AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icysB_ecoli_hinf_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 topA 300 DNA topoisomerase type I, omega protein #2 cysB 209 positive transcriptional regulator for cysteine regulon #3 cysZ 229 required for sulfate transport #4 cysK 184 cysteine synthase A, O-acetylserine sulfhydrolase A #5 HI1102 152 cysteine synthetase, putative (cysZ) #6 HI1103 98 cysteine synthetase (cysK) #7 HI1194 300 glycine cleavage system transcriptional activator (gcvA) #8 HI1196 35 succinyl-CoA synthetase, beta subunit (sucC) #9 HI1198 120 conserved hypothetical protein #10 HI1199 47 conserved hypothetical protein Motif number 1 TCTGTCAGGTTTTTATAAACAAAGGGTCGCGAAAGCGGC 2 19 1 TTTAAAGGCG 0.963373 -191 CACTATTAACTTTCACAGCACAAAGATAGATGAAATCGT 3 96 1 TTTAAAAGAG 0.977206 -134 TACCGGGTAATTGCGCAATGGACAGTTAGGATATGTTCG 3 152 0 TTGAACAGAG 0.90785 -78 ACACAAACGGTTTACAAAATAACCGGTAGATTG 4 5 0 TTTAACCGAG 0.842601 -180 ACTGTATGAAATTGGGATACAACAGGTAGCATACCCGCT 4 144 0 ATTAACAGAG 0.929378 -41 AAAGTGTGGAATTTTAAAGGAAAAGTGCGGTCTGTTTTA 5 96 1 ATTAAAAGCG 0.960192 -57 TTTTAAGCATATTTTTATTGAAAGGAAAGAAAA 5 130 1 ATTAAAGGAG 0.909247 -23 AAATAACTATTTTTTTAATCAAAAGTGCGGTACTATAAA 6 31 1 TTTAAAAGCG 0.981168 -68 ACCAAATCGGTTTAATAATATACAGGAAGTAAATGAGTA 7 56 1 TTTAACAGAG 0.966017 -245 GTATGGTTGTATTGTAAGGAAAAGGGTAGGAAAGGACAA 7 195 1 ATTAAAGGAG 0.909248 -106 GTGAACTGTTTTCATAACCAAAAAGGACGTCGCGA 8 11 1 TTCAAAAGCG 0.947526 -25 CAATCTACGCTTTAGAAAACTAAAGTGCGG 9 2 0 TTTAAAAGCG 0.981168 -119 TTTTTATATGCTCGCCATTATAAAGTGAGCACAAAATTG 9 57 1 CTCAAAAGAG 0.755243 -64 TGTTTTCCTTGAATAATGGAAAGGTCGCTTTCACAAG 10 21 0 TTGAAAAGCG 0.947526 -27 *** * **** ** Masking position 12 Map Score: 17.501 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 73 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 TCAGGTACAGTGTGACGCTTTCGTCAATCTGGCAAT 1 65 1 TGCGTTTCTA 0.865791 -236 GCAATAAAAAAGGGCCGCTTTCGCGACCCTTTGTTT 2 35 0 AGCGTTTCCA 0.979373 -175 GGTTATAGTTAGCACCTTTTTTATTATTAAATCGTA 2 120 1 AGCTTTTTTA 0.853556 -90 ACGCCATCAGAACATCGTTTTTTCGTCACACCTGGC 2 166 0 AACGTTTTCT 0.913056 -44 AAACAGCAAAAAGCACGATTTCATCTATCTTTGTGC 3 113 0 AACGTTTCTT 0.937754 -117 AAATAGATCAAATAACTATTTTTTTAATCAAAAGTG 6 22 1 AACTTTTTTA 0.812848 -77 GCTCTCATTGAGTGGCGTTTTTTTCATCCCGATTTT 7 12 0 AGCGTTTTTA 0.974249 -289 ATTGTTACTCAAGTTCGGTTTCCCGAACTATATGCA 7 99 1 AACGTTTCCA 0.972514 -202 GGAAAGGACAAGTGACGTTTTTTTATTTGAGGTATT 7 223 1 AGCGTTTTTT 0.93777 -78 GATTTATTTCAAATTAGTTTTTCTAATACCTCAAAT 7 247 0 AAAGTTTTTA 0.68957 -54 GAATAATGGAAAGGTCGCTTTCACAAGCGTCTATAA 10 12 0 AACGTTTCCA 0.972514 -36 ** ** **** * * Masking position 9 Map Score: 7.06242 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 401 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 