AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_Glycolysis_+_PPS_ecoli_hinf_reg_100.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 asnS 168 asparagine tRNA synthetase #2 glk 203 glucokinase #3 pgi 300 glucosephosphate isomerase #4 HI0556 85 oxidoreductase, putative (devB) #5 HI0557 82 H. influenzae predicted coding region HI0557 #6 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #7 HI0559 194 sulfite synthesis pathway protein (cysQ) #8 HI1302 147 asparaginyl-tRNA synthetase (asnS) #9 HI1573 300 pyruvate kinase, type II (pykA) #10 HI1574 33 replicative DNA helicase (dnaB) #11 HI1576 54 glucose-6-phosphate isomerase (pgi) Motif number 1 ACAACCGCCCCGCTCACCCTTTATTTATAA 3 95 0 CGCTCACCCT 0.963046 -206 ACGATCATCACCCCACCAAAAATGCAGAT 4 67 0 ACCCCACCAA 0.974529 -19 GCGTGGCTAAAGCCCACCCTACATTAGATT 5 13 0 AGCCCACCCT 0.992882 -70 GGTGGGCTTTAGCCCACAATTTATTATGTT 5 50 0 AGCCCACAAT 0.937437 -33 TGTGGGCTAAAGCCCACCCTACGGAAAATC 5 62 1 AGCCCACCCT 0.992882 -21 TTGTTCATAACCCGCACCAACACTATATTT 8 83 1 CCCGCACCAA 0.913746 -65 GAACCAGTGACCCCCACCATGTCAAGGTGG 9 26 1 CCCCCACCAT 0.990672 -275 ********** Masking position 6 Map Score: 8.87437 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 125 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 GTCACACAATTACTTTATCGTTTCAGCACC 2 77 0 TACTTTATCG 0.665351 -127 GAATTATTTTGACTTTAGCGGAGCAGTTGA 2 181 1 GACTTTAGCG 0.960453 -23 TCTTCTGGCCTGCGCTAGCGCAGGTAGTAC 3 63 1 TGCGCTAGCG 0.949446 -238 CACTCAACATTACGCTAACGGCACTAAAAC 3 209 1 TACGCTAACG 0.881338 -92 ATGTAGGGTGGGCTTTAGCCACGCTCTTAC 5 19 1 GGCTTTAGCC 0.911115 -64 CCGTAGGGTGGGCTTTAGCCCACAATTTAT 5 56 0 GGCTTTAGCC 0.911115 -27 ATTTTATGCTGACGCTAACGAACATTTACT 7 78 1 GACGCTAACG 0.945664 -117 ATATTAATAAGGCTTTACCCTATTTTATTT 8 28 1 GGCTTTACCC 0.915462 -120 CGACTAGCTGGACTCGAACCAGTGACCCCC 9 11 1 GACTCGAACC 0.832293 -290 GTCAAGGTGGTGCTCTAACCAACTGAGCTA 9 46 1 TGCTCTAACC 0.942992 -255 ********** Masking position 7 Map Score: 7.36946 Number of sites scoring better than the average of aligned sites = 732 Number in coding regions = 680 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TATCATCAGGGAGCTAATCGGCTC 1 1 1 TATTCAGGGC 0.961148 -168 GAATTAAAGGTAAAAAAAGGGAGCCGATTAGCTC 1 21 0 TAAAAAGGGC 0.847042 -148 TTTTTCCGACTATTAACAGAGAGAATATT 1 150 1 TATACAGGGA 0.992063 -19 CCCAGATCGATATTTACAGGGAGCCTGCCTTTCC 2 106 1 TATACAGGGC 0.988888 -98 TGCCCCCAGGTATTTACAGTGTGAGAAAGAATTA 2 153 1 TATACAGGGA 0.992063 -51 AGTACATTTATAAATAAAGGGTGAGCGGGGCGGT 3 88 1 TAAAAAGGGA 0.886075 -213 TCACGACTACTTCACACAGTGCGACTATAGCTCA 9 69 0 TTCACAGGGA 0.937627 -232 ATTTTGTAATTATTGACGGAGTAAATA 9 284 1 TATACGGGAA 0.694878 -17 CACTGCATTTTTTGAACAGAGGGAGTCATTCTCC 11 12 1 TTTACAGGGA 0.982638 -43 TTTCTGGAATTTTTATTAGGGAGAATGACTCCCT 11 31 0 TTTTTAGGGA 0.637269 -24 *** **** * ** Masking position 1 Map Score: 6.75776 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 167 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 CAGAATTCGCAAATGCAGCGAAAGATTTCGG 1 54 0 AATGCAGCGA 0.988324 -115 TTTCAGCACCAATTGCAGCGATGCCTTTTTG 2 56 