AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_ctra_reg_100.orf -o00130_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ubiA 111 4-hydroxybenzoate octaphenyltransferase #2 CT355 300 hypothetical protein #3 CT426 196 Fe-S oxidoreductase #4 gidA 293 FAD-dependent oxidoreductase #5 ygcA 85 rRNA Methyltransferse #6 hctA 300 Histone-Like Developmental Protein #7 CT793 62 hypothetical protein Motif number 1 CAACGTACTTTTTTCAGCAAGAAAAGCTCCTTCT 1 35 1 TTTAGAAAAA 0.923593 -77 CGTCAGAACACTTTTAACAAAAAAGCGTTATATC 2 95 0 CTTAAAAAAA 0.977439 -206 GCAGCTTATATTCTAAAAAAGAACCTACCCTCGT 2 164 0 TTTAAAAAAC 0.759722 -137 GATTTGTAGTTTTTAGGTAGAAAAACCTTAAGAA 2 273 0 TTTGGAGAAA 0.751991 -28 GATAGGGGTCTTCCTAGTAGGAAAGACCCTATCA 3 90 0 TTCAGAGAAA 0.8261 -107 GCAGCGACTGCTGTCAGAAAAAGAAGTCTTGTCC 3 138 1 CTTAGAAAGA 0.943431 -59 AGTCTTGTCCCCGTGAAAAGCAAAACTCACAAAC 3 162 1 CCTAAAGAAA 0.914159 -35 TGGCTGTCAATTTTTGGGAATAAACTTGT 4 6 0 TTTGGAAAAA 0.755933 -288 CGGCGATACACTTTGAGAAGAAAACCTATGAGGA 4 72 1 CTTAGAGAAA 0.976624 -222 CTTGCGTAAACCATTAAGAAGAAAACCATGTCAT 4 169 1 CCTAAAAAAA 0.915764 -125 ACCATGTCATCTGTTAAGAAAAAACGAAGACTTA 4 193 1 CTTAAAAAAA 0.977547 -101 AAAGTGCCCTCTATAAAAAAGAGAAAGCGCTAAA 5 14 0 CTTAAAAAGA 0.944522 -72 GAATCTTCTAACAAGAGAACAAGCTCCT 6 5 1 CTCAAAAAGA 0.8694 -296 TCAGCGCTTTCTATTAAAAGAAACCCTATTCAGA 6 61 1 CTTAAAGAAC 0.914159 -240 TATTTTTCCTCTGTTAATAGAAAAATTTTTTATA 6 115 0 CTTAAAGAAA 0.977088 -186 TGTTCCCCTACTACGAATAAAAAATTTTTTCGAT 7 32 0 CTCAAAAAAA 0.944522 -31 ** * ** ** *** Masking position 9 Map Score: 17.8712 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 387 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 CGGCTGGGTCCCTCCTCCCCTATAGCTTTTA 2 127 1 CCTCCTCCCT 0.992362 -174 TAAAAAAGAACCTACCCTCGTCCTAGGTAAA 2 154 0 CCTACCCTCT 0.912123 -147 TTGGATCTTACCGCCTCCCTAGAGATGTGGC 2 213 0 CCGCCTCCCA 0.866142 -88 TTGGGTTGTTCCTCCTCCCCTTTTTCTTTGG 2 240 0 CCTCCTCCCT 0.992362 -61 AAAAAGAAGTCTTGTCCCCGTGAAAAGCAAA 3 155 1 CTTGTCCCCT 0.929543 -42 CCATTGTAAACTTCTTCCCATCGCCTGGTGA 4 37 1 CTTCTTCCCT 0.972116 -257 GGGCAAGCACCCGATCCTCATAGGTTTTCTT 4 89 0 CCGATCCTCT 0.844361 -205 CGGGTGCTTGCCCGTTCTCATAGGCATTAGC 4 107 1 CCCGTTCTCT 0.966352 -187 GGCCCTCTTTCCTCTTCTCATTGATCCCTTC 5 57 1 CCTCTTCTCT 0.989967 -29 TTCTCATTGATCCCTTCTCTTTTTT 5 71 1 TCCCTTCTCT 0.752735 -15 AAGAAAGGAGCTTGTTCTCTTGTTAGAAGAT 6 13 0 CTTGTTCTCT 0.936485 -288 AAGAGCCTGTTCCCCTACTACGAATA 7 47 0 CCTGTTCCCT 0.990732 -16 ********* * Masking position 7 Map Score: 16.5907 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 