AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_mthe_reg_300.orf -o00760_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH1192 76 conserved protein #2 MTH1193 146 transcriptional regulator #3 MTH1194 35 acetylpolyamine aminohydolase #4 MTH1492 51 5'-nucleotidase #5 MTH1493 78 cation transporting P-type ATPase related protein #6 MTH1494 266 conserved protein #7 MTH1495 194 ornithine cyclodeaminase #8 MTH1510 109 NH(3)-dependent NAD+ synthetase #9 MTH1639 163 cell division control protein Cdc48 #10 MTH1832 92 quinolinate phosphoribosyltransferase Motif number 1 AACTTTGTAGCGATTTATATCTTTCTCTAA 1 36 1 CGATTTATAT 0.882299 -41 CAGATTAGGCAGTTTTATAT 1 67 1 AGTTTTATAT 0.839742 -10 CTTCAGATAAACATTTATAAGGGAACATCC 2 39 1 ACATTTATAA 0.882466 -108 GAAGTCATCAACTTTTATAAGATAGGGGAT 2 65 0 ACTTTTATAA 0.584887 -82 GACTTCTTCTAAACTTATATTCACTTAAAA 2 89 1 AAACTTATAT 0.949811 -58 TATGCCTATGAAAGTTATATTATAAAGTTT 2 118 0 AAAGTTATAT 0.908187 -29 ATACCATAAAAAACATATATTGGTCCG 5 62 1 AAACATATAT 0.633919 -17 TGAGTGATAGAAATTGATATGGAGCTGATA 6 68 1 AAATTGATAT 0.777594 -199 AAGGTTGATCAGACTTATATCTCACTTCAA 7 25 0 AGACTTATAT 0.953495 -170 AGAGGTAGAAAAACTTATATCAGTGATGCT 8 49 0 AAACTTATAT 0.949811 -61 ACCTCTTTTGATAGTTATATAAAATATACC 8 73 1 ATAGTTATAT 0.672383 -37 TGTTTCGGTAAAGTTTATATACTATTAGAT 9 41 0 AAGTTTATAT 0.802573 -123 CTTTACCGAAACATTTATATATGATTACCT 9 58 1 ACATTTATAT 0.96522 -106 TCTGGACATAAGATTTATAATTCTTCCATT 10 51 1 AGATTTATAA 0.882466 -42 TATAATTCTTCCATTTATATTAATTTAGGG 10 66 1 CCATTTATAT 0.882299 -27 ********** Masking position 7 Map Score: 13.7075 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 33 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 ATTTATAAGGGAACATCCCCTATCTTATAAA 2 51 1 GAACATCCCT 0.978738 -96 TTCAGCCATAAAACACCCCCCTTACAGGTTT 4 16 0 AAACACCCCC 0.989064 -36 GTATATGAATGAACTCCTCACAAGGATGGAC 6 117 1 GAACTCCCAC 0.948331 -150 CGAAGAGATAGACCACCACCTCTCAGAGATA 6 207 1 GACCACCCCT 0.954813 -60 CATGGACCGGAAACTCCACCCTCGAGGCAGT 7 68 0 AAACTCCCCC 0.979356 -127 TTTAAATATTGAACATCTCACATTTATTAGT 7 154 0 GAACATCCAC 0.946833 -41 TATACTCCTCCTGTAAAATTAA 8 2 1 ATACTCCCCT 0.812285 -108 CTCTTCTTTTGCAGATCTCCCTTCTGGACAT 10 29 1 GCAGATCCCC 0.879758 -64 AAAGATCCCCTAAATTAATAT 10 82 0 AAAGATCCCT 0.877094 -11 ******* *** Masking position 7 Map Score: 6.85704 Number of sites scoring better than the average of aligned sites = 660 Number in coding regions = 612 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 TTTATTTTCCCATCTTCAGATAAACATTTATAAGGGA 2 26 1 CTCGTAACAT 0.983104 -121 TCCCCTGAATCAGAAAATGATAACCAT 3 19 1 CAAGTAACAT 0.96972 -17 TGGAGGCACCCTGCCGCCGATAATCATCACAGATGAC 6 12 1 CCCGTAACAT 0.966033 -255 TTTAAGGGACCTTGTCCGGCTAACTATCCTCATCCTC 6 159 0 CTCGTAATAT 0.927768 -108 GTCATGGCAGCTATTAAGGTTGATCAGACTTATATCT 7 33 0 CTAGTGACAG 0.887601 -162 ATCTACCAATCTTTAAATATTGAACATCTCACATTTA 7 159 0 CAAATGACAT 0.834264 -36 