AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_ecoli_mtub_300.orf -o259_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -x5 -e 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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 flgB 154 flagellar biosynthesis, cell-proximal portion of basal-body rod #2 flgE 24 flagellar biosynthesis, hook protein #3 BIME65 28 BIME #4 flgG 44 flagellar biosynthesis, cell-distal portion of basal-body rod #5 flhB 130 putative part of export apparatus for flagellar proteins #6 BIME88 37 BIME #7 tap 45 methyl-accepting chemotaxis protein IV, peptide sensor receptor #8 tar 144 methyl-accepting chemotaxis protein II, aspartate sensor receptor #9 motA 126 proton conductor component of motor; no effect on switching #10 flhD 300 regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor #11 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #12 BIME89 108 BIME #13 fliC 265 flagellar biosynthesis; flagellin, filament structural protein #14 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #15 fliL 104 flagellar biosynthesis #16 fliO 62 flagellar biosynthesis Motif number 1 CACTATGCTTGATGTGTGGCAGCAAAAGCCCTA 5 18 1 GGGTGGCAGC 0.993335 -113 TCAATTTCGCGGCGGGTGGCATCAGCAATAAAG 8 69 1 GGGTGGCATC 0.974043 -76 TTATCGGCAAGGAGGGGGGAAACTTTATTGCTG 8 91 0 GGGGGGAAAC 0.99637 -54 CTGATACGGTGAGGCGCAACATTCCAGCAG 9 8 1 GGGGCGCAAC 0.987911 -119 CACATACAACGGAGGGGGGCTGCGATTTTCAAT 10 63 0 GGGGGGCTGC 0.991722 -238 ACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAA 10 240 0 GGCGGGAAGC 0.984972 -61 GACATCACGGGGTGCGGTGAAACCGCATAAAAA 10 260 1 GGGGTGAAAC 0.968324 -41 AACCCCGCCGGTGGCGGGGAAGCACGTTGCTGA 11 29 0 GGGGGGAAGC 0.997867 -150 CGATTGAGCCGACGGGTGGAAACCCAATACGTA 13 212 1 GGGTGGAAAC 0.987256 -54 CTGCAGCAGTGGCGCAGCAGAAACCGGC 16 45 0 GGGGCGCAGC 0.978735 -18 * * ******** Masking position 13 Map Score: 23.0333 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 138 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 CTTTACGCGCGCGTTATCGGCGGAATAAACG 1 91 0 GCGTTACGGC 0.997325 -64 CAAGTTGATCTCGTTATCGGCAAGGAGGGGG 8 106 0 TCGTTACGGC 0.986712 -39 CAGCGGTACGTCGTTACCGCTGCTGGAATGT 9 29 0 TCGTTACGCT 0.760606 -98 CCCCAATCGCGCGTTAACGCCTGACGACTGA 9 70 1 GCGTTACGCC 0.987616 -57 TTTTTACCGGGGCTTCCCGGCGACATCACGG 10 239 1 GGCTTCCGGC 0.937632 -62 GGTTATTTGGGGGTTACAGGTAAATTCCAGG 11 70 0 GGGTTAAGGT 0.854033 -109 TGCGTTATATGAGTTATCGGCATGATTATCC 11 146 0 GAGTTACGGC 0.979748 -33 AGGCAATTTGGCGTTGCCGTCAGTCTCAGTT 12 27 0 GCGTTGCGTC 0.910595 -82 ACGAATACCGGGGTTATCGGTCTGAATTGCG 13 41 1 GGGTTACGGT 0.986712 -225 GACGATAACAGGGTTGACGGCGATTGAGCCG 13 192 1 GGGTTGCGGC 0.992238 -74 CAAAAAAACGGGTTTATTGGCGGATAGAAAA 14 83 1 GGTTTATGGC 0.803274 -132 ATTATGGACGGCGTTATTGGCAAAGTGGAAC 14 