AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02030_ecoli_reg_100.orf -o02030_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/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 trg 300 methyl-accepting chemotaxis protein III, ribose sensor receptor #2 tap 45 methyl-accepting chemotaxis protein IV, peptide sensor receptor #3 tar 144 methyl-accepting chemotaxis protein II, aspartate sensor receptor #4 motA 126 proton conductor component of motor; no effect on switching #5 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #6 fliL 104 flagellar biosynthesis #7 mglB 279 galactose-binding transport protein; receptor for galactose taxis #8 aer 300 aerotaxis sensor receptor, flavoprotein #9 dppA 300 dipeptide transport protein #10 rbsD 300 D-ribose high-affinity transport system; membrane-associated protein #11 rbsB 24 D-ribose periplasmic binding protein #12 malE 300 periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis #13 tsr 300 methyl-accepting chemotaxis protein I, serine sensor receptor Motif number 1 TCCCCATCAGGCGGCAATGACCGCGTTAGTAAATA 2 15 0 GCGGAAGCCG 0.983801 -31 GATCTCGTTATCGGCAAGGAGGGGGGAAACTTTAT 3 96 0 TCGGAAGGGG 0.979695 -49 CTGATACGGTGAGGCGCAACATTCCAGCAG 4 6 1 ACGGGAGGCC 0.659822 -121 CATTCCAGCAGCGGTAACGACGTACCGCTGCTTTT 4 30 1 GCGGAAGCGC 0.988591 -97 TAAGACAAAGGCGCTAAATAGCAACAAAAAAACGG 5 59 1 GCGCAATGCC 0.598905 -156 GACGGCGTTATTGGCAAAGTGGAACAAGACTCACT 5 167 0 TTGGAAGGGC 0.841607 -48 GCAACAAAGCGGGGAAAAGACGCGGATTACGGTGC 6 22 0 GGGGAAGCGG 0.975999 -83 CCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGC 6 45 1 GCGCCAGCGG 0.886094 -60 TGTGTTTAAATCGCAAATTGCGATCTAAATCAAAT 8 192 1 TCGCAATCGC 0.598977 -109 ACGTTATGAGGTGGGGATGCCGTACTAATTAACAT 9 185 0 GTGGGAGCGC 0.921602 -116 TCGTTGATCCTCGCAAACGCCCGTGGTATTTGCGT 10 35 1 TCGCAAGCCG 0.879842 -266 GGCTTTTTTATGGGGGAGGAGGCGGGAGGATGAGA 12 42 1 TGGGGAGGGG 0.911488 -259 TACAGAATTGGCGGTAATGTGGAGATGCGCACATA 12 151 0 GCGGAAGGGA 0.909227 -150 GTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGGTT 12 208 1 GGGGAAGGGG 0.973148 -93 ATGGTCCTTGTTGGTGAAGTGCTCGTGAAAACACC 12 271 0 TTGGGAGGCG 0.736035 -30 TTGCGGTTGAGCGGCAAAGGCGTCGTTTAAGTGAC 13 103 1 GCGGAAGCGG 0.993038 -198 TGAATATCCCGCGGAGATTACGCCGAGTGAATTTT 13 219 0 GCGGGATCGG 0.93853 -82 **** ** * ** * Masking position 7 Map Score: 17.494 Number of sites scoring better than the average of aligned sites = 2960 Number in coding regions = 2865 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 TCCCGGTTAGCCTGAAAACAGAAAGTCTCA 1 22 1 CCTGAAAACA 0.974279 -279 AAGGCACCTTCCTGAAAACAAGTTGATCTC 3 125 0 CCTGAAAACA 0.974279 -20 CGGGTTACAACGTTAAAACGGTGCAATCAT 7 61 0 CGTTAAAACG 0.76405 -219 TCACTTTTGCCGAGGTAACAGCGTCATAAC 7 108 1 CGAGGTAACA 0.576141 -172 GAGGTAACAGCGTCATAACAACAATTAAAG 7 119 1 CGTCATAACA 0.756908 -161 CGGTAACGCTCCAGAAAACGGCTTTAATTG 7 140 0 CCAGAAAACG 0.942485 -140 TTCTTCCATGCCCGGTAACGCTCCAGAAAA 7 152 0 CCCGGTAACG 0.79244 -128 CAATTATTGCCCTGAAAACGTGCATTTGCG 8 86 0 CCTGAAAACG 0.987593 -215 GTCAACAGAATGTGAAAACGTCAATACAGC 9 104 0 TGTGAAAACG 0.755411 -197 GGCATCCCCACCTCATAACGTTGACCCGAC 9 199 1 CCTCATAACG 0.910076 -102 GGTGATTAACCATGAAAACAAAAACGCCCC 10 207 0 CATGAAAACA 0.787878 -94 ATGTGATCAACCTCGAAACGTTTTACATGG 10 235 0 CCTCGAAACG 0.943351 -66 GTGAAGTGCTCGTGAAAACACCTAAACGGA 12 263 0 CGTGAAAACA 0.959951 -38 AGATTTTCGGCCTGGAAAGGAAAAACTTTA 13 254 0 CCTGGAAAGG 0.827571 -47 ********** Masking position 7 Map Score: 13.0628 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 884 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 TCTCAGGCACCCGCAGGCATCCTATGAGGTTTCCT 1 47 1 CCGCAGGCTT 0.835388 -254 CCGTCAAGTGCCGATGACTTTCTATCAGGAGTAAA 1 255 1 CCGATGACTT 0.858191 -46 AATAAAAAACCCGATGCGCAGATCATCGGGTTCAT 3 34 0 CCGATGCATA 0.889458 -111 CTGATGCCACCCGCCGCGAAATTGAAATAAAAAAC 3 59 0 CCGCCGCTTA 0.942925 -86 TACGTCGTTACCGCTGCTGGAATGTTGCGCCTCAC 4 19 0 CCGCTGCATT 0.984046 -108 TAACGACGTACCGCTGCTTTTTTTTGCCCCAATCG 4 44 1 CCGCTGCTTT 0.991567 -83 TTACTGAACGCCGAAGCTCACTTTTTAAAATTCGT 7 181 0 CCGAAGCTTT 0.970086 -99 CTCTACTGCCCCGCCGAGCATTTATCTCAAGCACT 7 227 1 CCGCCGATTT 0.920066 -53 TATGTCGGCCCCGCTGCGGTTATCTTTAACCGATT 8 228 0 CCGCTGCATT 0.984046 -73 GTTTAGTTCACAGAAGCCGTGTTCTCATCCTCCCG 12 64 0 CAGAAGCTTT 0.718723 -237 TTCCTGTGGACCGATGCAAGATTTTCGGCCTGGAA 13 267 0 CCGATGCTTT 0.984082 -34 ******* ** * Masking position 13 Map Score: 7.70176 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 535 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 GTCATTGCCGCCTGATGGGGAGCGTTG 2 29 1 CCTGAGGGGA 0.824267 -17 AAATAAAAAACCCGATGCGCAGATCATCGGG 3 39 0 CCCGAGCGCA 0.990861 -106 GCTGATGCCACCCGCCGCGAAATTGAAATAA 3 64 0 CCCGCGCGAA 0.970621 -81 GCGCAACATTCCAGCAGCGGTAACGACGTAC 4 24 1 CCAGCGCGGT 0.920237 -103 ACTCTACTGCCCCGCCGAGCATTTATCTCAA 7 226 1 CCCGCGAGCA 0.988772 -54 TTATGTCGGCCCCGCTGCGGTTATCTTTAAC 8 233 0 CCCGCGCGGT 0.855272 -68 GATTGTAGGTCACGAGGGGCATTTTATGGAG 9 135 1 CACGAGGGCA 0.884142 -166 GCAAGTACAGCTTGCCGCGCAGACGCAAATA 10 61 0 CTTGCGCGCA 0.895104 -240 TGATCTGGTGCACGCAGCGCATTACGTTGCA 10 95 0 CACGCGCGCA 0.986795 -206 TTATGAATATCCCGCGGAGATTACGCCGAGT 