AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_mthe_reg_100.orf -o00380_mthe_100.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 MTH127 199 deoxyhypusine synthase #2 MTH147 23 phenylacrylic acid decarboxylase #3 MTH148 47 conserved protein #4 MTH150 75 conserved protein #5 MTH248 195 conserved protein #6 MTH249 64 conserved protein #7 MTH250 23 tRNA intron endonuclease #8 MTH251 54 tryptophanyl-tRNA synthetase #9 MTH1014 127 conserved protein #10 MTH1348 139 precorrin-2 methyltransferase #11 MTH1496 194 amidase #12 MTH1514 125 precorrin-6Y methylase Motif number 1 CATATCACCCCTCCACGAAAAGATTTTAGGAGTC 1 63 1 CCCCGAAAAT 0.836778 -137 GTCTTGCCCCGTTAATCTGTTCCAGGAGGT 3 28 0 CCCTTAATCT 0.969613 -20 TCGCCACCGGCTCCATGAATATATACTAGAAGCA 4 11 1 CCCTGAATAT 0.991483 -65 CCATGGAAGACCCCTTTAACAGATGCAGCCATAC 6 24 1 CCCTTAACAT 0.972221 -41 TCATATCACCGTTATTAAGTCATTTCTGTT 8 35 0 CCCTTATTAT 0.985094 -20 ACAAAGTCCTCCTTTATTAACTATATTTACTA 9 106 0 CCCTTATTAT 0.985094 -22 ATAGTTCCACCCCCTTAAATAGGTCC 10 3 0 CCCTAAATAT 0.966999 -137 TATCCAGACCCGCCTTTATTATCATTATTTTTCT 10 57 0 CCCTTATTAA 0.884452 -83 TAGAACACCTTTAATAACTCTGTAGACAT 10 121 0 CCCTTAATAT 0.994649 -19 ATTTCATTTCCAACACTAATAAATGTGAGATGTT 11 42 0 CACCTAATAT 0.899503 -153 TAAGTCTGATCAACCTTAATAGCTGCCATGACTG 11 144 0 CACTTAATAT 0.962722 -51 ATTGCTGAGACCCAGTGAATATCTGCCTCCGTGC 12 76 1 CCATGAATAT 0.893086 -50 * ** ****** * Masking position 8 Map Score: 17.2848 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 58 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 GCTAAGGCATGCACTCGAGATCTGTTATTT 1 148 1 GCACTCGAGA 0.886061 -52 GGACCCGGGGCCCCTCAAGGTATAATATTC 5 41 0 CCCCTCAAGG 0.984949 -155 GTCCCGTGATGCCCGGGAGGCCTTCCGTGT 5 67 1 GCCCGGGAGG 0.996652 -129 TTCCCCAGGAACACGGAAGGCCTCCCGGGC 5 77 0 ACACGGAAGG 0.948659 -119 GGGGAATATTCCGCTGGAGGGGTGCTGGTT 5 101 1 CCGCTGGAGG 0.988337 -95 GGGTGTCAGCGCCCTGAAGGATTTCCCCTG 5 150 1 GCCCTGAAGG 0.992316 -46 TGAAGGATTTCCCCTGGAGGGTCAGGGTTT 5 164 1 CCCCTGGAGG 0.996747 -32 CAACCAGCACTCACGGGAGGT 7 13 1 TCACGGGAGG 0.968522 -11 CGGAAACTCCACCCTCGAGGCAGTCATGGC 11 124 1 ACCCTCGAGG 0.988747 -71 ********** Masking position 8 Map Score: 16.587 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 527 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 ATATCCTTGTCCAGGACTCCTAAAATCTTT 1 81 0 CCAGGACTCC 0.993435 -119 ATCACGGGACCCGGGGCCCCTCAAGGTATA 5 47 0 CCGGGGCCCC 0.982244 -149 GGAAGGCCTCCCGGGCATCACGGGACCCGG 5 63 0 CCGGGCATCA 0.705748 -133 GGAATATTCCCCAGGAACACGGAAGGCCTC 5 83 0 CCAGGAACAC 0.901984 -113 CCCTGGAAAACCAGCACCCCTCCAGCGGAA 5 109 0 CCAGCACCCC 0.990148 -87 CTCAACCAGCACTCACGGGAGGT 7 6 1 CCAGCACTCA 0.931045 -18 CTGGAAATATCCAGACCCGCCTTTATTATC 10 68 0 CCAGACCCGC 0.882154 -72 CCATGGACCGCCGGGACAGCCATGACAGTA 11 92 0 CCGGGACAGC 0.961355 -103 TTAATAGCTGCCATGACTGCCTCGAGGGTG 