177 0 GCGTTATGGC 0.981067 -38 GTGTCGCTACTGCTTATCGGCTAATTATCCT 15 68 0 TGCTTACGGC 0.941033 -37 ****** **** Masking position 5 Map Score: 20.3523 Number of sites scoring better than the average of aligned sites = 1324 Number in coding regions = 1252 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 AGAATTTTGATACCTGCGGAGGAGAT 1 139 1 TACCGGGGGG 0.973097 -16 CCCTAAATCCCGCCTGTTTTGCCCCTTACTCAAA 5 46 1 CGCCGTTGCC 0.907975 -85 TTTGTATTGCCTGATGTGGCGTGACCACGTC 6 8 1 TGCCGTGGGG 0.988739 -30 CGGTCATTGCCGCCTGATGGGGAGCGTTG 7 27 1 CGCCGTGGGG 0.995121 -19 TGAAATAAAAAACCCGATGCGCAGATCATCGGGT 8 38 0 AACCGTGGCG 0.900249 -107 ATCTCGTTATCGGCAAGGAGGGGGGAAACTTTAT 8 96 0 CGGCAGAGGG 0.818616 -49 CAGGCGTTAACGCGCGATTGGGGCAAAAAAAAGC 9 59 0 CGCGGTTGGC 0.793615 -68 CACGCACATACAACGGAGGGGGGCTGCGATTTTC 10 66 0 CAACGGGGGC 0.742288 -235 CCGGCGACATCACGGGGTGCGGTGAAACCGCATA 10 255 1 CACGGTGGGG 0.978007 -46 AAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTG 11 33 0 CGCCGGGGGG 0.996924 -146 AACGCCAAATTGCCTGATGCGCTGCGCTTATCAG 12 43 1 TGCCGTGGCG 0.985715 -66 ACAGGGTTGACGGCGATTGAGCCGACGGGTGGAA 13 199 1 CGGCATGGCG 0.942238 -67 GGGGAAAAGACGCGGATTACGGTGCTACCTCTGA 15 13 0 CGCGATAGGG 0.777878 -92 GCAGGATAATTAGCCGATAAGCAGTAGCGACACA 15 66 1 TAGCGTAGCG 0.708541 -39 CTGCAGCAGTGGCGCAGCAGAAACCGG 16 46 0 CAGCGGGGCG 0.974784 -17 **** * ** ** * Masking position 11 Map Score: 16.8695 Number of sites scoring better than the average of aligned sites = 4684 Number in coding regions = 4107 Number in noncoding regions = 577 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 4 CACTAATCCACTACAGGACATTTT 4 31 1 CCAGGCTTTT 0.839421 -14 AAAGCCCTAAATCCCGCCTGTTTTGCCCCTTACT 5 42 1 ACCGCTTTTT 0.836702 -89 ATGCGCAGATCATCGGGTTCATTTCAATTGAGGA 8 22 0 CCGGGTATTT 0.978946 -123 ATGATCTGCGCATCGGGTTTTTTATTTCAATTTC 8 43 1 CCGGGTTTTA 0.974188 -102 TAACGACGTACCGCTGCTTTTTTTTGCCCCAATC 9 44 1 CCTGCTTTTT 0.843843 -83 TCCCCGCCACCGGCGGGGTTTTTTTCTGCCTGGA 11 42 1 CCGGGTTTTT 0.989045 -137 AGTGGGTGAAATGAGGGGTTATTTGGGGGTTACA 11 83 0 AAGGGTATTT 0.822043 -96 TTATCCGTTTCTGCAGGGTTTTTAATCGGACGAT 11 118 0 CCAGGTTTTA 0.941542 -61 ACTCATATAACGCAGGGCTGTTTATC 11 163 1 CAGGGTTTTA 0.899087 -16 CGACTAACAAAAAATGGCTGTTTTTGAAAAAAAT 13 137 1 AATGGTTTTT 0.667112 -129 GAAAAAAATTCTAAAGGTTGTTTTACGACAGACG 13 162 1 CAAGGTTTTT 0.900943 -104 TCTCGTCTCCCGGATAATTTCTGGTAGCAA 14 7 1 CCCGGTATTT 0.95994 -208 AGCAACAAAAAAACGGGTTTATTGGCGGATAGAA 14 78 1 ACGGGTATTG 0.786552 -137 GTAGCACCGTAATCCGCGTCTTTTCCCCGCTTTG 15 19 1 ACCGCTTTTT 0.8367 -86 TGCGCTCAAGACGCAGGATAATTAGCCGATAAGC 15 54 1 ACAGGTATTA 0.777327 -51 * **** * **** Masking position 12 Map Score: 11.1175 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 859 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 5 TGCTGCCACACATCAAGCATAGTGTGCGTT 