AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i066_ecoli_bsub_300.orf -o066_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 lysA 121 diaminopimelate decarboxylase #2 dapF 300 diaminopimelate epimerase #3 lysA 105 diaminopimelate decarboxylase #4 spoVAA 121 mutants lead to the production of immature spores (stage V sporulation) #5 spoIIAA 95 anti-anti-sigma factor (antagonist of SpoIIAB) #6 dacF 154 D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) #7 drm 160 phosphodeoxyribomutase #8 ripX 300 integrase/recombinase #9 yutL 122 similar to diaminopimelate epimerase #10 yutK 136 similar to Na+/nucleoside cotransporter #11 yuzB 262 yuzB Motif number 1 TAAATCGATATTTTTTATTCTTTTTATGATG 1 63 1 TTTTTTATCT 0.954069 -59 AGATAAGTGCTTTTTTATGATTACGCCACAT 1 91 0 TTTTTTATAT 0.65941 -31 CTTAAACACGTTTTTCATTATGGATTGCCTG 2 61 0 TTTTTCATAT 0.814931 -240 TGGCGCGATCGTTTTTATCCGGCACCGTGGA 2 215 0 GTTTTTATCG 0.865383 -86 TAAGACATACATTATCATACTCTTCAGTCAG 3 22 0 ATTATCATCT 0.660253 -84 ACAGCTGTCTTTTTTTATGCCCAAAATTCGA 6 56 1 TTTTTTATCC 0.905294 -99 AGTATAAACCGTTTTCATTCCCGTTGACAAT 7 81 0 GTTTTCATCC 0.955151 -80 TGCATTGAAAGTTTTCATCCTGTTTACCGGT 8 106 1 GTTTTCATCT 0.978849 -195 ACCGCTTTGTTCTATTATGCTATGATATGGG 8 140 1 TCTATTATCT 0.775522 -161 ACCGATGATAGTTTTCATACTCTTGATTCAC 8 170 0 GTTTTCATCT 0.978848 -131 GAGCTTCCGGTTTATCATACCGATGATAGTT 8 188 0 TTTATCATCC 0.875562 -113 ACCATCCGCCTTTTTCATCCTGATCCATTTC 8 235 0 TTTTTCATCT 0.979272 -66 TTATCCCCCGTTTTTCATACATAAAAGCTCC 9 39 0 TTTTTCATCA 0.845489 -84 GCTTATAATAGCTTTTATACTAAGAAAAAGA 9 83 1 GCTTTTATCT 0.912672 -40 TAAAAAAATATCTTTTATACGATAACAATAA 10 87 0 TCTTTTATCG 0.7712 -50 CTTCAATGTATCTATCATACTCTTCGGATTA 11 24 0 TCTATCATCT 0.887101 -239 ACTAATTTGTGTTTTCAGGCTAAATTGTAGG 11 132 0 GTTTTCAGCT 0.84637 -131 ******** ** Masking position 5 Map Score: 18.9775 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 341 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 2 AACAAACTCCAGATAAGTGCTTTTTTAT 1 104 0 AAACTCGTGT 0.909052 -18 CTGCGGTCTGAAAGGTCCGCTCTATTTCCCGCCTG 2 130 1 AAAGGCGTAT 0.945486 -171 GTGAATTACTAAAAGTCAGTTTCTGTACCCGCGTG 2 266 1 AAAAGCGTTG 0.926171 -35 CTTATGGATGAAAGGACAGTTTTATGGACTGTCCC 3 61 0 AAAGGCGTAT 0.945097 -45 TTTTTTGTGCAAAAGCGTGGTAATTTATGGTCTTT 4 29 1 AAAAGGGTTT 0.9639 -93 CACCGTGACAAAACTAGTGGTCATTCGGCATAA 5 9 0 AAACTGGTTT 0.818974 -87 ATGCAGGACCAAAAGACAGCTGTGTCTGATATCAC 6 21 1 AAAAGCGTGT 0.982117 -134 TGGGCATAAAAAAAGACAGCTGTGTGATATCAGAC 6 44 0 AAAAGCGTGT 0.982117 -111 ATCAGGATGAAAAAGGCGGATGGTTCGACCGGTTG 8 242 1 AAAAGCGTTT 0.982442 -59 TATGTATGAAAAACGGGGGATAATTGTATTGTGTC 9 47 1 AAACGGGTTT 0.963197 -76 ***** * * * ** Masking position 11 Map Score: 6.86842 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 193 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 CCAGATAAGTGCTTTTTTATGATTACGCCA 1 94 0 GCTTTTTTAT 0.942895 -28 GCGGCGGTGCGTTTTTATCTGCAGGCGGGA 2 156 0 GTTTTTATCT 0.865362 -145 GTGCAGGCTAGCTTTTTTGTGCAAAAGCGT 4 17 1 GCTTTTTTGT 0.971512 -105 ACACAGCTGTCTTTTTTTATGCCCAAAATT 6 54 1 CTTTTTTTAT 0.749467 -101 GGTGGCTGCGGCTTTTTTGTTTAGAGCGAC 7 16 1 GCTTTTTTGT 0.971512 -145 TGAAAGCCTCCTTTTTTTCTATACGTCTAT 7 139 0 CTTTTTTTCT 0.90126 -22 