AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icpxR_ecoli_opreg_100.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 htrA 129 periplasmic serine protease Do; heat shock protein HtrA #2 ybaU 191 putative protease maturation protein #3 cydD 122 ATP-binding component of cytochrome-related transport, Zn sensitive #4 motA 126 proton conductor component of motor; no effect on switching #5 ygjT 283 putative transport protein #6 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #7 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #8 yihD 69 orf, hypothetical protein #9 yihE 77 orf, hypothetical protein #10 cpxR_b3913 146 cpxR: transcriptional regulator in 2-component system, b3913: orf, hypothetical protein #11 proP 263 low-affinity transport system; proline permease II Motif number 1 CGTATCGATGCGCGCAAAGGCCTATTGTGA 2 128 0 CGCGCAAAGG 0.920615 -64 TGATAACTCACCTGCTAAGCGTGCA 3 108 1 CCTGCTAAGC 0.981004 -15 TACTTTGTTACCTGCAAAGGGGAGTAACTT 5 74 1 CCTGCAAAGG 0.98082 -210 CGCGGCATATCCCGCTATGCCATTTTATTT 6 28 0 CCCGCTATGC 0.977141 -243 CCTAAAATCGCCCGCTCGCGGCATATCCCG 6 44 0 CCCGCTCGCG 0.930536 -227 ATACTCTTTCCCTGCAATGGGTTCCGTAGC 7 23 1 CCTGCAATGG 0.957852 -222 GGTCTCTTTCCCTGCTACGGAACCCATTGC 7 36 0 CCTGCTACGG 0.988599 -209 TGGGATTGACCCTGCTAACGTGTCTGTCTC 8 31 1 CCTGCTAACG 0.980964 -39 TGTAAGCAAACCCGCTACGCTTGTTACAGA 11 152 1 CCCGCTACGC 0.989724 -112 TCCTGCAATTCCCGCTCCCCTTTTGCGGCC 11 189 1 CCCGCTCCCC 0.955636 -75 TTGGCCCATTTCCGCAAACGCCAGAAAAAT 11 228 0 TCCGCAAACG 0.820301 -36 ********** Masking position 5 Map Score: 14.6029 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 676 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 CAAGACGCAGAAAGTCACCGAATACAAATAAAA 2 68 0 AAAGTCACGT 0.967424 -124 CAACGGGGAAAAAATAAAGGCGACCCATAGTCG 3 52 0 AAAATAAGGA 0.700549 -71 TGGGGCAAAAAAAAGCAGCGGTACGTCGTTACC 4 42 0 AAAAGCACGA 0.971752 -85 TCTATGCATAAAAAGCAGCGGCTGGACGTCTTC 5 225 1 AAAAGCACGT 0.967422 -59 AACAGATCACAAAATCACCTAAAATCGCCCGCT 6 58 0 AAAATCACTA 0.903175 -213 TTCCGTGATCAAAATCACCTCTTAAAATGCAAT 6 119 0 AAAATCACTT 0.889512 -152 CACGGAATAAAAAGTGATCGTCAGGTTACATAT 6 145 1 AAAGTGACGA 0.880868 -126 AAAATTAGGTAAAGGGATGGCCTTGTTCTTGAA 6 191 1 AAAGGGAGGT 0.748108 -80 AGAGCAGAAAAAAAGCAAGTGAAGAGATTCTAA 6 230 0 AAAAGCAGTA 0.812753 -41 ACTTGTGGATAAAATCACGGTCTGATAAAACAG 7 137 1 AAAATCAGGT 0.962447 -108 CGGCGCCACCAAAATCATCGTGAAATGATAATC 9 22 1 AAAATCACGA 0.979103 -56 AAAACAACGTAAAGTCATGGATTAGCGACGTCT 10 89 1 AAAGTCAGGT 0.949545 -58 AAACGCCAGAAAAATCAGCGCGACGGCCGCAAA 11 210 0 AAAATCACGA 0.979103 -54 ******* ** * Masking position 7 Map Score: 14.5625 Number of sites