11 133 0 CCATGACTGC 0.890491 -62 TTATAATATCCCGGCACTACTTATTAAT 12 9 0 CCGGCACTAC 0.958475 -117 ********** Masking position 2 Map Score: 9.13359 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 1048 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 ACAGTTATCAATCCAGGGAA 1 190 1 ATCCAGGGAA 0.801094 -10 CCTCCCGGGCATCACGGGACCCGGGGCCCC 5 57 0 ATCACGGGAC 0.875265 -139 GCCTTCCGTGTTCCTGGGGAATATTCCGCT 5 86 1 TTCCTGGGGA 0.846344 -110 GGTGCTGGTTTTCCAGGGAACTCTATCTGG 5 121 1 TTCCAGGGAA 0.527595 -75 AACCCTGACCCTCCAGGGGAAATCCTTCAG 5 163 0 CTCCAGGGGA 0.941302 -33 CGCTGCAGTCATCCATGGAAGACCCCTTTA 6 12 1 ATCCATGGAA 0.70685 -53 ACCCCTCTTAATCAGGGGAACCACAATTTA 9 15 1 ATCAGGGGAA 0.864825 -113 GTCTGGATATTTCCAGAGAAGGATGACCAG 10 82 1 TTCCAGAGAA 0.759582 -58 GGAGTTTCCGGTCCATGGACCGCCGGGACA 11 104 0 GTCCATGGAC 0.487974 -91 TTATTATAATATCCCGGCACTACTTATTAA 12 12 0 ATCCCGGCAC 0.846978 -114 ********** Masking position 2 Map Score: 8.54368 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 648 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TGAGGGATATTAATTGCACCAGCTTTCATA 1 37 1 TAATTGCACC 0.956558 -163 GCACCAGCTTTCATATCACCCCTCCACGAA 1 52 1 TCATATCACC 0.961312 -148 CAAGGATATATAATTGCACCAGCTTAACAG 1 102 1 TAATTGCACC 0.956558 -98 GAATATATACTAGAAGCACCATAGTTCTAA 4 27 1 TAGAAGCACC 0.840809 -49 GCTTAAGCCGTCATAGTAGCCAAA 8 5 0 TCATAGTAGC 0.829802 -50 TCATATCACCGTTATTAAGT 8 45 0 TCATATCACC 0.961312 -10 TAAACTTATATAGTTCCACCCCCTTAAATA 10 16 0 TAGTTCCACC 0.799804 -124 TCAGGGTCAATCTACCAATCTTTAAA 11 7 1 TCAATCTACC 0.63021 -188 CTCGAGGCAGTCATGGCAGCTATTAAGGTT 11 137 1 TCATGGCAGC 0.911602 -58 CCCTATTCCATCAAATCAGCACGGAGGCAG 12 98 0 TCAAATCAGC 0.833107 -28 ********** Masking position 8 Map Score: 6.34995 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 521 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 GGTGCAATTAATATCCCTCAGGTGTTTGATGT 1 25 0 ATATCCTCGG 0.993008 -175 TCAAGGTATAATATTCCTCAGGAACTCAACAC 5 25 0 ATATCCTCGG 0.993008 -171 TTCCTGGGGAATATTCCGCTGGAGGGGTGCTG 5 96 1 ATATCCGCGG 0.991579 -100 TGGTCTGGTCATCCTTCTCTGGAAATATCCAG 10 84 0 ATCCTCTCGG 0.914418 -56 TTTCCGGTCCATGGACCGCCGGGACAGCCATG 11 98 0 ATGGCCGCGG 0.96886 -97 CCCAGTGAATATCTGCCTCCGTGCTGATTTGA 12 86 1 ATCTCCTCGT 0.959544 -40 **** **** ** Masking position 2 Map Score: 3.31267 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 120 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 TCAGGAACTCAACACTCTGTCTGACCTCA 5 10 0 AACACTCTGT 0.925602 -186 GGTTTTCCAGGGAACTCTATCTGGGGTGTC 5 127 1 GGAACTCTAT 0.959681 -69 TTAAGGGGGTGGAACTATATAAGTTTAGAG 10 19 1 GGAACTATAT 0.755349 -121 ATTTTTCTGTGGCACTCTCTAAACTTATAT 10 35 0 GGCACTCTCT 0.991052 -105 AACACCTTTAATAACTCTGTAGACATGATG 10 117 0 ATAACTCTGT 0.773551 -23 GTTGGTATGGGACACTCTCTTTAATGGAGA 12 45 1 GACACTCTCT 0.973978 -81 ACTGGGTCTCAGCAATCTCTCCATTAAAGA 