AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icrp_ctra_opreg_300.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 CT181 300 hypothetical protein #2 pdhA 221 Pyruvate Dehydrogenase Alpha #3 CT338 283 hypothetical protein #4 yrbH 31 GutQ/KpsF Family Sugar-P Isomerase #5 sucB_2 245 Dihydrolipoamide Succinyltransferase #6 ribC 300 Riboflavin Synthase #7 uhpC 300 Hexosphosphate Transport #8 CT565 90 hypothetical protein #9 CT569 61 predicted OMP [leader (16) peptide] #10 CT573 127 hypothetical protein #11 mutL 294 DNA Mismatch Repair #12 CT646 100 hypothetical protein Motif number 1 AAAAATAGTAAATAACATCATAAATCATACACTT 1 209 0 AAAACAAAAA 0.958789 -92 ACACCCAATGCAGAAAACCAAAAATCTCGAAATA 3 158 0 CAAAAAAAAA 0.84526 -126 CTCAAAGAGGAAAAAAATGACAAATACCAGGGAA 3 205 0 AAAAAAAAAA 0.979879 -79 TTGAGGGTTTAATAACATGAAAATCTGTACACTC 5 126 0 AAAACAAAAT 0.90274 -120 CTTTTGAAAAAAAATCACCACAAATCACAATCAA 6 22 0 AAATCAAAAA 0.834161 -279 GGTTACTTATAATCAAAAAATAATTATACTCCGA 6 171 0 AACAAAAAAT 0.868507 -130 AGGTGTGTCAAATAAAAGAAATAATAGAGAG 7 8 0 AAAAAAATAA 0.913261 -293 CTAGAAGCTTAAGAAAAATACAAATGCATACTGA 7 247 0 AAAAAAAAAA 0.979879 -54 AGATAATTTAAATATAAACATAAAAAACCAT 8 8 0 AAATAAAAAA 0.913261 -83 AGATTAATTTAATAAAAAGAAAAAAATCAGGTAT 8 62 1 AAAAAAAAAA 0.979879 -29 GGAAACTGTGAAGAAAACAAAAAAAAGAAAACAA 9 20 1 AAAAAAAAAA 0.979879 -42 TTTTTTGTTAAAAAACAAAAAAATCGGCTTTTAT 10 17 0 AAAACAAAAT 0.90274 -111 ATTTTTACAAAAGAAAATAAGAAAAGCCGTTTTT 10 47 0 AAAAAAAAAA 0.979879 -81 AACAACAGAGAAACAAAAAAGAATTGTATAAAGT 10 104 0 AACAAAAAAT 0.868507 -24 GATAATTCCTAAAAAAATAAAAATAACAAATTAC 11 14 1 AAAAAAAAAT 0.951049 -281 GTTTTATTAAAAGCAAAATATTAAAAACGTTTTT 11 96 0 AACAAAATAA 0.781629 -199 CATCTTTTTCAAGAAAAACATTAATTATAAACAG 12 21 0 AAAAAAATAA 0.913261 -80 TCATTTTAAAAAGATAAAGAAAAACGCTAA 12 81 1 AAATAAAAAA 0.913261 -20 ** **** * *** Masking position 7 Map Score: 28.2245 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 144 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 2 GTTTCATTCGTGAAAAATAATCAAATACATTA 1 118 0 TGAAAATAAC 0.455928 -183 ATTTTTCTTATAACAAAAAACCTCATGCGAGG 1 237 1 TAAAAAAAAC 0.949716 -64 AATAATTATAAAATATAAAAGCTTTTCGTTAC 1 279 0 AAAATAAAAC 0.907152 -22 AGTCTATGCTACAAAAAAAAACTTTTCGGCAC 2 51 0 ACAAAAAAAC 0.953559 -171 CCAATGCAGAAAACCAAAAATCTCGAAATAGC 3 156 0 AAACAAAAAC 0.788026 -128 AAGAAAACGAAGAGAGAAAACCCTCTTCGTTA 5 19 0 AGAAGAAAAC 0.751715 -227 TGGCTTTTACAGATAAAAAATGCCTTTTGAGG 5 154 0 AGAAAAAAAG 0.611975 -92 AGGCGACTTTTGAAAAAAAATCACCACAAATC 6 30 0 TGAAAAAAAC 0.928531 -271 TTTTATCCATTAAAATAAAAACCGTGGTATCT 6 81 0 TAAATAAAAC 0.833082 -220 AAAACTAGATACACGAAAAAGCCCTCTCCGGA 6 224 0 ACAGAAAAAC 0.673685 -77 TCTAGAAGCTTAAGAAAAATACAAATGCATAC 7 250 0 TAAAAAAATC 0.561653 -51 TTAAATATAAACATAAAAAACCAT 8 3 0 ACAAAAAAAC 0.953559 -88 ATTTAATAAAAAGAAAAAAATCAGGTATGGCT 8 68 1 AAGAAAAAAC 0.788026 -23 AAGAAAACAAAAAAAAGAAAACAATCCATTAC 9 30 1 AAAAAGAAAC 0.779469 -32 TTTCATATAAAAGCCGATTTTTTT 