13 226 0 CCCGCGAGAT 0.916086 -75 ***** ***** Masking position 1 Map Score: 10.7502 Number of sites scoring better than the average of aligned sites = 921 Number in coding regions = 877 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 TGATTATTTTCGTCCCTAAGGAAACCTCATAGGATG 1 64 0 CCCTAAGACC 0.95842 -237 CGGGTGGCATCAGCAATAAAGTTTCCCCCCTCCTTG 3 81 1 CCATAAATCC 0.957148 -64 GTAGGCTTTGCTACCAGAAATTATCCGGGAGACGAG 5 12 0 CCCGAAATCC 0.981477 -203 CAGTGCGGATCCTCCATAAAATGCCCCTCGTGACCT 9 141 0 CCCTAAATCC 0.994226 -160 CCCGCCTCCTCCCCCATAAAAAAGCCAGGGGGTGGA 12 32 0 CCCTAAAACC 0.986827 -269 TGTGGAGATGCGCACATAAAATCGCCACGATTTTTG 12 133 0 CACTAAATCC 0.957148 -168 TGACCGCTTACATCCCTAAAATAACCACTCAGTTAT 13 64 0 CCCTAAATCC 0.994226 -237 * ** **** * ** Masking position 8 Map Score: 5.9741 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 = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 CTTTCTGATTCCCGGTTAGCCTGAAAACAG 1 13 1 CCCGGTTAGC 0.991837 -288 TTTTCGTCATTCGGGTTAGCCAGTTTAGCC 1 131 1 TCGGGTTAGC 0.945502 -170 AGACTCACTCCCGGGTCAGCAAACTCGAAA 5 146 0 CCGGGTCAGC 0.977141 -69 TGGTGTAAATCCCGGTTGGCTGTATTGACG 9 86 1 CCCGGTTGGC 0.993178 -215 TTGTTTTTTGCCCGGTCGGGTCAACGTTAT 9 213 0 CCCGGTCGGG 0.920667 -88 GTTCGATAACCCTGTTTGGCGGGATTTCAA 10 128 0 CCTGTTTGGC 0.884762 -173 GAAACTAGAGTCCGTTTAGGTGTTTTCACG 12 253 1 TCCGTTTAGG 0.792549 -48 ********** Masking position 6 Map Score: 4.60477 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 405 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 TTACTGGTAGGCTTTGCTACCAGAAATTAT 5 24 0 GCTTTGCTAC 0.800781 -191 TCTTTTCCCCGCTTTGTTGCGCTCAAGACG 6 37 1 GCTTTGTTGC 0.871513 -68 AAGTGATTATTCACTGTTACATACGGGTTA 7 84 0 TCACTGTTAC 0.955667 -196 CAGTGAATAATCACTTTTGCCGAGGTAACA 7 98 1 TCACTTTTGC 0.635455 -182 TGTTGTTATGACGCTGTTACCTCGGCAAAA 7 112 0 ACGCTGTTAC 0.871418 -168 AAATACTTTCACTCTGTTACTATACGAAAA 8 143 0 ACTCTGTTAC 0.948809 -158 AGCACAAATTTCTCTGCTGCAAATAGCTGT 9 17 1 TCTCTGCTGC 0.933079 -284 TGGAGGATCCGCACTGTTACACTGATGTTA 9 161 1 GCACTGTTAC 0.963006 -140 CTTTGTGTGATCTCTGTTACAGAATTGGCG 12 173 0 TCTCTGTTAC 0.971896 -128 ********** Masking position 5 Map Score: 5.19489 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 330 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 TTTTCCAGAATTTTTCGTCATTCGGGTTAG 1 120 1 TTTTTCGTCA 0.887511 -181 CGCAAAGAGGTTTTTGGTCATAAGTAATTA 1 225 1 TTTTTGGTCA 0.85728 -76 CTGATAGAAAGTCATCGGCACTTGACGGTA 1 253 0 GTCATCGGCA 0.926636 -48 AGTTGATCTCGTTATCGGCAAGGAGGGGGG 3 105 0 GTTATCGGCA 0.967078 -40 TGAACATCCTGTCATGGTCAACAGTGGAAG 