TGCGTATCGGATTTTATCAGGTACAGTGTGACG 1 49 1 ATTTTAGGTA 0.962823 -252 ACCTAATTTGATTCTTCCAGGAATGCGTCGCAC 1 269 0 ATTTCAGGAA 0.976132 -32 CCTTTAATTCTGTCAGGTTTTTATAAACA 2 7 1 ATTTTAGGTT 0.904569 -203 AATTCTGCGTATTTTACCGGGTAATTGCGCAAT 3 172 0 ATTTCGGGTA 0.958782 -58 AATACGCAGAATTTTCCTGGGATTGGTCAAAAG 3 192 1 ATTTCGGGAT 0.89491 -38 GTGACGTTTTTTTATTTGAGGTATTAGAAAAAC 7 234 1 TTTTTAGGTA 0.82273 -67 ATCAGCGCACATTTTTTAAGGAAGAAACAC 9 101 1 ATTTTAGGAA 0.96282 -20 CGACCTTTCCATTATTCAAGGAAAACA 10 31 1 ATTTCAGGAA 0.976233 -17 *** * * ***** Masking position 5 Map Score: 5.74468 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 47 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TCCATATCGGTAACTCGTTGCCAGTGGAAGG 1 229 1 TAATCGTTGC 0.957007 -72 TCTGTTGTTCTAACACCTTGCCACCACGGCA 3 18 1 TAAACCTTGC 0.959713 -212 ATAGATATGCTAAATCCTTACTTCCGCATAT 4 107 1 TAATCCTTAC 0.986413 -78 TTTTATTCCTTACGCGCGATAGT 5 3 1 TTATCCTTAC 0.956649 -150 TAATGATTGGTAATTCCTTACTAGTTAATGA 7 163 0 TAATCCTTAC 0.986414 -138 *** ******* Masking position 8 Map Score: 1.99321 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TTATCAGGTACAGTGTGACGCTTTCGTCAA 1 62 1 CAGTGTGACG 0.985817 -239 AATCTATTGCCAGATTGACGAAAGCGTCAC 1 76 0 CAGATTGACG 0.873799 -225 TTTTCGTGAACAGAGTCACGACAAGGGGTT 1 180 1 CAGAGTCACG 0.911206 -121 AGGTTTATCAACGTGCGACGCATTCCTGGA 1 257 1 ACGTGCGACG 0.950294 -44 CTTAGTGTATAGGTGTGAAGAAAAAATAAT 2 73 0 AGGTGTGAAG 0.889617 -137 GTCACCCGCCAGGTGTGACGAAAAAACGAT 2 159 1 AGGTGTGACG 0.984161 -51 GTAGGAAAGGACAAGTGACGTTTTTTTATT 7 220 1 ACAAGTGACG 0.860907 -81 ********** Masking position 8 Map Score: 1.33484 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 425 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 AGTGAGTAAATGTTTGCCGTGGTGGCAAGG 3 33 0 TGTTTGCCGT 0.966077 -197 TCACTAAGAGTATTTGCCGATTACCTCAAG 3 58 1 TATTTGCCGA 0.917574 -172 TGCATGTCATTATTTCCCTTCTGTATATAG 4 81 1 TATTTCCCTT 0.886324 -104 AATATTTTCCTTTCGTTGGACT 6 87 0 TATTTTCCTT 0.878386 -12 ACTCAAGTTCGGTTTCCCGAACTATATGCA 7 105 1 GGTTTCCCGA 0.838526 -196 TATGATGTTGTGTTTGCATATAGTTCGGGA 7 119 0 TGTTTGCATA 0.869205 -182 GTGAACTGTTTTCATAACCAAAAAGG 8 7 1 TGTTTTCATA 0.80866 -29 TGTTTTCCTTGAATAATGGA 10 38 0 TGTTTTCCTT 0.948659 -10 ********** Masking position 5 Map Score: 2.18183 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 589 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 CCTCAAGTGCAAGTGCACTATTAACTTTCA 3 81 1 AAGTGCACTA 0.870963 -149 TTTACCGGGTAATTGCGCAATGGACAGTTA 3 163 0 AATTGCGCAA 0.896827 -67 AAATACTTCAAAGTGTGGAATTTTAAAGGA 5 87 1 AAGTGTGGAA 0.91502 -66 TTTAAAGGAAAAGTGCGGTCTGTTTTAAGC 5 108 1 AAGTGCGGTC 0.978931 -45 TTTTAATCAAAAGTGCGGTACTATAAATAA 6 43 1 AAGTGCGGTA 0.98246 -56 CGCCATTATAAAGTGAGCACAAAATTGCTA 9 69 1 AAGTGAGCAC 0.899259 -52 ********** Masking position 4 Map Score: 0.840241 