5 12 0 CATCAAGCAT 0.947363 -119 GGTCACGCCACATCAGGCAATACAAA 6 7 0 CATCAGGCAA 0.984973 -31 CAACGCTCCCCATCAGGCGGCAATGACCGC 7 26 0 CATCAGGCGG 0.991898 -20 GATGTTCAGTCGTCAGGCGTTAACGCGCGA 9 76 0 CGTCAGGCGT 0.972145 -51 GTGTGATCTGCATCACGCATTATTGAAAAT 10 42 1 CATCACGCAT 0.980037 -259 TTCCCGGCGACATCACGGGGTGCGGTGAAA 10 252 1 CATCACGGGG 0.924828 -49 AAGCGCAGCGCATCAGGCAATTTGGCGTTG 12 42 0 CATCAGGCAA 0.984973 -67 ********** Masking position 5 Map Score: 7.40567 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 413 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 TTTCGCCCCCAGCCATTTCTACAACGTGAA 1 11 1 AGCCATTTCT 0.973471 -144 ATAAATAGCGACCCATTTTGCGTTTATTCC 1 71 1 ACCCATTTTG 0.932258 -84 TACCCATTTATGTTAAGTAAT 10 2 1 ACCCATTTAT 0.946526 -299 AAGTGTAAAGACCCATTTCTATTTGTAAGG 10 143 1 ACCCATTTCT 0.985977 -158 CGGCATGATTATCCGTTTCTGCAGGGTTTT 11 130 0 ATCCGTTTCT 0.900679 -49 TTTCAAAAACAGCCATTTTTTGTTAGTCGC 13 136 0 AGCCATTTTT 0.958973 -130 CCGCCAATAAACCCGTTTTTTTGTTGCTAT 14 76 0 ACCCGTTTTT 0.967842 -139 ********** Masking position 1 Map Score: 6.71895 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 60 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 GCGGAATAAACGCAAAATGGGTCGCTATTTA 1 72 0 CGCAAATGGG 0.910251 -83 AGTGGATTAGTGACAAAGTGCATATGTCTTC 4 12 0 TGAAAAGTGC 0.769017 -33 TGCCACCCGCCGCGAAATTGAAATAAAAAAC 8 59 0 CGCAAATTGA 0.955175 -86 AGCACGTTGCTGACAAATTGCGCTTTATGTT 11 11 0 TGAAAATTGC 0.934424 -168 CTGACGGCAACGCCAAATTGCCTGATGCGCT 12 35 1 CGCAAATTGC 0.98938 -74 TGTGCAAATTCAATAAATTGCAATTCAACTT 12 83 0 CAAAAATTGC 0.934424 -26 CGGCGACTAACAAAAAATGGCTGTTTTTGAA 13 134 1 CAAAAATGGC 0.889735 -132 AAGACAAAGGCGCTAAATAGCAACAAAAAAA 14 60 1 CGCAAATAGC 0.95084 -155 TCAGCAAACTCGAAAAATTGACGCTCCCATT 14 130 0 CGAAAATTGA 0.943025 -85 *** ******* Masking position 6 Map Score: 6.48635 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 625 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 8 GACCATCAACGGCATAAATAGCGACCCATTTTGC 1 58 1 GGCTATGCGA 0.906273 -97 CAGCTTAAATGCCTTTACGCGCGCGTTATCGGCG 1 100 0 GCCTAGGCGC 0.98555 -55 GGCAGCAAAAGCCCTAAATCCCGCCTGTTTTGCC 5 35 1 GCCTATCCGC 0.977787 -96 TTTGCGCTCTGGCATCATTCACGCTTAATACTCT 5 91 1 GGCTATACGC 0.876509 -40 ATTTACTAACGCGGTCATTGCCGCCTGATGGGGA 7 16 1 GCGTATCCGC 0.551827 -30 TGAAATGAACCCGATGATCTGCGCATCGGGTTTT 8 30 1 CCGTACGCGC 0.911324 -115 CAGTCGTCAGGCGTTAACGCGCGATTGGGGCAAA 9 66 0 GCGTAGGCGA 0.865355 -61 GCCACCGGCGGGGTTTTTTTCTGCCTGGAATTTA 11 47 1 GGGTTTCTGC 0.606397 -132 TCAACTTGTAGGCCTGATAAGCGCAGCGCATCAG 12 56 0 GGCTAAGCGC 0.909121 -53 CGGGGTTATCGGTCTGAATTGCGCAAAGTTTACG 13 49 1 GGTTATGCGC 0.898267 -217 CTTTTCTCTGCCCCTTATTCCCGCTATTAAAAAA 13 93 0 CCCTATCCGC 0.971861 -173 ACAAAAAAACGGGTTTATTGGCGGATAGAAAAAA 14 82 1 GGGTATGCGG 0.876356 -133 