AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00510_aquae_reg_300.orf -o00510_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mtfB 300 mannosyltransferase B #2 mtfA 263 mannosyltransferase A #3 lytB 79 LytB protein #4 trxA2 168 thioredoxin #5 dmt 27 dolichol-phosphate mannosyltransferase #6 rfaG 300 glucosyl transferase I Motif number 1 GTGGAAGGAGAAAGTGGTGTAT 1 3 1 GGAAGGAGAA 0.960756 -298 TCGAAGGTTGAAAAGAAGCTCTCAATAAGC 1 44 0 AAAAGAAGCT 0.909886 -257 GGTAACATAAGGAATGAGCATGTGTTTAAA 1 111 1 GGAATGAGCA 0.906447 -190 CAGATTTATTGGACAGAGCATGGAATTTAT 1 240 1 GGACAGAGCA 0.82176 -61 GAAAGGAAAAGAAAAAAGCTTTTCCATTAA 2 181 1 GAAAAAAGCT 0.792671 -83 ATCTTGATTTAGAAGAAGAAATAATCTACT 2 225 1 AGAAGAAGAA 0.951236 -39 TAGAAGAAGTATTTTATCTTA 5 17 0 AGAAGAAGTA 0.885325 -11 GCAAAATTGCAGAAAAAGCAGGCATAACCA 6 26 1 AGAAAAAGCA 0.951236 -275 GGCATAACCAAGAAGGAGCTGACGCAGCTA 6 46 1 AGAAGGAGCT 0.974438 -255 TCTTCGAAAAGGAAGAAGCTCAGAATTCCC 6 106 1 GGAAGAAGCT 0.982047 -195 AAAATTTTAGAAAAGAAGAAAAGCGGGAAA 6 275 0 AAAAGAAGAA 0.828533 -26 ********** Masking position 7 Map Score: 12.014 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 876 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 TTGAATTTATAGGTATTCAGTT 1 289 0 GAATTTATAG 0.685267 -12 CCATAATTGAAAAATTATAGCTTAAAATAA 2 18 0 AAAATTATAG 0.853908 -246 AAATATGCTTGAAAATTTAGCATTATAAAC 2 65 0 GAAAATTTAG 0.971683 -199 AAATTTTCAAGCATATTTAGGGTAATTATA 2 77 1 GCATATTTAG 0.855052 -187 ATACGTGTTTATATATTTAGTAAAAACTTG 2 151 1 ATATATTTAG 0.697027 -113 CCCTCCCTTTAAAAATTTAGGCGGATAAAT 3 21 1 AAAAATTTAG 0.973462 -59 TCCCCCTTTTAAAAATAAAGGATAATTCTC 4 13 0 AAAAATAAAG 0.896394 -156 TATCATTTTTGAAAATTAAGACATTTTATG 4 91 1 GAAAATTAAG 0.95308 -78 ACAAATTAAGATAAAATACT 5 1 1 ACAAATTAAG 0.903285 -27 GAAAAGCGGGAAAAATTAAGAAATCTGCTT 6 258 0 AAAAATTAAG 0.955986 -43 AAATAAAAAATTTTAGAAAAGAAGAA 6 285 0 AAAATTTTAG 0.936199 -16 ********** Masking position 3 Map Score: 11.1392 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 106 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 TTCTTTTAATTTATCCCTTAATAAGGGAAT 2 122 0 TTATCCCTTA 0.889892 -142 AGCTTTTTTCTTTTCCTTTCCAAGTTTTTA 2 171 0 TTTTCCTTTC 0.702504 -93 AAGAGCACCTCCCTCCCTTTAAAAATTTAG 3 11 1 CCCTCCCTTT 0.900377 -69 AAGAGAATTATCCTTTATTTTTAAAAG 4 8 1 TTATCCTTTA 0.785328 -161 TAAGTCCTTGTCCCCCTTTTAAAAATAAAG 4 23 0 TCCCCCTTTT 0.90144 -146 ATTTACCATTTTATCATTTTTGAAAATTAA 4 80 1 TTATCATTTT 0.694324 -89 TAATAGTCCTTTAACCCTTTGTCCTGTATC 4 138 1 TTAACCCTTT 0.820894 -31 ATTCTGAGCTTCTTCCTTTTCGAAGAGTTC 6 102 0 TCTTCCTTTT 0.903054 -199 TTCTGGGATTTCTTCCCTTTCTTGCACTCC 6 163 0 TCTTCCCTTT 0.953659 -138 TTTGTATAACTTCTCCCGTTCTGGGATTTC 6 181 0 TTCTCCCGTT 0.91657 -120 GCAAGAAAGGTTCTCACTTTCAAACCTGCA 6 216 1 TTCTCACTTT 0.907912 -85 TTCTTAATTTTTCCCGCTTTTCTTCTTTTC 6 266 1 TTCCCGCTTT 0.760791 -35 ********** Masking position 9 Map Score: 5.80506 Number of sites scoring better than the average of aligned sites = 1912 Number in coding regions = 1771 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 4 GCTCTGTCCAATAAATCTGTTATGATCTCCC 1 228 0 ATAAATCTGT 0.86329 -73 CCAGAGGGTTATAAATTCCATGCTCTGTCCA 1 249 0 ATAAATTCCT 0.819772 -52 TGCTGTTGTTATAATTACCCTAAATATGCTT 2 85 0 ATAATTACCT 0.786869 -179 AACAGCAAATAAAATTCCCTTATTAAGGGAT 2 109 1 AAAATTCCCT 