10 3 1 TCAATAAAAC 0.734869 -125 TTTGTTAAAAAACAAAAAAATCGGCTTTTATA 10 16 0 AACAAAAAAC 0.788026 -112 TTTTGTTTTTTAACAAAAAAACGGCTTTTCTT 10 31 1 TAAAAAAAAC 0.949716 -97 AACTGATTTGAGAAAAAAAATCAATTTTTACA 10 72 0 AGAAAAAAAC 0.962169 -56 AACAACAGAGAAACAAAAAAGAATTGTATAAA 10 106 0 AAAAAAAAAA 0.607371 -22 GCTCATTTTAAAAAATAAAAACATCTTTTTCA 12 44 0 AAAATAAAAC 0.907152 -57 TTAAAAAGATAAAGAAAAACGCTAA 12 86 1 AAAAAAAACC 0.788026 -15 *** ****** * Masking position 9 Map Score: 17.1418 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 270 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 3 TATTTGATTATTTTTCACGAATGAAACGCG 1 123 1 TTTTTCACGA 0.798637 -178 AAAAGTTTTTTTTTGTAGCATAGACTTGGC 2 57 1 TTTTGTAGCA 0.775531 -165 CATTCTAGAATTTTTCAGGAACCCTTTATC 2 191 1 TTTTTCAGGA 0.933154 -31 AAGACATTTTTTTAATATAGCGGTGAA 4 8 1 TTTTTTAATA 0.750133 -24 GTGGTGATTTTTTTTCAAAAGTCGCCTAAT 6 35 1 TTTTTCAAAA 0.846489 -266 AGAAGAGGTTCTTTTCAACACAAGACACAG 6 115 0 CTTTTCAACA 0.89902 -186 GTGTATCTAGTTTTTCAAGATTGCTAAAAA 6 242 1 TTTTTCAAGA 0.952977 -59 GACAACAATACTTTTTAGCAATCTTGAAAA 6 253 0 CTTTTTAGCA 0.844813 -48 GATTTTTTTGTTTTTTAACAAAAAAACGGC 10 26 1 TTTTTTAACA 0.950876 -102 TCTTATTTTCTTTTGTAAAAATTGATTTTT 10 59 1 TTTTGTAAAA 0.612463 -69 TTATTTTTATTTTTTTAGGAATTATCGCG 11 10 0 TTTTTTAGGA 0.927928 -285 CCTTGCAATTTTTTTTAACAGGAGGTACCG 11 182 1 TTTTTTAACA 0.950876 -113 TAAAAACATCTTTTTCAAGAAAAACATTAA 12 31 0 TTTTTCAAGA 0.952977 -70 GATGTTTTTATTTTTTAAAATGAGCGCTCT 12 51 1 TTTTTTAAAA 0.901266 -50 TTTTCTTTATCTTTTTAAAATGAAGAGCGC 12 74 0 CTTTTTAAAA 0.806777 -27 ********** Masking position 7 Map Score: 15.5506 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 220 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 4 CGACACCTCCCGCGTTTCATTCGTGAAAAAT 1 132 0 CCGTTTCATT 0.906302 -169 TTCTCATAGGCTCTCTTCGTTCCTATATTCG 1 161 0 CCTCTTCGTT 0.991216 -140 AAAATATAAAAGCTTTTCGTTACTTTATGAT 1 271 0 ACTTTTCGTT 0.876341 -30 AGAGAGAAAACCCTCTTCGTTAAAAGATCT 5 10 0 CCTCTTCGTT 0.991216 -236 AGAGGGTTTTCTCTCTTCGTTTTCTTTAAGG 5 25 1 CCTCTTCGTT 0.991216 -221 GTCGTCAATACTCCTTTCATTTAGCTTAATA 7 128 0 CCCTTTCATT 0.906302 -173 TTAAAATGAGCGCTCTTCATTTTAAAAAGAT 12 65 1 CCTCTTCATT 0.982026 -36 * ********* Masking position 6 Map Score: 7.89448 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 16 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 5 TTTGATTATTTTTCACGAATGAAACGCGGGAG 1 125 1 TTTCCGATGA 0.751113 -176 CCGGTTACTTTTCCGCGCCGGCCTTGCATAGC 2 127 1 TTCCCGCGGC 0.976108 -95 ATCTTTTGAATTTCACTCTGGCTATGCAAGGC 2 147 0 TTTCCTCGGC 0.984833 -75 GTAGAAGTGCTTTCTCTCGAGCAGATGCGCAG 3 31 1 TTTCCTCAGC 0.942341 -253 TTTGCTAAAGTTCCACGGTTGCCCAGAGGATG 3 85 1 TTCCCGGTGC 0.936507 -199 TTCTTCACAGTTTCCCTCCTGTAG 9 3 0 TTTCCTCTGT 0.947567 -59 TTCTTTTTTGTTTCTCTGTTGTT 10 115 1 TTTCCTGTGT 0.864751 -13 AGTCCAAGCCTTTCGCGCAGGAGGTAACGGTA 11 207 0 TTTCCGCGGA 0.957954 -88 GACTTCACGCTTTCTCTCGTGCTGTCTCTCAC 11 235 1 TTTCCTCTGC 0.985129 -60 **** *** *** Masking