4 98 1 GTCATGGTCA 0.857754 -29 AAAAAACGGGTTTATTGGCGGATAGAAAAA 5 85 1 TTTATTGGCG 0.79317 -130 TATGGACGGCGTTATTGGCAAAGTGGAACA 5 176 0 GTTATTGGCA 0.934309 -39 ATTTTGCACGGTTTTTGTCGGGTATGGATT 8 44 1 GTTTTTGTCG 0.723711 -257 AATTGCCTGATTTTTGGGCAAGATAATTAA 8 111 1 TTTTTGGGCA 0.905473 -190 GAATCACATATTTATCGTCACTTAAACGAC 13 124 0 TTTATCGTCA 0.920324 -177 ********** Masking position 5 Map Score: 4.779 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 540 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 TTGCCGCCTGATGGGGAGCGTTG 2 33 1 AGGGGACGTG 0.944614 -13 CAAAAAAAAGCAGCGGTACGTCGTTACCGCTGC 4 37 0 CGCGGTCGTG 0.881282 -90 TCATGGTCAACAGTGGAAGGATGATGTC 4 109 1 CGTGGAGGAG 0.985353 -18 TGGAGCGTTACCGGGCATGGAAGAACGAATTTT 7 157 1 CGGGCAGGAG 0.939411 -123 TAACCCTTTGCAGTGGGTTGTCGCTGCCTGACC 9 247 0 CGTGGGTGTG 0.943172 -54 ATAAAAAAGCCAGGGGGTGGAGGATTTAAGCCA 12 20 0 CGGGGGGGAG 0.994126 -281 TGGCTTTTTTATGGGGGAGGAGGCGGGAGGATG 12 41 1 AGGGGGGGAG 0.97087 -260 CACAAAGCGACGGTGGGGCGTAGGGGCAAGGAG 12 196 1 CGTGGGCGTG 0.988578 -105 TTTCTCTTTCCTGTGGACCGATGCAAGATTTTC 13 276 0 CGTGGACGAG 0.985127 -25 * ***** *** * Masking position 5 Map Score: 6.63873 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 370 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 ATAATTGTTGTAAAAATGTGACGCAAAGAGG 1 204 1 TAAAATGTGA 0.950575 -97 CCGCTTTCAATCTGTGAGTGATTTCAC 7 7 1 TCAATTGTGA 0.885761 -273 CACAGTATCTTAACAATGTGATAGCTATGAT 7 35 1 TAACATGTGA 0.729601 -245 TTTCGTATAGTAACAGAGTGAAAGTATTTTA 8 144 1 TAACAAGTGA 0.609372 -157 CAATCTGTCAACAGAATGTGAAAACGTCAAT 9 109 0 ACAGATGTGA 0.749865 -192 TATTCTGCTCCAATTGTGATGTTTGTTGT 9 282 0 TCCAATGTGA 0.862885 -19 TAAGTGACGATAAATATGTGATTCATATCAC 13 130 1 TAAATTGTGA 0.922803 -171 ATTCACAATATAAATATGTGATATGAATCAC 13 147 0 TAAATTGTGA 0.922803 -154 CTTTTTAAATTCAGAGTGTGAATAAAATTCA 13 196 1 TCAGATGTGA 0.738859 -105 ***** ***** Masking position 9 Map Score: 3.65499 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 51 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 11 ACCCGATGATCTGCGCATCGGGTTTTTTAT 3 38 1 CTGCGCATCG 0.90226 -107 TTTATTTCAATTTCGCGGCGGGTGGCATCA 3 63 1 TTTCGCGGCG 0.941432 -82 TGCTGGAATGTTGCGCCTCACCGTATCAG 4 10 0 TTGCGCCTCA 0.855082 -117 CTTGAGATAAATGCTCGGCGGGGCAGTAGA 7 228 0 ATGCTCGGCG 0.896082 -52 AAACGTGCATTTGCGCAGCAATCATCAAAT 8 71 0 TTGCGCAGCA 0.968445 -230 GTATTTGCGTCTGCGCGGCAAGCTGTACTT 10 60 1 CTGCGCGGCA 0.986795 -241 CTGCAACGTAATGCGCTGCGTGCACCAGAT 10 94 1 ATGCGCTGCG 0.936696 -207 AGTTTTGCGGTTGAGCGGCAAAGGCGTCGT 13 99 1 TTGAGCGGCA 0.910249 -202 ********** Masking