206 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 GCTCTTAGTTACCCCTCTTTTCGATATTTAAGT 2 18 1 ACCTCTTTCG 0.92982 -283 CCAGAAAAATACATTTTTGTTTCCTTTGGCTTG 2 60 1 ACTTTTTTTC 0.931857 -241 TAGAATATAAGCTGCTTTGTTTGGGTGTTTGCC 2 183 1 GCCTTTTTTG 0.977184 -118 GTTCCTCCTCCCCTTTTTCTTTGGATCTTACCG 2 231 0 CCTTTTTTTG 0.79829 -70 GGCCTTCATGACTTCTTTATTTCTACTCGTCTG 3 16 1 ACCTTTTTTC 0.982208 -181 CGGGGACAAGACTTCTTTTTCTGACAGCAGTCG 3 142 0 ACCTTTTCTG 0.921502 -55 ACAAGTTTATTCCCAAAAATTGA 4 1 1 ACGTTTTTCC 0.817664 -293 GATCTCTTCGACGTCTTTTTTTACGCTTATGCT 4 236 0 ACCTTTTTTA 0.963938 -58 AAGAGAACAAGCTCCTTTCTTTCTTTTCTAAAC 6 23 1 GCCTTTTTTC 0.971892 -278 ATCTCCTTGTACCGCTCTGTTTATCAATAGGTT 6 148 0 ACCTCTTTTA 0.90257 -153 GGATCCTAAAGCAGCTTTATTTGACATCTCCTT 6 173 0 GCCTTTTTTG 0.977184 -128 GTTGTTTTAAACTATTTTTTTCAGTTTTAATTT 6 259 0 ACTTTTTTCA 0.787303 -42 ** **** **** Masking position 6 Map Score: 11.2048 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 4 CTATAGGGGAGGAGGGACCCAGCCGTCAGAACAC 2 118 0 GGAGACCCGC 0.984497 -183 TAGAGATGTGGCAAACACCCAAACAAAGCAGCTT 2 191 0 GCAAACCCAC 0.996025 -110 AAGGGGAGGAGGAACAACCCAAAATTCTTAAGGT 2 249 1 GGAAACCCAA 0.986697 -52 CTTCCTAGTAGGAAAGACCCTATCAAAACAGCTG 3 81 0 GGAAACCCAC 0.997915 -116 TTTCCTACTAGGAAGACCCCTATCTAAAGGATGT 3 100 1 GGAACCCCAC 0.994325 -97 ATGAGAACGGGCAAGCACCCGATCCTCATAGGTT 4 94 0 GCAAACCCAC 0.996025 -200 **** **** * * Masking position 3 Map Score: 7.83852 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 TATTGTAATCAGAAGGAGCTTTTCTTGCTG 1 49 0 AGAAGGAGCT 0.973238 -63 TTTTTCTGACAGCAGTCGCTGCGGCCACAT 3 130 0 AGCAGTCGCT 0.927693 -67 GCCGGCTTTCACCAGGCGATGGGAAGAAGT 4 46 0 ACCAGGCGAT 0.938304 -248 GCCTGGTGAAAGCCGGCGATACACTTTGAG 4 59 1 AGCCGGCGAT 0.938856 -235 TATAAAAAAGAGAAAGCGCTAAAATA 5 7 0 AGAAAGCGCT 0.97309 -79 TCTTTTTTATAGAGGGCACTTTTATCAACA 5 26 1 AGAGGGCACT 0.921058 -60 AGAAGAGGAAAGAGGGCCCTGTTGATAAAA 5 45 0 AGAGGGCCCT 0.945309 -41 TTCTTTTAATAGAAAGCGCTGAACCTTGTT 6 53 0 AGAAAGCGCT 0.97309 -248 ACAGAGCGGTACAAGGAGATGTCAAATAAA 6 161 1 ACAAGGAGAT 0.784054 -140 ********** Masking position 1 Map Score: 7.60838 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 237 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 AAACCCTTCGAATATTATGG 1 102 0 AAACCCTTCG 0.863119 -10 ATTCTAAAAAAGAACCTACCCTCGTCCTAG 2 159 0 AGAACCTACC 0.94074 -142 CTAGTAGGAAAGACCCTATCAAAACAGCTG 3 81 0 AGACCCTATC 0.97989 -116 CTTTGAGAAGAAAACCTATGAGGATCGGGT 4 82 1 AAAACCTATG 0.956243 -212 CTATTAAAAGAAACCCTATTCAGACCCTAT 6 71 1 