AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifur_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 entD 165 enterochelin synthetase, component D #2 fepA_fes 320 fepA: outer membrane receptor for ferric enterobactin (enterochelin) and colicins B and D, fes: enterochelin esterase #3 entF 217 ATP-dependent serine activating enzyme (may be part of enterobactin synthase as component F) #4 fepE 215 ferric enterobactin (enterochelin) transport #5 fepB_entC 374 fepB: ferric enterobactin (enterochelin) binding protein; periplasmic component, entC: isochorismate hydroxymutase 2, enterochelin biosynthesis #6 fur 288 negative regulator #7 tonB 127 energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins #8 cirA 293 outer membrane receptor for iron-regulated colicin I receptor; porin; requires tonB gene product #9 sodA 284 superoxide dismutase, manganese Motif number 1 CGCCGTCACACCATAACCCCATGTTTACTG 2 80 1 CCATAACCCC 0.876086 -241 CCACGGCGCGCCATTACGCTATTGCAAATG 2 165 0 CCATTACGCT 0.819887 -156 CCGTTCTGCCCCCTCTCCCTTCCAGGGTGA 5 209 1 CCCTCTCCCT 0.994672 -166 CTCACCCCAGCCCTCACCCTGGAAGGGAGA 5 222 0 CCCTCACCCT 0.996354 -153 CGAACATTAACCCTCACCCCAGCCCTCACC 5 234 0 CCCTCACCCC 0.996103 -141 CTGGCTGTTCCCCTCACCCTAACCCTCTCC 5 272 1 CCCTCACCCT 0.996354 -103 CTCACCCTAACCCTCTCCCCAAAGGGGCGA 5 284 1 CCCTCTCCCC 0.994305 -91 ACAATCCGTCCCCTCGCCCCTTTGGGGAGA 5 297 0 CCCTCGCCCC 0.987445 -78 TGTCATTACGCCCTTAACCTTATTAATAAC 5 342 1 CCCTTAACCT 0.858681 -33 ATTGAAAAAGCCCTCTCGGTTGAGAGGGCT 8 31 0 CCCTCTCGGT 0.838584 -263 TTTTTCAATTCCATTTCCCTGACAAATCAT 8 52 1 CCATTTCCCT 0.928813 -242 ********** Masking position 4 Map Score: 22.3938 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 150 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 AAGTGCGCGTCGTTCATGCCGGATGCGGCGT 1 33 1 CGTTATGCCG 0.96553 -133 CCGGATAAGGCGTTCACGCCGCATCCGGCAT 1 48 0 CGTTACGCCG 0.981135 -118 CACTTCCTACTTTTAACGCCGTCACACCATA 2 64 1 TTTTACGCCG 0.930179 -257 GGATGCGTCGTGTTGATGACGACCATGCCCG 2 262 1 TGTTATGACG 0.839789 -59 TAGGGGGAAATCTCCACGGCGCTCACTTTAC 4 169 0 TCTCACGGCG 0.851541 -47 CGTAGACATGAGTCTACGCCGCATCACA 6 8 0 AGTCACGCCG 0.971667 -281 CGTAGACTCATGTCTACGCCGTATTAATAGA 6 21 1 TGTCACGCCG 0.992778 -268 GGTGTTCAAGTGGCCTTGCCGTTGTAAATGT 6 116 1 TGGCTTGCCG 0.726982 -173 GTTTGCATTATCGTTACGCCGCAATCAAAAA 8 122 1 TCGTACGCCG 0.943574 -172 ACCTTTCGCCTGTTGCCGCCGTTGTCGATTT 9 83 1 TGTTCCGCCG 0.95889 -202 CAAATCACCCACTTAATGCCGTGATTGCCAG 9 115 0 ACTTATGCCG 0.875995 -170 TGAAAATGATTATCAATGCCGTACTTTTCGT 9 185 0 TATCATGCCG 0.879535 -100 GGCGGCCGATTGTTAATGCCGCGTAAGCAGT 9 244 0 TGTTATGCCG 0.986489 -41 **** ****** Masking position 10 Map Score: 16.8295 Number of sites scoring better than the average of aligned sites = 1220 Number in coding regions = 970 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 TCAGATTGTTGACAAAGTGCGCGTCGTTCATG 