AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ipurR_ctra_opreg_100.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 CT035 300 Biotin Protein Ligase #2 clpB 300 Clp Protease ATPase #3 CT114 25 hypothetical protein #4 mgtE 300 Mg++ Transporter (CBS Domain) #5 ubiA 111 4-hydroxybenzoate octaphenyltransferase #6 CT283 170 hypothetical protein #7 glyA 300 Serine Hydroxymethyltransferase Motif number 1 TTTACCAACTCTTTTTGTCTTTATCTGACTTTCG 1 40 0 CTTTTTTCTT 0.969666 -261 AAAAAAGCCTCTCTTTTTTCTCCTCTTCGTTTGA 1 73 1 CTCTTTTTTT 0.943115 -228 CAGTAAATAGCCCTTCTTGGTACTGTTTACGAAA 1 161 0 CCCTTCTGTT 0.785652 -140 TTACAAAAAGCTTTTTCTCATTATACCAAAAAAA 1 268 0 CTTTTTTCTT 0.969666 -33 CTCTTTGCCTTACAAAAAGCTTTT 1 287 0 CTCTTTCCTA 0.926865 -14 TTAGAGGAAGCTGTTTATGTTTGTGTCAGCTAAA 2 19 1 CTGTTTTGTT 0.772997 -282 ACAGCTAACTCTCTTCCCCTTACTGGCTATCCTA 2 69 0 CTCTTCCCTT 0.925788 -232 ATCGAAACTACTCTCTTTGATCAAGAAACAGCTA 2 96 0 CTCTCTTGTA 0.852468 -205 TGTAAAGTATCTTTTTATAGTGAAGGACTCTTGT 4 71 1 CTTTTTTATA 0.643504 -230 TCTCGGAAGACTTTTTGTCGTTTTCGTAAAAAAG 4 112 1 CTTTTTTCTT 0.969666 -189 CTCTTTCACGCCCTTCTCCGTTCTTTATATAAAG 4 226 0 CCCTTCCCTT 0.732117 -75 TCAGAAGGAGCTTTTCTTGCTGAAAAAAGTACGT 5 37 0 CTTTTCTGTA 0.857 -75 AGAGGGATCTCTTTCTCTCTTCGTAAAGGAATTC 6 112 1 CTTTCTTCTT 0.915734 -59 AGTAGTTTTCCTTTTTTTTCTTAAAAGGA 6 152 1 CTTTTTTTTA 0.855884 -19 AGCATCGTTTCTTTTTCTTATAGTTATAGTTAAA 7 140 1 CTTTTTTTTT 0.901851 -161 AAAATAAATCCTCTTTCTCCTAGAAAGTTTAGAC 7 171 1 CTCTTTTCTA 0.973876 -130 CCTCTACCCACTCTCCCTTATCCTTTATGGGAAT 7 224 0 CTCTCCTTTT 0.781937 -77 TGCAGAGGCACTCTTTATCCTCTACCCACTCTCC 7 242 0 CTCTTTTCTA 0.973876 -59 ****** ** * * Masking position 4 Map Score: 19.4922 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 441 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 TTACGAAAAATCTTTATGGGAATATAATTGCC 1 137 0 TTTTAGGGAA 0.920519 -164 TTCTTGGTACTGTTTACGAAAAATCTTTATGG 1 150 0 TTTTAGAAAA 0.955734 -151 AACTTCAAACCATTTATGAAAATAGTTTAAAA 1 208 0 CTTTAGAAAA 0.975678 -93 TAAACAGCTTCCTCTAAGGAGAGAT 2 4 0 CTCTAGGAGA 0.904721 -297 TTAAGAGACTTTTTTACGAAAACGACAAAAAG 4 122 0 TTTTAGAAAA 0.95458 -179 CTTCGGTCTTTGTCCATGAAAACTTGATAATA 6 49 1 TTCCAGAAAA 0.740287 -122 CTACAGAATTCCTTTACGAAGAGAGAAAGAGA 6 119 0 CTTTAGAAGA 0.926952 -52 TCCTTTTAAGAAAAAAAAGGAAAA 6 157 0 CTTTAGAAAA 0.975683 -14 AAGAAGCTTCCTACTAGGAAAAAAGCTT 7 7 0 CACTAGAAAA 0.893168 -294 TTATGGTAAGCGACTAGGGAAAATGGGGCGCT 7 92 1 CACTAGGAAA 0.859927 -209 AAGTCTAAACTTTCTAGGAGAAAGAGGATTTA 7 175 0 TTCTAGAGAA 0.941728 -126 GAATCTAATCTTTTGATGAGAAAGTCTAAACT 7 196 0 TTTGAGAGAA 0.730386 -105 TCTCCCTTATCCTTTATGGGAATCTAATCTTT 7 215 0 CTTTAGGGAA 0.955859 -86 * **** ***** Masking position 6 Map Score: 13.3726 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 187 