AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icoldbox_ecoli_opreg_300.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 cspB 300 cold shock protein; may affect transcription #2 deaD 128 inducible ATP-independent RNA helicase #3 yhbM 108 putative control proteins #4 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #5 rpsO 148 30S ribosomal subunit protein S15 #6 rbfA 163 ribosome-binding factor A #7 infB 24 protein chain initiation factor IF-2 #8 nusA 27 transcription pausing; L factor #9 yhbC 300 orf, hypothetical protein #10 yiaG 300 orf, hypothetical protein #11 cspA 280 cold shock protein 7.4, transcriptional activator of hns Motif number 1 GGGCCACTCAGGCCCCCTTTTCTGAAACTCG 4 17 0 GGCCCCTTTT 0.995639 -161 GGGCCTGAGTGGCCCCTTTTTTCAAGCTGAC 4 33 1 GGCCCCTTTT 0.995639 -145 AGGGGCTGTTAGCCCCTTTTTAAAATTAATT 6 122 0 AGCCCCTTTT 0.995725 -42 AGGGGCTAACAGCCCCTTTTTTGTCAGGAGA 6 136 1 AGCCCCTTTT 0.995725 -28 GTGGTTGCGGGGGCCGGATTTGAACCGACGA 9 81 0 GGGCCGATTT 0.894759 -220 AGTTATATAAAGCCCCGATTTATCGGGGTTT 9 224 1 AGCCCCATTT 0.988408 -77 ACTGGGCTTTAGGCCCTTTTTTTATGTCTTG 9 277 1 AGGCCCTTTT 0.993063 -24 TCCTGATGACAGGACCGTTTTCCAACCGATT 11 40 1 AGGACCTTTT 0.941125 -241 ****** **** Masking position 9 Map Score: 16.4615 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 22 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 CCGCAGCGGAGGGCAAATGGCAACC 3 4 0 GGGCATGGCA 0.91135 -105 CTGCGGCGGGGGGCTTTTAACCGGGCAGGACG 3 30 1 GGGCTTAACC 0.990961 -79 GCTTTTAACCGGGCAGGACGCCTTGTTAGCAA 3 42 1 GGGCAACGCC 0.983503 -67 TCAGGTGGAAGGGCTGTTCACGTTGACCTGAT 6 90 0 GGGCTTCACG 0.955395 -74 GACAAAAAAGGGGCTGTTAGCCCCTTTTTAAA 6 129 0 GGGCTTAGCC 0.993972 -35 CGCGGGCTTTTCACCTCATCCAGAC 8 13 0 GGGCTTCACC 0.992347 -15 GTAGCTCGTCGGGCTCATAACCCGAAGATCGT 9 53 1 GGGCTTAACC 0.990961 -248 CTTCTGGAAAGTGCTCCAGACCGCAGTTGCGG 9 181 1 GTGCTAGACC 0.943765 -120 CAGAATAACTGGGCTTTAGGCCCTTTTTTTAT 9 270 1 GGGCTAGGCC 0.904492 -31 AACCGTTGATGTGCATTAAGCCACGCATTGGC 11 106 0 GTGCAAAGCC 0.912324 -175 ***** ***** Masking position 4 Map Score: 15.4974 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 294 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 CGGTTAAAAGCCCCCCGCCGCAGCGGAGGGC 3 22 0 CCCCCGCCGC 0.983515 -87 TTCCCACTCCCGAAGACCACGGT 3 96 0 CCCCTCCCGA 0.960296 -13 TAATGACAACCCTAACCCAGCTCTATGTGGG 4 148 0 CCTACCCAGC 0.982377 -30 AGCGTAAACGCCTTATCCCGCATGGAACCCT 6 18 0 CCTATCCCGC 0.991993 -146 GCAATCCATGCCGGATGCAGCGTAAACGCCT 6 36 0 CCGATGCAGC 0.885658 -128 GGGCTTTTCACCTCATCCAGACTA 8 4 0 