AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i002_Purine_Nucleotides_Metabolism_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yohJ 238 orf, hypothetical protein #2 cdd 129 cytidine/deoxycytidine deaminase #3 yeiM 93 putative transport system permease protein #4 yeiC 300 putative kinase #5 deoC 257 2-deoxyribose-5-phosphate aldolase #6 deoA 83 thymidine phosphorylase #7 deoB 51 phosphopentomutase #8 deoD 56 purine-nucleoside phosphorylase #9 HI0518 83 purine-nucleoside phosphorylase (deoD) #10 HI0519 98 transport protein, putative #11 HI0521 212 conserved hypothetical protein #12 HI1116 110 deoxyribose-phosphate aldolase (deoC) #13 HI1350 273 cytidine deaminase (cdd) Motif number 1 TAACATAGCGCCTCATTTTTTTGCGGGTGAT 1 14 0 CCTCATTTTT 0.956679 -225 AGATTATTTTCTGCCCTTTTTTATTGTTCTG 4 50 1 CTGCCCTTTT 0.969668 -251 AGGCATTTAATCGCATTTTGTGAGCCTGCTC 4 121 1 TCGCATTTTT 0.897261 -180 CTGCTCAAATCTGCCCATTTTGCCTCTCTGG 4 146 1 CTGCCCATTT 0.758825 -155 CTTCTTTTCCTTTTATGCCGAAGGTG 5 6 1 TTTCCTTTTT 0.613302 -252 AGCGTTGACTCCGCCTTTGTTATGTCACAAA 8 24 1 CCGCCTTTGT 0.92865 -33 TCATTTTTTACCGCACTTTTTAATTGATTAA 9 17 0 CCGCACTTTT 0.986681 -67 TAAAAAATGACCGCACTTTATTCATTTTTAT 9 38 1 CCGCACTTTT 0.986681 -46 CGAATTTTCACCGCACTTTTTGTAAACGT 10 9 0 CCGCACTTTT 0.986681 -90 TGAAAATTCGCCGACTTTTCATAAGAAAACA 10 30 1 CCGACTTTTA 0.641196 -69 GTAGAATAAGCCGAATTTTATTAACTTAACT 10 62 1 CCGAATTTTT 0.849234 -37 TTTTTGCATCTTTCCTTTTATGATAAAACGG 11 30 0 TTTCCTTTTT 0.613302 -183 CTGTGATCTTCCTCACGTTTTCAAAATTGTC 11 142 1 CCTCACGTTT 0.819743 -71 TATTTTCCTCCTTTTATTTATGTTTTA 12 94 0 CCTCCTTTTT 0.975827 -17 GAGCTAATGCCCTCCCTTTGATATGGGTATT 13 40 1 CCTCCCTTTA 0.908177 -234 ********* * Masking position 8 Map Score: 16.9044 Number of sites scoring better than the average of aligned sites = 957 Number in coding regions = 780 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 2 GATTTCTTAATGTGATCGGTAGCACGTTTTACG 1 174 1 TGTGATCGGC 0.993644 -65 AATTTGCGATGCGTCGCGCATTTTTGA 2 5 1 TGCGATGGGC 0.975237 -125 TGGCTTTATATGTGATCTGAATCTCATTAATTA 2 58 0 TGTGATCGTC 0.994752 -72 GCGAGGAATTTGTGACGGGATGCACAGAACAGA 4 77 0 TGTGACGGGC 0.955357 -224 AATCGCATTTTGTGAGCCTGCTCAAATCTGCCC 4 129 1 TGTGAGCTTC 0.942856 -172 ATCACTGTAATGCGATCTGGTTCAAATAATTCA 5 115 0 TGCGATCGTC 0.989322 -143 TTTCCTTAATTGTGATGTGTATCGAAGTGTGTT 5 165 1 TGTGATGGTC 0.989866 -93 TTTCTAAAACTGTGATCTTCCTCACGTTTTCAA 11 133 1 TGTGATCTTC 0.984157 -80 TCATTAAAACTGTGATCTTGATCACTTATTTGA 13 164 0 TGTGATCTTC 0.984157 -110 ******* * ** Masking position 5 Map Score: 14.2783 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 55 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 GATCGGTAGCACGTTTTACGAATTAATTGT 1 187 1 ACGTTTTACG 0.900847 -52 TTTTTGATGTATGTTTCACGCGTTGCATAA 2 31 1 ATGTTTCACG 0.943567 -99 CATAGTATGCATGTTTTACGTAAAGTAAAT 4 182 0 ATGTTTTACG 0.967242 -119 AGGGTTGGTAATTTTTTACCAGAGGACGTG 4 279 1 ATTTTTTACC 0.968038 -22 AAGTGCGGTCATTTTTTACCGCACTTTTTA 9 26 0 ATTTTTTACC 0.968038 -58 AAAGTCGGCGAATTTTCACCGCACTTTTTG 10 18 0 AATTTTCACC 0.780728 -81 ATTTATTACCTTTTATATTC 11 1 1 ATTTATTACC 