AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iaraC_ecoli_hinf_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 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 araH_2 23 high-affinity L-arabinose transport system; membrane protein, fragment 2 #5 araG 69 ATP-binding component of high-affinity L-arabinose transport system #6 araF 300 L-arabinose-binding periplasmic protein #7 araE 300 low-affinity L-arabinose transport system proton symport protein #8 HI1027 58 L-xylulose kinase (lyx) #9 HI1028 30 conserved hypothetical protein #10 HI1030 71 conserved hypothetical transmembrane protein #11 HI1031 175 conserved hypothetical protein Motif number 1 GTAGCCGCATCCGGTATGTAACGCCTG 1 6 1 CGCATCGGTT 0.986551 -279 GCGTCAGCGTCGCATCAGGCGTTACATACCGG 1 21 0 CGCATCGGCT 0.999103 -264 GCTGACGCGTCTTATCTGGCCTACACGCTGCG 1 45 1 CTTATCGGCT 0.996906 -240 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 74 0 CTTATCGGCT 0.996906 -211 ATAAGCAAAGCGCATCCGGCATTCAACGCCTG 1 91 1 CGCATCGGCT 0.999103 -194 GCGCCAGCGTCGCATCAGGCGTTGAATGCCGG 1 106 0 CGCATCGGCT 0.999103 -179 GCTGGCGCGTCTTATCAGGCCTACGCGCTGCG 1 130 1 CTTATCGGCT 0.996906 -155 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 159 0 CTTATCGGCT 0.996906 -126 ATAAGCAAAGCGCATCCGGCATTCAACGCCTG 1 176 1 CGCATCGGCT 0.999103 -109 GCGCCAGCGTCGCATCAGGCGTTGAATGCCGG 1 191 0 CGCATCGGCT 0.999103 -94 GCTGGCGCGTCTTATCAGGCCTACACGCTGCG 1 215 1 CTTATCGGCT 0.996906 -70 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 244 0 CTTATCGGCT 0.996906 -41 ATAAGCAAAGCGCATCCGGCACGAAGGAGTCA 1 261 1 CGCATCGGCC 0.994339 -24 ****** *** * Masking position 4 Map Score: 59.1465 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 0.998734 -236 GCTTTGCTTATCCGGCCTACAAAATCGCAGC 1 71 0 TCGGCCTACA 0.998739 -214 GCAAAGCGCATCCGGCATTCAACGCCTGATG 1 95 1 TCGGCATTCA 0.980123 -190 GCGCGTCTTATCAGGCCTACGCGCTGCGATT 1 134 1 TCGGCCTACG 0.994628 -151 GCTTTGCTTATCCGGCCTACAAAATCGCAGC 1 156 0 TCGGCCTACA 0.998739 -129 GCAAAGCGCATCCGGCATTCAACGCCTGATG 1 180 1 TCGGCATTCA 0.980123 -105 GCGCGTCTTATCAGGCCTACACGCTGCGATT 1 219 1 TCGGCCTACA 0.998738 -66 GCTTTGCTTATCCGGCCTACAAAATCGCAGC 1 241 0 TCGGCCTACA 0.998739 -44 GTCATTCGTTTTTGCCCTACACAAAACGACA 6 262 1 TTGCCCTACA 0.918617 -39 ** ******** Masking position 8 Map Score: 30.1659 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 CCTACACGCTGCGATTTTGTAGGCCGGATA 1 64 1 GCGATTTTGT 0.960991 -221 AATGCCGGATGCGCTTTGCTTATCCGGCCT 1 84 0 GCGCTTTGCT 0.984964 -201 CCTACGCGCTGCGATTTTGTAGGCCGGATA 1 149 1 GCGATTTTGT 0.960991 -136 AATGCCGGATGCGCTTTGCTTATCCGGCCT 1 169 0 GCGCTTTGCT 0.984964 -116 CCTACACGCTGCGATTTTGTAGGCCGGATA 1 234 1 GCGATTTTGT 0.960991 -51 CGTGCCGGATGCGCTTTGCTTATCCGGCCT 1 254 0 GCGCTTTGCT 0.984964 -31 GGCTTTGGTCCCGCTTTGTTACAGAATGCT 2 132 0 CCGCTTTGTT 0.896065 -207 CTTTTGTTACGCGTTTTTGTCATGGCTTTG 2 155 0 GCGTTTTTGT 0.969769 -184 TTCTCCATACCCGTTTTTTTGGATGGAGTG 2 314 1 CCGTTTTTTT 0.773161 -25 TGATTGGTAGCCGTTCTGGTGGTTGTGATG 3 101 1 CCGTTCTGGT 0.789574 -25 TTATATTATGGCGTTTTACTGGAAACATAT 10 16 0 GCGTTTTACT 0.864663 -56 ********** Masking position 5 Map Score: 17.7896 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 422 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 GAAGAAACCAATTGTCCATATTGCATCAGA 2 36 1 ATTGTCCATA 0.933839 -303 CCATAGCATTTTTATCCATAAGATTAGCGG 2 247 1 TTTATCCATA 0.969071 -92 CTCTCTACTGTTTCTCCATACCCGTTTTTT 2 303 1 TTTCTCCATA 0.968466 -36 GCACAGCAGATTAATCCATAAGATTAGCCT 6 38 0 TTAATCCATA 0.962167 -263 CGAGAAATTAATTCTCCATAGGAGAGCAAT 6 157 0 ATTCTCCATA 0.974251 -144 GTAGATCATCATAATCCATATCATGGTTAT 7 49 1 ATAATCCATA 0.969072 -252 TGGTTATGAAATAATCCATATTAATTATCA 7 72 1 ATAATCCATA 0.969072 -229 TCGCAGCAATTTAATCCATATTTATGCTGT 7 209 1 TTAATCCATA 0.962167 -92 ATATTCTCCTTAGTTTTTTATG 8 47 0 ATTCTCCTTA 0.856419 -12 ********** Masking position 5 Map Score: 15.2853 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 5 ACGCCTGATGCGACGCTGACGCGTCTTATCTGGC 1 31 1 CGCCTGCGCT 0.998552 -254 ACGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 1 116 1 CGCCTGCGCT 0.998544 -169 ACGCCTGATGCGACGCTGGCGCGTCTTATCAGGC 1 201 1 CGCCTGCGCT 0.998544 -84 CAGACATTGCCGTCACTGCGTCTTTTACTGGCTC 2 62 1 CGCCTGGTCT 0.973096 -277 ATTAGCGGATCCTACCTGACGCTTTTTATCGCAA 2 269 1 CCACTGCGCT 0.989791 -70 TCGTTCACACCCCCTCTGCATCATGCAGAGGGGA 5 25 0 CCCCTGATCT 0.937498 -45 TTTTATGACCCTGCCGCATGGCAGGGTTT 7 6 1 TGCCTGCGCT 0.987182 -295 TATGCTGTTTCCGACCTGACACCTGCGTGAGTTG 7 231 1 CCACTGCACT 0.937498 -70 ** * *** *** * Masking position 7 Map Score: 14.2363 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 317 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 GCCTACAAAATCGCAGCGTGTAGGCCAGATA 1 57 0 TCGCAGCGGT 0.995627 -228 GCCTACAAAATCGCAGCGCGTAGGCCTGATA 1 142 0 TCGCAGCGGT 0.995544 -143 GCCTACAAAATCGCAGCGTGTAGGCCTGATA 1 227 0 TCGCAGCGGT 0.995627 -58 TGCTATGGCATAGCAAAGTGTGACGCCGTGC 2 224 0 TAGCAAAGGT 0.934446 -115 TATGGAGAAACAGTAGAGAGTTGCGATAAAA 2 292 0 CAGTAGAGGT 0.921983 -47 TTTTTCCTGCCAGCAGAGAGTAAGACATAGT 7 280 0 CAGCAGAGGT 0.987078 -21 ******** ** Masking position 5 Map Score: 6.96062 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 7 TCGCAGCGTGTAGGCCAGATAAGACGCGTCAG 1 46 0 TAGCAGATAA 0.931841 -239 TGCGATTTTGTAGGCCGGATAAGCAAAGCGCA 1 73 1 TAGCGGATAA 0.984074 -212 TGCGATTTTGTAGGCCGGATAAGCAAAGCGCA 1 158 1 TAGCGGATAA 0.984074 -127 TGCGATTTTGTAGGCCGGATAAGCAAAGCGCA 1 243 1 TAGCGGATAA 0.984074 -42 ACCGGTTGGGTTAGCGAGAAGAGCCAGTAAAA 2 84 0 TTGCAGAAGA 0.774377 -255 CTATTCAGCAGGATAATGAATACAGA 3 5 1 TCGCGGATAA 0.980785 -121 AAAGTGATAGCTTGCAGGATAACGACCAGCAA 3 58 0 CTGCGGATAA 0.96916 -68 TTTGCCGGAAAAATTCCCCTCT 5 1 1 TTGCGGAAAA 0.956227 -69 GTGCATAAATTTAGCGGGAAAAGACATAAGGG 6 98 0 TTGCGGAAAA 0.988372 -203 TGACATAGTTTTAGCGAGAAATTAATTCTCCA 6 169 0 TTGCAGAAAT 0.698779 -132 ATGAATTTTATCTGCTGTAAAATTAGGTGGTT 7 115 1 TCGCGTAAAA 0.786611 -186 TTACTCTCTGCTGGCAGGAAAAA 7 288 1 CTGCGGAAAA 0.969179 -13 ** ** ****** Masking position 9 Map Score: 20.7377 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 342 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 8 ATAAGCGGGGTTACCGGTTGGGTTAGCGAGA 2 97 0 TTACCGGTGG 0.889469 -242 TAGGATCCGCTAATCTTATGGATAAAAATGC 2 252 0 TAATCTTTGG 0.95388 -87 GAGGGGCGAATTATCTCTTGGCCTTGCTGGT 3 35 1 TTATCTCTGG 0.953653 -91 ATTTCCAGGCTAATCTTATGGATTAATCTGC 6 32 1 TAATCTTTGG 0.95388 -269 TCTTATGGATTAATCTGCTGTGCATTCGACA 6 45 1 TAATCTGTGT 0.875384 -256 ACACAGTCACTTATCTTTTAGTTAAAAGGTA 6 201 1 TTATCTTTAG 0.799624 -100 TTTATGAATTTTATCTGCTGTAAAATTAGGT 7 112 1 TTATCTGTGT 0.939444 -189 CGACATGTCGTTATGTGATGGATATTCCAAT 7 181 0 TTATGTGTGG 0.964705 -120 CCTTAGTTTTTTATGGGCTGGATTTTTATTA 8 31 0 TTATGGGTGG 0.921589 -28 GTGATTCGTTTTATATTATGGCGTTTTACTG 10 25 0 TTATATTTGG 0.836084 -47 ******* *** Masking position 3 Map Score: 6.03266 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 561 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 TAGGCCAGATAAGACGCGTCAGCGTCGCAT 1 38 0 AAGACGCGTC 0.991145 -247 CCGGATAAGCAAAGCGCATCCGGCATTCAA 1 87 1 AAAGCGCATC 0.95859 -198 TAGGCCTGATAAGACGCGCCAGCGTCGCAT 1 123 0 AAGACGCGCC 0.989303 -162 CCGGATAAGCAAAGCGCATCCGGCATTCAA 1 172 1 AAAGCGCATC 0.95859 -113 TAGGCCTGATAAGACGCGCCAGCGTCGCAT 1 208 0 AAGACGCGCC 0.989303 -77 CCGGATAAGCAAAGCGCATCCGGCACGAAG 1 257 1 AAAGCGCATC 0.95859 -28 TTGGGTTAGCGAGAAGAGCCAGTAAAAGAC 2 81 0 GAGAAGAGCC 0.294365 -258 AGCCATGACAAAAACGCGTAACAAAAGTGT 2 158 1 AAAACGCGTA 0.895159 -181 GAGTTGCGATAAAAAGCGTCAGGTAGGATC 2 276 0 AAAAAGCGTC 0.944905 -63 ********** Masking position 2 Map Score: 10.6824 Number of sites scoring better than the average of aligned sites = 1049 Number in coding regions = 898 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 10 ATCCGGTATGTAACGCCTGATGCGACGCTG 1 19 1 TAACGCCTGA 0.986809 -266 ATCCGGCATTCAACGCCTGATGCGACGCTG 1 104 1 CAACGCCTGA 0.996773 -181 ATCCGGCATTCAACGCCTGATGCGACGCTG 1 189 1 CAACGCCTGA 0.996773 -96 GCAGTGACGGCAATGTCTGATGCAATATGG 2 51 0 CAATGTCTGA 0.952094 -288 ********** Masking position 3 Map Score: 4.42076 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 TACGCGTTTTTGTCATGGCTTTGGTCCCGCTT 2 146 0 TGTCATGGTT 0.969268 -193 TTCTGGTGGTTGTGATGGTGGT 3 114 1 TGTGATGGGT 0.906583 -12 TCCATAAGATTAGCCTGGAAATCCTTGTTGTC 