AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -irpoH_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 MTH218 140 chaperonin #2 MTH219 51 unknown #3 MTH220 227 flavoprotein A homolog (II) #4 MTH221 97 unknown #5 MTH222 51 unknown #6 MTH223 163 unknown #7 MTH224 300 conserved protein #8 MTH283 107 protein kinase #9 MTH728 106 ATP-dependent 26S protease regulatory subunit 4 #10 MTH785 150 ATP-dependent protease LA #11 MTH786 139 sensory transduction histidine kinase related protein #12 MTH794 121 chaperonin #13 MTH890 145 conserved protein #14 MTH891 59 conserved protein #15 MTH983 104 unknown #16 MTH986 157 conserved protein #17 MTH987 41 conserved protein #18 MTH988 28 conserved protein #19 MTH989 26 conserved protein #20 MTH1009 300 glyceraldehyde 3-phosphate dehydrogenase #21 MTH1289 107 heat shock protein GrpE #22 MTH1291 150 DnaJ protein #23 MTH1639 163 cell division control protein Cdc48 #24 MTH1774 230 conserved protein Motif number 1 GGGTTTAAGGTTCTATAAATAATTTGTGTAGAAGAT 1 107 0 TTATAAATAG 0.518843 -34 GGATGTTCATATTTATATTTATGGATATAGTGTCCA 4 46 0 ATATATTTAT 0.567618 -52 ACACCTGTTATAAATAACTCTGTTATAGATA 6 143 0 TTATAAATAT 0.799321 -21 GAATGACCACAGATTAATATAAAAATTGCAAATGGT 7 186 0 ATTAATATAT 0.485384 -115 ATGGACCAAAATTTTTAAATAATAAGTTTAATACAC 7 247 1 ATTTAAATAG 0.798364 -54 CTAATCATCATTTTATAAATAAAGTTAAAAACAATT 8 61 1 TTATAAATAT 0.755137 -47 TCCCACCCCAATATTTAAATATTACTAGAAACAAGA 9 42 1 ATTTAAATAT 0.917359 -65 GTATACAACAAAATTTAAATAGGAGTGTTCTAAAAT 9 80 1 ATTTAAATAT 0.935659 -27 GAACCCCCATATATTAAAATAAAAATTTGTAAGTAA 10 45 1 ATTAAAATAT 0.596614 -106 GGGTTAGAGGTTCTATAAATAGTTTTCGCTGCTTCT 12 51 0 TTATAAATAT 0.80002 -71 CAATCACCTCAGTTTTAATTATAAATCAGTATGCAG 12 95 0 ATTTAATTAT 0.527139 -27 TTTCTGGGCTATATTTAAATATCTATGTTATCATAA 13 45 0 ATTTAAATAT 0.917359 -101 CACCTCTGATTATTTTATATATCAGTATCGTCATAT 13 83 1 TTTTATATAT 0.877762 -63 CCATTTAATAAGGTTTAATTAAGAGTATACCTCCTT 15 12 1 ATTTAATTAT 0.793506 -93 GCACCCCATGTTCTATATATAAGGAGGTATACTCTT 15 32 0 TTATATATAG 0.429947 -73 AGATACAAAAACCTTTATTTAACCCTTCAAGCCTTT 16 74 0 ATTTATTTAT 0.687634 -84 TTTAATGGATTATTTTATATACTTATCTAAAAGTGC 20 195 0 TTTTATATAT 0.878506 -106 TTATGTCGAAAGGTTTATATAACCTTTTGTAAGTAT 21 16 1 ATTTATATAT 0.811139 -92 TGTTTCGGTAAAGTTTATATACTATTAGATGGATTT 23 35 0 ATTTATATAT 0.909351 -129 CTTTACCGAAACATTTATATATGATTACCTGTACAT 23 58 1 ATTTATATAT 0.866428 -106 TTATCTCTGTTCCTTTAATTAGTTTTTTCATTTAGA 24 89 0 TTTTAATTAT 0.800014 -142 