCA 11 84 1 CGCTACAATA 0.970947 -96 TACGTTTATCCGGCCTACATGATCTCTGCAATATA 11 120 0 CGCTACAGTT 0.974188 -60 * ** **** * * * Masking position 7 Map Score: 6.24721 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 322 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 AGCGCAAGATTGTTGGTTTTTGCGTGATGG 2 10 1 TTGTGGTTTT 0.960416 -64 GGTTTCGGGCTGTTTTTTTACACGGGG 6 7 1 GGGTGTTTTT 0.917022 -69 CCCTGAGGATGCGGTGGCTTTATTGACCTGT 8 26 0 GCGTGGCTTT 0.967707 -56 CTCAGGGATGTCGGTGGTTTTCTTTTTCTAT 8 50 1 TCGTGGTTTT 0.985114 -32 ACACAGCTTGTGGCTGGTTTATCATCAATAT 10 147 1 TGGTGGTTTA 0.963352 -58 CATCCAAATCTGGATGGCTTTTCATAATTCT 12 17 0 TGGTGGCTTT 0.988399 -110 CATCCAGATTTGGATGGTTTTTTTTTGTCTA 12 32 1 TGGTGGTTTT 0.992164 -95 *** ******* Masking position 5 Map Score: 7.77358 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 100 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 GACCGTTCGCATGAGGATAATCACGT 3 96 1 ATGAGGATAA 0.941615 -16 CGACTGATTAATGAGGGTTAATCAGTATGC 4 234 1 ATGAGGGTTA 0.947605 -67 AGGCATATAACAGAGGGTTAATAAC 4 286 1 CAGAGGGTTA 0.913083 -15 AAATAAGCATATAAGGAAAAGAGAGA 5 70 1 ATAAGGAAAA 0.595172 -16 CTGATCTATTTAGAGGGTTATACGC 6 61 1 TAGAGGGTTA 0.871654 -15 CTTTCGACGCCAGAGGATATGACTCCACGC 7 27 0 CAGAGGATAT 0.69919 -59 TTCTTTTTCTATAAGGATAATGA 8 69 1 ATAAGGATAA 0.855602 -13 ATCAACCTCAAAAGGGAAATCGGGAAAAA 10 186 0 AAAAGGGAAA 0.768672 -19 TCTTCTTTTAAAGAGGGTATTGA 11 4 0 AAGAGGGTAT 0.90044 -176 TCTTTAAAAGAAGAGGGTTAGATTGCTGAC 11 20 1 AAGAGGGTTA 0.955539 -160 GGCAACTATTTTAAGGATAAAAT 13 38 1 TTAAGGATAA 0.651862 -13 ********** Masking position 4 Map Score: 7.58905 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 269 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 7 ATGAAAAAAGGGCCCGCAGGCCCTTTGTTCG 3 24 0 GCCCGCAGGC 0.991514 -88 GGGGAACGCAGGATCGCTGGCTCCCCGTGTA 6 29 0 GATCGCTGGC 0.973569 -47 TTATTGACCTGTACCGCAGTCGTTATA 8 7 0 GACCGCAGTC 0.95076 -75 TTCTGGTACGCCTGGCAGATATTTTG 10 6 1 GACGCCTGGC 0.975938 -199 CACACTGTTCGCCCGGCAGGCAAAATATCTG 10 26 0 GCCGGCAGGC 0.731898 -179 CAGCCTTTTAGCGAGGCTGGCAAAAAAA 13 8 0 GGAGGCTGGC 0.771124 -43 CAGCCTCGCTAAAAGGCTGGCAACTATTTTA 13 20 1 AAAGGCTGGC 0.916636 -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 8 TGATGTTAGGTGCTTATTTCGCCATTCCGC 4 77 1 TGCTTATTTC 0.878894 -224 TGGATTATTCTGCATTTTTGGGGAGAATGG 4 198 1 TGCATTTTTG 0.969373 -103 TGCCTTTATTTGCTTTTTTATGCCACTGCA 4 261 0 TGCTTTTTTA 0.843314 -40 TTTCCTTATATGCTTATTTGTACTTTGAAC 5 59 0 TGCTTATTTG 0.969373 -27 