scoring better than the average of aligned sites = 848 Number in coding regions = 761 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 CCAGGCTTTTGTAAAGACGAACAATAAATTTT 1 11 1 GTAAGAGAAC 0.92058 -119 CAGTGGGGATGTGACGAAGTTCAAGGGCGCAT 2 21 1 GTGAGAGTTC 0.983668 -171 TCCAGCAGCGGTAACGACGTACCGCTGCTTTT 4 33 1 GTAAGAGTAC 0.941021 -94 TGTTGACCATGACAGGATGTTCAGTCGTCAGG 4 89 0 GACAGAGTTC 0.830795 -38 TTCACACATCGTAATGACGATCGACCGGCAAT 5 105 0 GTAAGAGATC 0.97024 -179 TTTTTTATGTGTAAGGAACTTCT 5 271 1 GTAAGACTTC 0.965016 -13 TTTTTATTCCGTGATCAAAATCACCTCTTAAA 6 126 0 GTGACAAATC 0.827169 -145 AAAAAAGCAAGTGAAGAGATTCTAAATAGCCT 6 223 0 GTGAGAATTC 0.968411 -48 ATGTGACATAGAGATGAAATACCGGGAAGAGA 7 72 0 GAGAGAATAC 0.794875 -173 TGTCTCAAGAGTAAGGAGCATCACT 8 55 1 GTAAGACATC 0.952469 -15 AAATCATCGTGAAATGATAATCCTTCGTCATT 9 33 1 GAAAGAAATC 0.855067 -45 GTTTAAATTTGTGATCAACTTCACACATGGAT 11 43 0 GTGACACTTC 0.888348 -221 **** ** **** Masking position 7 Map Score: 11.0873 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 357 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 TCTTCAGATTCGTTTTATAGCCTGAAGTTCCGAAC 1 63 0 CGTTGCCTGA 0.917809 -67 GCGTTGTCCCCAGTGGGGATGTGACGAAGTTC 2 8 1 CCAGGGATGT 0.907608 -184 TGACTTTCTGCGTCTTGTGGGCTGACAATTGCCCC 2 84 1 CGTTGGCTGA 0.956192 -108 TACGTCGTTACCGCTGCTGGAATGTTGCGCCTCAC 4 19 0 CCTGGAATGT 0.94103 -108 GCCCCAATCGCGCGTTAACGCCTGACGACTGAACA 4 69 1 CGTTGCCTGA 0.917809 -58 TCCACTGTTGACCATGACAGGATGTTCAGTCGTCA 4 91 0 ACTGGGATGT 0.914686 -36 GTCATGGTCAACAGTGGAAGGATGATGTC 4 108 1 ACTGGGATGA 0.890588 -19 ATGTAACAGACCATTGACTGGCTGAATGGTCTGTC 5 38 1 CCTGGGCTGA 0.988397 -246 TTCGGGTTGCCCGGTGACCGGATGTGTTTTTTCAC 5 132 0 CCTGGGATGT 0.989282 -152 CAGAAGATATCGATTGAGAGGATTTGA 7 228 1 CGTGGGATTT 0.697932 -17 TTGTTTTACACCCCCTGACGCATGTTTGCAGCCTG 10 61 0 CCCTGCATGT 0.822742 -86 TACAATCAAACCAGTTGACGCCTGAATTGGGCAGT 11 99 0 CCTTGCCTGA 0.964485 -165 CTTACACCCTCCGGTTAAGGAATGTACAATCAAAC 11 123 0 CCTTGAATGT 0.90862 -141 ATTCCCGCTCCCCTTTTGCGGCCGTCGCGCTGATT 11 196 1 CCTTGGCCGT 0.910696 -68 ** ** ****** Masking position 10 Map Score: 12.1829 Number of sites scoring better than the average of aligned sites = 948 Number in coding regions = 850 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 CACCGAATACAAATAAAAAAGGCACATCAGT 2 55 0 AAAAAAAAAG 0.785171 -137 AAATCAGTAACAAAAGTAAAGAAGGCGACAC 3 17 1 CAAAGTAAAG 0.691047 -106 TACAACGGGGAAAAAATAAAGGCGACCCATA 3 56 0 AAAAATAAAG 0.623343 -67 CAAAGTAAAACAGTGTAAAAGGTATGTAACA 5 15 1 CAGGTAAAAG 0.79642 -269 GTCTCACTTACAACAAAAAAGGAATACGTCT 5 177 0 CAAAAAAAAG 0.954837 -107 ACAAACAGAGCAGAAAAAAAGCAAGTGAAGA 6 238 0 CAGAAAAAAG 0.958169 -33 