0 AATGCAGCGA 0.988324 -148 TCTTCAACTGCTCCGCTAAAGTCAAA 2 188 0 AATGCTCCGC 0.949684 -16 GACTTTGGAAGATTGTAGCGCCAGTCACAGA 3 250 0 GATGTAGCGC 0.892507 -51 TTTCCAGTTAATTTGTTCCGCATAAGGTGAT 4 35 0 ATTGTTCCGC 0.83442 -51 TTTTTGATAAAACTGTTGCAAATGCTTACCT 7 138 0 AATGTTGCAA 0.689014 -57 TAAGCGTATAATGTGCACCGATTTTTTATCT 9 217 1 ATTGCACCGA 0.958129 -84 TATCTGGCTAATATGTAGCGAAGTAAAATAA 9 243 1 ATTGTAGCGA 0.957627 -58 TCTGTTCAAAAAATGCAGTGA 11 1 0 AATGCAGTGA 0.892453 -54 ** ******** Masking position 4 Map Score: 6.06913 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 832 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 GTATCTGACCCCGCATAAGGAATAGAAC 2 9 0 CCGCATAAGG 0.969997 -195 GATGAAAAATCCGCATGACCCCATCGTTGA 3 124 0 CCGCATGACC 0.976784 -177 TTAATTTGTTCCGCATAAGGTGATTTGGCT 4 29 0 CCGCATAAGG 0.969997 -57 TACTCGGAAGCCGAATAAGGAATAATT 6 59 1 CCGAATAAGG 0.973152 -17 AAATACCATTCCGCATGTGC 7 1 0 CCGCATGTGC 0.958795 -194 ********** Masking position 5 Map Score: 4.98372 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 66 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 CATCAGGGAGCTAATCGGCTCCCTTTTTTT 1 14 1 CTAATCGGCT 0.764339 -155 GTTACTTGGGCAACGCGCCTCTTCTGGCCT 3 44 1 CAACGCGCCT 0.868352 -257 AAACCCTAGCCAAATCACCTTATGCGGAAC 4 22 1 CAAATCACCT 0.935618 -64 CAGTTTTATCAAAAACAGGTTCATGTTGAA 7 154 1 AAAAACAGGT 0.708272 -41 TGAAAGAAGACAACACGCCT 7 185 1 CAACACGCCT 0.93607 -10 AAAATCGCGTATATTCAATA 8 1 1 AAAATCGCGT 0.89367 -147 TATGAACAATAAAATCGCCTTAAAAATGAG 8 62 0 AAAATCGCCT 0.969165 -86 AAAAGTAAACAAAACCAGCTTAAATAACTG 9 162 1 AAAACCAGCT 0.803543 -139 TTTGGAAATCAAAAACGGCTCAGTTATTTA 9 182 0 AAAAACGGCT 0.955108 -119 AGCGAAGTAAAATAACACCTTTAAAATTTT 9 259 1 AATAACACCT 0.653666 -42 ********** Masking position 10 Map Score: 3.06619 Number of sites scoring better than the average of aligned sites = 969 Number in coding regions = 837 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 7 CAATACTCTTCTGATTTTGAGAATTGTGAC 3 278 0 CTGATTTTGA 0.9152 -23 TGATTTGGCTAGGGTTTTAAATAATAAC 4 9 0 AGGGTTTTAA 0.758084 -77 CAACATGAACCTGTTTTTGATAAAACTGTT 7 152 0 CTGTTTTTGA 0.950077 -43 AGTGTTGGTGCGGGTTATGAACAATAAAAT 8 77 0 CGGGTTATGA 0.948416 -71 CCAGTTATATCGGGTTTTAAGAAAAATACT 9 129 0 CGGGTTTTAA 0.960253 -172 GTTATTTAAGCTGGTTTTGTTTACTTTTTT 9 160 0 CTGGTTTTGT 0.921214 -141 AATAACTGAGCCGTTTTTGATTTCCAAAAG 9 184 1 CCGTTTTTGA 0.917785 -117 ********** Masking position 5 Map Score: 2.34119 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 386 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 GCGAAAGATTTCGGAATTAAAGGTAAAAAA 1 38 0 TCGGAATTAA 0.820519 -131 GGGTTTACACTCAACATTACGCTAACGGCA 3 202 1 TCAACATTAC 0.883171 -99 CATTACGCTAACGGCACTAAAACCATCACA 3 216 1 ACGGCACTAA 0.887034 -85 TCTCTAGAATACGGCATTATTTTCGACATT 6 30 1 ACGGCATTAT 0.909908 -46 GGCATTATTTTCGACATTACTCGGAAGCCG 6 42 1 TCGACATTAC 0.950834 -34 GGCAGCAACCACGGCATTACAAATAGAGCA 7 33 0 ACGGCATTAC 0.98138 -162 TTCGTTAGCGTCAGCATAAAATTATTCTCT 7 70 0 TCAGCATAAA 0.741452 -125 TGGTAAGCAATCAGCAATACTTGGTTAAGT 7 105 0 TCAGCAATAC 0.872799 -90 ********** Masking