AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iaraC_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 araD 284 L-ribulose-5-phosphate 4-epimerase #2 araB_araC 338 araB: L-ribulokinase, araC: transcriptional regulator for ara operon #3 araJ 125 involved in either transport or processing of arabinose polymers #4 sbcD 189 ATP-dependent dsDNA exonuclease #5 araH_2 23 high-affinity L-arabinose transport system; membrane protein, fragment 2 #6 araG 69 ATP-binding component of high-affinity L-arabinose transport system #7 araF 300 L-arabinose-binding periplasmic protein #8 araE 300 low-affinity L-arabinose transport system proton symport protein #9 HI1027 58 L-xylulose kinase (lyx) #10 HI1028 30 conserved hypothetical protein #11 HI1030 71 conserved hypothetical transmembrane protein #12 HI1031 175 conserved hypothetical protein Motif number 1 GTAGCCGCATCCGGTATGTAACGCCTG 1 6 1 CGCATCGGTT 0.984102 -279 GCGTCAGCGTCGCATCAGGCGTTACATACCGG 1 21 0 CGCATCGGCT 0.998937 -264 GCTGACGCGTCTTATCTGGCCTACACGCTGCG 1 45 1 CTTATCGGCT 0.996336 -240 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 74 0 CTTATCGGCT 0.996336 -211 ATAAGCAAAGCGCATCCGGCATTCAACGCCTG 1 91 1 CGCATCGGCT 0.998937 -194 GCGCCAGCGTCGCATCAGGCGTTGAATGCCGG 1 106 0 CGCATCGGCT 0.998937 -179 GCTGGCGCGTCTTATCAGGCCTACGCGCTGCG 1 130 1 CTTATCGGCT 0.996336 -155 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 159 0 CTTATCGGCT 0.996336 -126 ATAAGCAAAGCGCATCCGGCATTCAACGCCTG 1 176 1 CGCATCGGCT 0.998937 -109 GCGCCAGCGTCGCATCAGGCGTTGAATGCCGG 1 191 0 CGCATCGGCT 0.998937 -94 GCTGGCGCGTCTTATCAGGCCTACACGCTGCG 1 215 1 CTTATCGGCT 0.996336 -70 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 244 0 CTTATCGGCT 0.996336 -41 ATAAGCAAAGCGCATCCGGCACGAAGGAGTCA 1 261 1 CGCATCGGCC 0.993299 -24 ****** *** * Masking position 4 Map Score: 57.809 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 61 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 ACGCGTCTTATCTGGCCTACACGCTGCGATT 1 49 1 TCGGCCTACA 0.998428 -236 GCTTTGCTTATCCGGCCTACAAAATCGCAGC 1 71 0 TCGGCCTACA 0.998433 -214 GCAAAGCGCATCCGGCATTCAACGCCTGATG 1 95 1 TCGGCATTCA 0.975394 -190 GCGCGTCTTATCAGGCCTACGCGCTGCGATT 1 134 1 TCGGCCTACG 0.993326 -151 GCTTTGCTTATCCGGCCTACAAAATCGCAGC 1 156 0 TCGGCCTACA 0.998433 -129 GCAAAGCGCATCCGGCATTCAACGCCTGATG 1 180 1 TCGGCATTCA 0.975394 -105 GCGCGTCTTATCAGGCCTACACGCTGCGATT 1 219 1 TCGGCCTACA 0.998431 -66 GCTTTGCTTATCCGGCCTACAAAATCGCAGC 1 241 0 TCGGCCTACA 0.998433 -44 GTCATTCGTTTTTGCCCTACACAAAACGACA 7 262 1 TTGCCCTACA 0.900736 -39 ** ******** Masking position 8 Map Score: 29.2411 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 45 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 TATCCGGCCTACAAAATCGCAGCGTGTAGG 1 64 0 ACAAAATCGC 0.981949 -221 AGGCCGGATAAGCAAAGCGCATCCGGCATT 1 84 1 AGCAAAGCGC 0.985144 -201 TATCCGGCCTACAAAATCGCAGCGCGTAGG 1 149 0 ACAAAATCGC 0.981949 -136 AGGCCGGATAAGCAAAGCGCATCCGGCATT 1 169 1 