AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_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 CTTATGCGGGGTCAGATACTTAGTTTGCCCAGCTTGCAAA 2 20 1 GTCAACTTCC 0.917043 -184 CGTTGCCCAAGTAACGGTGTTGGAGGAGCCAGTCCTGTGA 3 19 0 GTAAGGTACC 0.972394 -282 CGTTACTTGGGCAACGCGCCTCTTCTGGCCTGCGCTAGCG 3 43 1 GCAAGCTTCC 0.940672 -258 CAACGATGGGGTCATGCGGATTTTTCATCCACTCCTGGCG 3 125 1 GTCAGGTTCC 0.994602 -176 TGCCGTTAGCGTAATGTTGAGTGTAAACCCTTAGCGCAGT 3 192 0 GTAAGGGTCC 0.995455 -109 TATTATGTTAGTAAGAGCGTGGCTAAAGCCCACCCTACAT 5 19 0 GTAAAGGTCC 0.977338 -64 CGGCTTCCGAGTAATGTCGAAAATAATGCCGTATTCTAGA 6 32 0 GTAAGGATCC 0.982167 -44 TGCTCTATTTGTAATGCCGTGGTTGCTGCCAAAAACAAGA 7 33 1 GTAAGGGTCC 0.995444 -162 CCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA 9 36 1 GTCAGGTTCC 0.994603 -265 **** * * * * ** Masking position 4 Map Score: 9.87915 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 137 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 ACAACCGCCCCGCTCACCCTTTATTTATAA 3 95 0 CGCTCACCCT 0.967176 -206 ACGATCATCACCCCACCAAAAATGCAGAT 4 67 0 ACCCCACCAA 0.977406 -19 GCGTGGCTAAAGCCCACCCTACATTAGATT 5 13 0 AGCCCACCCT 0.993699 -70 GGTGGGCTTTAGCCCACAATTTATTATGTT 5 50 0 AGCCCACAAT 0.944263 -33 TGTGGGCTAAAGCCCACCCTACGGAAAATC 5 62 1 AGCCCACCCT 0.993699 -21 TTGTTCATAACCCGCACCAACACTATATTT 8 83 1 CCCGCACCAA 0.922945 -65 GAACCAGTGACCCCCACCATGTCAAGGTGG 9 26 1 CCCCCACCAT 0.991741 -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 3 GGTGCTGAAACGATAAAGTAATTGTGTGAC 2 77 1 CGATAAAGTA 0.680965 -127 TCAACTGCTCCGCTAAAGTCAAAATAATTC 2 181 0 CGCTAAAGTC 0.963057 -23 GTACTACCTGCGCTAGCGCAGGCCAGAAGA 3 63 0 CGCTAGCGCA 0.952744 -238 GTTTTAGTGCCGTTAGCGTAATGTTGAGTG 3 209 0 CGTTAGCGTA 0.888562 -92 GTAAGAGCGTGGCTAAAGCCCACCCTACAT 5 19 0 GGCTAAAGCC 0.908643 -64 ATAAATTGTGGGCTAAAGCCCACCCTACGG 5 56 1 GGCTAAAGCC 0.908643 -27 AGTAAATGTTCGTTAGCGTCAGCATAAAAT 7 78 0 CGTTAGCGTC 0.949198 -117 AAATAAAATAGGGTAAAGCCTTATTAATAT 8 28 0 GGGTAAAGCC 0.920619 -120 GGGGGTCACTGGTTCGAGTCCAGCTAGTCG 9 11 0 GGTTCGAGTC 0.841478 -290 TAGCTCAGTTGGTTAGAGCACCACCTTGAC 9 46 0 GGTTAGAGCA 0.946647 -255 ********** Masking position 4 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 4 TATCATCAGGGAGCTAATCGGCTC 1 1 1 TATTCAGGGC 0.956234 -168 GAATTAAAGGTAAAAAAAGGGAGCCGATTAGCTC 1 21 0 TAAAAAGGGC 0.830245 -148 TTTTTCCGACTATTAACAGAGAGAATATT 1 150 1 TATACAGGGA 0.991023 -19 CCCAGATCGATATTTACAGGGAGCCTGCCTTTCC 2 106 1 TATACAGGGC 0.987437 -98 TGCCCCCAGGTATTTACAGTGTGAGAAAGAATTA 2 153 1 TATACAGGGA 0.991023 -51 AGTACATTTATAAATAAAGGGTGAGCGGGGCGGT 3 88 1 TAAAAAGGGA 0.872921 -213 TCACGACTACTTCACACAGTGCGACTATAGCTCA 9 69 0 TTCACAGGGA 0.929954 -232 ATTTTGTAATTATTGACGGAGTAAATA 