position 6 Map Score: 1.72978 Number of sites scoring better than the average of aligned sites = 919 Number in coding regions = 851 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 9 AGCCGATTAGCTCCCTGATGATA 1 3 0 CTCCCTGATA 0.972013 -166 ACATAGGTATCCCCCCATTTACGGGTGGACA 1 110 1 CCCCCCATTA 0.934911 -59 AATATTCTCTCTGTTAATAGTCGGAAA 1 152 0 CTCTCTGTTA 0.974783 -17 GAAAGGCAGGCTCCCTGTAAATATCGATCTG 2 108 0 CTCCCTGTAA 0.943101 -96 GCCCCGCTCACCCTTTATTTATAAATGTACT 3 88 0 CCCTTTATTA 0.745655 -213 GAGAATGACTCCCTCTGTTCAAAAAATGCAG 11 14 0 CCCTCTGTTA 0.979027 -41 GGGAGTCATTCTCCCTAATAAAAATTCCAGA 11 32 1 CTCCCTAATA 0.943872 -23 ********* * Masking position 11 Map Score: 1.75369 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 159 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 TATCATCAGGGAGCTAATCGGCTCCCTTT 1 10 1 GGAGCTAATC 0.796846 -159 ATATTTACAGGGAGCCTGCCTTTCCGGCGT 2 115 1 GGAGCCTGCC 0.959618 -89 CGGTGTTGGAGGAGCCAGTCCTGTGATAAC 3 15 0 GGAGCCAGTC 0.985493 -286 GGCCAGAAGAGGCGCGTTGCCCAAGTAACG 3 43 0 GGCGCGTTGC 0.852745 -258 GGGTGAGCGGGGCGGTTGTCAACGATGGGG 3 106 1 GGCGGTTGTC 0.912916 -195 GGAAGATTGTAGCGCCAGTCACAGAAAAAT 3 245 0 AGCGCCAGTC 0.963099 -56 TATGTTAGTAAGAGCGTGGCTAAAGCCCAC 5 26 0 AGAGCGTGGC 0.947147 -57 TTTTTTGAACAGAGGGAGTCATTCTCCCTA 11 19 1 AGAGGGAGTC 0.904052 -36 ********** Masking position 4 Map Score: 1.55215 Number of sites scoring better than the average of aligned sites = 1022 Number in coding regions = 967 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 11 AATCTTTCGCTGCATTTGCGAATTCTGCTT 1 58 1 TGCATTTGCG 0.844588 -111 TTGCGAATTCTGCTTGTCTGATTGCAGATG 1 73 1 TGCTTGTCTG 0.889219 -96 ATTGCAGCGATGCCTTTTTGCAAGCTGGGC 2 46 0 TGCCTTTTTG 0.941917 -158 ACAGGGAGCCTGCCTTTCCGGCGTTGTTGT 2 121 1 TGCCTTTCCG 0.981622 -83 TAGCAATACTCTTCTGATTTTGAGAA 3 285 0 TACTCTTCTG 0.74941 -16 TGGAAAAATCTGCATTTTTGGTGGGGTGAT 4 60 1 TGCATTTTTG 0.87801 -26 TGATTTTCCGTAGGGTGGGC 5 73 0 TGATTTTCCG 0.812596 -10 GAGCATAAAATACCATTCCGCATGTGC 7 8 0 TACCATTCCG 0.758282 -187 TGGTTTTGTTTACTTTTTTGCCAGTTATAT 9 149 0 TACTTTTTTG 0.814856 -152 ********** Masking position 7 Map Score: 1.48038 Number of sites scoring better than the average of aligned sites = 1038 Number in coding regions = 918 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 12 CAAATAGAGCATAAAATACCATTCCGCATG 7 14 0 ATAAAATACC 0.885087 -181 TGAGTCCTAAATAAAATAGGGTAAAGCCTT 8 36 0 ATAAAATAGG 0.946114 -112 GTTATGAACAATAAAATCGCCTTAAAAATG 8 64 0 ATAAAATCGC 0.973164 -84 ATAAAATTGCCGATAGTTTA 8 138 0 ATAAAATTGC 0.930044 -10 TTAGCCAGATAAAAAATCGGTGCACATTAT 9 224 0 AAAAAATCGG 0.823817 -77 ATATGTTAAAATAAAAGAGCG 10 23 1 ATAAAAGAGC 0.924715 -11 ********** Masking position 5 Map Score: 0.797672 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 = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 ********** No masking Map Score: 6.56131e-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: 6.56131e-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: 6.56131e-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