AGCAAAGCGC 0.985144 -116 TATCCGGCCTACAAAATCGCAGCGTGTAGG 1 234 0 ACAAAATCGC 0.981949 -51 AGGCCGGATAAGCAAAGCGCATCCGGCACG 1 254 1 AGCAAAGCGC 0.985144 -31 CAAAGCCATGACAAAAACGCGTAACAAAAG 2 155 1 ACAAAAACGC 0.952185 -184 CCTATTTATTACAACAGGGCAAATC 4 6 0 ACAACAGGGC 0.876389 -184 CGCAGAAAAAAGCAAATGGCACATCTGTTT 4 130 1 AGCAAATGGC 0.955048 -60 AATTTGTCTGACAAATTGGCTTTCCCTTAT 7 75 1 ACAAATTGGC 0.686185 -226 GGAGAGCAATATCACATCGCAGAATTACAG 7 137 0 ATCACATCGC 0.766445 -164 ATATGTTTCCAGTAAAACGCCATAATATAA 11 16 1 AGTAAAACGC 0.776106 -56 ********** Masking position 4 Map Score: 18.8227 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 399 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 GCCAGATAAGACGCGTCAGCGTCGCATCAGGCGT 1 31 0 AGCGCAGGCG 0.998076 -254 GCCTGATAAGACGCGCCAGCGTCGCATCAGGCGT 1 116 0 AGCGCAGGCG 0.998073 -169 GCCTGATAAGACGCGCCAGCGTCGCATCAGGCGT 1 201 0 AGCGCAGGCG 0.998073 -84 GAGCCAGTAAAAGACGCAGTGACGGCAATGTCTG 2 62 0 AGACCAGGCG 0.945172 -277 TTGCGATAAAAAGCGTCAGGTAGGATCCGCTAAT 2 269 0 AGCGCAGTGG 0.989006 -70 CGACGTCATTATGCGTCAGATTTATGACAGATTT 4 51 1 AGCGCAGTTA 0.87345 -139 TCCCCTCTGCATGATGCAGAGGGGGTGTGAACGA 6 25 1 AGATCAGGGG 0.877286 -45 ACTAAAAGATAAGTGACTGTGTTGACATAGTTTT 7 189 0 AGTGCTGGTG 0.819952 -112 AAACCCTGCCATGCGGCAGGGTCATAAAA 8 6 0 AGCGCAGGCA 0.988971 -295 CAACTCACGCAGGTGTCAGGTCGGAAACAGCATA 8 231 0 AGTGCAGTGG 0.953652 -70 * *** *** * ** Masking position 1 Map Score: 14.7518 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 507 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 GAAGAAACCAATTGTCCATATTGCATCAGA 2 36 1 ATTGTCCATA 0.934124 -303 CCATAGCATTTTTATCCATAAGATTAGCGG 2 247 1 TTTATCCATA 0.969209 -92 CTCTCTACTGTTTCTCCATACCCGTTTTTT 2 303 1 TTTCTCCATA 0.968606 -36 GCACAGCAGATTAATCCATAAGATTAGCCT 7 38 0 TTAATCCATA 0.962335 -263 CGAGAAATTAATTCTCCATAGGAGAGCAAT 7 157 0 ATTCTCCATA 0.974367 -144 GTAGATCATCATAATCCATATCATGGTTAT 8 49 1 ATAATCCATA 0.96921 -252 TGGTTATGAAATAATCCATATTAATTATCA 8 72 1 ATAATCCATA 0.96921 -229 TCGCAGCAATTTAATCCATATTTATGCTGT 8 209 1 TTAATCCATA 0.962335 -92 ATATTCTCCTTAGTTTTTTATG 9 47 0 ATTCTCCTTA 0.856985 -12 ********** Masking position 5 Map Score: 14.3614 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 59 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 CAGATAAGACGCGTCAGCGTCGCATCAGGC 1 33 0 GCGTCAGCGT 0.988867 -252 CTGATAAGACGCGCCAGCGTCGCATCAGGC 1 118 0 GCGCCAGCGT 0.994194 -167 CTGATAAGACGCGCCAGCGTCGCATCAGGC 1 203 0 GCGCCAGCGT 0.994194 -82 GCGATAAAAAGCGTCAGGTAGGATCCGCTA 2 271 0 GCGTCAGGTA 0.955085 -68 ACGTCATTATGCGTCAGATTTATGACAGAT 4 53 1 GCGTCAGATT 0.879009 -137 GTCGCACATATCTTCAGGTTATTGATTTCC 4 96 1 TCTTCAGGTT 0.696107 -94 GCTTTTTTCTGCGCCACGGAAATCAATAAC 4 113 0 GCGCCACGGA 0.926877 -77 CCATGCTTTTTCGCCAGGGAACCGTT 4 174 1 TCGCCAGGGA 0.964783 -16 GGTTCTCTCCAGCTTTAGTGTCGTT 7 286 0 TCTCCAGCTT 0.784167 -15 ACCCTGCCATGCGGCAGGGTCATAAAA 8 8 0 GCGGCAGGGT 0.980226 -293 ********** Masking position 6 Map Score: 