CCTATCCAGA 0.858012 -24 TACCAGGCTGCTCCACCCCGCGCCTGAAACG 9 25 0 CTCACCCCGC 0.984053 -276 CGGTTCAAATCCGGCCCCCGCAACCACTTTC 9 85 1 CCGCCCCCGC 0.991469 -216 CATGCCCTGACTTCACCCCGCTGTGTCTGCT 10 212 1 CTTACCCCGC 0.974939 -89 CGATGCAATTCACGATCCCGCAGTGTGATTT 10 268 1 CACATCCCGC 0.956415 -33 *** ******* Masking position 8 Map Score: 13.5783 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 607 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 AAAAATTCCTTAATACTGATAAC 1 2 1 AAATTCCTAA 0.75267 -299 GCACTATACACACGTTCCTGAAGAAAGCTATA 1 39 1 CACTTCCGAA 0.977702 -262 GTCTAAAATAAACATTGCTTCATATGTTCAAC 1 101 1 AACTTGCTCA 0.863876 -200 TCTACATTCCTTAACTTGAGCCTT 1 287 0 TACTTCCTAA 0.886593 -14 ACTGCCGCTTAACGTCGCGTAAATTGTTTAAC 5 51 1 AACTCGCTAA 0.747021 -98 AATTGTTTAACACTTTGCGTAACGTACACTGG 5 72 1 CACTTGCTAA 0.964624 -77 CCCCCGCAACCACTTTCCCTTAGAGTCCTTTT 9 99 1 CACTTCCTTA 0.962447 -202 CGGTCTGGAGCACTTTCCAGAAGGATTTTTTC 9 172 0 CACTTCCGAA 0.977702 -129 CGATGCAATTCACGATCCCGCAGTGTGATTTG 10 268 1 CACATCCGCA 0.821284 -33 TGTAGTAAGGCAAGTCCCTTCAAGAGTTATCG 11 161 1 CAATCCCTCA 0.773466 -120 CCTCGTAGTGCACATTCCTTTAACGCTTCAAA 11 201 1 CACTTCCTTA 0.962447 -80 *** **** *** Masking position 2 Map Score: 6.92545 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 352 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 GCAGAGGTTCGCGCGGCTAATGAGAGGCTTT 4 116 1 GCGCGCTAAT 0.991916 -62 CCTCGCGACTAATGACAACCCTA 4 165 0 TCGCGCTAAT 0.949955 -13 TGTGACGCTGGCGCGTCTTATCAGGTCAACG 6 71 1 GCGCGCTTAT 0.99378 -93 CGCGCCTGAAACGTGGCAAATTCTACT 9 7 0 ACGTGCAAAT 0.799919 -294 CTGTCATTTAGCGTGACTTATAGCCACCTAA 10 158 0 GCGTGCTTAT 0.987238 -143 ACCCGCCAATGCGTGGCTTAATGCACATCAA 11 102 1 GCGTGCTTAA 0.941383 -179 AATCTGTAAAGCACGCCATATCGCCGAAAGG 11 232 1 GCACGCATAT 0.90015 -49 ***** ***** Masking position 10 Map Score: 4.94898 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 204 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 TCGTATATCGTCTGTTCTTCAAACCGACGCAATCA 1 143 0 TCTGTTCACC 0.992507 -158 ACTTATTCCTTCTTTGAGTCTCTCCAATTAAGTAC 1 217 1 TCTTTTCTCC 0.94027 -84 CGAAGTCGTTTCTGTTATGCAAACCATTTATGCCG 1 251 1 TCTGTGCACC 0.993787 -50 CAGCCCGTAATCTTTTTTGATTGCCATCACCTTAA 2 24 1 TCTTTGATCC 0.838342 -105 AACCCAGCTCTATGTGGGTAAAGCCTCTCATTAGC 4 131 0 TATGTTAACC 0.824369 -47 GCTTTAATGGTCTGTACGTCAAACCGTTGATGTGC 11 124 0 TCTGTTCACC 0.992516 -157 CGCTTCAAAATCTGTAAAGCACGCCATATCGCCGA 11 224 1 TCTGTGCACC 0.993796 -57 ***** *** ** Masking position 5 Map Score: 3.84448 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 