AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00670_ecoli_reg_300.orf -o00670_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.51 -x5 -e 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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 fixA 300 probable flavoprotein subunit, carnitine metabolism #2 fixC 50 flavoprotein; electron transport #3 yaaU 56 putative transport protein #4 yabF 107 putative NAD(P)H oxidoreductase #5 folA 191 dihydrofolate reductase type I; trimethoprim resistance #6 panB 113 3-methyl-2-oxobutanoate hydroxymethyltransferase #7 yadC 49 putative fimbrial-like protein #8 yadK 26 putative fimbrial protein #9 htrE 34 probable outer membrane porin protein involved in fimbrial assembly #10 ecpD 97 probable pilin chaperone similar to PapD #11 yadN 300 putative fimbrial-like protein #12 folD 300 5,10-methylene-tetrahydrofolate dehydrogenase; 5,10-methylene-tetrahydrofolate cyclohydrolase #13 purU 49 formyltetrahydrofolate deformylase; for purT-dependent FGAR synthesis #14 ychJ 73 orf, hypothetical protein #15 purM 297 phosphoribosylaminoimidazole synthetase = AIR synthetase #16 glyA 300 serine hydroxymethyltransferase #17 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #18 ygdP 300 putative invasion protein #19 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #20 def 129 peptide deformylase #21 metB 276 cystathionine gamma-synthase #22 BIME202 79 BIME #23 metF 234 5,10-methylenetetrahydrofolate reductase #24 purH 300 phosphoribosylaminoimidazolecarboxamideformyltransferase = AICAR formyltransferase; IMP cyclohydrolase #25 metH 160 B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase, repressor of metE and metF Motif number 1 GTTTTTTCGTTAATTTTGATTAATAATCAG 1 56 1 TAATTTTGAT 0.725431 -245 TATGGATCACCAATATTGAAAGTCAGATGT 1 116 0 CAATATTGAA 0.963591 -185 ATCCATAAAACAATATTGAAAATTTCTTTT 1 139 1 CAATATTGAA 0.963591 -162 AGTTCCTCACCAATATTGAAAACACGGCGT 1 173 0 CAATATTGAA 0.963591 -128 AGGAACTTAACAATATTGAAAGTTGGATTT 1 196 1 CAATATTGAA 0.963591 -105 CTTTAATCACCAATATTGAAAATGTCACAC 1 232 0 CAATATTGAA 0.963591 -69 TCACGCCCTTTAATTTTGAAATAAAACTTT 1 258 0 TAATTTTGAA 0.904803 -43 TTATAGTCAATAATATTGATTCAGAAAAGA 4 27 0 TAATATTGAT 0.79458 -81 TATTTTTACTTAATTTTGAATTAAGTAAAT 11 102 1 TAATTTTGAA 0.904803 -199 ATGGTGATCACAATTTTGACTGTGGTTACC 24 133 0 CAATTTTGAC 0.808564 -168 TCCGATGAGTTAATGTTGAACAAATCTCAT 25 47 1 TAATGTTGAA 0.810665 -114 ********** Masking position 3 Map Score: 13.9519 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 76 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 GGGCCAAAATGCAGCCCTGCCAGAGTGGA 2 9 0 GCAGCCCTGC 0.987822 -42 