position 2 Map Score: 5.90211 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 43 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 6 ATTGTTAACGATCTCCTTGTTAGGATGGTCGGGT 1 42 0 ATCCTTGTAG 0.93667 -259 CGTTCTGCGCATCTGCTCGAGAGAAAGCACTTCT 3 33 0 ATCCTCGAAA 0.80436 -251 GCTCGATACGATCTGCTTGAGACAGACCTACCAA 3 124 0 ATCCTTGAAA 0.905319 -160 GAAATAGTTTATCCGCTCCTTATGATGTGCAA 3 262 1 ATCCTCCTAG 0.887355 -22 CCAGTTGATAATCTTCTTCTCATATTGAGTTAAC 5 183 1 ATCCTTCTAA 0.977068 -63 TGTTGAAAAGAACCTCTTCTTAGAAAGGTTTTCT 6 125 1 AACCTTCTAA 0.857045 -176 CAGCAAACGTATTGTCTTCTAAAAGCTATTAAGC 7 102 1 ATTCTTCTAA 0.923206 -199 AGACGAAAGTATCAGCTTCTAAGACCTCGTTTTT 7 214 0 ATCCTTCTAA 0.977068 -87 TTATATTTAAATTATCTTTTGATAATTGTTTAGT 8 25 1 ATTCTTTTAA 0.650327 -66 GTTTTTATTAATTAACTTGTTAAATCAGATCGTT 11 68 0 ATTCTTGTAA 0.906579 -227 *** ***** * * Masking position 7 Map Score: 4.39976 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 54 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 7 CGAATGAAACGCGGGAGGTGTCGAATATAGGAA 1 140 1 GCGGGTGTCG 0.983709 -161 TGCGAGGTTATCATAAAGTAACGAAAAGCTTTT 1 262 1 TCATGTAACG 0.745839 -39 TCTGTCTCAAGCAGATCGTATCGAGCTATTTCG 3 132 1 GCAGGTATCG 0.985343 -152 TTGGTTTTCTGCATTGGGTGTTGAGAATACTGA 3 171 1 GCATGTGTTG 0.843909 -113 GGATGGATAAGCGGAGAGTAAGGTGTGTCAAAT 7 29 0 GCGGGTAAGG 0.879788 -272 AAATACAAATGCATACTGAGACGAAAGTATCAG 7 233 0 GCATGAGACG 0.881931 -68 ACATCGTGCAGCAGCGTGTGTCGTTGCCTTGCA 11 156 1 GCAGGTGTCG 0.990709 -139 AGCCTTTCGCGCAGGAGGTAACGGTACCTCCTG 11 200 0 GCAGGTAACG 0.985343 -95 **** ****** Masking position 8 Map Score: 2.54269 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 22 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 8 ATAATATATACTGCTGGGCGCCAAGTCTAT 2 76 0 CTGCTGGGCG 0.994745 -146 CGCCTAATATCTGCAGGACGCTCAAGATAC 6 57 1 CTGCAGGACG 0.980081 -244 ACGACACACGCTGCTGCACGATGTTAACTT 11 150 0 CTGCTGCACG 0.992025 -145 GTACCGTTACCTCCTGCGCGAAAGGCTTGG 11 206 1 CTCCTGCGCG 0.986217 -89 ********** Masking position 2 Map Score: 1.82649 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 4 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 ATCATAAATCATACACTTCTAGATATTTAC 1 197 0 ATACACTTCT 0.962698 -104 GCTCGAGAGAAAGCACTTCTACCGGTTGTT 3 23 0 AAGCACTTCT 0.931142 -261 GAACTTTAGCAAACACTTCTTCCCAAGAAA 3 68 0 AAACACTTCT 0.973672 -216 TAACACAATTCTTGATTGTGAT 6 3 1 ACACAATTCT 0.932414 -298 ATCTCGTACTAAACAATTATCAAAAGATAA 8 36 0 AAACAATTAT 0.78441 -55 CAGTTACTTTATACAATTCTTTTTTGTTTC 10 99 1 ATACAATTCT 0.942572 -29 ********** Masking position 5 Map Score: 1.98776 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 38 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 ********** No masking Map Score: 3.19987e-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 11 ********** No masking Map Score: 3.19987e-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: 3.19987e-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