9 284 1 TATACGGGAA 0.667921 -17 CACTGCATTTTTTGAACAGAGGGAGTCATTCTCC 11 12 1 TTTACAGGGA 0.980386 -43 TTTCTGGAATTTTTATTAGGGAGAATGACTCCCT 11 31 0 TTTTTAGGGA 0.608093 -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 5 CCGAAATCTTTCGCTGCATTTGCGAATTCTG 1 54 1 TCGCTGCATT 0.988571 -115 CAAAAAGGCATCGCTGCAATTGGTGCTGAAA 2 56 1 TCGCTGCATT 0.988571 -148 TTTGACTTTAGCGGAGCAGTTGAAGA 2 188 1 GCGGAGCATT 0.95071 -16 TCTGTGACTGGCGCTACAATCTTCCAAAGTC 3 250 1 GCGCTACATC 0.894568 -51 ATCACCTTATGCGGAACAAATTAACTGGAAA 4 35 1 GCGGAACAAT 0.837392 -51 AGGTAAGCATTTGCAACAGTTTTATCAAAAA 7 138 1 TTGCAACATT 0.693637 -57 AGATAAAAAATCGGTGCACATTATACGCTTA 9 217 0 TCGGTGCAAT 0.958989 -84 TTATTTTACTTCGCTACATATTAGCCAGATA 9 243 0 TCGCTACAAT 0.958498 -58 TCACTGCATTTTTTGAACAGA 11 1 1 TCACTGCATT 0.894515 -54 ******** ** Masking position 8 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 6 GTTCTATTCCTTATGCGGGGTCAGATAC 2 9 1 CCTTATGCGG 0.991039 -195 AGCCAAATCACCTTATGCGGAACAAATTAA 4 29 1 CCTTATGCGG 0.991039 -57 TTATTTTCGACATTACTCGGAAGCCGAATA 6 46 1 CATTACTCGG 0.952106 -30 AATTATTCCTTATTCGGCTTCCGAGTA 6 59 0 CCTTATTCGG 0.988457 -17 ********** Masking position 5 Map Score: 4.20024 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 10 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 CTAATCGGCTCCCTTTTTTTACCTTTAATT 1 24 1 CCCTTTTTTT 0.951363 -145 GCCCCGCTCACCCTTTATTTATAAATGTAC 3 89 0 CCCTTTATTT 0.693779 -212 CAATACTCTTCTGATTTTGAGAATTGTGAC 3 278 0 CTGATTTTGA 0.803354 -23 GTATTTTATGCTCTATTTGTAATGCCGTGG 7 25 1 CTCTATTTGT 0.814216 -170 TAAAATTATTCTCTTGTTTTTGGCAGCAAC 7 54 0 CTCTTGTTTT 0.743508 -141 CAACATGAACCTGTTTTTGATAAAACTGTT 7 152 0 CTGTTTTTGA 0.911161 -43 TAAGGCTTTACCCTATTTTATTTAGGACTC 8 35 1 CCCTATTTTA 0.760967 -113 TTATTTAGGACTCATTTTTAAGGCGATTTT 8 52 1 CTCATTTTTA 0.830096 -96 GTTATTTAAGCTGGTTTTGTTTACTTTTTT 9 160 0 CTGGTTTTGT 0.767383 -141 AATAACTGAGCCGTTTTTGATTTCCAAAAG 9 184 1 CCGTTTTTGA 0.922366 -117 ATAATGTGCACCGATTTTTTATCTGGCTAA 9 224 1 CCGATTTTTT 0.849033 -77 CGCTCTTTTATTTTAACATATT 10 22 0 CTCTTTTATT 0.661684 -12 ********** Masking position 1 Map Score: 3.30989 Number of sites scoring better than the average of aligned sites = 746 Number in coding regions = 509 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 8 TATCATCAGGGAGCTAATCGGCT 1 3 1 TATCAGGGAG 0.972013 -166 TGTCCACCCGTAAATGGGGGGATACCTATGT 1 110 0 TAATGGGGGG 0.934911 -59 TTTCCGACTATTAACAGAGAGAATATT 1 152 1 TAACAGAGAG 0.974783 -17 CAGATCGATATTTACAGGGAGCCTGCCTTTC 2 108 1 TTACAGGGAG 0.943101 -96 AGTACATTTATAAATAAAGGGTGAGCGGGGC 3 88 1 TAATAAAGGG 0.745655 -213 CTGCATTTTTTGAACAGAGGGAGTCATTCTC 11 14 1 TAACAGAGGG 0.979027 -41 