0.890787 -155 ATTTAGGCGGATAAATCTCATTGACATTTAT 3 35 1 ATAAATCTCT 0.953981 -45 AAAATAAAGGATAATTCTCTT 4 1 0 ATAATTCTCT 0.943907 -168 GAAGAAGCTCAGAATTCCCGGACTCGGACCT 6 117 1 AGAATTCCCG 0.940619 -184 AAGAAAGGGAAGAAATCCCAGAACGGGAGAA 6 170 1 AGAAATCCCG 0.951257 -131 GGAAAAATTAAGAAATCTGCTTAACGAGTTC 6 249 0 AGAAATCTGT 0.860907 -52 ********* * Masking position 6 Map Score: 4.54282 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 299 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 AAAGCTTTTCCATTAAGAATCTTGAAGGTA 2 195 1 CATTAAGAAT 0.875964 -69 TCTTCTTCTAAATCAAGATTACCTTCAAGA 2 214 0 AATCAAGATT 0.749738 -50 GGGGACAAGGACTTAAGACTTAAACTAATT 4 38 1 ACTTAAGACT 0.915071 -131 CATTTTTGAAAATTAAGACATTTTATGCAT 4 94 1 AATTAAGACA 0.950065 -75 ATTAAGAAATACTTATGAATGCATAAAATG 4 112 0 ACTTATGAAT 0.699559 -57 GTTAAAGGACTATTAAGAAATACTTATGAA 4 123 0 TATTAAGAAA 0.826534 -46 ACAAATTAAGATAAAATACTTCT 5 4 1 AATTAAGATA 0.924722 -24 AAGCGGGAAAAATTAAGAAATCTGCTTAAC 6 255 0 AATTAAGAAA 0.958245 -46 ********** Masking position 5 Map Score: 2.18002 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 47 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 GCTTCTTTTCAACCTTCGAGCGATGGTTTG 1 55 1 AACCTTCGAG 0.970998 -246 AAATCAAGATTACCTTCAAGATTCTTAATG 2 205 0 TACCTTCAAG 0.982782 -59 GTTATACAAATACCTGCAAGAAAGGTTCTC 6 201 1 TACCTGCAAG 0.9888 -100 CTCACTTTCAAACCTGCAAAGGAACTCGTT 6 228 1 AACCTGCAAA 0.956937 -73 ********** Masking position 5 Map Score: 1.40538 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 48 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 7 TCTTTTTGGTTTATAATGCTAAATTTTCAAGCATA 2 57 1 TTATTTAATT 0.965198 -207 ATATAAACACGTATTCTTTTAATTTATCCCTTAAT 2 130 0 GTATTTAATT 0.958321 -134 TTTATGTTCTTAAGCTTTGAGTAGAT 2 248 0 TTATTTAACT 0.910243 -16 TCAATGAGATTTATCCGCCTAAATTTTTAAAGGGA 3 24 0 TTATGTAATT 0.977584 -56 AAACTAATTTTTATATGTTTAATTTACCATTTTAT 4 59 1 TTATGTAATT 0.977584 -110 TTTCTTGCAGGTATTTGTATAACTTCTCCCGTTCT 6 189 0 GTATGTAATT 0.973086 -112 **** * *** ** Masking position 10 Map Score: 1.04233 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 10 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: 3.60488e-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 9 ********** No masking Map Score: 3.60488e-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 10 AAAAGAAGCTCTCAATAAGCCATCTGTTGCCAT 1 31 0 CTAAAGCCAT 0.935401 -270 TCACTACATACTCTCCAAACCATCGCTCGAAGG 1 67 0 CTCAAACCAT 0.925741 -234 CATTCCTTATGTTACCAAGCCTTTTGCTCACTA 1 94 0 GTCAAGCCTT 0.948656 -207 CACATCAACTCCACCACAGCCATCTCTCATACC 1 174 0 CCCCAGCCAT 0.971156 -127 TTTTCTTTTCCTTTCCAAGTTTTTACTAAATAT 2 163 0 CTCAAGTTTT 0.740351 -101 AATTTTGCTACGAGCTCAGCCTT 6 1 0 CGCCAGCCTT 0.971151 -300 CAAGAAGGAGCTGACGCAGCTATCAAGGCTTTC 6 54 1 CTCCAGCTAT 0.961554 -247 TGTATGGCTTCTACGAAAGCCTTGATAGCTGCG 6 68 0 CTGAAGCCTT 0.955479 -233 ** * ******* Masking position 8 Map Score: 0.426066 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 206 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ********** No masking Map Score: 3.60488e-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 12 ********** No masking Map Score: 3.60488e-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: 3.60488e-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