AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ilexA_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 MTH1 170 conserved protein #2 MTH5 22 ribosomal protein L8 (E.coli L2) #3 MTH9 46 ribosomal protein L35 (E.coli L29) #4 MTH21 109 ribosomal protein L19 #5 MTH31 30 ribosomal protein L14 #6 MTH34 236 ribosomal protein S18 (E.coli S13) #7 MTH40 58 DNA-dependent RNA polymerase, subunit N #8 MTH442 195 excinuclease ABC subunit B #9 MTH443 41 excinuclease ABC subunit A #10 MTH472 140 DNA helicase II #11 MTH511 240 DNA helicase II #12 MTH543 107 unknown #13 MTH544 194 conserved protein #14 MTH1208 220 DNA-dependent DNA polymerase family B (PolB1) #15 MTH1692 113 conserved protein Motif number 1 TTAAACTTTCCGCTGGTGAGG 1 1 0 CGCTGGTGGG 0.938067 -170 GGAGGACTGGAAGGGGCATATTTTC 4 5 1 GACTGGAAGG 0.775731 -105 AAAGTTTTTTCGCTGGACTGGAAAATATGCC 4 25 0 CGCTGGACGG 0.985772 -85 GCTAGGCTATCCCGGCACAGGATGTATCATA 6 57 0 CCCGGCACGG 0.97775 -180 GGATAGCCTAGCCAGGTAAGGCGCAAGACTG 6 76 1 GCCAGGTAGG 0.894257 -161 CCAGGTAAGGCGCAAGACTGGAAATCTTGTG 6 87 1 CGCAAGACGG 0.880903 -150 GGGATTTGAACCCAGGAGGAGCAAAGCTCCA 6 116 0 CCCAGGAGAG 0.801149 -121 TTTAACCGACGCCGGGACTGGGATTTGAACC 6 135 0 GCCGGGACGG 0.991693 -102 AGAGTGAATTCGCGGGACGGGGGTTTGCGAA 6 200 0 CGCGGGACGG 0.991864 -37 CTTTATGTATCCTGGCAAAGGTATATATAAG 8 121 1 CCTGGCAAGG 0.743735 -75 ATGGCAGTGCCCCGACTGAGGCCCTTCACCA 12 32 1 CCCGACTGGG 0.691142 -76 AGGGTATGAGGCCTGGAACGGTGAGATCTGA 13 102 1 GCCTGGAAGG 0.968722 -93 ******** ** Masking position 11 Map Score: 9.6304 Number of sites scoring better than the average of aligned sites = 830 Number in coding regions = 777 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 GCAGACTGGGCAAGTAAAACCACAGACCACA 1 107 0 CAAGAAAACC 0.978772 -64 AGGCCCTTCACCAGAAAAACCACAAACTATT 12 50 1 CCAGAAAACC 0.995861 -58 TCCAACACCCCCAGGAAATCCTAAACACTAT 14 95 1 CCAGAAATCC 0.986511 -126 AACCACCACACCACGAAAACCGGCACACCTA 15 24 0 CCACAAAACC 0.993983 -90 ACCACTACAACCACGAAAACCGGCAGGGTGA 15 75 0 CCACAAAACC 0.993983 -39 **** ****** Masking position 6 Map Score: 6.60594 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 10 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 3 ACCACATCGTATCAGAGCATACAATGTGAG 1 83 0 ATCAGAGCAT 0.968864 -88 ACAGATTCATATCAGTGAATAATAGAAAGG 3 20 1 ATCAGTGAAT 0.901349 -27 TTAAACATAAATCAGAGGATGGTAATGATA 8 13 0 ATCAGAGGAT 0.987728 -183 TGGGGGTATCATCACAGGATTATGGAACAC 8 54 1 ATCACAGGAT 0.987728 -142 ATTAATACTGATCACAGGATTAAACTGTTC 14 30 1 ATCACAGGAT 0.987728 -191 TTAATCTCACATAACAGAATAGGTAC 14 205 1 ATAACAGAAT 0.851419 -16 ********** Masking position 4 Map Score: 5.02279 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 56 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 GTTTAAATATGGATACCATACAATTTTTAG 1 26 1 GGATACCATA 0.966845 -145 CTTTTTAAGGGGATACCTGAAATTTTTCGG 4 52 1 GGATACCTGA 0.928353 -58 AAAAGTGGATGGAAACCATAGAATAACATT 11 215 1 GGAAACCATA 0.981953 -26 GGTAACCTTATTATAACAAG 13 1 1 GGTAACCTTA 0.966845 -194 TCTCTTCACTCGTAACCATAATAACACCAT 13 48 0 CGTAACCATA 0.92579 -147 CTTGTAGAACGGTAACCAGAGATAAACGCA 14 161 1 GGTAACCAGA 0.978312 -60 ********** Masking position 5 Map Score: 4.49337 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 