AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -irpoH_mthe_opreg_100.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 MTH283 107 protein kinase #3 MTH728 106 ATP-dependent 26S protease regulatory subunit 4 #4 MTH785 150 ATP-dependent protease LA #5 MTH794 121 chaperonin #6 MTH890 145 conserved protein #7 MTH891 59 conserved protein #8 MTH986 157 conserved protein #9 MTH987 41 conserved protein #10 MTH988 28 conserved protein #11 MTH989 26 conserved protein #12 MTH1009 300 glyceraldehyde 3-phosphate dehydrogenase #13 MTH1289 107 heat shock protein GrpE #14 MTH1291 150 DnaJ protein #15 MTH1639 163 cell division control protein Cdc48 #16 MTH1774 230 conserved protein Motif number 1 AATTGTTTTTAACTTTATTTATAAAATGATGATTAG 2 61 0 ATATTTATAA 0.72621 -47 TCTTGTTTCTAGTAATATTTAAATATTGGGGTGGGA 3 42 0 ATATTTAAAT 0.949397 -65 ATTTTAGAACACTCCTATTTAAATTTTGTTGTATAC 3 80 0 ATATTTAAAT 0.968491 -27 TTACTTACAAATTTTTATTTTAATATATGGGGGTTC 4 45 0 ATATTTTAAT 0.667044 -106 GCTTCTCCAGAAGAATATTTAACGAAGATGGAACTT 5 21 0 ATATTTAACA 0.772682 -101 AGAAGCAGCGAAAACTATTTATAGAACCTCTAACCC 5 51 1 ATATTTATAA 0.812523 -71 CTGCATACTGATTTATAATTAAAACTGAGGTGATTG 5 95 1 ATAATTAAAT 0.568065 -27 TTATGATAACATAGATATTTAAATATAGCCCAGAAA 6 45 1 ATATTTAAAT 0.859837 -101 ATATGACGATACTGATATATAAAATAATCAGAGGTG 6 83 0 ATATATAAAA 0.9351 -63 AAAGGCTTGAAGGGTTAAATAAAGGTTTTTGTATCT 8 74 1 ATAAATAAAT 0.508185 -84 GCACTTTTAGATAAGTATATAAAATAATCCATTAAA 12 195 1 ATATATAAAA 0.942487 -106 ATACTTACAAAAGGTTATATAAACCTTTCGACATAA 13 16 0 ATATATAAAT 0.560747 -92 AAATCCATCTAATAGTATATAAACTTTACCGAAACA 15 35 1 ATATATAAAT 0.945807 -129 ATGTACAGGTAATCATATATAAATGTTTCGGTAAAG 15 58 0 ATATATAAAT 0.897129 -106 TCTAAATGAAAAAACTAATTAAAGGAACAGAGATAA 16 89 1 ATAATTAAAA 0.903786 -142 AGATCCCGGAAAAACTAATTAAAGGAATAGAGATAA 16 144 1 ATAATTAAAA 0.903786 -87 * ******** * Masking position 7 Map Score: 19.9608 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 14 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 AGAAGATCCTGTGGGTTTCTGGTTTCTGCAGA 1 82 0 GTGGGTTTGG 0.996541 -59 TTATCCATGGGTTTAAGGTTCTATAAAT 1 123 0 ATGGGTTTGG 0.995826 -18 GCAGTTATCAATGGGTTAGAGGTTCTATAAAT 5 67 0 ATGGGTTAGG 0.983294 -55 ATAATCAGAGGTGTGTTTCTGGGCTATATTTA 6 64 0 GTGTGTTTGG 0.973938 -82 AATGCTTCTCATGGGCTTCTGAGGGAAAAGGA 12 119 0 ATGGGCTTGA 0.90496 -182 ATAAAAAAATGTGGGTTGGGGGCTAGTTCTTG 14 71 0 GTGGGTTGGG 0.990596 -80 AATGATGGGTATGGGTTTAAGGAGTTTGTAGG 16 16 1 ATGGGTTTGG 0.995826 -215 ******** ** Masking position 7 Map Score: 9.75552 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 22 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 3 TCAGTATGCAGTTATCAATGGGTTAGAGGTTC 5 74 0 GTATCAAGGG 0.898601 -48 ATATTATCAAGTTATTAAAGGGCCAGAT 6 128 1 GTATTAAGGG 0.91485 -18 TTATAATGCTTTCCATGGGCTTTGATGGG 8 139 0 GTTTCCAGGG 0.991931 -19 GTGGTTAAGATGTTCCGGGATATTCCTGTC 9 9 1 GTGTTCCGGA 0.881638 -33 AATCTTTAATGCTTCTCATGGGCTTCTGAGGG 12 126 0 GTTCTCAGGG 0.975361 -175 AAGCATTAAAGATTATCACGGGAACCCCTGAT 12 144 1 GTTATCAGGG 0.963911 -157 AACTCAAAGAGGTTTCCCTGGGAACAGCGTTT 12 254 1 GTTTCCCGGG 0.990235 -47 TGGGAACAGCGTTTTTCAGGGGATAGGAGGTT 12 272 1 GTTTTCAGGG 0.993335 -29 CCTTTAATTAGTTTTTCCGGGATCTGGATGGA 16 137 0 GTTTTCCGGA 0.960329 -94 * ****** *** Masking position 3 Map Score: 8.97585 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 227 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 ATGATGATTAGTTAACTTTATTAGATGAATG 2 41 0 GTAACTTTAT 0.919905 -67 TTTAATTGTTTTTAACTTTATTTATAAAATG 2 69 0 TTAACTTTAT 0.848455 -39 GAAGATCCCTTTTTATTTTATACTAGATTTA 3 11 1 TTTATTTTAT 0.639824 -96 ACATGGTGGAGATACCTTTATAAGGGGAACC 4 19 1 GTACCTTTAT 0.904056 -132 ACTTACAAATTTTTATTTTAATATATGGGGG 4 48 0 TTTATTTTAA 0.776057 -103 TAACTGTGATTTTAATTTTAACCACTTCACT 4 108 1 TTAATTTTAA 0.776028 -43 AGATTACTTTAAGTTCCATCTT 5 2 1 GTTACTTTAA 0.957276 -120 TCACCTCAGTTTTAATTATAAATCAGTATGC 5 97 0 TTAATTATAA 0.444921 -25 ACACACCTCTGATTATTTTATATATCAGTAT 6 80 1 GTTATTTTAT 0.78466 -66 TGCACCCCCTATTTCCTTTAAATCCCGGGTC 12 78 1 ATTCCTTTAA 0.739041 -223 GAGGGAAAAGGATACCTCTAAGGACCCGGGA 12 100 0 GTACCTCTAA 0.713808 -201 ATTTTTAATGGATTATTTTATATACTTATCT 12 203 0 GTTATTTTAT 0.78466 -98 GTTACCGGAGGTTACCTATAACCTTATAGCT 13 55 0 GTACCTATAA 0.809597 -53 GGTAACCTCCGGTAACTTTAATTTCTGTAAA 13 70 1 GTAACTTTAA 0.957276 -38 AGTAAATTTAGGTTACTATAATACATGTACA 15 87 0 GTTACTATAA 0.838258 -77 ATGTTATCTCTGTTCCTTTAATTAGTTTTTT 16 97 0 TTTCCTTTAA 0.899618 -134 TAGTTATCTCTATTCCTTTAATTAGTTTTTC 16 152 0 TTTCCTTTAA 0.899618 -79 AATAGAGATAACTAACTTTAAAGCATACATC 16 169 1 ATAACTTTAA 0.775375 -62 * ********* Masking position 7 Map Score: 15.4859 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 75 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 TGACAGGAATATCCCGGAACATCTTAACCA 9 12 0 ATCCCGGAAC 0.974943 -30 TTTCCTTTAAATCCCGGGTCCTTAGAGGTA 12 89 1 ATCCCGGGTC 0.962696 -212 ATTAAAGATTATCACGGGAACCCCTGATCC 12 148 1 ATCACGGGAA 0.908548 -153 GGAACCCCTGATCCCGGATCCGCCATTCAC 12 164 1 ATCCCGGATC 0.988381 -137 CTCCATCCAGATCCCGGAAAAACTAATTAA 16 136 1 ATCCCGGAAA 0.966001 -95 ********** Masking position 2 Map Score: 5.74475 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 25 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 TTCCAGTAAGTCTGCAGAAACCAGAAACCCA 1 72 1 TCTGCAGAAC 0.957109 -69 ACACAAATTATTTATAGAACCTTAAACCCAT 1 114 1 TTTATAGAAC 0.959822 -27 TAAATATTCTTCTGGAGAAGCAGCGAAAACT 5 36 1 TCTGGAGAAC 0.810967 -86 GCGAAAACTATTTATAGAACCTCTAACCCAT 5 58 1 TTTATAGAAC 0.959822 -64 GAATCGGATCTTTACAGAATCC 10 2 0 TTTACAGAAC 0.986467 -27 TTGACAGAATCGGATCTTTAC 10 18 0 TTGACAGAAC 0.969081 -11 TATAAACCTTTCGACATAATCTAC 13 4 0 TCGACATAAC 0.794142 -104 TGTCGAAAGGTTTATATAACCTTTTGTAAGT 13 19 1 TTTATATAAC 0.80506 -89 CCTTTGATTTTTTACAGAAATTAAAGTTACC 13 80 0 TTTACAGAAT 0.864282 -28 GTATATAAACTTTACCGAAACATTTATATAT 15 49 1 TTTACCGAAC 0.938275 -115 ********* * Masking position 8 Map Score: 7.1022 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 64 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 ATTGACTGGAGATGGTGGCGTGTGG 1 6 0 GATGGTGGCG 0.952641 -135 ACCATGCAACATGGTGGAGATACCTTTAT 4 10 1 CATGGTGGAG 0.926296 -141 TATCTCTGCAGGTGGTGAAGGGTCATTTCA 8 105 1 GGTGGTGAAG 0.981503 -53 AAAGGAAATAGGGGGTGCAGCTTCATCCAC 12 67 0 GGGGGTGCAG 0.966517 -234 ATGGGCTTCTGAGGGAAAAGGATACCTCTA 12 111 0 GAGGGAAAAG 0.843095 -190 CACAGCCTCTGAGGGTGAAGACAGGGGCGG 14 11 1 GAGGGTGAAG 0.989608 -140 CCGGGATCTGGATGGAGAAGGGAACATGTT 16 123 0 GATGGAGAAG 0.971675 -108 ********** Masking position 5 Map Score: 4.2121 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 362 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ATTTAATCTAATCATCACACTGTAAAAG 2 8 0 ATCATACACT 0.97232 -100 ATTATGGTATGATTATACTTTAATTGTTT 2 89 0 ATGATATACT 0.956163 -19 TATCTATGTTATCATAATACTATATCATTTT 6 31 0 ATCATATACT 0.976271 -115 TATATCTTATATGACGATACTGATATATAAA 6 96 0 ATGACATACT 0.890175 -50 ATGCTGTTATCATCACACTTCAATTTGAT 7 9 1 ATCATACACT 0.97232 -51 ATCAACCGGAATCATAATAATAATCATAAAG 15 141 1 ATCATATAAT 0.855481 -23 ***** ***** Masking position 7 Map Score: 2.64624 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 9 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 CCCTTATAAAGGTATCTCCACCATGTTGCA 4 15 0 GGTATCTCCA 0.880317 -136 TCTATAAATAGTTTTCGCTGCTTCTCCAGA 5 46 0 GTTTTCGCTG 0.922566 -76 TAAAGGTTTTTGTATCTCTGCAGGTGGTGA 8 93 1 TGTATCTCTG 0.919135 -65 CAATAACTGCGGTTTCTCTGTGGATGAAGC 