TTATCTCTATTCCTTTAATTAGTTTTTCCGGGATCT 24 144 0 TTTTAATTAT 0.800014 -87 * ******** * Masking position 10 Map Score: 21.2387 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 18 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 2 GCCACCATCTCCAGTCAATTATTTATTTCCAGGAA 1 17 1 CCACATTTTA 0.887181 -124 AAAAATCAGCACCACAAATTGTATAATCACCCCCC 3 136 1 ACCAATTATA 0.863073 -92 CCACCTCACCCCATAAAATTGTATAATTTAATAAT 3 183 1 CCAAATTATA 0.863073 -45 ATATGAACATCCATTCATATGTAAACTGAGGTGAT 4 70 1 CCACATTAAA 0.860617 -28 AGCAGTGGTGCCAGCCACATATTTATTACTTATAC 6 56 1 CCACATTTTA 0.887181 -108 TCCGGTGTGCCCCCTAAATTCTTAAAAGGGAATGG 7 51 0 CCCAATTTAA 0.942747 -250 CATCTAATGGACCAAAATTTTTAAATAATAAGTTT 7 241 1 ACCAATTAAA 0.863073 -60 GATTTATCCCACCCCAATATTTAAATATTACTAGA 9 36 1 ACCAATTAAA 0.863073 -71 AAGATAGTATACAACAAAATTTAAATAGGAGTGTT 9 74 1 ACAAATTAAA 0.754476 -33 TATAAGGGGAACCCCCATATATTAAAATAAAAATT 10 37 1 ACCCATTTAA 0.887181 -114 AATATTTTCACCAGCAATGTATTTAAGATTTTAGT 11 84 0 CCAAATTTTA 0.88923 -56 CTTTCCTCCATGAATCTGTTAAAATGATATAG 13 8 1 CCAAATTTAA 0.88923 -138 CTTTATTTAACCCTTCAAGCCTTTAATAAAGCTTG 16 63 0 CCCCACTTTA 0.671655 -95 ACAGGAATATCCCGGAACATCTTAACCAC 17 5 0 CCCAATTTAA 0.942747 -37 CTAGCCCCCAACCCACATTTTTTTATTCTTGATGA 22 77 1 ACCCATTTTA 0.887181 -74 TATAAACTTTACCGAAACATTTATATATGATTACC 23 52 1 ACCAATTATA 0.863073 -112 *** ** * **** Masking position 7 Map Score: 15.2221 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 96 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 ATTATTTATTTCCAGGAAGAGGAATCCATC 1 34 1 TCCAGGAAGA 0.792607 -107 GAACCTTAAACCCATGGATAA 1 130 1 CCCATGGATA 0.943736 -11 TCCAGTGAAAAAGTTAGGGC 7 1 1 TCCAGTGAAA 0.891037 -300 TTTGAAGAATTCCAGTAATATAAACATTTA 7 97 1 TCCAGTAATA 0.7873 -204 TGGAATTCATCCCATGGATATGACTACCAT 7 161 1 CCCATGGATA 0.943736 -140 GAACCTCTAACCCATTGATAACTGCATACT 12 74 1 CCCATTGATA 0.85591 -48 CCCATCAAAGCCCATGGAAAGCATTATAA 16 139 1 CCCATGGAAA 0.958491 -19 GACAGGAATATCCCGGAACATCTTAACCAC 17 11 0 TCCCGGAACA 0.717044 -31 CCCTCAGAAGCCCATGAGAAGCATTAAAGA 20 126 1 CCCATGAGAA 0.67731 -175 GATCAGGGGTTCCCGTGATAATCTTTAATG 20 147 0 TCCCGTGATA 0.797519 -154 TATAAAATAATCCATTAAAAATAGTATCAG 20 212 1 TCCATTAAAA 0.760493 -89 AAACGCTGTTCCCAGGGAAACCTCTTTGAG 20 256 0 CCCAGGGAAA 0.973723 -45 AACCTCCTATCCCCTGAAAAACGCTGTTCC 20 274 0 CCCCTGAAAA 0.905131 -27 TCCATCCAGATCCCGGAAAAACTAATTAAA 24 137 1 TCCCGGAAAA 0.905131 -94 ********** Masking position 10 Map Score: 11.2479 