AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifis_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH174 169 sensory transduction histidine kinase #2 MTH175 128 conserved protein #3 MTH176 168 tRNA-guanine transglycosylase #4 MTH846 170 N-acetyl-gamma-glutamyl-phosphate reductase #5 MTH847 59 unknown #6 MTH848 103 protein-export membrane protein, SecF Motif number 1 GATGAAATTCTGGATGGAAACTGATTGAACAGAATAC 1 17 0 TGGAATGATG 0.857856 -153 TATAAATTGATGGAATTGATGAAATTCTGGATGGAAA 1 34 0 TGGATAAATC 0.874701 -136 CCTCCACAGAGGGGCATGATGTAAATCGGGGGGTGAT 1 125 1 GGGATTAATC 0.970338 -45 GATGTAAATCGGGGGGTGATGTAGGTGGGGGTTTTCC 1 142 1 GGGATTAGTG 0.983031 -28 TGTGATTTGAGGGTATTCCTGTGGGTCTTGGAGGGTC 2 16 1 GGGCTTGGTC 0.979505 -113 CTGTGGGTCTTGGAGGGTCTGAAAATCATAACTTGAT 2 34 1 TGGCTAAATC 0.907875 -95 TTGATGAGCAGGCACCGACTCTGATTCAGGGGTAATG 2 66 1 GGCCTTGATC 0.820102 -63 TCAGGGGTAATGGCAAAATTTAAGTTGTAATTACTGT 2 91 1 TGGTTAAGTG 0.660876 -38 AAGTATTTCATGGACAACCTTTAACTGTCCATGGGGA 4 21 0 TGGCTTAATG 0.987503 -150 GGGTCAGTGATGGACATTATATGGGTGGGAGGCCCCA 4 80 1 TGGATTGGTG 0.983031 -91 CTGGGTACTCTGGATAGTCTGCGAGGGTATGGTGGGG 4 112 0 TGGCTCGAGG 0.859965 -59 AGGTCAGTGATGGACATTATATAGGTGGGTATAG 4 147 1 TGGATTAGTG 0.978712 -24 GTTATTAAATGGGCAGAAATATATATGATGCCATCAA 5 20 1 GGGATTATTG 0.899618 -40 CTAGGGATGAGATTTGATGGCATCATATAT 5 40 0 GGGATTGAGG 0.972031 -20 TTTGACAGATGGGAGAAACTTTAAAGGTGATCGTCTT 6 15 1 GGGCTTAAGG 0.97496 -89 TTATGGCTGCTGGTATGGCTATGAGTGGCCTGTATGA 6 71 0 TGGCTTGATG 0.990057 -33 *** ** *** ** Masking position 2 Map Score: 21.4502 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 590 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 AGCATGTCTGCCCCACTATGTTATTAATTATATC 1 81 0 CCCACATTAT 0.891371 -89 GGGAAAACCCCCACCTACATCACCCCCCGATTT 1 147 0 CCCCCATCAC 0.987768 -23 TAAAAATCCTCCCACATAATCCATGCCTCAGAAA 3 37 0 CCCCAACCAT 0.984308 -132 GCAGTGGCTACCACCAGATACTACATGCTCAGAT 3 116 0 CCACAACTAC 0.940414 -53 CCGGTCGTGGCCACCAAAATTTATAAGTATTTCA 4 48 0 CCACAATTAT 0.968879 -123 GGTGGGGCCTCCCACCCATATAATGTCCATCACT 4 85 0 CCCCCATAAT 0.986326 -86 CCCCACCATACCCTCGCAGACTATCCAGAGTACC 4 112 1 CCCCGACTAT 0.949981 -59 CTATACCCACCTATATAATGTCCATCACT 4 152 0 CCCCCATAAT 0.986326 -19 ATATATGATGCCATCAAATCTCATCCCTAG 5 40 1 CCACAATCAT 0.97409 -20 CATAGCCATACCAGCAGCCATAACTGTAA 6 85 1 CCACACTAAC 0.78023 -19 *** ** * **** Masking position 13 Map Score: 10.3329 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 166 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 CGGGGGGTGATGTAGGTGGGGGTTTTCCC 1 151 1 TGTGGGGTTT 0.989699 -19 GATTTGAGGGTATTCCTGTGGGTCTTGGAGGGTCT 2 19 1 TATGGGGTCT 0.987999 -110 AGGCATGGATTATGTGGGAGGATTTTTAGGGTGCT 