12 48 1 GGTTTCTCTG 0.985358 -253 AACTCAAAGAGGTTTCCCTGGGAACAGCGT 12 254 1 GGTTTCCCTG 0.960948 -47 AAGGGAACATGTTATCTCTGTTCCTTTAAT 16 106 0 GTTATCTCTG 0.976973 -125 TTTAAAGTTAGTTATCTCTATTCCTTTAAT 16 161 0 GTTATCTCTA 0.920472 -70 ********** Masking position 5 Map Score: 4.31098 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 140 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 CACGCCACCATCTCCAGTCAATTATTTATT 1 14 1 TCTCCAGTCA 0.9568 -127 CAATTATTTATTTCCAGGAAGAGGAATCCA 1 32 1 TTTCCAGGAA 0.776619 -109 ATCTGCAACTCTTCCAGTAAGTCTGCAGAA 1 61 1 CTTCCAGTAA 0.929685 -80 TATTCAAATGCCTCCATTAAGTGAAGTGGT 4 128 0 CCTCCATTAA 0.973295 -23 CTTTCCTCCATGAATCTGTTAAAA 6 5 1 CCTCCATGAA 0.960822 -141 GATCCCGGATCCGCCATTCACCGCACTTTT 12 173 1 CCGCCATTCA 0.904656 -128 TTATAGGTAACCTCCGGTAACTTTAATTTC 13 65 1 CCTCCGGTAA 0.938847 -43 CATGTTCCCTTCTCCATCCAGATCCCGGAA 16 125 1 TCTCCATCCA 0.836221 -106 ********** Masking position 10 Map Score: 2.775 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 344 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 11 TGAGGAATGACTGGTTATCAAATTGAAGTG 7 26 0 CTGGTTATCA 0.973952 -34 TATTGTTCAGCTGGTTAGCAGCGATCAGTA 12 23 0 CTGGTTAGCA 0.975824 -278 AAAATAGTATCAGGTTAGGAATTTAAACTC 12 229 1 CAGGTTAGGA 0.942615 -72 AATACATGTACAGGTAATCATATATAAATG 15 69 0 CAGGTAATCA 0.942145 -95 TTATGGTGGGCAGGTTATCCTACAAACTCC 16 36 0 CAGGTTATCC 0.960216 -195 ********** Masking position 5 Map Score: 1.46627 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 12 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 TATATAAAATAATCAGAGGTGTGTTTCTGG 6 74 0 AATCAGAGGT 0.892704 -72 TTCATGGCCCCATCAAAGCCCATGGAAAGC 8 131 1 CATCAAAGCC 0.904913 -27 GGGCCTCAGAGCTCAGTGAACTT 11 4 1 CCTCAGAGCT 0.975166 -23 AATCCCGGGTCCTTAGAGGTATCCTTTTCC 12 98 1 CCTTAGAGGT 0.912217 -203 TATCCTTTTCCCTCAGAAGCCCATGAGAAG 12 117 1 CCTCAGAAGC 0.942802 -184 TTCTGTAAAAAATCAAAGGTGAACTG 13 92 1 AATCAAAGGT 0.764828 -16 CTGTCTTCACCCTCAGAGGCTGTG 14 5 0 CCTCAGAGGC 0.993271 -146 TAGTTCTTGACCTCAAAGTCTGCATCTATG 14 50 0 CCTCAAAGTC 0.899254 -101 ********** Masking position 5 Map Score: 4.48655 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 647 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 ********** No masking Map Score: 6.18415e-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: 6.18415e-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: 6.18415e-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