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 480 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 4 GCCTGAAAAATCAGCACCACAAATTGTATAA 3 131 1 TCAGCACCCA 0.956278 -97 ACAAATTGTATAATCACCCCCCCCAAAATCA 3 149 1 TAATCACCCC 0.964635 -79 CCCCCCAAAATCAGCACCACCTCACCCCATA 3 167 1 TCAGCACCCC 0.963744 -61 TTAATCACCTCAGTTTACATAT 4 86 0 TAATCACCCA 0.957344 -12 CCAAATTAAGGAATGACCACAGATTAATATA 7 201 0 GAATGACCCA 0.71061 -100 AAATTTAATCTAATCATCACACTGTAAAAG 8 10 0 TAATCATCCA 0.577376 -98 TCAATCACCTCAGTTTTAATTA 12 110 0 CAATCACCCA 0.926182 -12 ATGAAATGACCCTTCACCACCTGCAGAGATA 16 105 0 CCTTCACCCC 0.948501 -53 AAGGGTCATTTCATGGCCCCATCAAAGCCCA 16 122 1 TCATGGCCCA 0.797276 -36 TGTGGATGAAGCTGCACCCCCTATTTCCTTT 20 66 1 GCTGCACCCC 0.853346 -235 CCGGATCCGCCATTCACCGCACTTTTAGATA 20 177 1 CATTCACCCA 0.877393 -124 GCCGCCCCTGTCTTCACCCTCAGAGGCTGTG 22 11 0 TCTTCACCTC 0.66727 -140 ATCTATGGTATCATCGCCGCCCCTGTCTTCA 22 26 0 TCATCGCCCC 0.943714 -125 GGGGGCTAGTTCTTGACCTCAAAGTCTGCAT 22 55 0 TCTTGACCCA 0.885423 -96 ******** ** Masking position 8 Map Score: 11.5588 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 645 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 AGAAGATCCTGTGGGTTTCTGGTTTCTGCAGA 1 82 0 GTGGGTTTGG 0.991317 -59 TTATCCATGGGTTTAAGGTTCTATAAAT 1 123 0 ATGGGTTTGG 0.989534 -18 TCACTTAAACATTGGTTGATGGTTGGAATTCA 7 138 1 ATTGGTTGGG 0.91045 -163 GCAGTTATCAATGGGTTAGAGGTTCTATAAAT 12 67 0 ATGGGTTAGG 0.966372 -55 ATAATCAGAGGTGTGTTTCTGGGCTATATTTA 13 64 0 GTGTGTTTGG 0.936747 -82 ATAAAAAAATGTGGGTTGGGGGCTAGTTCTTG 22 71 0 GTGGGTTGGG 0.989546 -80 AATGATGGGTATGGGTTTAAGGAGTTTGTAGG 24 16 1 ATGGGTTTGG 0.989534 -215 ******** ** Masking position 6 Map Score: 8.83266 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 18 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 TTGAACTTCATTATTAAATTATACAATTTT 3 197 0 TTATTAAATT 0.672625 -31 ATTCTTCAAATTATTAAATGATCCGGTGTG 7 77 0 TTATTAAATG 0.959211 -224 TTAGTTAACTTTATTAGATGAATGAAATTT 8 35 0 TTATTAGATG 0.910006 -73 TTAACTTTATTTATAAAATGATGATTAGTT 8 59 0 TTATAAAATG 0.767929 -49 TATTATCAAGTTATTAAAGGGCCAGAT 13 129 1 TTATTAAAGG 0.962233 -17 TAATTAAACCTTATTAAATGGT 15 3 0 TTATTAAATG 0.959211 -102 GTCTCAAGCTTTATTAAAGGCTTGAAGGGT 16 59 1 TTATTAAAGG 0.962233 -99 AGTTTATATACTATTAGATGGATTTTGTGC 23 30 0 CTATTAGATG 0.678332 -134 ATGAAAAAACTAATTAAAGGAACAGAGATA 24 94 1 TAATTAAAGG 0.876272 -137 CCGGAAAAACTAATTAAAGGAATAGAGATA 24 149 1 TAATTAAAGG 0.876272 -82 ********** Masking position 6 Map Score: 10.049 