59 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 CCGCTGCGGCGGGGGGCTTTTAACCGGGCA 3 27 1 GGGGGGCTTT 0.885844 -82 ATTAGAGATCGGCGTCCTTTCATTCTATAT 5 113 1 GGCGTCCTTT 0.95473 -36 AAGACGCGCCAGCGTCACATCAGGCAATCC 6 60 0 AGCGTCACAT 0.522252 -104 CGCGGGCTTTTCACCTCATC 8 18 0 CGCGGGCTTT 0.926607 -10 ACTTTCCCTTAGAGTCCTTTTTCAAATATA 9 110 1 AGAGTCCTTT 0.798119 -191 CGGCCTTCGTAGTGGGATTTGAAAAAATCC 9 152 1 AGTGGGATTT 0.872524 -149 CCTGTCATTTAGCGTGACTTATAGCCACCT 10 160 0 AGCGTGACTT 0.945976 -141 ACGATCCCGCAGTGTGATTTGAGGAGTTTT 10 279 1 AGTGTGATTT 0.905778 -22 TCGGCGATATGGCGTGCTTTACAGATTTTG 11 229 0 GGCGTGCTTT 0.979396 -52 TTAATAATTAAGTGTGCCTTTCGGCGATAT 11 249 0 AGTGTGCCTT 0.94131 -32 ********** Masking position 10 Map Score: 3.97474 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 767 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 8 ATGGGGTTGAAGATGGCTGGATGTCTAAAATAA 1 79 1 AGATCGGATG 0.977826 -222 CAATCAAAAAAGATTACGGGCTGATGTGTACGT 2 14 0 AGATCGGCTG 0.995673 -115 GAGCCCGACGAGCTACCAGGCTGCTCCACCCCG 9 36 0 AGCTCGGCTG 0.990446 -265 GCGAAGGCGTAAATCTCTGGCTACAAAAAAGGC 10 56 0 AAATCGGCTA 0.95139 -245 AAGTCACGCTAAATGACAGGCTGAATCGAATCA 10 170 1 AAATCGGCTG 0.990304 -131 **** * ***** Masking position 4 Map Score: 1.80853 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 67 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ACTATACACACGTTCCTGAAGAAAGCTATAG 1 41 1 CGTTCCTGAG 0.975788 -260 AAGCAGTTCTCATTTCAGGTGTTATTCACTT 1 190 1 CATTTCAGGG 0.841373 -111 AATGATCTTCCGTTGCAGAGGTTCGCGCGGC 4 102 1 CGTTGCAGAG 0.984512 -76 GAATTTGCCACGTTTCAGGCGCGGGGTGGAG 9 15 1 CGTTTCAGGG 0.964731 -286 GTCTGGAGCACTTTCCAGAAGGATTTTTTCA 9 171 0 CTTTCCAGAG 0.968903 -130 AGATTTACGCCTTCGCAGAAGGTTAGATTTT 10 73 1 CTTCGCAGAG 0.863094 -228 TTGCTGTTTACGGTCCTGATGACAGGACCGT 11 27 1 CGGTCCTGAG 0.925443 -254 ********* * Masking position 6 Map Score: 1.78977 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 302 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 GTTATCAGTATTAAGGAATTTTT 1 4 0 TTAAGGAATT 0.897774 -297 GTTGAACATATGAAGCAATGTTTATTTTAG 1 103 0 TGAAGCAATG 0.890114 -198 AGTAGTTTACTAAAGCAGTTCTCATTTCAG 1 178 1 TAAAGCAGTT 0.889799 -123 AAGGCTCAAGTTAAGGAATGTAGA 1 287 1 TTAAGGAATG 0.947749 -14 GCAGTGTGATTTGAGGAGTTTTCA 10 287 1 TTGAGGAGTT 0.765439 -14 TACAGACCATTAAAGCAGTGTAGTAAGGCA 11 143 1 TAAAGCAGTG 0.943427 -138 TTTGAAGCGTTAAAGGAATGTGCACTACGA 11 203 0 TAAAGGAATG 0.947749 -78 ********** Masking position 4 Map Score: 1.56986 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 