GAACCCATTGCAGGGAAAGAGTATAACACGC 7 16 0 CAGGAAAGAG 0.96414 -229 GGTTCCGTAGCAGGGAAAGAGACCCCGTTGT 7 42 1 CAGGAAAGAG 0.96414 -203 GTCAATCCCACAATAAAAGAGGCGATATCG 8 10 0 CAAAAAAGAG 0.958169 -60 TGTCGCGATTCAACGATAGAGAGTTTACGAT 10 29 1 CAAGATAGAG 0.91828 -118 *** ******* Masking position 8 Map Score: 6.81388 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 233 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 GTATTTCAGTCTCGATTAACAGA 1 117 0 TTTCAGTCTC 0.909227 -13 ATTCGGTGACTTTCTGCGTCTTGTGGGCTG 2 78 1 TTTCTGCGTC 0.909197 -114 CAATCGATATCTTCTGGCGCTTCAGTGGTA 7 214 0 CTTCTGGCGC 0.950867 -31 CCTGCTAACGTGTCTGTCTCAAGAGTAAGG 8 41 1 TGTCTGTCTC 0.936892 -29 TCCCAAAATCTTTCTGTCGCGATTCAACGA 10 15 1 TTTCTGTCGC 0.983126 -132 GATGACGTAATTTCTGCCTCGGAGGTATTT 10 122 1 TTTCTGCCTC 0.981162 -25 CGCGCTGATTTTTCTGGCGTTTGCGGAAAT 11 221 1 TTTCTGGCGT 0.890808 -43 ********** Masking position 3 Map Score: 3.65034 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 479 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 AAAGGCCTATTGTGACAAGAAACGGGGGCAATTGTCA 2 106 0 TGAAAACGGG 0.969636 -86 TATTTGCAGAGCAATGTTACAACGGGGAAAAAATAAA 3 67 0 GCTCAACGGG 0.968921 -56 CTGAACATCCTGTCATGGTCAACAGTGGAAGGATGAT 4 97 1 TGACAACGTG 0.980235 -30 TTGCCAAAGTAAAACAGTGTAAAAGGTAT 5 3 1 GCAAAACGTG 0.942717 -281 TGTCATACTTTGTTACCTGCAAAGGGGAGTAACTTCA 5 69 1 TGACAAAGGG 0.905233 -215 ATGAAATACCGGGAAGAGACAACGGGGTCTCTTTCCC 7 54 0 GGACAACGGG 0.994803 -191 ATAAAATCACGGTCTGATAAAACAGTGAATGATAACC 7 145 1 GGTAAACGTG 0.909839 -100 CTGTGCCAGAGCTTAAGAGCAACGAGGTTATCATTCA 7 170 0 GCACAACAGG 0.906294 -75 GGCGCTTCAGTGGTAGCAACAACTGTGCCAGAGCTTA 7 192 0 TGACAACGTG 0.980235 -53 ** * **** *** Masking position 11 Map Score: 5.26313 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 335 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 GCGACCCATAGTCGCATGGTGTCGCCTTCTT 3 35 0 GTCGCAGGTG 0.926469 -88 GCGCGTTAACGCCTGACGACTGAACATCCTG 4 78 1 GCCTGAGACT 0.891208 -49 GTGAGACCTTGCCGGAAGGCGAGGTCTATGC 5 201 1 GCCGGAGGCG 0.996436 -83 AACGGCCAACGTCGGAAGACGTCCAGCCGCT 5 241 0 GTCGGAGACG 0.991158 -43 CGTAATGTTTTCCGGATGATGGG 9 65 1 TCCGGAGATG 0.945477 -13 GATTAGCGACGTCTGATGACGTAATTTCTGC 10 108 1 GTCTGAGACG 0.968333 -39 ACATTCCTTAACCGGAGGGTGTAAGCAAACC 11 133 1 ACCGGAGGTG 0.954423 -131 ****** **** Masking position 6 Map Score: 3.43236 Number of sites scoring better than the average of aligned sites = 844 Number in coding regions = 782 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 TTCTTTACTTTTGTTACTGATTTGTAAAA 3 10 0 TTGTTACTGA 0.960116 -113 TGTAAAAGGTATGTAACAGACCATTGACTG 5 28 1 ATGTAACAGA 0.94382 -256 TCCTTTTTTGTTGTAAGTGAGACCTTGCCG 