1 19 1 GACAAGTCGC 0.988349 -147 TCATCAACACGACGCATCCCGCTACCGCGAAA 2 249 0 GACGATCCGC 0.971402 -72 GGGAGCGTTTTACATATTGCGCAATGCGCAGG 3 45 1 TACAATTCGC 0.91235 -173 ATTCGTCGGTGTCAGAGTACGCCAGTGGGCTT 3 173 0 GTCAAGTCGC 0.950016 -45 CTCTGACACCGACGAATTTTACCCAGTTGCAG 3 188 1 GACGATTTAC 0.760811 -30 CTCAAGAGTTGACATAGTGCGCGTTTGCTTTT 5 77 0 GACAAGTCGC 0.988349 -298 CTCTTGAGGTAACGCAATCTGCAACTCGGGGT 5 101 1 AACGAATTGC 0.68353 -274 GGCGCAGGACATCACATTGCGCTTATGCGAAT 5 179 0 ATCAATTCGC 0.804401 -196 GGGGCGAGGGGACGGATTGTGCGCTTTGTCGA 5 307 1 GACGATTTGC 0.977956 -68 TAGAAGAAGTGACAGAATTTGCTCTTGAGATA 6 231 0 GACAAATTGC 0.944573 -58 TTAGTAACAGGACAGATTCCGC 6 277 1 GACAATTCGC 0.991669 -12 CCATTTCCCTGACAAATCATGCGGATATAAAA 8 62 1 GACAATCTGC 0.949212 -232 **** *** *** Masking position 6 Map Score: 14.1391 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 446 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 GCCCGGAATGGCAGCGTCTGAATGACGAA 2 6 0 GCCGTCAATG 0.945684 -315 GTAGCGGGATGCGTCGTGTTGATGACGACCATGC 2 256 1 GCCGTGGATG 0.84263 -65 ACGCATTGTTGCGGCCACAGACTGAATTGCCCCT 3 74 0 GCCCACACTG 0.978119 -144 TGTGACTGCGGCTGACACACAATGTCCCAGCCTG 3 116 0 GCACACAATG 0.722048 -102 ACGCCAGTGGGCTTCCAGCCACTGCTGGCAGGAC 3 153 0 GCCCAGACTG 0.953986 -65 TGTGCCTCCTGCAACTGGGTAAAATTC 3 201 0 GCCCTGACTG 0.903733 -17 TTTGTAAATTCCTTCCACTGAATGCAACATTCAC 4 106 0 CCCCACAATG 0.957278 -110 ATCATCCTCCACAAAATGATAAAGGCTT 5 5 1 TCCCACAATG 0.915606 -370 ACAACCAGATGCAACCCCGAGTTGCAGATTGCGT 5 112 0 GCCCCCGTTG 0.917838 -263 AATGTGATGTCCTGCGCCGTTCTGCCCCCTCTCC 5 193 1 CCCGCCTCTG 0.831532 -182 ACAATCCGTCCCCTCGCCCCTTTGGGGAGAGGGT 5 293 0 CCCGCCTTTG 0.573829 -82 TTATAGAATTGCCACGCCTAAATGAAAACCACAA 6 187 0 GCCGCCAATG 0.981524 -102 AAAAATAAGTCCACCGCGATGCTGCCGTACGCAA 8 204 1 CCCGCGGCTG 0.871382 -90 TCGCGTCACATCTCCGACGAGATGAGTGTAAAAA 9 34 1 TCCGACGATG 0.84913 -251 GTGAAGCAAATCACCCACTTAATGCCGTGATTGC 9 118 0 TCCCACAATG 0.915606 -167 TTAACAATCGGCCGCCCGACAATACTGGAGATGA 9 259 1 GCCCCGAATA 0.624712 -26 ** **** **** Masking position 13 Map Score: 13.1867 Number of sites scoring better than the average of aligned sites = 1805 Number in coding regions = 1718 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 AATAGTTATCAATAATATTATCAATATATTTCTGCAATCAA 2 122 0 AAATTTCATT 0.925374 -199 AATATTATTGATAACTATTTGCATTTGCAATAGCGTAATGG 2 144 1 ATATTGCATT 0.972757 -177 TAAAAAACCCATAATTATTTTCTGTAATTATGGGTTTATAA 4 22 0 ATATTTCTTT 0.880844 -194 AAAGGCTTTAATAATGATTATCATTTATATTTTCGGTCGCT 5 31 1 ATATTTCATT 0.980986 -344 GAATCCATCAATAATGCTTCTCATTTTCATTGTAACCACAA 5 142 0 ATCTTTCATT 0.916377 -233 TGTAGCAATTATTTTGATTGGCATTATCTATTAATACGGCG 6 37 0 ATATTGCATT 0.916508 -252 TTACGCCAAAAATGACATTTTCACTGATCCTGATCGTCTTG 7 24 1 AAATTTCATT 0.935889 -104 ATTGAATATGATTGCTATTTGCATTTAAAATCGAGACCTGG 7 69 1 ATATTGCATT 0.972757 -59 AATGCAAACGATAACAATTATCAATCCAAATGTTAAATTTT 8 