GTTTGTGCTCCATATTTGTTATGCGGTG 7 68 0 TCCATATTTG 0.96895 -18 GATGGTAGAATCCATTTTTAAGCAAACGGT 9 73 1 TCCATTTTTA 0.841444 -31 TGAAAAGCCATCCAGATTTGGATGGTTTTT 12 24 1 TCCAGATTTG 0.892349 -103 ATTAATAAAATGAATATTTGCAATACGTAA 12 78 0 TGAATATTTG 0.850011 -49 ********** Masking position 7 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 9 TAGCCTTTAGGCTGCCCGGTCACCATCACG 2 33 0 GCTGCCCGGT 0.984576 -41 AATCAGCTCCCTGGTTAAGGATAGC 2 59 0 GCTCCCTGGT 0.990075 -15 AGGATCGCTGGCTCCCCGTGTAAAAAAACA 6 21 0 GCTCCCCGTG 0.984953 -55 GCGATCCTGCGTTCCCCGCTGATCTATTTA 6 43 1 GTTCCCCGCT 0.968495 -33 GTTATGCGGTGATCCCTGTTGTCTTTCGAC 7 49 0 GATCCCTGTT 0.94197 -37 ********** Masking position 3 Map Score: 1.69746 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 94 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TTTTTGCGTGATGGTGACCGGGCAGCCTAA 2 27 1 ATGGTGACCG 0.982671 -47 TCCGGCCTACATGATCTCTGCAATATATTG 11 117 0 ATGATCTCTG 0.905928 -63 CACCATTAGTATGGTCACTGCCATGGATTC 14 39 0 ATGGTCACTG 0.989762 -30 GACCATACTAATGGTGACTGCCATTG 14 53 1 ATGGTGACTG 0.989762 -16 ********** Masking position 5 Map Score: 1.09751 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 46 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 TGCGCTTTGCTTTCATATTCCGG 1 4 0 TTTCATATTC 0.928595 -67 GCTATAGATGTTTCAAAATGTAAATGCAAG 4 126 0 TTTCAAAATG 0.827862 -175 AAAGTTTTAGTATCATATTCGTGTTGGATT 4 174 1 TATCATATTC 0.729719 -127 TGCGCAATTTTTTCAGAATCGAAAGGTTCA 5 34 1 TTTCAGAATC 0.963226 -52 ACCATCGCTTTTTCAGAGTTACAGCACTTT 9 49 0 TTTCAGAGTT 0.799482 -55 TTTTCAAAATCACCGTTTGCT 9 93 0 TTTCAAAATC 0.944239 -11 CTGGATGGCTTTTCATAATTCTGAGAAA 12 9 0 TTTCATAATT 0.891291 -118 ********** Masking position 5 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 12 TTGACATTCAGTGCTGTCAAATACTTAA 4 9 1 CAGTGCTGTC 0.982667 -292 ACCGCATCCTCAGGGATGTCGGTGGTTTTC 8 42 1 CAGGGATGTC 0.932986 -40 TGAGTGCAAAAAGTGCTGTAACTCTGAAAA 9 40 1 AAGTGCTGTA 0.829559 -64 CAGTGTGATACATTGCTGTGTCGGGTAAGC 10 50 1 CATTGCTGTG 0.958079 -155 GTCATGAATCCATGGCAGTGACCATACTAA 14 34 1 CATGGCAGTG 0.949786 -35 CAATGGCAGTCACCATTAGTA 14 58 0 AATGGCAGTC 0.911992 -11 ********** Masking position 2 Map Score: 0.412282 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 380 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 ********** 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 Motif number 14 ********** 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 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