GATACGTAACGCCGCACTGACTCTCATTGCA 3 20 1 GCCGCACTGC 0.99628 -37 TAACGTAGCAGCACTGTCACCTTCTGGC 6 8 1 GCAGCACTGC 0.995515 -106 TTTATCCGTAGCAGCACTGCCAGAAGGTGAC 6 26 0 GCAGCACTGC 0.995514 -88 GCGAAGGTGAGGCGCACCGTCGCTGAGACTG 12 169 0 GGCGCACCGC 0.97195 -132 TCAGAAGCGGGGCGCGCTGTCAGGTTTCGTT 12 228 0 GGCGCGCTGC 0.976369 -73 CTGATTGACAGCATCACTGACCAATCGCAAA 20 45 0 GCATCACTGC 0.966434 -85 ********* * Masking position 5 Map Score: 9.81796 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 158 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 TGGTATCACATTTTTGTTTCGGGTGAATAG 1 21 1 TTTTTGTTTC 0.916134 -280 TGAAAATTTCTTTTTGCTACGCCGTGTTTT 1 155 1 TTTTTGCTAC 0.573742 -146 TGTTGGTTTGATACGTAACG 3 1 1 TGTTGGTTTG 0.604392 -56 TAACTGTTTGTTTTTGTTTCATTGTAATGC 5 41 1 TTTTTGTTTC 0.916134 -151 GTTTGCGCTGTTTTTGTTTG 7 1 0 TTTTTGTTTG 0.887453 -49 TTCTTTATTGTTATGGTTTGCGCTGTTTTT 7 16 0 TTATGGTTTG 0.858528 -34 TAATACGCCGTTATTGTTTCCAGGGAGATT 14 50 1 TTATTGTTTC 0.937649 -24 GCCAAAAATTTTATTGTTAGCTGAGTCAGG 16 273 1 TTATTGTTAG 0.79421 -28 TATATACGAATGATTGTTTCATACTCCAGG 18 258 0 TGATTGTTTC 0.839016 -43 GTTTTCGGGTTTATGGTTTCTAATGAAATA 22 42 1 TTATGGTTTC 0.893697 -38 AACCATGTACTTATTGCTTCT 23 2 0 TTATTGCTTC 0.839016 -233 TTTTATTGTTAGCTAATGCAAT 25 3 1 TTATTGTTAG 0.79421 -158 ********** Masking position 4 Map Score: 8.19224 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 125 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 TTAAAGGGCGTGATATCTGTAATTAACACCACCGAT 1 275 1 TTCTGTTTAC 0.944193 -26 GGTTATTCCTGTTTTTTGCAATGAGAGTC 3 38 0 TTCTGTTTTC 0.961195 -19 AATCGTTCTCTTTTGCCTGAACTTACCACCGAAACAG 19 180 0 TTCTGATTAC 0.961195 -121 ATGTTTACTCTGGTGCCTGACATTTCACCGACAAAGC 21 233 1 TTCTGATTTA 0.760092 -44 AGTTTTTTCATCTTCCCTGATTTTTCCTCACCATCAT 23 93 1 TTCTGATTTC 0.973164 -142 ATCATCAATGTAATTTCTGTATTTTGCCCACGGTAAC 24 102 1 TTCTGTTTTC 0.961195 -199 GTGATCACAATTTTGACTGTGGTTACCGTGGGCAAAA 24 123 0 TTCTGTTTAC 0.944193 -178 CCGTTAGGGGCGTTAGCTGAGTTTTTCGCGAAAAATT 24 232 1 CTCTGATTTC 0.939733 -69 TTACAGAGAGCGTTAGCTGAATTTTTCGCGAAAAACT 24 251 0 CTCTGATTTC 0.939733 -50 GCTAATGCAATAGTTACTGAACTGATCCGATGAGTTA 25 22 1 TTCTGATGAC 0.837812 -139 * * **** *** * Masking position 8 Map Score: 7.07722 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 42 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 ACGTAACGCCGCACTGACTCTCATTGCAAAAAACA 3 23 1 GCACATCCTT 0.795185 -34 CCTCACCTTCGCAAGAGGTCGCTTCACGCGATAAA 12 188 1 GCAAGTCCTC 0.949822 -113 CTTTACCCTGGCACAAGTCTTCTTTCGCCGCGCGC 15 155 1 GCACGCTCTT 0.93764 -143 AAGCAGTCTCGCAAACGTTTGCTTTCCCTGTTAGA 15 221 1 GCAAGTTCTT 0.984358 -77 CTTGCAACCGGAAACGGATTTCTTTTCAGGTTTGT 16 110 0 GAAAGTTCTT 0.860517 -191 