45 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 ACCAAACAAAACATTAATATTCCCATCAATC 10 82 1 ACATTAAATT 0.955091 -59 ATAATAATGTACATTAAAATTATTGAATATA 11 62 1 ACATTAAATT 0.955058 -179 AAATACATTAACATTAAAATTAAAGTTATTA 11 132 0 ACATTAAATT 0.955058 -109 CCCATAAATGTTATTCTATGGT 11 229 0 CCATAAAGTT 0.924404 -12 ATTGAATAGAAAATAAATGTTATAAATAGTT 12 74 0 AAATAAAGTT 0.83802 -34 GTGGTGGTTGACATAAAGGTTTGCAATGATC 15 46 1 ACATAAAGTT 0.970966 -68 ******* *** Masking position 6 Map Score: 1.0152 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 AGCGGAAAGTTTAAATATGGATACCATACA 1 18 1 TTAAATATGG 0.648637 -153 ATATTTATAAATAAATCCGGACAGATATTA 1 147 1 ATAAATCCGG 0.927907 -24 CAGTTATATGATACATCCTGTGCCGGGATA 6 51 1 ATACATCCTG 0.777172 -186 AACTCTTTAATCCTGCCTTAATTCT 9 27 0 TTTAATCCTG 0.97126 -15 GTTCAGGCCCTTTAATCCGGTACAGATTTA 10 49 1 TTTAATCCGG 0.970695 -92 GTGAATGTTTAATATTGAATAGAAAAT 12 91 0 TTTAATATTG 0.75133 -17 CTCCCCGTGTATTAATACTGATCACAGGAT 14 20 1 ATTAATACTG 0.891708 -201 AAATGAACAGTTTAATCCTGTGATCAGTAT 14 34 0 TTTAATCCTG 0.97126 -187 ********** Masking position 5 Map Score: 3.8164 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 73 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 TGCGGTGGATCCGCTCACATTGTATGCTCTGAT 1 70 1 CCCTCATTGT 0.911169 -101 CACATTGTATGCTCTGATACGATGTGGTCTGTG 1 85 1 GCCTGACGAT 0.853912 -86 GATGATACCCCCACTGAACTTGTTTTAAACATA 8 34 0 CCCTGATTGT 0.984121 -162 AACATCACCTCTGAAATTATAGATGCACAG 11 8 1 CCCTGATTAT 0.984431 -233 AATTATAGATGCACAGCCCTTATAGTCTGAGTA 11 25 1 GCCAGCTTAT 0.872228 -216 CCGGTAGCCTCCCCTGAGATTATTGAAAATACA 11 156 0 CCCTGATTAT 0.984431 -85 CTCAGTCGGGGCACTGCCATGGTCTCTGCTCTA 12 19 0 GCCTGCTGGT 0.954835 -89 TAAAGTGTTCCCGCTGCGTTTATCTCTGGTTAC 14 172 0 CCCTGCTTAT 0.984121 -49 ** **** **** Masking position 13 Map Score: 3.83648 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 103 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GGAGGACTGGAAGGGGCATATT 4 1 1 GGAGGACGAA 0.943158 -109 CAGCAAATGCTGAATACAAGGAGGTTTCTTGA 4 88 1 TGAATACGGA 0.817039 -22 CAGGTAAGGCGCAAGACTGGAAATCTTGTGGA 6 88 1 GCAAGACGAA 0.751098 -149 GACTGGGATTTGAACCCAGGAGGAGCAAAGCT 6 119 0 TGAACCCGAG 0.949715 -118 ACAGGATTATGGAACACGTGGGATACCCTGTC 8 67 1 GGAACACGGG 0.898347 -129 TTAAAGGGCCTGAACACAAGGAATTATTAAAG 10 32 0 TGAACACGGA 0.966517 -109 GATGAACCCCTGAATGATATATCA 10 127 0 TGAACCCGAA 0.97774 -14 TGGTTACGAGTGAAGAGATGAAGAGGAGACTC 13 60 1 TGAAGAGGAA 0.809096 -135 AAAAAGGGTATGAGGCCTGGAACGGTGAGATC 13 98 1 TGAGGCCGAA 0.961902 -97 CGGTGAGATCTGAGCCCGAGAAAGCTGAGAAG 13 120 1 TGAGCCCGAA 0.969015 -75 ******* *** Masking position 3 Map Score: 4.24543 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 435 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 CGGATTTATTTATAAATATTTCCACAATGCA 1 135 0 TATAAATATT 0.908815 -36 GGTATCCCCTTAAAAAGTTTTTTCGCTGGAC 4 38 0 TAAAAAGTTT 0.665576 -72 CTACGACTCTTATGAAGAATTCGCAAACCCC 6 181 1 TATGAAGATT 0.918424 -56 AATTATTGAATATAAATTTTTTTATTGAATT 11 79 1 TATAAATTTT 0.818224 -162 TTAAAGTTATTATGAAGAATTTAATAGGCTG 11 113 0 TATGAAGATT 0.918424 -128 AAATAAATGTTATAAATAGTTTGTGGTTTTT 12 64 0 TATAAATATT 0.908832 -44 CAAGCTGCAATAAAAATAATTATGGTGTTAT 13 27 1 TAAAAATATT 0.734773 -168 