90 0 ATATTTCATT 0.943705 -204 TACGGCATTGATAATCATTTTCAATATCATTTAATTAACTA 9 193 1 ATATTTCATT 0.97025 -92 ** *** *** * * Masking position 9 Map Score: 11.1269 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 31 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 CGTCGTTCATGCCGGATGCGGCGTGAACGCCT 1 40 1 GCCGGATCGC 0.612073 -126 CGGCGTGAACGCCTTATCCGGCCTACAAAAAT 1 58 1 GCCTTATCGC 0.64189 -108 GGGCAATTCAGTCTGTGGCCGCAACAATGCGT 3 76 1 GTCTGTGCGC 0.970079 -142 CTGGCAGGACGCCTGTGACTGCGGCTGACACA 3 131 0 GCCTGTGCGC 0.994947 -87 ACAAATCAGAGGCTGTTCCGGCTTTCTGGGAT 8 159 1 GGCTGTTCGC 0.98452 -135 TTAACCTTTCGCCTGTTGCCGCCGTTGTCGAT 9 80 1 GCCTGTTCGC 0.996727 -205 CACATCTCGGGCATTTTCCTGCAAAACCATAC 9 149 1 GCATTTTCGC 0.909291 -136 ******* * ** Masking position 9 Map Score: 6.9364 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 533 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 CGTTAAAAGTAGGAAGTGAGAGCTGGTGGC 2 52 0 AGGAAGTGAG 0.830075 -269 CTGCGGATCATCGAAGGGATTACTGAATGC 3 16 0 TCGAAGGGAT 0.890557 -202 CTTCGATGATCCGCAGGGAGCGTTTTACAT 3 30 1 CCGCAGGGAG 0.927275 -188 CAGCCACTGCTGGCAGGACGCCTGTGACTG 3 142 0 TGGCAGGACG 0.910976 -76 CTGCCAGCAGTGGCTGGAAGCCCACTGGCG 3 156 1 TGGCTGGAAG 0.873486 -62 TTGCATTCAGTGGAAGGAATTTACAAACTT 4 113 1 TGGAAGGAAT 0.899903 -103 GCCCTCACCCTGGAAGGGAGAGGGGGCAGA 5 213 0 TGGAAGGGAG 0.990153 -162 GGGCTTAGCAAGGAAGGGAGGAAAC 8 6 0 AGGAAGGGAG 0.977651 -288 ********** Masking position 6 Map Score: 3.07486 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 387 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 ACTATTTGCATTTGCAATAGCGTAATGGCGCG 2 157 1 TTTGCAAGCG 0.987973 -164 ATCAAAGGTTTTCGCGGTAGCGGGATGCGTCG 2 240 1 TTCGCGAGCG 0.990951 -81 TATTGATGGATTCGCATAAGCGCAATGTGATG 5 170 1 TTCGCAAGCG 0.995903 -205 AGGGTTAATGTTCGCACCAGTGCTGGCTGTTC 5 250 1 TTCGCAAGTG 0.974099 -125 TAATGACAAATTCGACAAAGCGCACAATCCGT 5 318 0 TTCGACAGCG 0.944265 -57 ATTGTTATCGTTTGCATTATCGTTACGCCGCA 8 113 1 TTTGCAATCG 0.92705 -181 ****** **** Masking position 9 Map Score: 2.94033 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 102 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GCATCCGGCATGAACGACGCGCACTTTGTCAAC 1 26 0 TGAGAGCGCA 0.983728 -140 GCGTCGTTCATGCCGGATGCGGCGTGAACGCCT 1 39 1 TGCGAGCGGC 0.936214 -127 AACGCAAAACTGCCTGATGCGCTACGCTTATCA 1 126 0 TGCGAGCGCT 0.983412 -40 CCTTTGATCCTGAAAGACACGCAGTGCAGTTGG 2 215 0 TGAGAACGCA 0.935027 -106 TTTTACATATTGCGCAATGCGCAGGGGCAATTC 3 52 1 TGCAAGCGCA 0.631217 -166 TGCCAGCAGTGGCTGGAAGCCCACTGGCGTACT 3 157 1 GGCGAGCCCA 0.936374 -61 TTTACCCAGTTGCAGGAGGCACA 3 205 1 TGCGAGCACA 0.973942 -13 GAAGCATTATTGATGGATTCGCATAAGCGCAAT 5 163 1 TGAGATCGCA 0.93593 -212 *** ** ***** Masking position 7 Map Score: 3.60753 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 599 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 ATAACTATTTGCATTTGCAATAGCGTAATGG 