AGGAATTTACGCAAACGATTACCTTCAGGCTACGC 16 166 0 GCAAGTTCTT 0.984358 -135 GGTCCCCAACGCAATCGTTCTCTTTTGCCTGAACT 19 194 0 GCAAGTCCTT 0.987808 -107 GCATTCCCCAGCAAAAGCCCGCTTTATACCTTTTT 24 48 1 GCAAGCCCTT 0.975371 -253 CGAGCGTTGCGCAAACGTTTTCGTTACAATGCGGG 24 180 1 GCAAGTTCTT 0.984358 -121 **** * ** * ** Masking position 3 Map Score: 6.73228 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 58 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GATGTTATTTTTTACTCACAACAGAGCATAA 1 90 0 TTTATCACAA 0.909 -211 ATATTGTTAAGTTCCTCACCAATATTGAAAA 1 181 0 GTTCTCACCA 0.939658 -120 GAAATAAAACTTTAATCACCAATATTGAAAA 1 240 0 TTTATCACCA 0.965761 -61 AATATAAAATTTTCCTCAACATCATCCTCGC 5 107 1 TTTCTCAACA 0.93292 -85 GTAAATTTAATTTGTTCAAAAGCTTCTAAAG 11 126 1 TTTGTCAAAA 0.717366 -175 TTTCGTTGACTTTAGTCAAAATGATAACGGT 15 60 1 TTTATCAAAA 0.721179 -238 AATAATCTTCTTTCATAACCATCTGAATATA 15 108 0 TTTCTAACCA 0.765572 -190 AGTGAAAAATTTGCATCACAAACCTGAAAAG 16 93 1 TTGCTCACAA 0.734849 -208 TTGCAAGCTCTTTATTCTCCAAAGCCTTGCG 16 138 1 TTTATCTCCA 0.735177 -163 TAATTCCGTAGTTCTTCACAACTCTATCCAC 18 108 1 GTTCTCACAA 0.846501 -193 GATAGCCGTTTTTATTCACCTTTTCTGTGGA 18 134 0 TTTATCACCT 0.735182 -167 TTCCCTGATTTTTCCTCACCATCATTGGTCA 23 105 1 TTTCTCACCA 0.981701 -130 CAGTCAAAATTGTGATCACCATTGAAAGAGA 24 141 1 TGTGTCACCA 0.801314 -160 CAACATGAGATTTGTTCAACATTAACTCATC 25 50 0 TTTGTCAACA 0.877559 -111 **** ****** Masking position 6 Map Score: 6.0656 Number of sites scoring better than the average of aligned sites = 749 Number in coding regions = 666 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 CCATCATGGACGAAAAATGAAGCTTTCAGT 12 143 1 CGAAAAATGA 0.974462 -158 AAATCTGAAACGAAACCTGACAGCGCGCCC 12 220 1 CGAAACCTGA 0.901155 -81 TTATTCCATCCGAAAACTAACCTTTACCCT 15 134 1 CGAAAACTAA 0.859408 -164 TACTTGCGGTAGAAAAATAAAATTCGGCGC 15 259 0 AGAAAAATAA 0.711192 -39 GACCTGTTATCGCACAATGATTCGGTTATA 16 208 1 CGCACAATGA 0.813355 -93 GGGCGTCAACCGAAAAATGACCAATGATGG 23 123 0 CGAAAAATGA 0.974462 -112 GAAAAATTGCAGAAAAATGACTGACTGCTG 24 19 1 AGAAAAATGA 0.882541 -282 ACAATGCGGGCGAAAAATAAGGATGCCCCG 24 205 1 CGAAAAATAA 0.925956 -96 GCGACCACCACGCAACATGAGATTTGTTCA 25 63 0 CGCAACATGA 0.901155 -98 ********** Masking position 4 Map Score: 4.7096 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 189 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 AGTCGACGACGGTTTACGCTTTACGTATAG 5 141 1 GGTTTACGCT 0.969294 -51 TTATTGTTATGGTTTGCGCTGTTTTTGTTT 7 12 0 GGTTTGCGCT 0.880604 -38 TGGTTGACGGTACGGTTTAGC 13 2 1 GGTTGACGGT 0.980592 -48 TGCAGAGAGTGGTTTACCGTCTTCCTGGAG 18 235 1 GGTTTACCGT 0.969294 -66 AAACTATGCGGGTTTACGGTCAGTACCCAC 21 63 0 GGTTTACGGT 0.983937 -214 AAACCCGCATAGTTTACCGTACAGGCGTTA 21 