6 22 0 TAGCCTGGAT 0.799165 -279 CCCTGCCGCATGGCAGGGTTTTTTATACCTGT 7 19 1 TGGCAGGGTT 0.930008 -282 TCATAATCCATATCATGGTTATGAAATAATCC 7 57 1 TATCATGGTT 0.924972 -244 CATGTCGTTATGTGATGGATATTCCAATTTTC 7 177 0 TGTGATGGTT 0.969268 -124 TCAATAGGCTGGATTTTACATAATAA 8 5 1 TAGGCTGGTT 0.950414 -54 TAGTTTTTTATGGGCTGGATTTTTATTATGTA 8 27 0 TGGGCTGGTT 0.980014 -32 ******** * * Masking position 1 Map Score: 3.45797 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 264 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 CAGAAAAGTCCACATTGATTATTTGCACGGC 2 200 1 CAATTGATTA 0.833166 -139 ATGTCTTTTCCCGCTAAATTTATGCACGTTC 6 103 1 CCCTAAATTT 0.821502 -198 GCTTTGTTTTCCGATTAATTTAACGAATGTC 6 234 1 CCATTAATTT 0.957764 -67 TGAAATAATCCATATTAATTATCAATTAATG 7 78 1 CAATTAATTA 0.858246 -223 TTATTATTAACCACCTAATTTTACAGCAGAT 7 124 0 CCCCTAATTT 0.872142 -177 CTCAATAATTCAACTTAATTTGAAAATTGGA 7 156 1 CACTTAATTT 0.936943 -145 TACACCTCCAATTGATTATCACAAATGT 10 54 0 CCATTGATTA 0.907508 -18 ATTATTTTAACATATTGATTTATAAATAATT 11 68 1 CAATTGATTT 0.904945 -108 TTTTTCCTCTCTTAATTTTATATAGTAA 11 158 0 TCCTTAATTT 0.741073 -18 ** ******** Masking position 8 Map Score: 2.32073 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 134 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 AAGCGGGACCAAAGCCATGACAAAAACGCGT 2 146 1 AAAGCCATGC 0.956727 -193 TATGGATAAAAATGCTATGGCATAGCAAAGT 2 236 0 AATGCTATGC 0.714118 -103 ATTTCTCGCTAAAACTATGTCAACACAGTCA 6 179 1 AAAACTATGC 0.934301 -122 ACAGGTATAAAAAACCCTGCCATGCGGCAGG 7 20 0 AAAACCCTGC 0.97281 -281 TTTATTATGTAAAATCCAGCCTATTGA 8 7 0 AAAATCCAGC 0.891107 -52 TTACATAATAAAAATCCAGCCCATAAAAAAC 8 26 1 AAAATCCAGC 0.891107 -33 CAGCCCATAAAAAACTAAGGAGAATAT 8 42 1 AAAACTAAGA 0.613606 -17 CAAAAATAAGAAAGCTCAGTCAATAAATGTA 11 108 0 AAAGCTCAGC 0.956727 -68 ********* * Masking position 2 Map Score: 1.74222 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 574 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 14 ********** No masking Map Score: -3.54318e-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 15 TCCCACCATTCAGAGAAGAAACCAATTGTC 2 22 1 CAGAGAAGAA 0.929123 -317 ATAATGAATACAGAGGGGCGAATTATCTCT 3 23 1 CAGAGGGGCG 0.968111 -103 CTGCATCATGCAGAGGGGAATTTTTCCGGC 5 14 0 CAGAGGGGAA 0.993226 -56 CTGCATGATGCAGAGGGGGTGTGAACGACC 5 31 1 CAGAGGGGGT 0.917562 -39 CGGGAAAAGACATAAGGGAAAGCCAATTTG 6 86 0 CATAAGGGAA 0.789252 -215 ATTAATTCTCCATAGGAGAGCAATATCACA 6 151 0 CATAGGAGAG 0.837706 -150 TTCCTGCCAGCAGAGAGTAAGACATAGTGA 7 278 0 CAGAGAGTAA 0.864868 -23 ATATAAAATTAAGAGAGGAAAAA 11 163 1 AAGAGAGGAA 0.864868 -13 ********** Masking position 4 Map Score: 2.89377 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 270 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706