12 62 0 AGCAATCTCT 0.874154 -64 ********** Masking position 4 Map Score: 1.89527 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 182 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 TGCAATTAATATCCCTCAGGTGTTTGATGT 1 25 0 ATCCCTCAGG 0.948818 -175 AAGGTATAATATTCCTCAGGAACTCAACAC 5 25 0 ATTCCTCAGG 0.983673 -171 CCAGCGGAATATTCCCCAGGAACACGGAAG 5 88 0 ATTCCCCAGG 0.994423 -108 CCTGGGGAATATTCCGCTGGAGGGGTGCTG 5 98 1 ATTCCGCTGG 0.985061 -98 CCCCAGATAGAGTTCCCTGGAAAACCAGCA 5 123 0 AGTTCCCTGG 0.902593 -73 CCCTGAAGGATTTCCCCTGGAGGGTCAGGG 5 161 1 TTTCCCCTGG 0.982841 -35 ATAAATTGTGGTTCCCCTGATTAAGAGGGG 9 16 0 GTTCCCCTGA 0.916745 -112 ********** Masking position 5 Map Score: 7.27723 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 211 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 CATCCATGGAAGACCCCTTTAACAGATGCA 6 21 1 AGACCCCTTT 0.97078 -44 ATAGACCCCTCTTAATCAGGGG 9 3 1 AGACCCCTCT 0.975413 -125 ACAAAGTCCTCCTTTATTAACTAT 9 114 0 AGTCCTCCTT 0.910362 -14 TTATATAGTTCCACCCCCTTAAATAGGTCC 10 11 0 CCACCCCCTT 0.940541 -129 GGAAATATCCAGACCCGCCTTTATTATCAT 10 66 0 AGACCCGCCT 0.96533 -74 TAGAACACCTTTAATAACTCT 10 129 0 AGAACACCTT 0.842265 -11 TGGACCGGAAACTCCACCCTCGAGGCAGTC 11 119 1 ACTCCACCCT 0.901241 -76 ********** Masking position 10 Map Score: 2.25507 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 328 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 GCCACCGGCTCCATGAATATATACTAGAAG 4 13 1 CCATGAATAT 0.791176 -63 GGTGTCAGCGCCCTGAAGGATTTCCCCTGG 5 151 1 CCCTGAAGGA 0.873041 -45 CTGCAGTCATCCATGGAAGACCCCTTTAAC 6 14 1 CCATGGAAGA 0.970214 -51 GTAATTAAAGCCATTAAAGTATCTGTTAAC 9 60 1 CCATTAAAGT 0.909305 -68 GAAATTAAAACCACGGATGAGTACTGTCAT 11 71 1 CCACGGATGA 0.869194 -124 GCCGGGACAGCCATGACAGTACTCATCCGT 11 83 0 CCATGACAGT 0.961565 -112 TTAATAGCTGCCATGACTGCCTCGAGGGTG 11 133 0 CCATGACTGC 0.918472 -62 AGCAATCTCTCCATTAAAGAGAGTGTCCCA 12 52 0 CCATTAAAGA 0.928708 -74 ********** Masking position 2 Map Score: 1.43894 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 548 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 GTTTGATGTTAAAAATAAAGAGT 1 4 0 AAAAATAAAG 0.917843 -196 AAAAAATCAGGACAGAAACCT 3 2 1 AAAAATCAGG 0.964505 -46 ACTATTAATAAAACATCATGGTTAACAGAT 9 80 0 AAACATCATG 0.911539 -48 AGTGCCACAGAAAAATAATGATAATAAAGG 10 49 1 AAAAATAATG 0.917841 -91 CCTTCTCTGGAAATATCCAGACCCGCCTTT 10 74 0 AAATATCCAG 0.817609 -66 CTTCAACTTGAAATATAAGG 11 185 1 AAATATAAGG 0.923429 -10 ********** Masking position 5 Map Score: 0.507917 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 55 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 ********** No masking Map Score: 1.97064e-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: 1.97064e-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: 1.97064e-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