TATACTCCTCCTGTAAAATTAATCATCGATCCAAGA 8 10 1 CTAATAACAT 0.939807 -100 AATTAATCATCGATCCAAGATCAGCATCACTGATATA 8 27 1 CCAGTCACAT 0.901793 -83 TACTATAATACATGTACAGGTAATCATATATAAATGT 9 68 0 CTCGTAACAT 0.983104 -96 CTAGAATATTCCGGTTAAATTAAATATCAACCGGAAT 9 116 1 CTAATAATAT 0.775036 -48 CTCTTTATGATTATTATTATGATTCCG 9 147 0 CTAGTTATAT 0.736645 -17 GAAGGGAGATCTGCAAAAGAAGAGCATTTATGAAAGA 10 16 0 CAAGAGACAT 0.725361 -77 * * * * *** *** Masking position 13 Map Score: 7.00059 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 159 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 CAGTTCACCTGCTCGAGATATTATTAACTT 1 7 1 ACCTGTGGAA 0.945702 -70 ATTATTTATCCCCTGAATCAGAAAATGATAACCA 3 11 1 CCCTGACGAA 0.991693 -25 ATACAGTGGCACCTGTAAGCGAGACCCATAAACA 5 13 0 ACCTGAGGAA 0.982848 -66 CTGGAGGCACCCTGCCGCCGATAATCATCACAG 6 10 1 CCCTGCCGAA 0.993111 -257 ATAGAAATTGATATGGAGCTGATAGCATGTACCC 6 74 1 ATATGACGAA 0.766648 -193 CAAGGATGGACCATGTCTTCGAGAGGATGAGGAT 6 137 1 CCATGCTGAA 0.915244 -130 ATAGACCACCACCTCTCAGAGATAATGAGGATAC 6 214 1 ACCTCCGGAA 0.919697 -53 TCCCGGCGGTCCATGGACCGGAAACTCCACCCTC 7 76 0 CCATGACGAA 0.97902 -119 ***** * * ** * Masking position 12 Map Score: 4.25136 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 274 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TTAATAATATCTCGAGCAGGTGAACTG 1 7 0 CCGAGCAGGT 0.964921 -70 TAAAACACCCCCCTTACAGGTTTTAACC 4 8 0 CCTTACAGGT 0.992229 -44 TTATGGGTCTCGCTTACAGGTGCCACTGTAT 5 16 1 CCTTACAGGT 0.992455 -63 TCCTCATTATCTCTGAGAGGTGGTGGTCTAT 6 214 0 CCTGAGAGGT 0.931365 -53 TACTATAATACATGTACAGGTAATCATATAT 9 74 0 CTGTACAGGT 0.973606 -90 AAATGCTCTTCTTTTGCAGATCTCCCTTCTG 10 24 1 CTTTGCAGAT 0.850893 -69 * ********* Masking position 8 Map Score: 2.45456 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 151 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TAATTACCCTCCTTTTTTATTT 2 2 1 AATTACCCTC 0.936718 -145 CTCCTTTTTTATTTTCCCATCTTCAGATAAA 2 19 1 ATTTTCCCAC 0.804098 -128 AAGATAGGGGATGTTCCCTTATAAATGTTTA 2 46 0 ATGTTCCCTA 0.950505 -101 CTCATAGTATAAGGATCCTTCCAGTCATCTG 6 41 0 AAGGATCCTC 0.826976 -226 AGCTGATAGCATGTACCCCACCAGGACGTAT 6 90 1 ATGTACCCCC 0.950432 -177 TCTCGAAGACATGGTCCATCCTTGTGAGGAG 6 130 0 ATGGTCCATC 0.880889 -137 TTAGCCGGACAAGGTCCCTTAAAAGAGAAGA 6 173 1 AAGGTCCCTA 0.928415 -94 AGATTGGTAGATTGACCCTGA 7 184 1 ATTGACCCTA 0.922521 -11 GTTATATAAAATATACCCTACTTACTTTTAA 8 86 1 ATATACCCTC 0.917817 -24 ********* * Masking position 1 Map Score: 2.13249 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 739 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 ATATCTTTCTCTAAACAGATTAGGCAGTTT 1 52 1 CTAAACAGAT 0.931278 -25 TGTTTTATGGCTGAACTGAGCATAATCTAG 4 32 1 CTGAACTGAG 0.971161 -20 AGAGAAGAGATCGAAGAGATAGACCACCAC 6 196 1 TCGAAGAGAT 0.829767 -71 AATGAGGATACTGAACAGATACAACTGAAG 6 237 1 CTGAACAGAT 0.975671 -30 ATATTTCAAGTTGAAGTGAGATATAAGTCT 7 15 1 TTGAAGTGAG 0.918259 -180 CGATGTGGTATTAAACAGAG 