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 8 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 CTGCAGAAACCAGAAACCCACAGGATCTTCTACAC 1 83 1 CAACACAGGA 0.827781 -58 ACAAATTGTATAATCACCCCCCCCAAAATCAGCAC 3 149 1 TAACCCCCCA 0.820396 -79 ATTCAGTGAACCCCCAGAGTAGAGGCAG 5 4 1 CAACCCCAGA 0.986083 -48 AGAGTAGAGGCAGAGAACGCCCGGAATGGTGATAA 5 26 1 CAACCCCGGA 0.994013 -26 TTAACCATCTCCCACAATGAACATCT 11 124 0 TAACCCCACA 0.910232 -16 CATAGATATTTAAATATAGCCCAGAAACACACCTC 13 54 1 TAAACCCAGA 0.905344 -92 ATGTACCTGACAGGAATATCCCGGAACATCTTAAC 17 14 0 CAAACCCGGA 0.983872 -28 CAGCTTCATCCACAGAGAAACCGCAGTTATTGTTC 20 45 0 CAAAACCGCA 0.89722 -256 CCGGTTAAATTAAATATCAACCGGAATCATAATAA 23 126 1 TAACACCGGA 0.957287 -38 TTCCCTTCTCCATCCAGATCCCGGAAAAACTAATT 24 129 1 CAAACCCGGA 0.983872 -102 AACTTTAAAGCATACATCCAGCAGATGTCTTAAAA 24 182 1 CAACAGCAGA 0.752485 -49 ** * * ****** Masking position 6 Map Score: 6.70541 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 233 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ATGGATTCCTCTTCCTGGAAATAAATAATT 1 33 0 CTTCCTGGAA 0.951794 -108 TTTCTGCAGACTTACTGGAAGAGTTGCAGA 1 62 0 CTTACTGGAA 0.984655 -79 TCACATCATATTTACTGGCAGACTAGTTGT 3 47 1 TTTACTGGCA 0.924689 -181 ACTGGCGGTTCTTGCTGGCATGTAGGAGGT 6 15 0 CTTGCTGGCA 0.917903 -149 CCACTGCTGACTAACTGGAACTGGCGGTTC 6 34 0 CTAACTGGAA 0.919996 -130 AAATGTTTATATTACTGGAATTCTTCAAAT 7 96 0 ATTACTGGAA 0.955913 -205 ATATTTAAATATTACTAGAAACAAGATAGT 9 52 1 ATTACTAGAA 0.832196 -55 GTAACCTAAATTTACTAGAATATTCCGGTT 23 102 1 TTTACTAGAA 0.832196 -62 ********** Masking position 10 Map Score: 4.64203 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 36 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 GGAGACTGAGGCTGGTAACC 7 291 1 GCTGGTAACC 0.915336 -10 TTGAGGAATGACTGGTTATCAAATTGAAGT 14 27 0 ACTGGTTATC 0.935559 -33 TTATTGTTCAGCTGGTTAGCAGCGATCAGT 20 24 0 GCTGGTTAGC 0.931046 -277 TAAAGTTACCGGAGGTTACCTATAACCTTA 21 60 0 GGAGGTTACC 0.861549 -48 TAATACATGTACAGGTAATCATATATAAAT 23 70 0 ACAGGTAATC 0.891586 -94 ATTATGGTGGGCAGGTTATCCTACAAACTC 24 37 0 GCAGGTTATC 0.975027 -194 GGAGAAGGGAACATGTTATCTCTGTTCCTT 24 110 0 ACATGTTATC 0.710318 -121 ********** Masking position 8 Map Score: 0.846503 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 102 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ATGGGTTTAAGGTTCTATAAATAATTTGTGT 1 114 0 GTTCTATAAA 0.962315 -27 ATGGGTTAGAGGTTCTATAAATAGTTTTCGC 12 58 0 GTTCTATAAA 0.962315 -64 GGATTCTGTAAAGATCCGATTC 