GCTGGCATGAAATGAACAGTTTAATCCTGTG 14 42 0 AATGAACATT 0.727113 -179 CAAGTAGCAGAATAAACACTTAAGTAGCACT 14 134 0 AATAAACATT 0.78913 -87 ATGTGAGATTAATAAAGTGTTCCCGCTGCGT 14 186 0 AATAAAGTTT 0.764212 -35 ******** ** Masking position 6 Map Score: 2.38211 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 24 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 10 GGAGGACTGGAAGGGGCATATTTTC 4 6 1 ACTGGAAGGG 0.733902 -104 GCTAGGCTATCCCGGCACAGGATGTATCAT 6 58 0 CCCGGCACAG 0.985905 -179 TTGCGCCTTACCTGGCTAGGCTATCCCGGC 6 72 0 CCTGGCTAGG 0.86723 -165 AGAGTGAATTCGCGGGACGGGGGTTTGCGA 6 201 0 CGCGGGACGG 0.872032 -36 GAGTCTCATATCTGACAGGGTATCCCACGT 8 82 0 TCTGACAGGG 0.760529 -114 CTTTATGTATCCTGGCAAAGGTATATATAA 8 121 1 CCTGGCAAAG 0.950208 -75 GGCCCTTTAATCCGGTACAGATTTAATAAC 10 54 1 TCCGGTACAG 0.659564 -87 ATGGCAGTGCCCCGACTGAGGCCCTTCACC 12 32 1 CCCGACTGAG 0.696856 -76 GGGTATGAGGCCTGGAACGGTGAGATCTGA 13 103 1 CCTGGAACGG 0.923699 -92 GAGATCTGAGCCCGAGAAAGCTGAGAAGTT 13 124 1 CCCGAGAAAG 0.654915 -71 CTGTCCAAACTGTGGCAAGGAGTATGGAGC 13 154 1 TGTGGCAAGG 0.663138 -41 CACCACGAAAACCGGCACACCTAATCATAT 15 17 0 ACCGGCACAC 0.658614 -97 AACCACGAAAACCGGCAGGGTGATCATTGC 15 68 0 ACCGGCAGGG 0.966761 -46 ********** Masking position 4 Map Score: 5.13923 Number of sites scoring better than the average of aligned sites = 1404 Number in coding regions = 1317 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 CTATTAATATCTGTCCGGATTTATTT 1 155 0 ATATCTGTCC 0.958679 -16 TCACTGATATGAATCTGTCCATATATA 3 8 0 GAATCTGTCC 0.984435 -39 AATTATTAAAGAATCTGTACATAGAATCTT 10 13 0 GAATCTGTAC 0.965615 -128 TTTGGTTATTAAATCTGTACCGGATTAAAG 10 58 0 AAATCTGTAC 0.962989 -83 AAAGCTGAGAAGTTCTGTCCAAACTGTGGC 13 140 1 AGTTCTGTCC 0.91268 -55 ********** Masking position 6 Map Score: 1.55132 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 29 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 AACAAGTTCAGTGGGGGTATCATCACAGGA 8 43 1 GTGGGGGTAT 0.949901 -153 ATTAATACACGGGGAGGTAGAGGGT 14 6 0 GGGGAGGTAG 0.9751 -215 AGGATTTCCTGGGGGTGTTGGACTTATAAT 14 87 0 GGGGGTGTTG 0.970661 -134 TTTTCGTGGTGTGGTGGTTGACATAAAGGT 15 36 1 GTGGTGGTTG 0.97809 -78 GCCGGTTTTCGTGGTTGTAGTGGTTGATGT 15 82 1 GTGGTTGTAG 0.965976 -32 ********** Masking position 8 Map Score: 0.844435 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 145 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 ********** No masking Map Score: -4.31056e-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 TTTTTAGTACCTATTGCAATCTGCGGTGGAT 1 49 1 CTATTGCATC 0.888908 -122 CTATTAATATCTGTCCGGATT 1 160 0 CTATTAATTC 0.885407 -11 TCATTAACCTCCAGTAAGAGT 6 226 0 TCATTAACTC 0.880747 -11 TTTATCATTACCATCCTCTGATTTA 8 5 1 TCATTACCTC 0.807032 -191 ATAAATTTTTTTATTGAATTCATCAGCCTAT 11 90 1 TTATTGAATC 0.899075 -151 ATTCATCAGCCTATTAAATTCTTCATAATAA 11 107 1 CTATTAAATC 0.935131 -134 TATAGTTTTTCCATTGAATTCTCATGGCCGG 11 185 0 CCATTGAATC 0.932659 -56 CGGGAACACTTTATTAATCTCACATAACAGA 14 192 1 TTATTAATTC 0.829678 -29 ******** ** Masking position 3 Map Score: 0.329097 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 64 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 ********** No masking Map Score: -4.31056e-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