AATTGACGCTCCCATTATTTGTGCTTTCGTTTTT 14 112 0 CCCTATGTGC 0.913636 -103 TCCATAATCAGCCACGAGGTGCGCG 14 200 1 GCCCAGGCGC 0.896419 -15 CGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCA 15 35 1 CCGTTTGCGC 0.936962 -70 ATCTTCCGCGCCGGTTTCTGCTGCGCCACTGCTG 16 36 1 CCGTTTCTGC 0.540481 -27 *** * * * **** Masking position 13 Map Score: 15.9627 Number of sites scoring better than the average of aligned sites = 2895 Number in coding regions = 2745 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 9 CAATTCACGTTGTAGAAATGGCTGGGGGCGA 1 13 0 TGTAGAATGG 0.780271 -142 GACTGACTCCTGAAATGTGAAGGC 2 7 0 TCCTGAATGT 0.781192 -18 AAAATGTCCTGTAGTGGATTAGTGACA 4 28 0 TCCTGAGTGG 0.977767 -17 TAATACTCTTTCCAGGATTGGCGAC 5 116 1 TCCAGATTGG 0.931681 -15 GGCGCAACATTCCAGCAGCGGTAACGACGTA 9 23 1 TCCAGAGCGG 0.978114 -104 CGACTGAACATCCTGTCATGGTCAACAGTGG 9 94 1 TCCTGCATGG 0.946797 -33 TTAAAAACCCTGCAGAAACGGATAATCATGC 11 127 1 TGCAGAACGG 0.967614 -52 TTTTCGAGTTTGCTGACCCGGGAGTGAGTCT 14 145 1 TGCTGCCCGG 0.842272 -70 CTGCAGCAGTGGCGCAGCAGAA 16 51 0 TGCAGAGTGG 0.97765 -12 ***** ***** Masking position 1 Map Score: 6.03144 Number of sites scoring better than the average of aligned sites = 783 Number in coding regions = 734 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 10 TCCGCAATGACCATCAACGGCATAAATAGC 1 50 1 CCATCAACGG 0.911738 -105 CAACGCTCCCCATCAGGCGGCAATGACCG 7 27 0 CCATCAGGCG 0.946068 -19 ATTGCTGATGCCACCCGCCGCGAAATTGAA 8 68 0 CCACCCGCCG 0.990607 -77 GCGCAACATTCCAGCAGCGGTAACGACGTA 9 24 1 CCAGCAGCGG 0.99116 -103 TGCTTCCCCGCCACCGGCGGGGTTTTTTTC 11 38 1 CCACCGGCGG 0.642311 -141 TATTGGGTTTCCACCCGTCGGCTCAATCGC 13 211 0 CCACCCGTCG 0.956776 -55 CTGCAGCAGTGGCGCAGCAGAA 16 51 0 GCAGCAGTGG 0.890393 -12 ********** Masking position 3 Map Score: 4.68294 Number of sites scoring better than the average of aligned sites = 938 Number in coding regions = 906 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 TCAATGGTTTGAGTAAGGGGCAAAACAGGC 5 57 0 GAGTAAGGGG 0.96266 -74 TTAGTGGGTGAAATGAGGGGTTATTTGGGG 11 89 0 AAATGAGGGG 0.942514 -90 CACGTAAAACGAATACCGGGGTTATCGGTC 13 33 1 GAATACCGGG 0.946521 -233 TTAATAGCGGGAATAAGGGGCAGAGAAAAG 13 97 1 GAATAAGGGG 0.986015 -169 AATAGCAACAAAAAAACGGGTTTATTGGCG 14 75 1 AAAAAACGGG 0.883645 -140 ACGAAAGCACAAATAATGGGAGCGTCAATT 14 116 1 AAATAATGGG 0.918606 -99 ********** Masking position 2 Map Score: 1.47164 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 40 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 ********** No masking Map Score: 7.21444e-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 13 ********** No masking Map Score: 7.21444e-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 14 ********** No masking Map Score: 7.21444e-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