114 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 TTAATGATTGCGTCGGTTTGAAGAACAGACG 1 139 1 CGTCGGTTGA 0.979455 -162 ACCTACTTTGAGCCGGTTCACACTTTTCAAT 2 88 1 AGCCGGTTAC 0.862903 -41 CTCCCGAAGACCACGGTTGAATGAACGTCCT 3 82 0 CCACGGTTAA 0.899734 -27 TGTTATCGCAAGACGGTTAACA 5 2 0 AGACGGTTAC 0.933209 -147 ACCCGAAGATCGTCGGTTCAAATCCGGCCCC 9 72 1 CGTCGGTTAA 0.9678 -229 ACGCCTTCGCAGAAGGTTAGATTTTCGAAAT 10 79 1 AGAAGGTTGA 0.813792 -222 ATTTATGATTAATCGGTTGGAAAACGGTCCT 11 50 0 AATCGGTTGA 0.891294 -231 TAATGCACATCAACGGTTTGACGTACAGACC 11 120 1 CAACGGTTGA 0.94424 -161 ******** ** Masking position 7 Map Score: 1.94174 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 390 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 CTAAAATAAACATTGCTTCATATGTTCAAC 1 103 1 CATTGCTTCA 0.758209 -198 GCTGTTCCTTCCTGCTACAGTTTA 7 6 0 TCCTGCTACA 0.897894 -19 TTTTTTGTTATCTGACTACAGAATAACTGG 9 252 1 TCTGACTACA 0.960079 -49 GGCGTAAATCTCTGGCTACAAAAAAGGCAA 10 54 0 TCTGGCTACA 0.974119 -247 CAGAGCATGCCCTGACTTCACCCCGCTGTG 10 207 1 CCTGACTTCA 0.952986 -94 AAGGGACTTGCCTTACTACACTGCTTTAAT 11 151 0 CCTTACTACA 0.960083 -130 ********** Masking position 7 Map Score: 0.586669 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 157 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 AGACGATATACGAAGTAGTTTACTAAAGCA 1 165 1 CGAAGTAGTT 0.932486 -136 CAATTAAGTACGAAGTCGTTTCTGTTATGC 1 241 1 CGAAGTCGTT 0.988923 -60 CACATCAGCCCGTAATCTTTTTTGATTGCC 2 19 1 CGTAATCTTT 0.825575 -110 CTACGAAGGCCGAAGTCTTCACAGTATATT 9 134 0 CGAAGTCTTC 0.962374 -167 TAACCTTCTGCGAAGGCGTAAATCTCTGGC 10 68 0 CGAAGGCGTA 0.908443 -233 GTTAGATTTTCGAAATCTTTACAAAACAGG 10 94 1 CGAAATCTTT 0.950459 -207 ********** Masking position 4 Map Score: 0.678715 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 179 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 TTCTGTTATGCAAACCATTTATGCCGAAAGGCTCAA 1 260 1 CAATATGCCG 0.990872 -41 CATTAGTTTCCAGTGAATTGCTGCCGTCAGCTTGAA 4 53 0 CAATCTGCCG 0.989007 -125 AGGTCGCTACGAGTAGAATACTGCCGCTTAACGTCG 5 32 1 GAAACTGCCG 0.979686 -117 AAAGTATATAGAATGAAAGGACGCCGATCTCTAATT 5 112 0 GAAAACGCCG 0.955105 -37 AGCGTCACATCAGGCAATCCATGCCGGATGCAGCGT 6 44 0 CAATATGCCG 0.990872 -120 GCCACCTAACGATCTGATAAATGCCGATATATCTCT 10 131 0 GAATATGCCG 0.990872 -170 ** ** ****** Masking position 7 Map Score: 2.63024 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 98 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ********** No masking Map Score: 3.13593e-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