13.5225 Number of sites scoring better than the average of aligned sites = 2126 Number in coding regions = 1990 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 CTGGCCTACACGCTGCGATTTTGTAGGCCG 1 60 1 CGCTGCGATT 0.986342 -225 GTTGAATGCCGGATGCGCTTTGCTTATCCG 1 88 0 GGATGCGCTT 0.973228 -197 CAGGCCTACGCGCTGCGATTTTGTAGGCCG 1 145 1 CGCTGCGATT 0.986342 -140 GTTGAATGCCGGATGCGCTTTGCTTATCCG 1 173 0 GGATGCGCTT 0.973228 -112 CAGGCCTACACGCTGCGATTTTGTAGGCCG 1 230 1 CGCTGCGATT 0.986342 -55 CCTTCGTGCCGGATGCGCTTTGCTTATCCG 1 258 0 GGATGCGCTT 0.973228 -27 CCTGCCGCATGGCAGGGTTTTTTATACCTG 8 20 1 GGCAGGGTTT 0.909951 -281 AACGACATGTCGCAGCAATTTAATCCATAT 8 200 1 CGCAGCAATT 0.849946 -101 TCAATAGGCTGGATTTTACATAATAA 9 7 1 GGCTGGATTT 0.911166 -52 GTTTTTTATGGGCTGGATTTTTATTATGTA 9 27 0 GGCTGGATTT 0.911166 -32 ********** Masking position 9 Map Score: 15.6113 Number of sites scoring better than the average of aligned sites = 875 Number in coding regions = 798 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 8 TGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 74 0 TTATCCGGCT 0.950728 -211 TGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 159 0 TTATCCGGCT 0.950728 -126 TGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 244 0 TTATCCGGCT 0.950728 -41 TCAATGTGGACTTTTCTGCCGTGATTATAGA 2 187 0 CTTTTCTGCG 0.72382 -152 TCTGTATTCATTATCCTGCTGAATAG 3 6 0 TTATCCTGCG 0.979775 -120 TTGCTGGTCGTTATCCTGCAAGCTATCACTT 3 58 1 TTATCCTGCA 0.974111 -68 GCCATTTGCTTTTTTCTGCGCCACGGAAATC 4 119 0 TTTTTCTGCC 0.825152 -71 AGAGGGGAATTTTTCCGGCAAA 6 2 0 TTTTCCGGCA 0.963925 -68 ATCTTATGGATTAATCTGCTGTGCATTCGAC 7 44 1 TTAATCTGCG 0.79723 -257 CCCTTATGTCTTTTCCCGCTAAATTTATGCA 7 98 1 TTTTCCCGCA 0.883568 -203 GTTCTCACTGTAATTCTGCGATGTGATATTG 7 130 1 TAATTCTGCA 0.614073 -171 CTTTATGAATTTTATCTGCTGTAAAATTAGG 8 111 1 TTTATCTGCG 0.772409 -190 TTTTTCCTGCCAGCAGAGAGTA 8 289 0 TTTTCCTGCA 0.970131 -12 ********* * Masking position 6 Map Score: 14.692 Number of sites scoring better than the average of aligned sites = 1096 Number in coding regions = 851 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 9 TATCTGGCCTACACGCTGCGATTTTGTAGGC 1 57 1 ACCGCTGCGA 0.994599 -228 TATCAGGCCTACGCGCTGCGATTTTGTAGGC 1 142 1 ACCGCTGCGA 0.994532 -143 TATCAGGCCTACACGCTGCGATTTTGTAGGC 1 227 1 ACCGCTGCGA 0.994599 -58 GCACGGCGTCACACTTTGCTATGCCATAGCA 2 224 1 ACCTTTGCTA 0.920169 -115 TTTTATCGCAACTCTCTACTGTTTCTCCATA 2 292 1 ACCTCTACTG 0.905266 -47 ACTATGTCTTACTCTCTGCTGGCAGGAAAAA 8 280 1 ACCTCTGCTG 0.984069 -21 ** ******** Masking position 7 Map Score: 6.34418 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 170 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 ATCCGGTATGTAACGCCTGATGCGACGCTG 1 19 1 TAACGCCTGA 0.982676 -266 ATCCGGCATTCAACGCCTGATGCGACGCTG 1 104 1 CAACGCCTGA 0.995676 -181 ATCCGGCATTCAACGCCTGATGCGACGCTG 1 189 1 CAACGCCTGA 0.995676 -96 GCAGTGACGGCAATGTCTGATGCAATATGG 2 51 0 CAATGTCTGA 0.936359 -288 ********** Masking