2 154 1 GCATTTGAAT 0.775167 -167 TGTAATTATGGGTTTATAAATAATATTAAT 4 10 0 GGTTTATAAT 0.614071 -206 AATGATAAAGGCTTTAATAATGATTATCATT 5 25 1 GCTTTAAAAT 0.897937 -350 AAAATGAGAAGCATTATTGATGGATTCGCAT 5 156 1 GCATTATGAT 0.888792 -219 ATTTTGATTGGCATTATCTATTAATACGGCG 6 37 0 GCATTATTAT 0.745555 -252 ATTGCTATTTGCATTTAAAATCGAGACCTGG 7 79 1 GCATTTAAAT 0.918066 -49 AACCGAGAGGGCTTTTTCAATTCCATTTCCC 8 40 1 GCTTTTTAAT 0.77024 -254 TTTAACATTTGGATTGATAATTGTTATCGTT 8 94 1 GGATTGAAAT 0.72219 -200 GTTATCGTTTGCATTATCGTTACGCCGCAAT 8 116 1 GCATTATGTT 0.480711 -178 ATGATCACCTGCATAAAAAATAAGTCCACCG 8 189 1 GCATAAAAAT 0.741348 -105 GAAAAGTACGGCATTGATAATCATTTTCAAT 9 187 1 GCATTGAAAT 0.923639 -98 TGCTTACGCGGCATTAACAATCGGCCGCCCG 9 246 1 GCATTAAAAT 0.961158 -39 ******* *** Masking position 4 Map Score: 2.49511 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 289 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 CGGCGTAGACTCATGTCTACGCCGTATTAA 6 18 1 TCATGTCTAC 0.791616 -271 GCAAATTCTGTCACTTCTTCTAATGAAGTG 6 241 1 TCACTTCTTC 0.900027 -48 CACATCTTCTTCACGTCCCCTTGCGTACGG 8 228 0 TCACGTCCCC 0.957193 -66 GGGTTATCGCTCACATCTTCTTCACGTCCC 8 239 0 TCACATCTTC 0.967341 -55 TCCATATCTCCATGAGGTAAC 8 283 0 CCATATCTCC 0.880351 -11 TTTCGTCGCGTCACATCTCCGACGAGATGA 9 29 1 TCACATCTCC 0.98872 -256 GTGATTTGCTTCACATCTCGGGCATTTTCC 9 138 1 TCACATCTCG 0.943982 -147 ********** Masking position 3 Map Score: 2.4393 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 155 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 AGTCGAAACATGGCCCGGAATGGCAGCGTC 2 22 0 TGGCCCGGAA 0.818168 -299 ATGTCCGCGCTTCCCACGGCGCGCCATTAC 2 178 0 TTCCCACGGC 0.909332 -143 TCCTGCATTTTTGCCACGAATTGCAACTGT 2 293 0 TTGCCACGAA 0.967668 -28 ACAGACTGAATTGCCCCTGCGCATTGCGCA 3 62 0 TTGCCCCTGC 0.886987 -156 TTAACAATATTTGCCAGGGACTTGTGGTTT 6 166 1 TTGCCAGGGA 0.984075 -123 CATTATAGAATTGCCACGCCTAAATGAAAA 6 193 0 TTGCCACGCC 0.945086 -96 TCCGCATGATTTGTCAGGGAAATGGAATTG 8 57 0 TTGTCAGGGA 0.873477 -237 AATGCCGTGATTGCCAGTAAATCGACAACG 9 102 0 TTGCCAGTAA 0.87253 -183 ********** Masking position 1 Map Score: 1.60717 Number of sites scoring better than the average of aligned sites = 917 Number in coding regions = 859 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 13 GACACGCAGTGCAGTTGGTTAATTAATGTC 2 203 0 GCAGTTGGTT 0.989568 -118 GCTCACTTTACCAGTTGGTGATAATTATCC 4 150 0 CCAGTTGGTG 0.954037 -66 ACTCGGGGTTGCATCTGGTTGTGGTTACAA 5 124 1 GCATCTGGTT 0.933354 -251 TGCCGCGTAAGCAGTTGGTTCATTATAGTT 9 229 0 GCAGTTGGTT 0.989568 -56 ********** Masking position 6 Map Score: 0.121456 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 65 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 ********** No masking Map Score: -1.68155e-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 ********** No masking Map Score: -1.68155e-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