0.84442 -212 CCTTTTATTTATGTTTTACCTATTGTAGCA 12 82 0 ATGTTTTACC 0.979608 -29 ********** Masking position 8 Map Score: 7.62163 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 83 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 ATCACCCGCAAAAAAATGAGGCGCTATGTTA 1 14 1 AAAAAATAGG 0.822098 -225 CCGGGGAGCGAAAAAATAAGCGCTGATTTCT 1 150 1 AAAAAATAGC 0.969516 -89 CGATCACATTAAGAAATCAGCGCTTATTTTT 1 161 0 AAGAAATAGC 0.947395 -78 TCTGCCCTTGAGGAAATAACCTGAGTGTTTG 4 22 0 AGGAAATACC 0.968208 -279 AAAAAAGGGCAGAAAATAATCTGCCCTTGAG 4 41 0 AGAAAATATC 0.911549 -260 TTTTACGTAAAGTAAATTACCGCCAGAGAGG 4 168 0 AGTAAATACC 0.917536 -133 GTCCTCTGGTAAAAAATTACCAACCCTGTCA 4 275 0 AAAAAATACC 0.976619 -26 AAAGTGCGGTAAAAAATGACCGCACTTTATT 9 29 1 AAAAAATACC 0.976621 -55 TCACAGTTTTAGAAAATAAACATTATGCAAA 11 117 0 AGAAAATAAC 0.911549 -96 ******* *** Masking position 6 Map Score: 6.85558 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 161 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TCCCTCTCTATGCTTGATGTATGCCTGAGT 1 100 1 TGCTTGATGT 0.981921 -139 CGCTGCGCATTGCGTAATGCCGGGGAGCGA 1 131 1 TGCGTAATGC 0.814118 -108 AAGCGCTGATTTCTTAATGTGATCGGTAGC 1 167 1 TTCTTAATGT 0.853671 -72 ACGAATTAATTGTATGATGAATCCATCTCA 1 204 1 TGTATGATGA 0.828387 -35 GCGTCGCGCATTTTTGATGTATGTTTCACG 2 21 1 TTTTTGATGT 0.853671 -109 GGTTTTGGTATGCTTGATGAGTACGGGCGA 3 32 0 TGCTTGATGA 0.97131 -62 ATAACCTGAGTGTTTGATGAACGTTTG 4 8 0 TGTTTGATGA 0.917328 -293 TGTAAGAAGTTTCGTGATGTTCACTTTGAT 5 46 1 TTCGTGATGT 0.922947 -212 AGTAACCGTTTGCATAATGTTTATTTTCTA 11 109 1 TGCATAATGT 0.885632 -104 ********** Masking position 5 Map Score: 5.66955 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 467 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 6 GTGATCTGAATCTCATTAATTATGCAACGCGT 2 48 0 TCTATTATTA 0.878066 -82 TACCGCACTTTTTAATTGATTAAGATAAA 9 8 0 TTTATTATTA 0.959022 -76 CTTTATTCATTTTTATTCATTATTAAAAATAA 9 53 1 TTTATTATTA 0.959022 -31 AGTGAAATTGTTCTATTCAATATAATTGATAG 13 90 1 TTCATTAATA 0.923631 -184 ATTTGATAGCTTCTATTTATTACAATTTCTTA 13 138 0 TTCATTATTA 0.940292 -136 GCCGCGATAGTTTGATTAAATATTCATTAAAA 13 188 0 TTTATTAATA 0.947294 -86 AACAATAAATTTTGATTTAATAAGTACAGTTA 13 221 1 TTTATTAATA 0.947291 -53 *** *** **** Masking position 5 Map Score: 4.37795 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 28 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 7 AATGATTTTCCCTTCATGCCGGTA 3 80 0 ATTTTCCCTT 0.783008 -14 AACACTCAGGTTATTTCCTCAAGGGCAGAT 4 24 1 TTATTTCCTC 0.903941 -277 AAATCTGCCCATTTTGCCTCTCTGGCGGTA 4 152 1 ATTTTGCCTC 0.726004 -149 CTTCTTTTCCTTTTATGCCGAA 5 3 1 TCTTTTCCTT 0.913974 -255 ACTTGTAAGTAGATTTCCTTAATTGTGATG 5 152 1 AGATTTCCTT 0.669899 -106 CGCCTCATACTCTTTTCCTCGGGAGGTTAC 6 63 1 TCTTTTCCTC 0.886383 -21 TGTTTTATCCTTTTTGTGACAT 8 45 0 TTTTATCCTT 0.731511 -12 AATTTTTCCTTATTTTTAATA 9 73 0 ATTTTTCCTT 0.954586 -11 ATTTATTACCTTTTATATTCCG 11 3 1 TTATTACCTT 0.597481 -210 CTGTTTTTGCATCTTTCCTTTTATGATAAA 11 34 0 ATCTTTCCTT 0.814252 -179 TTTATTTATTCCTTATCTTGTTGA 12 5 1 TTTATTCCTT 0.731511 -106 TATTTTCCTCCTTTTATTTA 12 101 0 TATTTTCCTC 0.834534 -10 