AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i151_Transhydrogenase_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pntA 300 pyridine nucleotide transhydrogenase, alpha subunit #2 HI1354 300 glutaminyl-tRNA synthetase (glnS) #3 HI1355 65 conserved hypothetical protein #4 HI1356 61 4-alpha-glucanotransferase (malQ) #5 HI1358 95 glycogen operon protein (glgX) #6 HI1360 107 glycogen synthase (glgA) #7 HI1361 245 glycogen phosphorylase (glgP) #8 HI1362 261 NAD(P) transhydrogenase, subunit alpha (pntA) Motif number 1 TCACGGCGATACCGCTTTTTAATGTGATGT 2 28 0 ACCGCTTTTT 0.97272 -273 CAAAAAACTTACCGCACTTTGTGCATTTAT 2 124 1 ACCGCACTTT 0.998854 -177 GTTTGTTTTGACCGCACTTGGTTGATTAAA 3 12 0 ACCGCACTTG 0.995702 -54 CGTGATTTTGACCGCACTTTTTATTTGTAT 3 41 1 ACCGCACTTT 0.998854 -25 GTTAATTTTGACCGCACTTTTCCTAA 6 7 0 ACCGCACTTT 0.998854 -101 GTCAAAATTAACCGCACTTTCTGAACCTCC 6 25 1 ACCGCACTTT 0.998854 -83 TCAAAATTTGACCGCTCTTTGAGTACGTGA 7 141 0 ACCGCTCTTT 0.996877 -105 TCAAAAATTTACCGCACTTTCCATAAAAAA 8 52 0 ACCGCACTTT 0.998854 -210 ********** Masking position 1 Map Score: 32.4542 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 TATAAATGCACAAAGTGCGGTAAGTTTTTT 2 125 0 CAAAGTGCGG 0.998109 -176 TTTTAATCAACCAAGTGCGGTCAAAACAAA 3 11 1 CCAAGTGCGG 0.991957 -55 GATACAAATAAAAAGTGCGGTCAAAATCAC 3 42 0 AAAAGTGCGG 0.994425 -24 TAGCTAAGCTGAAAGTGATGACAACTGGCT 4 11 0 GAAAGTGATG 0.885814 -51 TTAGGAAAAGTGCGGTCAAAATTAA 6 6 1 AAAAGTGCGG 0.994425 -102 AGGAGGTTCAGAAAGTGCGGTTAATTTTGA 6 26 0 GAAAGTGCGG 0.997518 -82 TCCTCTTTAGCAAAGAGAGGAGTTGATCGA 6 52 1 CAAAGAGAGG 0.970454 -56 TTCACGTACTCAAAGAGCGGTCAAATTTTG 7 140 1 CAAAGAGCGG 0.99404 -106 TTTTTTTATGGAAAGTGCGGTAAATTTTTG 8 51 1 GAAAGTGCGG 0.997518 -211 ********** Masking position 4 Map Score: 26.3735 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 49 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 GATATTCCCTTCCATCGGTTTTATTGATGATG 1 279 0 TTCACGTTTT 0.884464 -22 TGATAGGAAATTTTGCTGTTTTTGCCTGCATTC 2 56 0 TTTGTGTTTT 0.977054 -245 CACGATAATTTCGTGGCGGTTTTTTATGGCAAG 2 161 1 TCGGCGTTTT 0.922832 -140 ATTTTTATCGATTTTGTAGGCAAAT 5 81 0 TTTACGTTTT 0.954414 -15 AGCGGTGTGATTGGGCTTGTTTTTTGCAAAGAT 7 64 1 TTGGTTTTTT 0.842526 -182 TCAATCAAAATTTGACCGCTCTTTGAGTACGTG 7 142 0 TTTACGTCTT 0.797684 -104 GCGGTCAAATTTTGATTGATTTTTGCAAACGTG 7 156 1 TTTATGTTTT 0.957241 -90 AGTAAAAAACTTGTGGTGCTTTTAATTTTATTA 8 11 0 TTGGTGTTTT 0.985487 -251 AGTTTTTTACTTGCGGTGTTTTTTTATGGAAAG 8 33 1 TTGGTGTTTT 0.985487 -229 CGGTAAATTTTTGAGATGTTTTTTATGTGGGAT 8 68 1 TTGGTGTTTT 0.985487 -194 AGGTAACGTTTTTAAGTGGTTTTACAAGATATT 8 120 0 TTTATGTTTT 0.957241 -142 *** * ** **** Masking position 10 Map Score: 14.1088 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 203 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 AGTAACAAACGCCCTATAACGTACTGAAAA 1 180 0 GCCCTATAAC 0.964039 -121 ACAGCAAAATTTCCTATCAAATGGGAGCTG 2 70 1 TTCCTATCAA 0.786919 -231 AAGCTAAACATTCAAAAAACTTACCGCACT 2 112 1 TTCAAAAAAC 0.507866 -189 GTAAAAACTTGCCATAAAAAACCGCCACGA 2 171 0 GCCATAAAAA 0.925669 -130 TCCTGTTCTTGCCATAGAAATACTAGATTT 2 213 0 GCCATAGAAA 0.792997 -88 ACCAAGTGCGGTCAAAACAAACGTGATTTT 3 20 1 GTCAAAACAA 0.622885 -46 TTAGCTATAATCCCTAACAAGAGTTATACA 4 34 1 TCCCTAACAA 0.952182 -28 AATTACATTTGCCCAAAAACATCGGTGGTT 5 54 0 GCCCAAAAAC 0.942955 -42 TTTTTTATTTTCCCTATAAATATAAATAAT 6 84 0 TCCCTATAAA 0.935332 -24 CAAAAAACAAGCCCAATCACACCGCTTGCA 7 60 0 GCCCAATCAC 0.941567 -186 TACCGCACTTTCCATAAAAAAACACCGCAA 8 43 0 TCCATAAAAA 0.886115 -219 TTTTTCGTGATCCCTATCACAATATCTTGT 8 100 1 TCCCTATCAC 0.950994 -162 ********** Masking position 6 Map Score: 8.98078 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 433 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 TTTTGGCGCTAGATCACAGGCATAATTTTCAGTAC 1 155 1 AGATCCATAA 0.817571 -146 TCCCTCCACTACATCACATTAAAAAGCGGTATCGC 2 18 1 ACATCCAAAA 0.98409 -283 GTGCATTTATACATCGCCACGATAATTTCGTGGCG 2 144 1 ACATCCATAA 0.951328 -157 TATTCTATACAAATCTAAGGGAAAATAAAGGTTCA 2 245 0 AAATCAAAAA 0.733367 -56 AAGCCCAATCACACCGCTTGCAAAATATTCTTTCA 7 47 0 ACACCCAAAA 0.989964 -199 AATGTTGTTTACACAGCCTACAAAAGTAGTTCGAA 7 107 0 ACACACAAAA 0.896024 -139 AGGTAAAACCTCTATTAGAATGCTAAGAAA 7 226 0 AAACCCAGAA 0.930239 -20 CCATAAAAAAACACCGCAAGTAAAAAACTTGTGGT 8 27 0 ACACCCAAAA 0.989964 -235 GGATCACGAAAAATCCCACATAAAAAACATCTCAA 8 78 0 AAATCCAAAA 0.969214 -184 ATATCTTGTAAAACCACTTAAAAACGTTACCTATT 8 121 1 AAACCCAAAC 0.912816 -141 ***** * **** Masking position 12 Map Score: 8.3731 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 202 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 AACTCGCAAAATATTAACGATTCAGCCGTG 1 108 0 ATATTAACGA 0.955393 -193 TTACTAATTTATTTTAACGGAGTAACATTT 1 205 1 ATTTTAACGG 0.969464 -96 ATATTTTTTTATTTTAACGAGAGAAA 2 285 1 ATTTTAACGA 0.986002 -16 ATTTTTATCGATTTTGTAGGC 5 85 0 TTTTTATCGA 0.866859 -11 ACTTTTTGTCATTTTAACGATGAATAGACG 8 190 1 ATTTTAACGA 0.986002 -72 ********** Masking position 5 Map Score: 4.16919 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 7 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 CTTAACAATCCACCGCTTGTGAAAGAATAT 7 28 1 CACCGCTTGT 0.992111 -218 AGCCCAATCACACCGCTTGCAAAATATTCT 7 51 0 CACCGCTTGC 0.986626 -195 AAATTAAAAGCACCACAAGTTTTTTACTTG 8 16 1 CACCACAAGT 0.969377 -246 CATAAAAAAACACCGCAAGTAAAAAACTTG 8 31 0 CACCGCAAGT 0.992111 -231 ********** Masking position 2 Map Score: 2.65315 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 25 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 AAGTAGTGATTCGTGCCGGGGCGATGTCT 1 10 1 TTCGTGCCGG 0.979076 -291 TTATCCCACTATCACGGCTGAATCGTTAAT 1 96 1 ATCACGGCTG 0.879429 -205 ATTTTGCGAGTTCACGCCGAAATACTGATT 1 126 1 TTCACGCCGA 0.974837 -175 TTTGCCTGCATTCACGGCGATACCGCTTTT 2 39 0 TTCACGGCGA 0.98073 -262 CCACGAAATTATCGTGGCGATGTATAAATG 2 147 0 ATCGTGGCGA 0.956787 -154 CCACGATAATTTCGTGGCGGTTTTTTATGG 2 160 1 TTCGTGGCGG 0.98399 -141 GCGAATGTAATTCGCCCCTACAATTTATCT 5 18 0 TTCGCCCCTA 0.807581 -78 ********** Masking position 2 