78 1 AGTTTACCGT 0.755781 -199 CATGTTTTCGGGTTTATGGTTTCTAATGAA 22 39 1 GGTTTATGGT 0.872453 -41 GTCATTTTTCGGTTGACGCCCTTCGGCTTT 23 132 1 GGTTGACGCC 0.858829 -103 ATTAAATCTGGGTTGAGCGTGTCGGGAGCA 25 138 1 GGTTGAGCGT 0.811657 -23 ********** Masking position 4 Map Score: 6.36174 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 234 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 AAGAGCTCCCTGTCAGCGGCAGG 2 38 0 AGCTCCCTGT 0.957758 -13 AGTCCACGCTCTCTCCCTGGACTCGCCGCA 5 68 0 CTCTCCCTGG 0.96818 -124 TAGAAATTATTATTCCCTGTATATTCATTC 10 33 0 TATTCCCTGT 0.787104 -65 TATTTTATATTATTCCCTGTTTTAATTAAC 10 61 1 TATTCCCTGT 0.787104 -37 AAATAATCTCCCTGGAAACAATAAC 14 59 0 ATCTCCCTGG 0.939345 -15 CAAACGTTTGCTTTCCCTGTTAGAATTGCG 15 232 1 CTTTCCCTGT 0.931285 -66 GACGGTAAACCACTCTCTGCAGGGCATTAC 18 226 0 CACTCTCTGC 0.762926 -75 GCATCGGAGCCACTCCCGGTCCCCAACGCA 19 216 0 CACTCCCGGT 0.874163 -85 CCTTATCTCCCTGCCATAAGCAGC 20 5 1 ATCTCCCTGC 0.91403 -125 GTGATGAAGTTCCCTGGGCTTTGTCGG 21 260 0 AGTTCCCTGG 0.872952 -17 ATTCAGCTAACGCTCTCTGTAATAGTCAAA 24 266 1 CGCTCTCTGT 0.872818 -35 ********** Masking position 4 Map Score: 5.72689 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 237 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 10 AGAAAAGAGAGAAATCTGAACAAT 4 5 0 GAAATCTGAA 0.760966 -103 ACAATGGTTGTAAATTTGGGTAACAAATAT 11 179 1 TAAATTTGGG 0.768 -122 GATGGCGTTGTAAATCTGGAACTGATTTAT 12 118 0 TAAATCTGGA 0.974309 -183 CTTCACGCGATAAATCTGAAACGAAACCTG 12 209 1 TAAATCTGAA 0.911863 -92 TGGACGTCAATACATCTGGACATCTAAACT 21 195 0 TACATCTGGA 0.962245 -82 CCTTCATCTTTACATCTGGACGTCTAAACG 23 163 1 TACATCTGGA 0.962245 -72 GAATTTTTATTAAATCTGGGTTGAGCGTGT 25 130 1 TAAATCTGGG 0.962294 -31 ********** Masking position 4 Map Score: 2.8778 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 27 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 CTGCATTTTGGCCCTGCCGCTGACAGGGAGCT 2 26 1 GCCCTGCCTG 0.982014 -25 TAAATCATTGCCCCCACCAATGTGACTGATAA 6 53 1 CCCCCACATG 0.843548 -61 CAGCGACGGTGCGCCTCACCTTCGCAAGAGGT 12 175 1 GCGCCTCCTT 0.88594 -126 CTGACAGCGCGCCCCGCTTCTGACAAAATAGG 12 236 1 GCCCCGCCTG 0.994033 -65 GTCTTCTTTCGCCGCGCGCCTGGGGAAAAGAC 15 171 1 GCCGCGCCTG 0.960325 -127 CGGCTATCCACCCCTTCCTCTGTTTATAACTC 18 157 1 CCCCTTCCTG 0.946636 -144 AAAGTTGTCAGCCCCGCTTATTCAATGAGGAC 19 276 1 GCCCCGCATT 0.965265 -25 CTAGACAAATCCCCCTCTGATTGACAGCATCA 20 60 0 CCCCCTCATT 0.900288 -70 TTCGGTTGACGCCCTTCGGCTTTTCCTTCATC 23 139 1 GCCCTTCCTT 0.946004 -96 ******* *** Masking position 11 Map Score: 4.48057 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 380 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 GGATCACCAATATTGAAAGTCAGATGTTAT 1 113 0 TATTGAAAGT 0.946863 -188 CATAAAACAATATTGAAAATTTCTTTTTGC 1 142 1 TATTGAAAAT 0.942879 -159 TCCTCACCAATATTGAAAACACGGCGTAGC 1 170 0 TATTGAAAAC 0.881462 -131 AACTTAACAATATTGAAAGTTGGATTTATC 1 199 1 TATTGAAAGT 0.946863 -102 TAATCACCAATATTGAAAATGTCACACGCA 1 229 0 TATTGAAAAT 0.942879 -72 ********** Masking position 6 Map Score: 1.69271 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 29 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 13 ACCCTAACCAATTGCACTTGTGAACTTATTTTTAC 11 76 1 ATGCACTGTC 0.940407 -225 ACACAACCTTTTTGCACGTCTTTTCCCCAGGCGCG 15 185 0 TTGCACTCTC 0.986217 -113 TGATGCAAATTTTTCACTTCATCACATTCTTTCTG 16 76 0 TTTCACTCAC 0.745232 -225 GACATCGTGTAATGCACCTGTCGGCGTGATAATGC 21 112 1 ATGCACTGTC 0.940407 -165 CGTCAATACATCTGGACATCTAAACTTCTTTGCGT 21 186 0 TTGGACTCTC 0.977768 -91 ACATTGTGTTAATGGACGTCAATACATCTGGACAT 21 202 0 ATGGACTCAC 0.909389 -75 CATCTTTACATCTGGACGTCTAAACGGATAGATGT 23 167 1 TTGGACTCTC 0.977768 -68 TATGTTGTGTTGTGCACATCTATCCGTTTAGACGT 23 182 0 TTGCACTCTC 0.986217 -53 * ***** *** * Masking position 6 Map Score: 2.97063 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 32 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 GGCGTAGCAAAAAGAAATTTTCAATATTGT 1 148 0 AAAGAAATTT 0.870248 -153 TAGTCTGACTAATGGAATTTTATTAAAGGA 11 276 1 AATGGAATTT 0.636157 -25 GAATTTTATTAAAGGATTTTT 11 290 1 AAAGGATTTT 0.878101 -11 GACAATATAAAAAGAATTTTCAGCCTGGTA 12 50 0 AAAGAATTTT 0.897256 -251 AAGTCAACGAAAAGAATATTGCCGCCTTGA 15 42 0 AAAGAATATT 0.820845 -256 GATGGTTATGAAAGAAGATTATTCCATCCG 15 116 1 AAAGAAGATT 0.7916 -182 AGGTCTTGACAAAGGAATTTACGCAAACGA 16 183 0 AAAGGAATTT 0.846915 -118 ATTGACTGATAATGAATATTTTAAAATGTC 18 38 1 AATGAATATT 0.591486 -263 ATCTATACGCAAAGAAGTTTAGATGTCCAG 21 180 1 AAAGAAGTTT 0.878643 -97 ********** Masking position 6 Map Score: 2.11642 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 71 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 15 ATCAGTTTGTTATGCTCTGTTGTGAGTAAAAA 1 81 1 TATGTCTGTG 0.962282 -220 AGGAAAATTTTATATTCTGCTGGCGAGTCCAC 5 91 0 TATATCTGTG 0.928496 -101 CTGATAAATTGATGTTGTGCTGTCTGGCATTT 6 84 0 GATGTGTGTG 0.954635 -30 AAAGTTATTTTATATTCAGATGGTTATGAAAG 15 98 1 TATATCAGTG 0.671811 -200 TCTATACAAAGATGATGTGATGAGAAAGTCAA 19 52 0 GATGTGTGTG 0.954635 -249 TTAACCATAAGCTAATGTGATGATCAATTTTA 19 132 1 GCTATGTGTG 0.739912 -169 TAACACAATGTTTACTCTGGTGCCTGACATTT 21 226 1 TTTATCTGTG 0.699434 -51 CTTGTAGTTATATGTTGTGTTGTGCACATCTA 23 195 0 TATGTGTGTG 0.962282 -40 TTTATGCCAGTATGGTTTGTTGAATTTTTATT 25 109 1 TATGTTTGTG 0.830185 -52 **** **** ** Masking position 6 Map Score: 1.68975 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 99 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234