AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -inagC_synecho_opreg_300.orf -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glmS 300 L-glutamine:D-fructose-6-P amidotransferase #2 leuA 185 2-isopropylmalate synthase #3 1001455 84 hypothetical protein #4 1001456 95 hypothetical protein #5 1001457 37 hypothetical protein #6 1001458 26 hypothetical protein #7 glmU 242 UDP-N-acetylglucosamine pyrophosphorylase #8 devB 44 glucose-6-P-dehydrogenase #9 1653816 147 hypothetical protein #10 1653817 181 hypothetical protein Motif number 1 TTCCTAAATCCCCCAATGCCATGCTGACGTCA 1 119 1 CCCCTGCCAT 0.976787 -182 ATATAGTCCGCCCCTGTGCCAAGTTCCTCCCG 1 160 1 CCCCTGCCAA 0.994704 -141 CCTCCCGAAAGCCCATTACCATACCCAGCTAA 1 185 1 GCCCTACCAT 0.62501 -116 AATCTATCGCCCCCCATGGCAATTAGCTGGGT 1 207 0 CCCCTGGCAA 0.993054 -94 TTTTCCTTCTGCCCAATGACAAATCTATCGCC 1 228 0 GCCCTGACAA 0.982833 -73 GGAGATTCCCCAATGATAGTGAAGATGAT 1 282 0 CCCCTGATAG 0.945177 -19 GTGTCTTTTTCACCCTTGAAAAGGTGCGTTTA 2 162 1 CACCTGAAAA 0.900187 -24 TGGCCCGGTGACAGTTACGCCAGG 3 3 1 GCCCTGACAG 0.952019 -82 GCTACTTCATCCCCGGTAAAAAATCGTTATTT 4 22 0 CCCCTAAAAA 0.873605 -74 ACCAGCCAGTCACCGTTGGCAAAACCTTAACA 7 149 0 CACCTGGCAA 0.962857 -94 ATTTGCCTTGCCCCAATCACGATATACTCAAT 7 195 1 CCCCTCACGA 0.926079 -48 CCTTGACAATCCCCGTTGGTGATTTATACTTA 9 31 1 CCCCTGGTGA 0.911354 -117 AATTTCCTCACACCTGTCCTAAGTATAAATCA 9 50 0 CACCTCCTAA 0.644466 -98 CCGGACAAGGCCTCTGTGAAAATCTTAAAAAA 10 51 0 CCTCTGAAAA 0.751745 -131 **** ****** Masking position 7 Map Score: 17.3101 Number of sites scoring better than the average of aligned sites = 2110 Number in coding regions = 1933 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 2 ACTTGGCACAGGGGCGGACTATATCCCCAAAA 1 152 0 GGGGCGCTAT 0.858492 -149 ATTTGTCATTGGGCAGAAGGAAAAAGCTAAAC 1 236 1 GGGCAGGGAA 0.979352 -65 CTAAACTGGAGGGCAATTTGATCATCTTCACT 1 262 1 GGGCAATGAT 0.801538 -39 GGAAGCAGAGGGGGAGAAGAAAGGGCAATGGG 2 18 1 GGGGAGGAAA 0.961175 -168 GGAGAAGAAAGGGCAATGGGACGATAAAGCAA 2 30 1 GGGCAAGGAC 0.965695 -156 AACGCATTAAGGGGAAACCAATCGCTACCGAT 2 72 1 GGGGAACAAT 0.942035 -114 TCTAGACTTTGGGCAACTCTAAACTTTTTGTT 7 121 1 GGGCAACTAA 0.982741 -122 GCAAATTCAGGGGGAAAACTACCAGCCAGTCA 7 169 0 GGGGAACTAC 0.934383 -74 ATCGTGATTGGGGCAAGGCAAATTCAGGGGGA 7 186 0 GGGCAACAAA 0.985946 -57 GCAATTTTTAGGGCAGTCCACAG 9 135 1 GGGCAGCACA 0.908321 -13 CCGGTCGGTCGGGCCATGGTAATTATCCATCG 10 122 1 GGGCCAGTAA 0.963887 -60 TCCATCGGCCGGGCCACTGAAATAATCAACCA 10 147 1 GGGCCAGAAA 0.970487 -35 ****** **** Masking position 3 Map Score: 13.2495 Number of sites scoring better than the average of aligned sites = 992 Number in coding regions = 886 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 3 TTAGCAATTCCTAAATCCCCCAATGCCATG 1 112 1 CTAAATCCCC 0.987649 -189 CAGGGGCGGACTATATCCCCAAAACTGACG 1 146 0 CTATATCCCC 0.972057 -155 AAGTTCCTCCCGAAAGCCCATTACCATACC 1 180 1 CGAAAGCCCA 0.930076 -121 AATGACAAATCTATCGCCCCCCATGGCAAT 1 216 0 CTATCGCCCC 0.951634 -85 CAATTTGTTGCTAAACCCCCTCCCATCCCC 3 65 1 CTAAACCCCC 0.99448 -20 TACAATTGTGCGAAACCACC 6 1 0 CGAAACCACC 