AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i002_Purine_Nucleotides_Metabolism_ecoli_hinf_reg_100.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 cdd 129 cytidine/deoxycytidine deaminase #2 yeiM 93 putative transport system permease protein #3 yeiC 300 putative kinase #4 deoC 257 2-deoxyribose-5-phosphate aldolase #5 deoA 83 thymidine phosphorylase #6 deoB 51 phosphopentomutase #7 deoD 56 purine-nucleoside phosphorylase #8 HI0518 83 purine-nucleoside phosphorylase (deoD) #9 HI0519 98 transport protein, putative #10 HI0521 212 conserved hypothetical protein #11 HI1116 110 deoxyribose-phosphate aldolase (deoC) #12 HI1350 273 cytidine deaminase (cdd) Motif number 1 GGGCAGATTATTTTCTGCCCTTTTTTATTGTTCTGTTCTGTG 3 46 1 TTCTCTTTTT 0.973199 -255 ATTCAGGCATTTAATCGCATTTTGTGAGCCTGCTCAAATCTG 3 117 1 TTTCCTTTTG 0.944291 -184 CTTCTTTTCCTTTTATGCCGAAGGTGATGCGCC 4 2 1 TTTTCTTTTG 0.923119 -256 GCGGTCATTTTTTACCGCACTTTTTAATTGATTAAGATAAA 8 10 0 TTCCCTTTTT 0.980865 -74 GCGGTAAAAAATGACCGCACTTTATTCATTTTTATTCATTAT 8 34 1 ATCCCTTTTT 0.972023 -50 AATTTTTCCTTATTTTTAATAATGAATAAAAAT 8 61 0 ATTTCATTTT 0.783542 -23 TCGGCGAATTTTCACCGCACTTTTTGTAAACGT 9 2 0 TTCCCTTTTG 0.968735 -97 ATTTATTACCTTTTATATTCCGTTTTATCATAA 10 2 1 TTTTCTTTTT 0.952072 -211 AACTGACAAAATTATTTCTGTTTTTGCATCTTTCCTTTTATG 10 39 0 ATTTCTTTTT 0.930861 -174 AACTGTGATCTTCCTCACGTTTTCAAAATTGTCTATTTTGTT 10 140 1 TTTCCTTTAT 0.829552 -73 CCCTTTGAAAATGGTTTCGTATTGTACGCAATGGTAACAAAA 10 175 0 ATTTCATTTT 0.783558 -38 TATTTTCCTCCTTTTATTTATGTTTTACCTATTG 11 87 0 TTCCCTTTTT 0.980865 -24 AATTGAGCTAATGCCCTCCCTTTGATATGGGTATTATACGTT 12 36 1 ATCCCTTTAT 0.857749 -238 ATAGAACAATTTCACTTCAAATTATAGAAACGTATAATACCC 12 64 0 TTCTCATTTG 0.855111 -210 CACTTATTTGATAGCTTCTATTTATTACAATTTCTTAACAAA 12 133 0 ATCTCTTTTT 0.960955 -141 ** ** * *** * * Masking position 12 Map Score: 17.1619 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 209 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 2 AATTTGCGATGCGTCGCGCATTTTTGATGT 1 3 1 TTTGCAGCCA 0.899192 -127 TCTCATTAATTATGCAACGCGTGAAACATACATCAAAA 1 32 0 TATGCAGACA 0.774255 -98 TGTGGCTTTATATGTGATCTGAATCTCATTAATTATGC 1 55 0 TATGTACCCA 0.988689 -75 AAGCGAGGAATTTGTGACGGGATGCACAGAACAGAACA 3 74 0 TTTGTAGCCA 0.896999 -227 AAAATGGGCAGATTTGAGCAGGCTCACAAAATGCGATT 3 129 0 GATTTACCCA 0.881174 -172 CATGTGTTCATATTTAAACATGTGCTCATAGTATGCAT 3 200 0 TATTTACCCA 0.979173 -101 TCCTGATGCGTTTGCCACCACTGACGCATTCATTTGAA 4 75 1 TTTGCACCCA 0.966191 -183 GAAAGTGAATTATTTGAACCAGATCGCATTACAGTGAT 4 110 1 TATTTACCCA 0.979174 -148 AGTTTGTTAGTATTCTAACATCTACTCCGCAACACACT 4 190 0 TATTCACCCC 0.891596 -68 AAATAAACATTATGCAAACGGTTACTCAAAATAAATAT 10 97 0 TATGCACCCA 0.977165 -116 GAGATGATTGTAATTGAGCGTAAAACCATAGTCAAAAA 11 33 1 TAATTACACA 0.656338 -78 TCTAGTTGAATAATTGAGCTAATGCCCTCCCTTTGATA 12 25 1 TAATTACCCT 0.636148 -249 AGCTATCAAATAAGTGATCAAGATCACAGTTTTAATGA 12 159 1 TAAGTACCCA 0.965591 -115 ***** * * * ** Masking position 7 Map Score: 10.1801 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 288 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 TACCGGCATGAAGGGAAAATCATT 