9 1 0 TTAAACAGAG 0.931278 -163 ********** Masking position 5 Map Score: 0.979112 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 97 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 CTTCAGATAAACATTTATAAGGGAACATCCCCT 2 39 1 ACATTATAAG 0.970654 -108 CCCCACCAGGACGTATATGAATGAACTCCTCAC 6 105 1 ACGTTATGAG 0.923965 -162 AGGATACTGAACAGATACAACTGAAGCCGTGGA 6 241 1 ACAGTACAAG 0.830835 -26 GGCAGTCATGGCAGCTATTAAGGTTGATCAGAC 7 41 0 GCAGTATTAG 0.920074 -154 GACCGCCGGGACAGCCATGACAGTACTCATCCG 7 99 1 ACAGCATGAG 0.885358 -96 TGAACATCTCACATTTATTAGTGTTGGAAATGA 7 143 0 ACATTATTAG 0.970654 -52 AGGTAGAAAAACTTATATCAGTGATGCTGATCT 8 44 0 ACTTTATCAG 0.753606 -66 GTACAGGTAATCATATATAAATGTTTCGGTAAA 9 59 0 TCATTATAAG 0.855648 -105 GATTACCTGTACATGTATTATAGTAACCTAAAT 9 80 1 ACATTATTAG 0.970654 -84 CAAAAGAAGAGCATTTATGAAAGAGTGAT 10 7 0 GCATTATGAG 0.962154 -86 **** ***** * Masking position 7 Map Score: 5.53689 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 89 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 CCATAAAACACCCCCCTTACAGGTTTTAACC 4 10 0 CCCCTTACAG 0.907039 -42 GTATAAGGATCCTTCCAGTCATCTGTGATGAT 6 34 0 CCTCAGTCAT 0.932216 -233 AGCATGTACCCCACCAGGACGTATATGAATGA 6 97 1 CCCCGGACGT 0.97717 -170 GGAAACTCCACCCTCGAGGCAGTCATGGCAGC 7 59 0 CCTCAGGCAG 0.964837 -136 GGTCCATGGACCGCCGGGACAGCCATGACAGT 7 91 1 CCCCGGACAG 0.952121 -104 TGCAGATCTCCCTTCTGGACATAAGATTTATA 10 38 1 CCTCGGACAT 0.989563 -55 ** ** ****** Masking position 5 Map Score: 0.909096 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 279 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 GAAAATAAAAAAGGAGGGTAATTA 2 5 0 AAGGAGGGTA 0.990653 -142 TAAAACCTGTAAGGGGGGTGTTTTATGGCT 4 14 1 AAGGGGGGTG 0.934082 -38 TCTTCGAGAGGATGAGGATAGTTAGCCGGA 6 152 1 GATGAGGATA 0.949703 -115 TCTCAGAGATAATGAGGATACTGAACAGAT 6 227 1 AATGAGGATA 0.95794 -40 AATTTTACAGGAGGAGTATA 8 1 0 GAGGAGTATA 0.896318 -109 GGTTAAAAGTAAGTAGGGTATATTTTATAT 8 89 0 AAGTAGGGTA 0.942517 -21 ********** Masking position 2 Map Score: 2.2551 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 495 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 TTCAGATAAACATTTATAAGGGAACATCCCC 2 40 1 CATTATAAGG 0.785388 -107 ATATTATAAAGTTTTTTAAGTGAATATAAGT 2 101 0 GTTTTTAAGT 0.891275 -46 TGTAAGGGGGGTGTTTTATGGCTGAACTGAG 4 21 1 GTTTTTATGG 0.981478 -31 GATGTTTATGGGTCTCGCTTA 5 1 1 GAGTTTATGG 0.912161 -78 ACCAATATATGTTTTTTATGGTATTAAGATT 5 55 0 GTTTTTATGG 0.981476 -24 TCGATCTCTTCTCTTTTAAGGGACCTTGTCC 6 179 0 CTTTTTAAGG 0.965149 -88 ** ******** Masking position 5 Map Score: 0.379603 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 98 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 ********** No masking Map Score: 1.65089e-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: 1.65089e-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: 1.65089e-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