CGGTTTTACCGCTTTGTTCTATTATGCTAT 8 133 1 GCTTTGTTCT 0.88822 -168 GACGCAAGGAGCTTTTATCGT 9 2 0 GCTTTTATCG 0.718396 -121 AGTGCAAGGAGCTTTTATGTATGAAAAACG 9 32 1 GCTTTTATGT 0.916307 -91 GTGCCTCCAACTTTTTTTCTTTTTCTTAGT 9 101 0 CTTTTTTTCT 0.90126 -22 GCCTGTCCAGGCCCTTTTCT 10 1 0 GCCCTTTTCT 0.715133 -136 CTGGACAGGCCCTTTTTTATTTTGCCGTAC 10 21 1 CCTTTTTTAT 0.882741 -116 CATTTTTTTAGTTCTTTTGTACGGCAAAAT 10 39 0 GTTCTTTTGT 0.810652 -98 ********** Masking position 5 Map Score: 11.4242 Number of sites scoring better than the average of aligned sites = 877 Number in coding regions = 652 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 4 ATGATATGGATTACCGGATTGCGAGAGAGC 1 15 0 TTACCGGATT 0.925587 -107 GTTTGCGTCTCTACCGGTTTGGTCGGCGGC 2 181 0 CTACCGGTTT 0.986929 -120 TTCATCCTGTTTACCGGTTTTACCGCTTTG 8 119 1 TTACCGGTTT 0.979966 -182 TACAGCGGAGCTTCCGGTTTATCATACCGA 8 196 0 CTTCCGGTTT 0.96906 -105 TCTTGATCTACTCCCCGTTTTGGTAAAAAA 8 281 0 CTCCCCGTTT 0.978208 -20 AATACAATTATCCCCCGTTTTTCATACATA 9 47 0 TCCCCCGTTT 0.912577 -76 ********** Masking position 9 Map Score: 4.10845 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 183 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TTTATGATGTGGCGTAATCATAAAAAAGCA 1 85 1 GGCGTAATCA 0.863112 -37 AGCGGAGAAAGAGGGAATGACA 3 94 1 GAGGGAATGA 0.941846 -12 CTTTTCGAGCGGATGAATGAGAACAAAATC 4 60 1 GGATGAATGA 0.946241 -62 TTTCGATTTCGACGGAATGAATTCCTTCAC 5 41 0 GACGGAATGA 0.917483 -55 ATCATATCAAGGAGGAATGAGC 5 84 1 GGAGGAATGA 0.978276 -12 GCTATGATATGGGTGAATCAAGAGTATGAA 8 158 1 GGGTGAATCA 0.965128 -143 TCGGATTAAAGGGGAATTCAA 11 2 0 GGGGAATTCA 0.770766 -261 CAAAGACAACGGATGATTCAAAATTTATTA 11 194 0 GGATGATTCA 0.865657 -69 ********** Masking position 6 Map Score: 3.02138 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 318 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 TCTATGCAAAAATGATATGGATTACCGGAT 1 26 0 AATGATATGG 0.920829 -96 TTATTCTTTTTATGATGTGGCGTAATCATA 1 77 1 TATGATGTGG 0.975053 -45 GTTATATATGTAGTATGTGGTTCGATTTTG 4 83 0 TAGTATGTGG 0.833688 -39 TAAAAAGGATTATGAAATGGAGGGCTTTTG 6 133 1 TATGAAATGG 0.934766 -22 AAGGATCGATTAGGACATGGGAAGATTCCT 8 61 1 TAGGACATGG 0.946257 -240 TCTATTATGCTATGATATGGGTGAATCAAG 8 150 1 TATGATATGG 0.979229 -151 ********** Masking position 5 Map Score: 2.8164 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 38 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 CTGCTTTCTATCATCGCAGGAGAAGACGTAAAAG 2 11 0 TCATCCGGGA 0.978186 -290 GACGCAAACGCAATCCACGGTGCCGGATAAAAAC 2 202 1 CAATCAGGGC 0.849568 -99 CTGGGATGGACCATCGCCAGTGGCGCGATCGTTT 2 232 0 CCATCCAGGC 0.968137 -69 TGGCGATGGTCCATCCCAGGTGAATTACTAAAAG 2 247 1 CCATCCGGGA 0.995631 -54 TTACTCCAATCACGCGGGTACAGAAACTGA 2 281 0 CAATCCCGGA 0.969243 -20 GTCCTTTCATCCATAAGCGGAGAAAGAGGGAATG 3 79 1 CCATAGGGGA 0.932115 -27 GAAACATTTTCCATCAGTGGCGTATAAAACCATC 6 85 1 CCATCGGGGA 0.992911 -70 GCGTATAAAACCATCACGCTTGGAAAAAATAAAA 6 104 1 CCATCCCTGA 0.904091 -51 AATTCCCCTTTAATCCGAAGAGTATGATAGATAC 11 14 1 TAATCGAGGA 0.711204 -249 ***** * ** * * Masking position 4 Map Score: 4.84402 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 473 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 GCTGCGGTCTGAAAGGTCCGCTCTATTTCC 2 129 1 GAAAGGTCCG 