18 2 1 GTTCTGTAAA 0.981392 -27 GTAAAGATCCGATTCTGTCAA 18 18 1 GTTCTGTCAA 0.941955 -11 ACTTACAAAAGGTTATATAAACCTTTCGACA 21 19 0 GTTATATAAA 0.768099 -89 GGTAACTTTAATTTCTGTAAAAAATCAAAGG 21 80 1 ATTCTGTAAA 0.872457 -28 ATATATAAATGTTTCGGTAAAGTTTATATAC 23 49 0 GTTCGGTAAA 0.941949 -115 * ********* Masking position 10 Map Score: 3.41977 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 11 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ATTCAGTGAACCCCCAGAGTAGAG 5 5 1 AGTGAACCCC 0.929464 -47 AAATATGTGGCTGGCACCACTGCTGACTAA 6 50 0 CTGGCACCAC 0.873156 -114 AAGAATTTAGGGGGCACACCGGATCATTTA 7 63 1 GGGGCACACC 0.873887 -238 ACCTTTATAAGGGGAACCCCCATATATTAA 10 32 1 GGGGAACCCC 0.75914 -119 AGATTTCATCATGGCACCCCATGTTCTATA 15 51 0 ATGGCACCCC 0.970323 -54 TGTGGATGAAGCTGCACCCCCTATTTCCTT 20 66 1 GCTGCACCCC 0.945139 -235 AAGATTATCACGGGAACCCCTGATCCCGGA 20 152 1 CGGGAACCCC 0.975815 -149 ********** Masking position 6 Map Score: 4.44738 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 208 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 ACAATTAAAGTATAATCATACCATAAT 8 91 1 TATATTCCAA 0.904348 -17 CTACTTAAAATATTTTACTTACAAATTTTTATTTT 10 60 0 TATTTTACAA 0.845902 -91 CATAATACTATATCATTTTAACAGATTCATGGAGG 13 15 0 TATATTACAA 0.96852 -131 AATGATATAGTATTATGATAACATAGATATTTAAA 13 33 1 TATATTACAA 0.967597 -113 GTATAAGGTGTATAATCCTCTCAGAACATTAAAAA 16 23 0 TATATTTCAA 0.864762 -135 ACCTTATAGCTATTATACTTACAAAAGGTTATATA 21 31 0 TATATTACAA 0.968384 -77 TCTAATAGTATATAAACTTTACCGAAACATTTATA 23 42 1 TATAATACCA 0.757622 -122 CCTGTACATGTATTATAGTAACCTAAATTTACTAG 23 85 1 TATATTACCA 0.944841 -79 *** ** * *** * Masking position 2 Map Score: 1.50576 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 11 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 TTCTGGTTTCTGCAGACTTACTGGAAGAGT 1 68 0 TGCAGACTTA 0.937683 -73 CAATTTGTGGTGCTGATTTTTCAGGCTGGA 3 127 0 TGCTGATTTT 0.946962 -101 GGTGAGGTGGTGCTGATTTTGGGGGGGGTG 3 163 0 TGCTGATTTT 0.946962 -65 CTGGCACCACTGCTGACTAACTGGAACTGG 6 40 0 TGCTGACTAA 0.873836 -124 GATAACTGCATACTGATTTATAATTAAAAC 12 90 1 TACTGATTTA 0.734192 -32 ATACCATAGATGCAGACTTTGAGGTCAAGA 22 46 1 TGCAGACTTT 0.937683 -105 ********** Masking position 6 Map Score: 0.536107 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ********** No masking Map Score: -4.15424e-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 15 ********** No masking Map Score: -4.15424e-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