3 43 1 TATGGGATTT 0.974564 -126 TATTAATCAGTATCATCGTGGATATACACTGATCT 3 85 1 TATGGGATAT 0.988773 -84 AACCTTTAACTGTCCATGGGGATATCTTCCCC 4 8 0 TGTGGGATAT 0.988549 -163 TACTCTGGATAGTCTGCGAGGGTATGGTGGGGCCT 4 109 0 AGTGGGGTAT 0.975356 -62 TGATGGACATTATATAGGTGGGTATAG 4 154 1 TATGGGGTAT 0.995581 -17 TTACAGTTATGGCTGCTGGTATGGCTATGAGT 6 82 0 TATGTGGTAT 0.961775 -22 *** * ****** Masking position 3 Map Score: 12.8154 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 103 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 TTCCAGTATTCTGTTCAATCAGTTTCCATCCAGAAT 1 12 1 CTGTTCAGTC 0.982225 -158 GAGTCGGTGCCTGCTCATCAAGTTATGATTTTCAGA 2 51 0 CTGCTCAGTT 0.987354 -78 GGCACCGACTCTGATTCAGGGGTAATGGCAAAATTT 2 76 1 CTGATTCGTT 0.960243 -53 TGATCCAGCCCTGCTTCCAGTGTTTCTGAGGCATGG 3 15 1 CTGCTTCGTC 0.974248 -154 CACGATGATACTGATTAATATGTAATCAGCACCCTA 3 69 0 CTGATTAGTT 0.971423 -100 ATACACTGATCTGAGCATGTAGTATCTGGTGGTAGC 3 108 1 CTGAGCAGTC 0.975053 -61 CAGAATGATACTGATTAACAGGTACTCTGCAGTGGC 3 142 0 CTGATTAGTT 0.971423 -27 CAACCTTTAACTGTCCATGGGGATATCTTCCCC 4 8 0 CTGTCCAGAT 0.800823 -163 ATGTCCATCACTGACCCGGTCGTGGCCACCAAAATT 4 61 0 CTGACCCGTC 0.986772 -110 ATATATATTTCTGCCCATTTAATAACGGTCCTGTG 5 10 0 CTGCCCAATC 0.899704 -50 ******* ** * Masking position 2 Map Score: 9.40437 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 158 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 CATGCCCCTCTGTGGAGGAACCTGACGCAGCATGTC 1 107 0 TTGGAGGCAC 0.987809 -63 CATAACTTGATGAGCAGGCACCGACTCTGATTCAGG 2 60 1 TAGCAGGCCT 0.914418 -69 GCATGTAGTATCTGGTGGTAGCCACTGCAGAGTACC 3 122 1 TTGGTGGCCT 0.996494 -47 ACTTATAAATTTTGGTGGCCACGACCGGGTCAGTGA 4 54 1 TTGGTGGCCC 0.98458 -117 TCTGCGAGGGTATGGTGGGGCCTCCCACCCATATAA 4 96 0 TTGGTGGCCC 0.99777 -75 AGGGATGAGATTTGATGGCATCATATATATTTCTGC 5 32 0 TTGATGGCAT 0.948514 -28 * ****** * ** Masking position 1 Map Score: 4.11749 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 101 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 CAGCATGTCTGCCCCACTATGTTATTAATT 1 86 0 GCCCCACTAT 0.987898 -84 TTTACATCATGCCCCTCTGTGGAGGAACCT 1 120 0 GCCCCTCTGT 0.934404 -50 CACCTACATCACCCCCCGATTTACATCATG 1 139 0 ACCCCCCGAT 0.979543 -31 TGGTGGGGCCTCCCACCCATATAATGTCCA 4 90 0 TCCCACCCAT 0.972411 -81 TGGGTGGGAGGCCCCACCATACCCTCGCAG 4 101 1 GCCCCACCAT 0.99227 -70 CTATACCCACCTATATAATGTCCA 4 157 0 ACCCACCTAT 0.975324 -14 AAGTCATACAGGCCACTCATAGCCATACCA 6 68 1 GGCCACTCAT 0.820999 -36 ********** Masking position 10 Map Score: 5.53874 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 192 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 GGGTGATGTAGGTGGGGGTTTTCCC 1 155 1 GGTGGGGGTT 0.915601 -15 CCTGAATCAGAGTCGGTGCCTGCTCATCAA 