position 3 Map Score: 4.01026 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 25 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 CATTTTTATCCATAAGATTAGCGGATCCTA 2 253 1 CATAAGATTA 0.879113 -86 CAGATTAATCCATAAGATTAGCCTGGAAAT 7 32 0 CATAAGATTA 0.879113 -269 TGAGAACGTGCATAAATTTAGCGGGAAAAG 7 107 0 CATAAATTTA 0.701075 -194 GAATGACATTCGTTAAATTAATCGGAAAAC 7 239 0 CGTTAAATTA 0.821679 -62 TTTTATCTGCTGTAAAATTAGGTGGTTAAT 8 120 1 TGTAAAATTA 0.934005 -181 TCACAAAATCAGTAAAATTATTTTAACATA 12 52 1 AGTAAAATTA 0.908062 -124 AGTCAATAAATGTAAAATAAATAAATTATT 12 92 0 TGTAAAATAA 0.690501 -84 AATTTTATATAGTAAAATTACGTTTCATAA 12 143 0 AGTAAAATTA 0.908062 -33 AATTTTACTATATAAAATTAAGAGAGGAAA 12 154 1 TATAAAATTA 0.878099 -22 ********** Masking position 5 Map Score: 3.40316 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 92 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 CAGAAAAGTCCACATTGATTATTTGCACGG 2 200 1 CACATTGATT 0.850824 -139 ATGATCGCAACCTATTTATTACAACAGGGC 4 16 0 CCTATTTATT 0.860319 -174 CATTATGCGTCAGATTTATGACAGATTTAT 4 57 1 CAGATTTATG 0.93065 -133 AGATTTATGACAGATTTATGAAAAGCTCGT 4 68 1 CAGATTTATG 0.93065 -122 GAATGCACAGCAGATTAATCCATAAGATTA 7 42 0 CAGATTAATC 0.749489 -259 GCTTTGTTTTCCGATTAATTTAACGAATGT 7 234 1 CCGATTAATT 0.858955 -67 TGAAATAATCCATATTAATTATCAATTAAT 8 78 1 CATATTAATT 0.883071 -223 CAATTTAATCCATATTTATGCTGTTTCCGA 8 215 1 CATATTTATG 0.906999 -86 TTACTGGAAACATATTGCTG 11 1 0 CATATTGCTG 0.760695 -71 TACACCTCCAATTGATTATCACAAATG 11 55 0 CCAATTGATT 0.706763 -17 ATTATTTTAACATATTGATTTATAAATAAT 12 68 1 CATATTGATT 0.93975 -108 ********** Masking position 4 Map Score: 5.48614 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 252 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 13 AATGGTGGGAGTATGAAAAGT 2 2 0 GTATGAAAAG 0.913741 -337 GTAACCCCGCTTATTAAAAGCATTCTGTAA 2 114 1 TTATTAAAAG 0.824789 -225 ACAAAAACGCGTAACAAAAGTGTCTATAAT 2 165 1 GTAACAAAAG 0.835894 -174 TATGACAGATTTATGAAAAGCTCGTCGCAC 4 73 1 TTATGAAAAG 0.949255 -117 ACAGACTTTCTTAACACAAGGAGACTTTT 10 12 1 TTAACACAAG 0.898133 -19 CTCCAATTGATTATCACAAATGTGATTCGT 11 47 0 TTATCACAAA 0.728954 -25 ATATGAAATATTATCACAAGAAAATAGGAT 12 17 1 TTATCACAAG 0.960134 -159 TTTTTGTAAATTATGAAACGTAATTTTACT 12 133 1 TTATGAAACG 0.832457 -43 ********** Masking position 6 Map Score: 2.19921 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 66 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 CAATTGGTTTCTTCTCTGAATGGTGGGAGTA 2 19 0 CTTCTCTGAT 0.959896 -320 AGATAATTCGCCCCTCTGTATTCATTATCCT 3 20 0 CCCCTCTGAT 0.99646 -106 CGGAAAAATTCCCCTCTGCATGATGCAGAGG 6 16 1 CCCCTCTGAT 0.99646 -54 TCGTTCACACCCCCTCTGCATCATGCAGAGG 6 28 0 CCCCTCTGAT 0.99646 -42 TTTTTCCTCTCTTAATTTTATATAGT 12 160 0 CCTCTCTTAT 0.959902 -16 ******** ** Masking position 5 Map Score: 7.29728 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 ********** No masking Map Score: -4.11161e-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