5 185 1 TTGTAAGTGA 0.907378 -99 GGACTCATTGATGTAACTGATTAT 11 5 0 ATGTAACTGA 0.960116 -259 CCCGCTACGCTTGTTACAGAGATTGCATCC 11 162 1 TTGTTACAGA 0.94382 -102 ********** Masking position 6 Map Score: 1.21056 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 42 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 TTCGGAACTTCAGGCTATAAAACGAATCTG 1 64 1 CAGGCTATAA 0.782756 -66 CAGAAAGTCACCGAATACAAATAAAAAAGG 2 64 0 CCGAATACAA 0.83591 -128 GGGCAATTGTCAGCCCACAAGACGCAGAAA 2 88 0 CAGCCCACAA 0.894807 -104 CTCCCCTTTGCAGGTAACAAAGTATGACAG 5 68 0 CAGGTAACAA 0.882906 -216 AACATTTAAACAGATCACAAAATCACCTAA 6 69 0 CAGATCACAA 0.889371 -202 AATTTAGCAACCGATTGCAATAAAACATTT 6 92 0 CCGATTGCAA 0.892906 -179 AAGTGATCGTCAGGTTACATATATTTCAGA 6 156 1 CAGGTTACAT 0.855499 -115 TTTGGTGGCGCCGCTTACAAGCTT 9 5 0 CCGCTTACAA 0.926692 -73 GTTTACGATTCAGGCTGCAAACATGCGTCA 10 51 1 CAGGCTGCAA 0.967066 -96 GCGGGAATTGCAGGATGCAATCTCTGTAAC 11 174 0 CAGGATGCAA 0.928736 -90 ********** Masking position 9 Map Score: 4.53887 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 370 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 CGGAACTTCAGGCTATAAAACGAATCTGAA 1 66 1 GGCTATAAAA 0.807703 -64 ATGTTACAACGGGGAAAAAATAAAGGCGAC 3 61 0 GGGGAAAAAA 0.971716 -62 ACGCGCGATTGGGGCAAAAAAAAGCAGCGG 4 54 0 GGGGCAAAAA 0.939308 -73 TCATTACGATGTGTGAAAAAACACATCCGG 5 120 1 GTGTGAAAAA 0.865484 -164 CATTGAACTTGTGGATAAAATCACGGTCTG 7 131 1 GTGGATAAAA 0.878012 -114 ATGCGTCAGGGGGTGTAAAACAACGTAAAG 10 73 1 GGGTGTAAAA 0.947681 -74 AACACTGGTAGGGTAAAAAGGTCATTAACT 11 72 1 GGGTAAAAAG 0.897477 -192 ********** Masking position 7 Map Score: 0.626952 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 279 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 12 ATAGTCGCATGGTGTCGCCTTCTTTACTTT 3 29 0 GGTGTCGCCT 0.99279 -94 CATGCGACTATGGGTCGCCTTTATTTTTTC 3 48 1 TGGGTCGCCT 0.946904 -75 GCTGCTGGAATGTTGCGCCTCACCGTATCA 4 12 0 TGTTGCGCCT 0.833426 -115 CCAATCGCGCGTTAACGCCTGACGACTGAA 4 72 1 GTTAACGCCT 0.906958 -55 ATTAGGTAAAGGGATGGCCTTGTTCTTGAA 6 194 1 GGGATGGCCT 0.86204 -77 CGATATCGCCTCTTTTATTGT 8 2 1 GATATCGCCT 0.911615 -68 CGATGATTTTGGTGGCGCCGCTTACAAGCT 9 12 0 GGTGGCGCCG 0.96807 -66 AATCAAACCAGTTGACGCCTGAATTGGGCA 11 101 0 GTTGACGCCT 0.95268 -163 ********** Masking position 7 Map Score: 3.7199 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 544 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 13 ********** No masking Map Score: -5.30475e-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: -5.30475e-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: -5.30475e-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