0.962902 -172 GGTGAATTACTAAAAGTCAGTTTCTGTACC 2 265 1 TAAAAGTCAG 0.720884 -36 TCTTAATTATGAAGGGACAGTCCATAAAAC 3 48 1 GAAGGGACAG 0.950526 -58 GCTTATGGATGAAAGGACAGTTTTATGGAC 3 67 0 GAAAGGACAG 0.986364 -39 TCATCCGCTCGAAAAGACCATAAATTACCA 4 46 0 GAAAAGACCA 0.8331 -76 AATGCAGGACCAAAAGACAGCTGTGTCTGA 6 20 1 CAAAAGACAG 0.912712 -135 TTGGGCATAAAAAAAGACAGCTGTGTGATA 6 50 0 AAAAAGACAG 0.875854 -105 GAACCATAGGGAAAGGATCGATTAGGACAT 8 49 1 GAAAGGATCG 0.88786 -252 ********** Masking position 3 Map Score: 3.8207 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 247 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 AATGAGAACAAAATCGAACCACATACTACAT 4 75 1 AATCGAACCA 0.987195 -47 CATTCCGTCGAAATCGAAACACTCATTATCC 5 52 1 AATCGAAACA 0.980012 -44 TTATGCCCAAAATTCGAAACATTTTCCATCA 6 70 1 AATCGAAACA 0.980012 -85 TGGTTTATATAACTGGAACCATAGGGAAAGG 8 34 1 AATGGAACCA 0.946458 -267 CATTGAAGAAAATACGAACTATGTAAAATAA 11 47 1 AAACGAACTA 0.865351 -216 TTTTAGATCAAATTCGATATAATTCTAGATG 11 78 0 AATCGATATA 0.803426 -185 ** ******** Masking position 7 Map Score: 2.04377 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 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 10 TCGACATAAATCGATATTTTTTATTCTTTTTA 1 57 1 TCATTTTTTT 0.770521 -65 TTCATAATCCTTTTTATTTTTTCCAAGCGTGA 6 117 0 TTTTTTTTTT 0.649047 -38 ATATTGAAGTTTCTCATTATTTCCAAATACAT 7 51 1 TTTCTTATTT 0.493605 -110 GTTCGACCGGTTGATCTTTTTTTACCAAAACG 8 264 1 TTATTTTTTT 0.881707 -37 TTTTGATGTCTACACATTTTTTTAGTTCTTTT 10 51 0 TAACTTTTTT 0.872357 -86 TACGATAACAATAATATTTTTTGATGTCTACA 10 69 0 ATATTTTTTT 0.814484 -68 TATCGTATAAAAGATATTTTTTTAAATAAAAT 10 94 1 AAATTTTTTT 0.865326 -43 GTACACCTCTTAAATTTTATTTAAAAAAATAT 10 107 0 TAATTTATTT 0.901795 -30 GATATAATTCTAGATGTTATTTTACATAGTTC 11 62 0 TAATTTATTT 0.901796 -201 ACAAATTAGTAAAACGTTATTTGAGAAATAAT 11 153 1 AAACTTATTT 0.772232 -110 TTATTATCGTAACATATTATTTCTCAAATAAC 11 168 0 AAATTTATTT 0.84406 -95 ** ** ****** Masking position 7 Map Score: 2.40467 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 134 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 11 GAAACTGACTGAAGAGTATGATAATGTATG 3 18 1 GAAGAGTATG 0.989643 -88 ATGGGTGAATCAAGAGTATGAAAACTATCA 8 166 1 CAAGAGTATG 0.981091 -135 CCTTTAATCCGAAGAGTATGATAGATACAT 11 20 1 GAAGAGTATG 0.989643 -243 ********** Masking position 5 Map Score: 1.33086 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 13 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 ACGCAATCCACGGTGCCGGATAAAAACGAT 2 209 1 CGGTGCCGGA 0.981404 -92 CATCCATAAGCGGAGAAAGAGGGAATGACA 3 86 1 CGGAGAAAGA 0.802597 -20 TCTGCAGTGCAGGCTAGCTTTTTT 4 5 1 CAGTGCAGGC 0.976382 -117 AGTTTTGTCACGGTGAAGGAATTCATTCCG 5 29 1 CGGTGAAGGA 0.979908 -67 ATATGAATCAATGCAGGACCAAAAGACA 6 9 1 CAATGCAGGA 0.934208 -146 CTCCTTGCGTCAGTGCAAGGAGCTTTTATG 9 21 1 CAGTGCAAGG 0.933028 -102 ********** Masking position 5 Map Score: 0.401865 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 651 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ********** No masking Map Score: -3.91266e-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: -3.91266e-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: -3.91266e-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