0.95092 -26 GATAATACAGCAAAGCCCCCCTTTGTTTGT 7 52 0 CAAAGCCCCC 0.952435 -191 ********** Masking position 3 Map Score: 5.73914 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 423 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 CATACCCAGCTAATTGCCATGGGGGGCGAT 1 204 1 TAATTGCCAT 0.834392 -97 GAAGATGATCAAATTGCCCTCCAGTTTAGC 1 261 0 AAATTGCCCT 0.94283 -40 GTTAAGGAGTAATTTGCTTTATCGTCCCAT 2 45 0 AATTTGCTTT 0.84185 -141 ACCGGGGATGAAGTAGCCTTTGTATGTCGG 4 37 1 AAGTAGCCTT 0.930375 -59 TTTCCCCCTGAATTTGCCTTGCCCCAATCA 7 184 1 AATTTGCCTT 0.979452 -59 ACTGCCCTAAAAATTGCCATAAAAAAACAC 9 122 0 AAATTGCCAT 0.965653 -26 AACAGTATTAAATTAGCCTTTCCGGACAAG 10 74 0 AATTAGCCTT 0.967439 -108 GGGCCATGGTAATTATCCATCGGCCGGGCC 10 132 1 AATTATCCAT 0.718175 -50 ********** Masking position 2 Map Score: 5.97186 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 484 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 CTGATGTCTGCCATAGCCAAGACGGCGATCGC 1 20 0 CCTAGCCAGA 0.870674 -281 AACCTATGACCATAAACAGAAACACCGTTTTG 1 82 0 CAAAACAAAA 0.67034 -219 TGTCATTGGGCAGAAGGAAAAAGCTAAACTGG 1 239 1 CAAAGGAAAA 0.701316 -62 TCAAAGTATGCCAACGTCTAAATAGACAAGAT 2 113 1 CCACGTCAAA 0.944129 -73 CGACTGGTCGCCGACATACAAAGGCTACTTCA 4 45 0 CCACATAAAA 0.868473 -51 AGACCTATGTAGAAAATGGAAAGCT 4 81 0 CCATGTAAAA 0.931097 -15 ATAACCTAACCCCAAATACAAACAAAGGGGGG 7 35 1 CCAAATAAAA 0.931075 -208 TTAGAGTTGCCCAAAGTCTAGAAAATTAAGTA 7 111 0 CCAAGTCAGA 0.922966 -132 GTTGGCAAAACCTTAACAAAAAGTTTAGAGTT 7 135 0 CCTAACAAAA 0.883593 -108 CAGCCAGTCACCGTTGGCAAAACCTTAACAAA 7 147 0 CCTTGGCAAA 0.821347 -96 TTCCACAATTCCTTTACCTAAACGGGAAACGA 8 16 1 CCTTACCAAA 0.799254 -29 TCACACCTGTCCTAAGTATAAATCACCAACGG 9 43 0 CCAAGTAAAA 0.967578 -105 ** ***** *** Masking position 10 Map Score: 5.04091 Number of sites scoring better than the average of aligned sites = 1486 Number in coding regions = 1317 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 6 CATAGCCAAGACGGCGATCGCCATCATTAG 1 9 0 ACGGCGACGC 0.985838 -292 ACGATTTTTTACCGGGGATGAAGTAGCCTTTG 4 27 1 ACCGGGGTGA 0.943524 -69 GGTTTTGCCAACGGTGACTGGCTGGTAGTTTT 7 155 1 ACGGTGATGC 0.974933 -88 CTTTACCTAAACGGGAAACGACTCCAAG 8 27 1 ACGGGAACGC 0.975235 -18 TAAATCACCAACGGGGATTGTCAAGGCTTCAG 9 25 0 ACGGGGATGC 0.996038 -123 ATAAAAAAACACCTGGGGCGTCTTTCCTTGTT 9 102 0 ACCTGGGCGC 0.952774 -46 GGCCCGACCGACCGGGATTTCCAGACCAGTTT 10 105 0 ACCGGGATTC 0.961282 -77 ******* ** * Masking position 1 Map Score: 3.48466 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 893 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 7 TTTAAAGCTGTTCTCACTTCCCACCCTGATG 1 46 0 TTTCACTTCC 0.954084 -255 TGGTCATAGGTTAGCAATTCCTAAATCCCCC 1 102 1 TTGCAATTCC 0.982748 -199 ATTACAATTCTTTGCACTTCCGTATAAATAC 7 83 1 TTGCACTTCC 0.983999 -160 TCCCCCTGAATTTGCCTTGCCCCAATCACGA 7 186 1 TTGCCTTGCC 0.908472 -57 AGAAATTCCACAATTCCTTTACCTAAA 8 7 1 TCACAATTCC 0.836402 -38 GTCTGAAGCCTTGACAATCCCCGTTGGTGAT 9 23 1 TTACAATCCC 0.855549 -125 CCAGATGTTTTTCTAATTTCCTCACACCTGT 9 65 0 TTTAATTTCC 0.682488 -83 CAGTATTAAATTAGCCTTTCCGGACAAGGCC 10 71 0 TTGCCTTTCC 0.969932 -111 ** ******** Masking position 8 Map Score: 2.70643 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 399 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 CAAGACGGCGATCGCCATCATTAG 1 4 0 ATCGCCACAT 0.963195 -297 CCCCAAAACTGACGTCAGCATGGCATTGGGG 1 129 0 GACGTCACAT 0.97452 -172 TGTCTATTTAGACGTTGGCATACTTTGAAGA 2 110 0 GACGTTGCAT 0.942899 -76 GAGCCGACTGGTCGCCGACATACAAAGGCTA 4 50 0 GTCGCCGCAT 0.992546 -46 TTCTGTCCTGATCGTCGCCATTGAGTATATC 7 215 0 ATCGTCGCAT 0.980518 -28 ******* *** Masking position 10 Map Score: 1.17918 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 160 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 TTTGCTCAGTTTAAAGCTGTTCTCACTTCCC 1 55 0 TTAAAGCTTT 0.938881 -246 TGGTTTCCCCTTAATGCGTTAAGGAGTAATT 2 61 0 TTAATGCGTA 0.873739 -125 ACAACAATAATTAATGCTCTTATT 5 4 0 TTAATGCTTT 0.980598 -34 TTTTAAAATCTTAATACTTTTTTAAGATTTT 10 34 1 TTAATACTTT 0.957322 -148 AAAGGCTAATTTAATACTGTTCAAACTGGTC 10 83 1 TTAATACTTT 0.957322 -99 ******** ** Masking position 4 Map Score: 0.599393 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 35 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 ATCGCCGTCTTGGCTATGGCAGACATCAGG 1 23 1 TGGCTATGGC 0.935449 -278 ACGGTGTTTCTGTTTATGGTCATAGGTTAG 1 86 1 TGTTTATGGT 0.920675 -215 GGCAATTAGCTGGGTATGGTAATGGGCTTT 1 192 0 TGGGTATGGT 0.901345 -109 GCATTAATTATTGTTGTGGTGGCATAACCT 5 18 1 TTGTTGTGGT 0.889453 -20 TCTAAACTTTTTGTTAAGGTTTTGCCAACG 7 138 1 TTGTTAAGGT 0.929469 -105 CCAACGGGGATTGTCAAGGCTTCAGACCTG 9 20 0 TTGTCAAGGC 0.847372 -128 CCCAGGTGTTTTTTTATGGCAATTTTTAGG 9 117 1 TTTTTATGGC 0.949449 -31 TTTATGGCAATTTTTAGGGCAGTCCACAG 9 129 1 TTTTTAGGGC 0.872895 -19 ********** Masking position 1 Map Score: 2.03342 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 343 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 GAAGAGGTAAAATCGGTAGCGATTGGTTTC 2 85 0 AATCGGTAGC 0.977337 -101 AAGTCGGATTAATTGGTAGCAAACATCACA 3 37 1 AATTGGTAGC 0.986581 -48 CAAACATCACAATTTGTTGCTAAACCCCCT 3 56 1 AATTTGTTGC 0.94873 -29 CTGACAGTGTAATTGGTTGATTATTTCAGT 10 162 0 AATTGGTTGA 0.94873 -20 ********** Masking position 7 Map Score: 0.54543 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 82 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 12 GCAATTCCTAAATCCCCCAATGCCATGCTG 1 115 1 AATCCCCCAA 0.98531 -186 GGGCGGACTATATCCCCAAAACTGACGTCA 1 143 0 TATCCCCAAA 0.940537 -158 GGAGATTCCCCAATGATAGTGAA 1 288 0 GATTCCCCAA 0.96157 -13 AACTATAACCTAACCCCAAATACAAACAAA 7 31 1 TAACCCCAAA 0.894487 -212 AGAAATTCCACAATTCCTTTACC 8 4 1 AATTCCACAA 0.868405 -41 TCCTAAGTATAAATCACCAACGGGGATTGT 9 36 0 AAATCACCAA 0.779583 -112 ********** Masking position 2 Map Score: 0.474757 Number of sites scoring better than the average of aligned sites = 1097 Number in coding regions = 918 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 13 ********** No masking Map Score: 4.7139e-13 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: 4.7139e-13 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: 4.7139e-13 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