AATAATTTCCTTTTTCTAGTTG 13 3 1 TAATTTCCTT 0.760751 -271 AATTTTTAATATTTTTCCTAAGGATATGTT 13 254 1 ATTTTTCCTA 0.747327 -20 ********** Masking position 9 Map Score: 6.76627 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 296 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 8 AAGGTCTGCAAAGAGGGATTGCTGCAAACT 1 66 1 AAGAGGGATT 0.948807 -173 ATCAAGCATAGAGAGGGATTGCAGTTTGCA 1 88 0 GAGAGGGATT 0.961376 -151 CACCCCAGATGAGATGGATTCATCATACAA 1 213 0 GAGATGGATT 0.893737 -26 ATGAGTACGGGCGACGGCTTTCTGCCCGTC 3 16 0 GCGACGGCTT 0.892654 -78 AATTACAAAAGCGAGGAATTTGTGACGGGA 4 90 0 GCGAGGAATT 0.778262 -211 AGATACTGCAAAGACGGTTTAAACATGTGT 4 231 0 AAGACGGTTT 0.802773 -70 ACAAACTCGCAAGGTGAATTTTATTGGCGA 5 221 1 AAGGTGAATT 0.713848 -37 AAAAGAGTATGAGGCGGCTTTTGCCGGATG 6 49 0 GAGGCGGCTT 0.956177 -35 TGACATAACAAAGGCGGAGTCAACGCTCCG 8 21 0 AAGGCGGAGT 0.904458 -36 CAAGTAGAATAAGCCGAATTTTATTAACTT 10 59 1 AAGCCGAATT 0.712469 -40 ACCATTTTCAAAGGGGACGTT 11 202 1 AAGGGGACGT 0.668507 -11 ********** Masking position 10 Map Score: 3.64227 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 561 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 9 AACAAACTCGCAAGGTGAATTTTATTGGCG 5 220 1 CAAGGTGAAT 0.969091 -38 TGGCGACAAGCCAGGAGAATGAA 5 245 1 CCAGGAGAAT 0.963441 -13 CATAAGAAAACAAGTAGAATAAGCCGAATT 10 49 1 CAAGTAGAAT 0.932955 -50 CTTAACTAATCTAGGGGAATCAA 10 86 1 CTAGGGGAAT 0.963441 -13 TTTCCTTTTTCTAGTTGAATAATTGAGCTA 13 16 1 CTAGTTGAAT 0.932955 -258 ********** Masking position 3 Map Score: 0.994182 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 37 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 AATTTGCGATGCGTCGCGCATTTTTGATGTATG 2 11 1 GCGTCGCATT 0.955394 -119 TATGTTTCACGCGTTGCATAATTAATGAGATTC 2 40 1 GCGTTGCATT 0.985837 -90 GGCGTTGCCTCATAATCATGTAAT 2 116 0 GCGTTGCCTA 0.953221 -14 TATGCCGAAGGTGATGCGCCATTGTAAGAAGTT 5 24 1 GTGATGCCTT 0.96752 -234 AAGAAGTTTCGTGATGTTCACTTTGATCCTGAT 5 49 1 GTGATGTATT 0.851677 -209 TCGCATTACAGTGATGCAAACTTGTAAGTAGAT 5 133 1 GTGATGCATT 0.977909 -125 GTATCGAAGTGTGTTGCGGAGTAGATGTTAGAA 5 183 1 GTGTTGCATA 0.961651 -75 ******* * ** Masking position 12 Map Score: 1.74767 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 176 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 TTGCAGCAATCCCTCTTTGCAGACCTTTAA 1 63 0 CCCTCTTTGC 0.988448 -176 ACTGCAATCCCTCTCTATGCTTGATGTATG 1 93 1 CTCTCTATGC 0.947163 -146 AATGATTTTCCCTTCATGCCGGTAAACCC 3 75 0 CCCTTCATGC 0.943642 -19 CTCAAATCTGCCCATTTTGCCTCTCTGGCG 4 149 1 CCCATTTTGC 0.936347 -152 CATGTTTAAACCGTCTTTGCAGTATCTATA 4 234 1 CCGTCTTTGC 0.978129 -67 CTTCTTTTCCTTTTATGCCGAAGGTGAT 5 9 1 CCTTTTATGC 0.91249 -249 AAAATTATTTCTGTTTTTGCATCTTTCCTT 11 44 0 CTGTTTTTGC 0.909932 -169 ********** Masking position 8 Map Score: 4.88854 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 172 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 ********** No masking Map Score: -5.02821e-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: -5.02821e-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: -5.02821e-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