position 2 Map Score: 3.46166 Number of sites scoring better than the average of aligned sites = 1487 Number in coding regions = 1425 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 12 TTACCGTCAAGTGCCGATGACTTTCTATCA 1 252 1 GTGCCGATGA 0.645267 -49 GGAAACTTTATTGCTGATGCCACCCGCCGC 3 77 0 TTGCTGATGC 0.747531 -68 CGGTACGTCGTTACCGCTGCTGGAATGTTG 4 27 0 TTACCGCTGC 0.917381 -100 CGGTAACGACGTACCGCTGCTTTTTTTTGC 4 41 1 GTACCGCTGC 0.953007 -86 ACTCGAAAAATTGACGCTCCCATTATTTGT 5 124 0 TTGACGCTCC 0.93134 -91 CGGTCTTCCTGTGTCGCTACTGCTTATCGG 6 79 0 GTGTCGCTAC 0.839028 -26 TCCATGCCCGGTAACGCTCCAGAAAACGGC 7 148 0 GTAACGCTCC 0.804565 -132 AGAGAAATTTGTGCTACTCCA 9 2 0 GTGCTACTCC 0.548156 -299 TTGCAGTGGGTTGTCGCTGCCTGACCTTTT 9 243 0 TTGTCGCTGC 0.92022 -58 CAAGCTGTACTTGCTGCTGCAACGTAATGC 10 78 1 TTGCTGCTGC 0.955178 -223 GAAAACCATCGTGACGTTACGGAAATGTGA 10 259 0 GTGACGTTAC 0.699464 -42 AAGGAATTTCGTGATGTTGCTTGCAAAAAT 12 110 1 GTGATGTTGC 0.755007 -191 TCCATCCTCCTTGCCCCTACGCCCCACCGT 12 205 0 TTGCCCCTAC 0.598577 -96 CTATCCTGTAGTGATGTTGCCAGAGTTACG 13 15 1 GTGATGTTGC 0.755007 -286 AACGACGCCTTTGCCGCTCAACCGCAAAAC 13 100 0 TTGCCGCTCA 0.785597 -201 ********** Masking position 8 Map Score: 10.2405 Number of sites scoring better than the average of aligned sites = 3764 Number in coding regions = 3611 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 13 GAGTAAACCTGGACGAGAGACAACGGTA 1 283 1 GGACGAGAGA 0.888075 -18 TCAATTTCGCGGCGGGTGGCATCAGCAATA 3 69 1 GGCGGGTGGC 0.902202 -76 TTATCGGCAAGGAGGGGGGAAACTTTATTG 3 94 0 GGAGGGGGGA 0.98925 -51 AAATTATCCGGGAGACGAGA 5 1 0 GGAGACGAGA 0.852489 -214 CGGGTTTATTGGCGGATAGAAAAAAACGAA 5 91 1 GGCGGATAGA 0.930782 -124 TTATGGGGGAGGAGGCGGGAGGATGAGAAC 12 49 1 GGAGGCGGGA 0.98925 -252 GTAGGGGCAAGGAGGATGGAAAGAGGTTGC 12 215 1 GGAGGATGGA 0.976344 -86 ********** Masking position 2 Map Score: 2.48237 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 249 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 CATTCCAATAGCATTAATTTTCTATGCAAT 1 176 1 GCATTAATTT 0.820638 -125 AATTTTCTATGCAATAATTGTTGTAAAAAT 1 191 1 GCAATAATTG 0.971609 -110 CAATGTGATAGCTATGATTGCACCGTTTTA 7 48 1 GCTATGATTG 0.914973 -232 CCAGAAAACGGCTTTAATTGTTGTTATGAC 7 130 0 GCTTTAATTG 0.943405 -150 CGTTTTCAGGGCAATAATTGCCTGATTTTT 8 96 1 GCAATAATTG 0.971609 -205 ********** Masking position 5 Map Score: 0.313226 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 52 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 ********** No masking Map Score: 6.78101e-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