TCTGGAATTTTTATTAGGGAGAATGACTCCC 11 32 0 TATTAGGGAG 0.943872 -23 * ********* Masking position 1 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 9 GATGGGGTCATGCGGATTTTTCATCCACTCC 3 129 1 TGCGATTTTT 0.972402 -172 CCACCAAAAATGCAGATTTTTCCAGTTAATT 4 53 0 TGCGATTTTT 0.972402 -33 TCGAAAATAATGCCGTATTCTAGAGAAAAAA 6 25 0 TGCGTATTCT 0.834143 -51 GCACATGCGGAATGGTATTTTATGCT 7 6 1 TGCGAATGGT 0.945706 -189 AACCAAGTATTGCTGATTGCTTACCAATCAG 7 109 1 TGCGATTGCT 0.983536 -86 ATAAAATTGCCGATAGTTTACCTTAATG 8 130 0 TGCGATAGTT 0.931826 -18 *** ******* Masking position 1 Map Score: 1.13423 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 197 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 AAAGGGAGCCGATTAGCTCCCTGATGATA 1 9 0 GTTAGCTCCC 0.936258 -160 AGGTAACATAGGTATCCCCCCATTTACGGGT 1 105 1 GTATCCCCCC 0.954283 -64 ACGCCGGAAAGGCAGGCTCCCTGTAAATATC 2 114 0 GCAGGCTCCC 0.931875 -90 CGGCGTTGTTGTTATGCCCCCAGGTATTTAC 2 139 1 GTATGCCCCC 0.975673 -65 GTTATCACAGGACTGGCTCCTCCAACACCGT 3 15 1 GCTGGCTCCT 0.858892 -286 CCCCATCGTTGACAACCGCCCCGCTCACCCT 3 105 0 GCAACCGCCC 0.94259 -196 AACAGAGGGAGTCATTCTCCCTAATAAAAAT 11 26 1 GCATTCTCCC 0.950364 -29 * ********* Masking position 7 Map Score: 1.50358 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 194 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 11 CAGCGATGCCTTTTTGCAAGCTGGGCAAAC 2 42 0 TTTTTGCAAG 0.954911 -162 AAAAATGCAGATTTTTCCAGTTAATTTGTT 4 49 0 ATTTTTCCAG 0.86554 -37 TATTCTCTTGTTTTTGGCAGCAACCACGGC 7 48 0 TTTTTGGCAG 0.969126 -147 TTTGTTTACTTTTTTGCCAGTTATATCGGG 9 145 0 TTTTTGCCAG 0.991033 -156 CTTCGCTACATATTAGCCAGATAAAAAATC 9 236 0 TATTAGCCAG 0.910796 -65 ********** Masking position 4 Map Score: 0.383893 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 463 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 12 ********** 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 13 TTTAATTCCGAAATCTTTCGCTGCATTTGCG 1 47 1 AAACTTTCGC 0.86963 -122 CAGCTTGCAAAAAGGCATCGCTGCAATTGGT 2 49 1 AAAGCATCGC 0.949479 -155 TTCAGCTAATAAATGCTTCACTGCGCTAAGG 3 173 1 AAAGCTTCAC 0.922171 -128 TGTTGAGTGTAAACCCTTAGCGCAGTGAAGC 3 187 0 AAACCTTAGC 0.957082 -114 TAACGGCACTAAAACCATCACATTTTTCTGT 3 224 1 AAACCATCAC 0.92494 -77 GTTATTATTTAAAACCCTAGCCAAATCACCT 4 11 1 AAACCCTAGC 0.964196 -75 GAGCGTGGCTAAAGCCCACCCTACATTAGAT 5 14 0 AAACCCACCC 0.95185 -69 ATTGTGGGCTAAAGCCCACCCTACGGAAAAT 5 60 1 AAACCCACCC 0.95185 -23 AAACTGTTGCAAATGCTTACCTGATTGGTAA 7 129 0 AAAGCTTACC 0.897431 -66 *** ******* Masking position 3 Map Score: 5.4856 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 434 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 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