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 190 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 GCTTGACATTCGACCAAAATTCCGTCGTGCTAT 1 107 1 CGCCAATTCC 0.93154 -194 GTCGCGAAAGCGGCCCTTTTTTATTGCATATTA 2 44 1 CGCCCTTTTA 0.957548 -166 CGGCATAAGCCACCCCTGTTTCACACAAACGGT 4 33 0 CACCCTTTCA 0.984306 -152 TGGCTTATGCCGCCCCTTATTCCATCTTGCATG 4 54 1 CGCCCATTCC 0.972075 -131 CTACCTGTTGTATCCCAATTTCATACAGTTAAG 4 154 1 TACCCTTTCA 0.934832 -31 GGTGCTAATGCTACCATATTTCAGTAGGTGAAA 5 54 1 CTCCATTTCA 0.944778 -99 GCGTTTTTTTCATCCCGATTTTA 7 1 0 CACCCTTTTA 0.934832 -300 GAAAGCGACCTTTCCATTATTCAAGGAAAACA 10 26 1 TTCCAATTCA 0.709244 -22 ** *** ***** Masking position 10 Map Score: 1.28822 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 361 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 ********** No masking Map Score: -1.25466e-13 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 10 AGTGTGACGCTTTCGTCAATCTGGCAATAGAT 1 73 1 TTTGTAATCT 0.702347 -228 TCACCTGAATTTTCGTGAACAGAGTCACGACA 1 171 1 TTTGTAACAG 0.934654 -130 CACCTTTTTTATTATTAAATCGTATTAGTCAC 2 132 1 ATTTTAATCG 0.828562 -78 ATTAAATCGTATTAGTCACCCGCCAGGTGTGA 2 145 1 ATTGTACCCG 0.943212 -65 TTTTCCTGGGATTGGTCAAAAGGAGCTCATCC 3 203 1 ATTGTAAAAG 0.82856 -27 CTACCGGTTATTTTGTAAACCGTTTGTGTGAA 4 15 1 TTTGTAACCG 0.98426 -170 ATTAAACCGATTTGGTTAAACGCTGCTCTCAT 7 40 0 TTTGTAAACG 0.954813 -261 CTTCCTGTATATTATTAAACCGATTTGGTTAA 7 53 0 ATTTTAACCG 0.934653 -248 *** ** ***** Masking position 8 Map Score: 1.29706 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 398 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 ********** No masking Map Score: -1.25466e-13 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 12 TTTGGATTTTGCATGCTAATAAAGTTGCGTAT 1 24 1 GCTGCTATAA 0.690534 -277 TCCGCAGAGAGCGAGTCCATATCGGTAACTCG 1 214 1 GCAGTCATAT 0.868858 -87 GGAATGCGTCGCACGTTGATAAACCTTCCACT 1 251 0 GCCGTTATAA 0.86981 -50 CGCGAAAGCGGCCCTTTTTTATTGCATATTAT 2 46 1 GCCTTTTTAT 0.736978 -164 GTCAAAAGGAGCTCATCCTGATT 3 217 1 GCCATCTGAT 0.775773 -13 ATTCCATCTTGCATGTCATTATTTCCCTTCTG 4 72 1 GCTGTCTTAT 0.975197 -113 TAAGGATTTAGCATATCTATATACAGAAGGGA 4 95 0 GCTATCATAT 0.897976 -90 GGCCTGTCCTTAACTGTATGAAA 4 172 0 GCTGTCTTAA 0.946817 -13 TCTGTTTTAAGCATATTTTTATTGAAAGGAAA 5 126 1 GCTATTTTAT 0.846132 -27 ATTTTTATATGCTCGCCATTATAAAGTGAGCA 9 56 1 GCCGCCTTAT 0.956073 -65 ** **** **** Masking position 11 Map Score: 0.907098 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 659 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 13 ********** No masking Map Score: -1.25466e-13 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 14 ********** No masking Map Score: -1.25466e-13 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: -1.25466e-13 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