2 80 1 AAGGGAAAAT 0.771495 -14 ATCTGCCCTTGAGGAAATAACCTGAGTGTT 3 24 0 GAGGAAATAA 0.909123 -277 TACCGCCAGAGAGGCAAAATGGGCAGATTT 3 152 0 GAGGCAAAAT 0.789728 -149 TTCGGCATAAAAGGAAAAGAAG 4 3 0 AAGGAAAAGA 0.959794 -255 CATCACAATTAAGGAAATCTACTTACAAGT 4 152 0 AAGGAAATCT 0.723823 -106 GTAACCTCCCGAGGAAAAGAGTATGAGGCG 5 63 0 GAGGAAAAGA 0.935188 -21 ATGTCACAAAAAGGATAAAACA 7 45 1 AAGGATAAAA 0.886396 -12 TATTAAAAATAAGGAAAAATT 8 73 1 AAGGAAAAAT 0.951615 -11 CGGAATATAAAAGGTAATAAAT 10 3 0 AAGGTAATAA 0.657181 -210 TTTATCATAAAAGGAAAGATGCAAAAACAG 10 34 1 AAGGAAAGAT 0.803982 -179 TCAACAAGATAAGGAATAAATAAA 11 5 0 AAGGAATAAA 0.726509 -106 TAAATAAAAGGAGGAAAATA 11 101 1 GAGGAAAATA 0.829807 -10 CAACTAGAAAAAGGAAATTATT 12 3 0 AAGGAAATTA 0.82145 -271 CTTAACAAACAAGGCTAAGACTATCAATTA 12 112 0 AAGGCTAAGA 0.669738 -162 TATTTTTCCTAAGGATATGTT 12 263 1 AAGGATATGT 0.712752 -11 ********** Masking position 2 Map Score: 9.13969 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 384 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 4 TTTTTGATGTATGTTTCACGCGTTGCATAA 1 31 1 ATGTTTCACG 0.921322 -99 CATAGTATGCATGTTTTACGTAAAGTAAAT 3 182 0 ATGTTTTACG 0.953873 -119 AGGGTTGGTAATTTTTTACCAGAGGACGTG 3 279 1 ATTTTTTACC 0.980391 -22 AAGTGCGGTCATTTTTTACCGCACTTTTTA 8 26 0 ATTTTTTACC 0.980391 -58 AAAGTCGGCGAATTTTCACCGCACTTTTTG 9 18 0 AATTTTCACC 0.835357 -81 ATTTATTACCTTTTATATTC 10 1 1 ATTTATTACC 0.948196 -212 CCTTTTATTTATGTTTTACCTATTGTAGCA 11 82 0 ATGTTTTACC 0.980003 -29 GATAGCTTCTATTTATTACAATTTCTTAAC 12 136 0 ATTTATTACA 0.739012 -138 ********** Masking position 8 Map Score: 7.48239 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 116 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TGACGGGCAGAAAGCCGTCGCCCGTACTCA 2 15 1 AAAGCCGTCG 0.975557 -79 AAGCATACCAAAACCTGGCGCTGACGCCGG 2 47 1 AAACCTGGCG 0.945918 -47 TCATGCCGGTAAACCCGGCGTCAGCGCCAG 2 61 0 AAACCCGGCG 0.992638 -33 GCATCCGGCAAAAGCCGCCTCATACTCTTT 5 48 1 AAAGCCGCCT 0.941646 -36 GTGACATAACAAAGGCGGAGTCAACGCTCC 7 22 0 AAAGGCGGAG 0.904797 -35 TTTCTTATGAAAAGTCGGCGAATTTTCACC 9 28 0 AAAGTCGGCG 0.988659 -71 TAAGTTAATAAAATTCGGCTTATTCTACTT 9 60 0 AAATTCGGCT 0.820045 -39 ********** Masking position 3 Map Score: 4.23929 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 574 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 TTTAAACATGTGTTCATATTTAAACATGTGCT 3 212 0 TGTTCAATTA 0.729214 -89 AGTTTCGTGATGTTCACTTTGATCCTGATGCG 4 53 1 TGTTCATTTA 0.954951 -205 TGGTTCAAATAATTCACTTTCAAATGAATGCG 4 99 0 AATTCATTTA 0.852363 -159 TATACTGATCTGATCATTTAAATTTGAAGCAC 6 14 1 TGATCATTAA 0.775283 -38 TTTATCTTAATCAATTAAAAAGTGCGGTA 8 8 1 TAATCATTAA 0.807463 -76 GACCGCACTTTATTCATTTTTATTCATTATTA 8 46 1 TATTCATTTA 0.96263 -38 TTACCTTTTATATTCCGTTTTATCATAAAAGG 10 16 1 TATTCCTTTA 0.815617 -197 TAATTTTGTCAGTTCATTTATATCAAAAACAT 10 67 1 AGTTCATTAA 0.775284 -146 ATCAAAAACATATTTATTTTGAGTAACCGTTT 10 88 1 TATTTATTTA 0.648984 -125 TTAGCTCAATTATTCAACTAGAAAAAGGAAAT 12 15 0 TATTCACTAA 0.779002 -259 GAAATTGTTCTATTCAATATAATTGATAGTCT 12 93 1 TATTCATATA 0.852363 -181 TTTGATTAAATATTCATTAAAACTGTGATCTT 12 178 0 TATTCATAAA 0.807398 -96 ****** *** * Masking position 12 Map Score: 4.90354 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 172 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 TAATGAGATTCAGATCACATATAAAGCCAC 1 62 1 CAGATCACAT 0.813321 -68 TTATTTCCTCAAGGGCAGATTATTTTCTGC 3 34 1 AAGGGCAGAT 0.951659 -267 AACAATAAAAAAGGGCAGAAAATAATCTGC 3 48 0 AAGGGCAGAA 0.80351 -253 GAGAGGCAAAATGGGCAGATTTGAGCAGGC 3 144 0 ATGGGCAGAT 0.940372 -157 CATGCATACTATGAGCACATGTTTAAATAT 3 199 1 ATGAGCACAT 0.925109 -102 ATGTTTAAATATGAACACATGTTTAAACCG 3 217 1 ATGAACACAT 0.820786 -84 TCAAATTTAAATGATCAGATCAGTATACCG 6 11 0 ATGATCAGAT 0.924343 -41 AAACGTGAGGAAGATCACAGTTTTAGAAAA 10 132 0 AAGATCACAG 0.91349 -81 ATAAGTGATCAAGATCACAGTTTTAATGAA 12 168 1 AAGATCACAG 0.91349 -106 ********** Masking position 7 Map Score: 5.89132 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 134 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 AAAAATGCGCGACGCATCGCAAATT 1 6 0 GACGCATCGC 0.87721 -124 CACATATAAAGCCACAACGGGTTCGTAAAC 1 77 1 GCCACAACGG 0.882454 -53 ACATGATTATGAGGCAACGCC 1 119 1 GAGGCAACGC 0.982028 -11 GGTAAACCCGGCGTCAGCGCCAGGTTTTGG 2 54 0 GCGTCAGCGC 0.978862 -40 TCAAATGAATGCGTCAGTGGTGGCAAACGC 4 82 0 GCGTCAGTGG 0.862944 -176 TTTGCCGGATGCGTCTACGCCTTATCCGGC 5 30 0 GCGTCTACGC 0.839043 -54 AACAAAGGCGGAGTCAACGCTCCGCCCAAA 7 15 0 GAGTCAACGC 0.980689 -42 ********** Masking position 5 Map Score: 3.69305 Number of sites scoring better than the average of aligned sites = 1288 Number in coding regions = 1240 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 9 CTCTGGCGGTAATTTACTTTACGTAAAACA 3 171 1 AATTTACTTT 0.634321 -130 TTTAAACATGTGTTCATATTTAAACATGTG 3 214 0 TGTTCATATT 0.695458 -87 AGTTTCGTGATGTTCACTTTGATCCTGATG 4 53 1 TGTTCACTTT 0.910433 -205 TGGTTCAAATAATTCACTTTCAAATGAATG 4 101 0 AATTCACTTT 0.699512 -157 GACCGCACTTTATTCATTTTTATTCATTAT 8 46 1 TATTCATTTT 0.937421 -38 TATTCATTTTTATTCATTATTAAAAATAAG 8 56 1 TATTCATTAT 0.655572 -28 ATCAAAAACATATTTATTTTGAGTAACCGT 10 88 1 TATTTATTTT 0.91778 -125 GTTTGCATAATGTTTATTTTCTAAAACTGT 10 116 1 TGTTTATTTT 0.923627 -97 TTTTCAAAATTGTCTATTTTGTTACCATTG 10 159 1 TGTCTATTTT 0.694886 -54 TAGCAAAAATTCTTTATTTTTGACTATGGT 11 57 0 TCTTTATTTT 0.774506 -54 TTCCTCCTTTTATTTATGTTTTACCTATTG 11 87 0 TATTTATGTT 0.699512 -24 ********** Masking position 6 Map Score: 3.62976 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 194 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 10 AACAAACTCGCAAGGTGAATTTTATTGGCG 4 220 1 CAAGGTGAAT 0.973265 -38 TGGCGACAAGCCAGGAGAATGAA 4 245 1 CCAGGAGAAT 0.968353 -13 CATAAGAAAACAAGTAGAATAAGCCGAATT 9 49 1 CAAGTAGAAT 0.941716 -50 CTTAACTAATCTAGGGGAATCAA 9 86 1 CTAGGGGAAT 0.968353 -13 TTTCCTTTTTCTAGTTGAATAATTGAGCTA 12 16 1 CTAGTTGAAT 0.941716 -258 ********** Masking position 3 Map Score: 1.65208 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 11 ********** No masking Map Score: -3.23054e-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 12 ********** No masking Map Score: -3.23054e-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: -3.23054e-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