AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00061_ctra_reg_100.orf -o00061_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 fabI 237 Enoyl-Acyl-Carrier Protein Reductase #2 araD 83 Ribulose-P Epimerase #3 fabH 137 Oxoacyl Carrier Protein Synthase III #4 accA 132 AcCoA Carboxylase/Transferase Alpha #5 accD 71 AcCoA Carboxylase/Transferase Beta #6 sodM 131 Superoxide Dismutase (Mn) #7 ybeB 300 iojap superfamily ortholog Motif number 1 TTAAGGATTTTTTATTTTTAACAGGAAATTCTAC 1 32 1 TTTTTTACAG 0.948846 -206 GAAAAACAGGTTTTATATGTAGAATTTCCTGTTA 1 50 0 TTTATTAGAA 0.759652 -188 ACAAGGAAACTCTTTACTCTAGAAACCTGGATCC 1 116 1 TCTTATAGAA 0.731237 -122 TAGCAGATTCTTTATTATTGAGAAACGGGCCTCA 1 178 0 TTTTTTAGAA 0.971409 -60 TCTGCTACTCTCCTCTCTCAAGAAGACAAAATGG 1 205 1 TCCCTTAGAA 0.804583 -33 TACACTCTCCTTCTTATCGTAGAGGGTTAAAATT 2 13 1 TTCTACAGAG 0.742921 -71 TTCCTTCTGTAGAGATGACGCACA 2 70 0 TTCTTTAGAG 0.984792 -14 TTTCTTTTTAAGAGAAATTAAAAT 4 1 1 TTTTTTAGAG 0.989489 -132 TTTATTGTAATTTTTTTTAACCAATCAATAATAA 5 13 0 TTTTTTCCAA 0.583364 -59 TATTGCTCAATTTTTTGTAAAGAGGATGGTTTT 5 49 1 TTTTTTAGAG 0.988575 -23 CAATAAAATATTCACTGTCAAGAGCTATCCACAT 6 26 0 TTCCTTAGAG 0.968514 -106 GAATATTTTATTGATAATCTAGAGGGATCTATCT 6 47 1 TTGTATAGAG 0.855221 -85 CGCCACCTTCTCTATTTTCTACAGGCTAGCTAGA 6 78 0 TCTTTTACAG 0.870908 -54 TGGACATATTTTTATTTCAAAGAGCTAAGGCTTT 7 53 0 TTTTTCAGAG 0.951057 -248 GTACGGTGACTAGGTTTTTGAGAAAGCTCTTCAA 7 138 1 TAGTTTAGAA 0.618481 -163 CGAGATCCCCTACTCTTTGAAGAGCTTTCTCAAA 7 154 0 TACCTTAGAG 0.833163 -147 AAATAGCCTCTTTCCTCTAGCGAGATCCCCTACT 7 174 0 TTTCTTCGAG 0.902756 -127 AAAGAGGCTATTTTTGGTAAAGAATATCCACGAG 7 195 1 TTTTGTAGAA 0.772788 -106 AGGTCGAGCTTTTTTTCTAAAGAGAAAAATCCCT 7 242 0 TTTTTTAGAG 0.98941 -59 *** ** * **** Masking position 1 Map Score: 21.8241 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 599 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 AACTCCCGGATTCTTTTAAGGATTTTTTATTT 1 17 1 TTTTTAAGGA 0.956866 -221 TAAGGATTTTTTATTTTTAACAGGAAATTCTA 1 33 1 TTTTTTAACA 0.893323 -205 AGCAGATTCTTTATTATTGAGAAACGGGCCTC 1 179 0 TTTTTTGAGA 0.964939 -59 ACCCCATTTTGTCTTCTTGAGAGAGGAGAGTA 1 210 0 GTTTTTGAGA 0.838267 -28 TTTCTTTTTAAGAGAAATTAAAA 4 2 1 TTTTTTAAGA 0.986193 -131 AAAATAACTCTTTTTTATAAGAAGGGAGCGTG 4 106 1 TTTTATAAGA 0.909702 -27 ATTGCTCAATTTTTTGTAAAGAGGATGGTTTT 5 50 1 TTTTTAAAGA 0.976856 -22 ATAGTAACCTTATTTTTTAGGATGGCT 6 115 1 TATTTTAGGA 0.77752 -17 GGACATATTTTTATTTCAAAGAGCTAAGGCTT 7 54 0 TTTTCAAAGA 0.926243 -247 AAGAGGCTATTTTTGGTAAAGAATATCCACGA 7 196 1 TTTGTAAAGA 0.918745 -105 GGTCGAGCTTTTTTTCTAAAGAGAAAAATCCC 7 243 0 TTTTTAAAGA 0.982593 -58 ** ** ****** Masking position 12 Map Score: 10.9893 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 181 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 GGAAACTCTTTACTCTAGAAACCTGGATCCAGCC 1 120 1 TCCTGAACCT 0.958217 -118 AAGGAGTAGATTCACTGGCTGGATCCAGGTTTCT 1 136 0 TCCTGCGGAT 0.945371 -102 TTCTCTATTTTCTACAGGCTAGCTAGATAGATCC 6 71 0 TTCAGCAGCT 0.987387 -61 ATAAGGTTACTATCCTCGCCACCTTCTCTATTTT 6 94 0 TTCTGCACCT 0.98341 -38 GAGCTAAGGCTTTTCTCGCAACATTTTGCGATCG 7 32 0 TTCTGCACAT 0.958628 -269 