AAACCCTATT 0.952454 -230 AACCCTATTCAGACCCTATGCAGCACATAG 6 82 1 AGACCCTATG 0.986106 -219 CAGAGGAAAAATAACCTATTGATAAACAGA 6 136 1 ATAACCTATT 0.793337 -165 ********** Masking position 3 Map Score: 4.03748 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 34 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 GTGTTTTGCTCTTAGTTACCCCT 2 4 1 TTTTGCTCTT 0.951456 -297 GGCTTGAGGATATAACGCTTTTTTGTTAAA 2 87 1 TATAACGCTT 0.902524 -214 CCTCCTCCCCTATAGCTTTTACCTAGGACG 2 137 1 TATAGCTTTT 0.817583 -164 TCTGTTGCGCTACAGCCCTTCTCAGTATAG 3 45 1 TACAGCCCTT 0.866848 -152 AGTTTGTGAGTTTTGCTTTTCACGGGGACA 3 167 0 TTTTGCTTTT 0.817617 -30 CGACGTCTTTTTTTACGCTTATGCTTGGCG 4 231 0 TTTTACGCTT 0.902524 -63 TATTTTAGCGCTTTCTCTTTTTT 5 4 1 TTTAGCGCTT 0.984835 -82 CTAAACAAGGTTCAGCGCTTTCTATTAAAA 6 50 1 TTCAGCGCTT 0.973526 -251 ********** Masking position 9 Map Score: 4.41296 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 151 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 TATATCCTCAAGCCAAAGGAAACAAAAATG 2 71 0 AGCCAAAGGA 0.891126 -230 TGTGGCAAACACCCAAACAAAGCAGCTTAT 2 189 0 ACCCAAACAA 0.963412 -112 AGGCGGTAAGATCCAAAGAAAAAGGGGAGG 2 228 1 ATCCAAAGAA 0.953965 -73 AGGTAGAAAAACCTTAAGAATTTTGGGTTG 2 263 0 ACCTTAAGAA 0.811735 -38 GAAGACCCCTATCTAAAGGATGTGGCCGCA 3 111 1 ATCTAAAGGA 0.895755 -86 AGAACCCAAACAATTTAACTATC 4 281 0 ACCCAAACAA 0.963412 -13 TTTCTTTCTTTTCTAAACAAGGTTCAGCGC 6 38 1 TTCTAAACAA 0.745804 -263 TAGGTAAGGATCCTAAAGCAGCTTTATTTG 6 183 0 TCCTAAAGCA 0.773715 -118 ********** Masking position 6 Map Score: 2.31529 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 190 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 GAACTTCAACGTACTTTTTTCAGCAAGAAAA 1 29 1 GACTTTTTTC 0.978037 -83 GTATTTTTCTGGAATTTTTTCACTTAAATAT 2 41 0 GAATTTTTTC 0.975551 -260 ACGAGGGTAGGTTCTTTTTTAGAATATAAGC 2 164 1 GTCTTTTTTA 0.756233 -137 TTTATAGAGGGCACTTTTATCAACAGGGCCC 5 31 1 GACTTTTATC 0.888715 -55 TAGTTTTATAAAAAATTTTTCTATTAACAGA 6 109 1 AAAATTTTTC 0.645679 -192 TTATCAATAGGTTATTTTTCCTCTGTTAATA 6 130 0 GTATTTTTCC 0.882663 -171 ACAACTAGAGGATATTTTTTC 6 290 1 GTATTTTTTC 0.963965 -11 CTACGAATAAAAAATTTTTTCGATCACGCAA 7 25 0 AAATTTTTTC 0.912006 -38 * ********* Masking position 6 Map Score: 3.75075 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 154 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: 1.80721e-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: 1.80721e-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: 1.80721e-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