Map Score: 5.20747 Number of sites scoring better than the average of aligned sites = 1229 Number in coding regions = 1168 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 GTCAGGAGCCACACAAGCTGCTCATGTACGA 1 238 0 ACACAGCTGC 0.986442 -63 GTGGCTCCTGACACAGGCAAACCATCATCAA 1 257 1 ACACAGCAAA 0.900139 -44 AGCTTACCAAACCCAGCCAGCTCCCATTTGA 2 86 0 ACCCACCAGC 0.970863 -215 AATGTTGTTTACACAGCCTACAAAAGTAGTT 7 111 0 ACACACCTAC 0.989917 -135 TTGAAAATTCACACACCCTACGTTAATTATT 7 197 1 ACACACCTAC 0.989917 -49 ***** ***** Masking position 5 Map Score: 1.23125 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 52 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 CGTTTGTTACTAATTTATTTTAACGGAGTA 1 199 1 TAATTTATTT 0.751999 -102 GTTTTTACAATCTTTTATTTAAATCTAGTA 2 193 1 TCTTTTATTT 0.89548 -108 AGCCGAATATTTTTTTATTTTAACGAGAGA 2 279 1 TTTTTTATTT 0.969931 -22 TTTGACCGCACTTTTTATTTGTATCAACT 3 47 1 CTTTTTATTT 0.882856 -19 TGATCGAGCATTATTTATATTTATAGGGAA 6 75 1 TTATTTATAT 0.751999 -33 TGAGTTTTTTATTTTCCCTATAAA 6 94 0 TTTTTTATTT 0.969931 -14 ACACCCTACGTTAATTATTTCTTAGCATTC 7 209 1 TTAATTATTT 0.727327 -37 GCACCACAAGTTTTTTACTTGCGGTGTTTT 8 25 1 TTTTTTACTT 0.882857 -237 TTTTGAGATGTTTTTTATGTGGGATTTTTC 8 76 1 TTTTTTATGT 0.89548 -186 ********** Masking position 5 Map Score: 5.40197 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 79 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 GTCTTCGACGGTCGGGTAAAACGAGACATC 1 33 0 GTCGGGTAAA 0.985036 -268 ACCTTAGAACGCCGGATAAAGACTGATAAT 1 64 0 GCCGGATAAA 0.985036 -237 AGCCGTGATAGTGGGATAAACACCTTAGAA 1 85 0 GTGGGATAAA 0.976671 -216 AATTACATTCGCCTGATAAACCACCGATGT 5 36 1 GCCTGATAAA 0.943081 -60 TTTATGGAAAGTGCGGTAAATTTTTGAGAT 8 55 1 GTGCGGTAAA 0.944005 -207 ********** Masking position 7 Map Score: 1.86007 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 122 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 ATTTAGCTCGTACATGAGCAGCTTGTGTGG 1 231 1 TACATGAGCA 0.937316 -70 AGGGGCGAATTACATTCGCCTGATAAACCA 5 29 1 TACATTCGCC 0.983191 -67 GTAGGCAAATTACATTTGCCCAAAAACATC 5 61 0 TACATTTGCC 0.985768 -35 CAATTAATGATACATTTGCATCCGTTTGAC 8 162 1 TACATTTGCA 0.977297 -100 ********** Masking position 5 Map Score: 0.579276 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 GGTTTTATTGATGATGGTTTGCCTGTGTCAGG 1 263 0 AGATGTTTGC 0.961431 -38 CCCATTTGATAGGAAATTTTGCTGTTTTTGCC 2 63 0 AGAATTTTGC 0.939858 -238 GTGCGGTCAAAATCACGTTTGTTTTGACCGCA 3 26 0 ATCAGTTTGT 0.814002 -40 GTGGATTGTTAAGAAAGTTTACGAATAAAA 7 9 0 AGAAGTTTAC 0.939858 -237 TTCAAAATTTACGCACGTTTGCAAAAATCAAT 7 170 0 AGCAGTTTGC 0.988057 -76 CGATGAATAGACGAAGGTTTGTTCATTAATCT 8 207 1 AGAAGTTTGT 0.969371 -55 * *** ****** Masking position 8 Map Score: 0.432726 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 238 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 14 ********** No masking Map Score: 1.70773e-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: 1.70773e-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