CTAGTCACCGTACTCAAGCTAACTTCCATGCCAG 7 117 0 TCCAGCAACT 0.959666 -184 ATAGCCTCTTTCCTCTAGCGAGATCCCCTACTCT 7 172 0 TCCTGCAGAT 0.986677 -129 TGGTAAAGAATATCCACGAGAGCTAGGGCTCAAA 7 209 1 TTCAGAAGCT 0.939049 -92 TAATCGGGTATTCTCAGGCCAGTTTC 7 285 1 TCCAGCAGTT 0.959666 -16 * * ** ** **** Masking position 1 Map Score: 7.80062 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 84 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 GAATTTCCTGTTAAAAATAAAAAATCCTTA 1 33 0 TTAAAAATAA 0.937761 -205 GGCCCGTTTCTCAATAATAAAGAATCTGCT 1 181 1 TCAATAATAA 0.914677 -57 GCACCCGCAAACAAAAAGAAAAAACCGAGT 3 104 0 ACAAAAAGAA 0.856464 -34 TTAATTTCTCTTAAAAAGAAA 4 2 0 TTAAAAAGAA 0.936688 -131 CAAACAATAATCAAAAACAACCAAAAACCA 4 72 0 TCAAAAACAA 0.933862 -61 TCCCTTCTTATAAAAAAGAGTTATTTTAAT 4 103 0 TAAAAAAGAG 0.81617 -30 TTTTAACCAATCAATAATAAAA 5 3 0 TCAATAATAA 0.914677 -69 TATTGATTGGTTAAAAAAAATTACAATAAA 5 17 1 TTAAAAAAAA 0.788309 -55 AGCCATCCTAAAAAATAAGGTTACTATC 6 114 0 TAAAAAATAA 0.913299 -18 ATATTCTTTACCAAAAATAGCCTCTTTCCT 7 192 0 CCAAAAATAG 0.795061 -109 ********** Masking position 6 Map Score: 5.79002 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 263 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 AGTAGATTCACTGGCTGGATCCAGGTTTCTA 1 135 0 CTGGCGGATC 0.994386 -103 ATAAACCTCCCTAGCAGTATACTCGGTTTTT 3 84 1 CTAGCGTATA 0.902065 -54 AAAATATTCACTGTCAAGAGCTATCCACATC 6 25 0 CTGTCAGAGC 0.907674 -107 TATTGATAATCTAGAGGGATCTATCTAGCTA 6 55 1 CTAGAGGATC 0.950059 -77 TTTCTACAGGCTAGCTAGATAGATCCCTCTA 6 66 0 CTAGCAGATA 0.978336 -66 CCTCTTTCCTCTAGCGAGATCCCCTACTCTT 7 171 0 CTAGCAGATC 0.989392 -130 GAAACTGGCCTGAGAATACCCGATT 7 286 0 CTGGCTGAGA 0.935583 -15 ***** ***** Masking position 9 Map Score: 3.92258 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 60 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 AGAAGACAAAATGGGGTTAGCTC 1 225 1 ATGGGGTTAG 0.96688 -13 ATAATCGATTATGAGGATAGATGCAAAATA 3 43 1 ATGAGGATAG 0.991797 -95 ATTTTTTGTAAAGAGGATGGTTTT 5 58 1 AAGAGGATGG 0.916017 -14 GTACGTAAAGATGTGGATAGCTCTTGACAG 6 16 1 ATGTGGATAG 0.97351 -116 ATCCTAAAAAATAAGGTTACTATCCTCGCC 6 108 0 ATAAGGTTAC 0.833881 -24 AAATATGTCCATAAGGATAGCAGAGAAGTC 7 76 1 ATAAGGATAG 0.976098 -225 ********** Masking position 8 Map Score: 3.77639 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 40 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 AAACTCTTTACTCTAGAAACCTGGATCCAG 1 122 1 CTCTAGAAAC 0.922347 -116 ATTTTGTCTTCTTGAGAGAGGAGAGTAGCA 1 207 0 CTTGAGAGAG 0.693485 -31 TGTGCGTCATCTCTACAGAAGGAA 2 70 1 CTCTACAGAA 0.948595 -14 ATTTTAATTTCTCTTAAAAAGAAA 4 5 0 CTCTTAAAAA 0.659497 -128 AAACCATCCTCTTTACAAAAAATTGAGCAA 5 51 0 CTTTACAAAA 0.917623 -21 ATGTGGATAGCTCTTGACAGTGAATATTTT 6 26 1 CTCTTGACAG 0.794773 -106 TCTAGCTAGCCTGTAGAAAATAGAGAAGGT 6 78 1 CTGTAGAAAA 0.881502 -54 TTTGAGAAAGCTCTTCAAAGAGTAGGGGAT 7 154 1 CTCTTCAAAG 0.868571 -147 AGCCTCTTTCCTCTAGCGAGATCCCCTACT 7 174 0 CTCTAGCGAG 0.913929 -127 CGTGGATATTCTTTACCAAAAATAGCCTCT 7 197 0 CTTTACCAAA 0.811032 -104 GGATTTTTCTCTTTAGAAAAAAAGCTCGAC 7 244 1 CTTTAGAAAA 0.942615 -57 ********** Masking position 9 Map Score: 5.04179 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 