2 66 0 AGTCGGTGCC 0.833164 -63 GCATGGATTATGTGGGAGGATTTTTAGGGT 3 45 1 TGTGGGAGGA 0.556922 -124 TGTAGTATCTGGTGGTAGCCACTGCAGAGT 3 125 1 GGTGGTAGCC 0.987981 -44 TCACTGACCCGGTCGTGGCCACCAAAATTT 4 60 0 GGTCGTGGCC 0.980387 -111 CGACCGGGTCAGTGATGGACATTATATGGG 4 75 1 AGTGATGGAC 0.906246 -96 ACATTATATGGGTGGGAGGCCCCACCATAC 4 93 1 GGTGGGAGGC 0.986442 -78 TACCCAGGTCAGTGATGGACATTATATAGG 4 142 1 AGTGATGGAC 0.906246 -29 AAACTTTAAAGGTGATCGTCTTGATTGACC 6 30 1 GGTGATCGTC 0.875174 -74 ********** Masking position 3 Map Score: 3.16262 Number of sites scoring better than the average of aligned sites = 1194 Number in coding regions = 1118 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 GTTATTAATTATATCATACATCAGATATAA 1 66 0 ATATCATACA 0.921542 -104 CCCCCGATTTACATCATGCCCCTCTGTGGA 1 127 0 ACATCATGCC 0.954723 -43 ACCCCCACCTACATCACCCCCCGATTTACA 1 144 0 ACATCACCCC 0.910964 -26 GAGGGTCTGAAAATCATAACTTGATGAGCA 2 46 1 AAATCATAAC 0.601791 -83 GGTTAAATGATACAGTAATTACAA 2 115 0 AAATGATACA 0.787836 -14 TATGTGATCCAGCCCTGCTTC 3 2 1 ATGTGATCCA 0.804474 -167 AAATCCTCCCACATAATCCATGCCTCAGAA 3 38 0 ACATAATCCA 0.725631 -131 AGCACCCTAAAAATCCTCCCACATAATCCA 3 48 0 AAATCCTCCC 0.902859 -121 GTCCATGGGGATATCTTCCCC 4 2 0 ATATCTTCCC 0.885399 -169 GCAGAAATATATATGATGCCATCAAATCTC 5 32 1 ATATGATGCC 0.893381 -28 ATGCCATCAAATCTCATCCCTAG 5 47 1 ATCTCATCCC 0.926905 -13 CCGCATTTTAAAGTCATACAGGCCACTCAT 6 58 1 AAGTCATACA 0.785361 -46 ********** Masking position 1 Map Score: 6.6059 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 960 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 9 TGAAATTCTGGATGGAAACTGATTGAACAG 1 22 0 GATGGAAACT 0.947877 -148 GCCCCTCTGTGGAGGAACCTGACGCAGCAT 1 110 0 GGAGGAACCT 0.936847 -60 AACTTGATGAGCAGGCACCGACTCTGATTC 2 63 1 GCAGGCACCG 0.847796 -66 AGTATCTGGTGGTAGCCACTGCAGAGTACC 3 128 1 GGTAGCCACT 0.911633 -41 TATAAATTTTGGTGGCCACGACCGGGTCAG 4 57 1 GGTGGCCACG 0.882433 -114 CCGGGTCAGTGATGGACATTATATGGGTGG 4 78 1 GATGGACATT 0.875278 -93 TATATGGGTGGGAGGCCCCACCATACCCTC 4 97 1 GGAGGCCCCA 0.959845 -74 CCAGGTCAGTGATGGACATTATATAGGTGG 4 145 1 GATGGACATT 0.875278 -26 GATGAGATTTGATGGCATCATATATATTTC 5 35 0 GATGGCATCA 0.792941 -25 ********** Masking position 5 Map Score: 4.09536 Number of sites scoring better than the average of aligned sites = 1274 Number in coding regions = 1216 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 10 ********** No masking Map Score: -3.17312e-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 11 ********** No masking Map Score: -3.17312e-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 ********** No masking Map Score: -3.17312e-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