425 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 ATAAAACCTGTTTTTCACACTTTAAAGATT 1 68 1 TTTTTCACAC 0.918562 -170 ATGAGGCCCGTTTCTCAATAATAAAGAATC 1 177 1 TTTCTCAATA 0.815332 -61 ATCTTTTTTCACACGCACCCGCAA 3 124 0 TTTTTCACAC 0.918562 -14 ACAATTTTAATTTCTCTTAAAAAGAAA 4 8 0 TTTCTCTTAA 0.839574 -125 ATGACCTTTGTTTCACGCAAACAATTTTAA 4 28 0 TTTCACGCAA 0.882677 -105 AGCTAAGGCTTTTCTCGCAACATTTTGCGA 7 35 0 TTTCTCGCAA 0.976147 -266 TTTGAAGAGCTTTCTCAAAAACCTAGTCAC 7 143 0 TTTCTCAAAA 0.953612 -158 GGTCGAGCTTTTTTTCTAAAGAGAAAAATC 7 245 0 TTTTTCTAAA 0.837175 -56 ********** Masking position 3 Map Score: 3.86716 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 176 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 TAGAGTAAAGAGTTTCCTTGTCAAATGTTT 1 107 0 AGTTTCCTTG 0.798062 -131 GGCTGGATCCAGGTTTCTAGAGTAAAGAGT 1 124 0 AGGTTTCTAG 0.809605 -114 TTTTTGTTTGCGGGTGCGTGTGAAAAAAGA 3 117 1 CGGGTGCGTG 0.959088 -21 AAATTAAAATTGTTTGCGTGAAACAAAGGT 4 25 1 TGTTTGCGTG 0.916095 -108 TTTTATAAGAAGGGAGCGTGCTACG 4 118 1 AGGGAGCGTG 0.970712 -15 AAAATAGAGAAGGTGGCGAGGATAGTAACC 6 94 1 AGGTGGCGAG 0.96842 -38 CGATCGCAAAATGTTGCGAGAAAAGCCTTA 7 32 1 ATGTTGCGAG 0.903525 -269 CTGGCATGGAAGTTAGCTTGAGTACGGTGA 7 117 1 AGTTAGCTTG 0.899426 -184 ********** Masking position 7 Map Score: 1.05068 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 129 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 10 TCAAATGTTTAATAGTTTTAATCTTTAAAG 1 87 0 AATAGTTTTA 0.934336 -151 TCTTGTGGTCAAAAATTTTAACCCTCTACG 2 30 0 AAAAATTTTA 0.874465 -54 GTTTCACGCAAACAATTTTAATTTCTCTTA 4 19 0 AACAATTTTA 0.94864 -114 AAAATTGAGCAATAATTTTATTGTAATTTT 5 33 0 AATAATTTTA 0.955729 -39 ********** Masking position 6 Map Score: 0.407786 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 11 GCCCGTTTCTCAATAATAAAGAATCTGCTA 1 182 1 CAATAATAAA 0.822168 -56 TCCTCATAATCGATTATCTAGGTGCTAGAC 3 30 0 CGATTATCTA 0.951952 -108 ACAAAGGTCATTATAATCAAATAGTTGGTT 4 47 1 TTATAATCAA 0.763398 -86 TTAATACAAACAATAATCAAAAACAACCAA 4 78 0 CAATAATCAA 0.95286 -55 TTTAACCAATCAATAATAAAA 5 2 0 CAATAATAAA 0.822168 -70 AATATTTTATTGATAATCTAGAGGGATCTA 6 48 1 TGATAATCTA 0.879078 -84 GCCACCTTCTCTATTTTCTACAGGCTAGCT 6 81 0 CTATTTTCTA 0.611775 -51 TGAGAATACCCGATTATCTAAGATAAGGTC 7 271 0 CGATTATCTA 0.951952 -30 ********** Masking position 3 Map Score: 2.58726 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 64 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 CTCCTTATGTATTATGAGGCCCGTTTCTCA 1 164 1 ATTATGAGGC 0.941128 -74 TAGATAATCGATTATGAGGATAGATGCAAA 3 40 1 ATTATGAGGA 0.972593 -98 TCAGTACGTAAAGATGTGGATAGCTCTTGA 6 13 1 AAGATGTGGA 0.944321 -119 TTTTATGTTCATGATGAGAACGATCGCAAA 7 12 1 ATGATGAGAA 0.938731 -289 ATGCCAGAGCAAGATTAGGACTTCTCTGCT 7 94 0 AAGATTAGGA 0.914476 -207 ********** Masking position 5 Map Score: 0.118796 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 44 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: -3.26606e-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: -3.26606e-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: -3.26606e-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