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 GAAAAAAGAGAGGCTTTTTTTTACCAACTC 1 63 0 AGGCTTTTTT 0.711721 -238 TTTCGGGCTAAAGCTCCCTCAAACGAAGAG 1 95 0 AAGCTCCCTC 0.928957 -206 TATTCCCATAAAGATTTTTCGTAAACAGTA 1 145 1 AAGATTTTTC 0.870468 -156 AGAGTTGATAAAGCGTTTTTTTTGGTATAA 1 252 1 AAGCGTTTTT 0.915309 -49 GCCTTACAAAAAGCTTTTTCTCATTATACC 1 275 0 AAGCTTTTTC 0.946544 -26 CAAACATAAACAGCTTCCTCTAAGGAGAGA 2 12 0 CAGCTTCCTC 0.831237 -289 GCTAAATCATCAGCTCCTTGGTTAGGATAG 2 47 1 CAGCTCCTTG 0.765229 -254 TTTGCACTGTAAGCTTCGTTTCTTCTG 4 8 0 AAGCTTCGTT 0.889993 -293 TCACTATAAAAAGATACTTTACAAACAGAT 4 64 0 AAGATACTTT 0.813169 -237 ACTCTTAAACAAGAGTCCTTCACTATAAAA 4 83 0 AAGAGTCCTT 0.818412 -218 ACTATCTATTAAGAGACTTTTTTACGAAAA 4 132 0 AAGAGACTTT 0.70696 -169 GACGACTTTTAAGAGTCTTTATATAAAGAA 4 210 1 AAGAGTCTTT 0.915309 -91 TCAGCAAGAAAAGCTCCTTCTGATTACAAT 5 48 1 AAGCTCCTTC 0.968687 -64 ATTACAATACAAGATCTTTTACACCTATAA 5 70 1 AAGATCTTTT 0.826736 -42 AAGCTTTTTTCCTAGTAGGA 7 1 1 AAGCTTTTTT 0.951133 -300 TCCTAGTAGGAAGCTTCTTGACTTTTGCTG 7 20 1 AAGCTTCTTG 0.95166 -281 ********** Masking position 9 Map Score: 14.3216 Number of sites scoring better than the average of aligned sites = 847 Number in coding regions = 846 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 GCCAGTAAGGGGAAGAGAGTTAGCTGTTTC 2 76 1 GGAAGAGAGT 0.728477 -225 TTTATTGACTGTAAGAGAATTAAGCTGTAT 2 193 1 GTAAGAGAAT 0.879557 -108 ATTTTGCACTGTAAGCTTCGTTTCTTCTG 4 10 0 GTAAGCTTCG 0.83623 -291 GGACTCTTGTTTAAGAGTCTCGGAAGACTT 4 95 1 TTAAGAGTCT 0.915778 -206 AGACTATCTATTAAGAGACTTTTTTACGAA 4 134 0 TTAAGAGACT 0.865066 -167 TAGACGACTTTTAAGAGTCTTTATATAAAG 4 208 1 TTAAGAGTCT 0.915778 -93 TACTTGTTGCGTAAGATTATTATCAAGTTT 6 68 0 GTAAGATTAT 0.802305 -103 TTTCCTAGTAGGAAGCTTCTTGACTTTTGC 7 18 1 GGAAGCTTCT 0.88818 -283 GACTTTTGCTGTAAGAATATGATCAACTGA 7 39 1 GTAAGAATAT 0.739102 -262 GCACCTTATGGTAAGCGACTAGGGAAAATG 7 87 1 GTAAGCGACT 0.960323 -214 TAATGGTCTTGGAAGCATCGTTTCTTTTTC 7 127 1 GGAAGCATCG 0.692855 -174 ********** Masking position 4 Map Score: 5.4832 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 261 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 AGGACTTACGAGAACGAAAGTCAGATAAAGA 1 26 1 AGAACGAAGT 0.934371 -275 AGGGAGCTTTAGCCCGAAAGGACCATTACAG 1 106 1 AGCCCGAAGG 0.993655 -195 CGTAAACAGTACCAAGAAGGGCTATTTACTG 1 164 1 ACCAAGAAGG 0.922878 -137 TGGTTAGGATAGCCAGTAAGGGGAAGAGAGT 2 65 1 AGCCAGTAGG 0.946505 -236 GCGAGACTTTAGACCGAATGTGTCGCTAATA 4 179 1 AGACCGAAGT 0.957595 -122 GAGTCTTTATATAAAGAACGGAGAAGGGCGT 4 222 1 ATAAAGAAGG 0.835802 -79 TACTTTTTTCAGCAAGAAAAGCTCCTTCTGA 5 40 1 AGCAAGAAAG 0.874228 -72 TCATGGACAAAGACCGAAGGGAGGATCTGTA 6 37 0 AGACCGAAGG 0.989973 -134 ******** ** Masking position 8 Map Score: 4.97717 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 74 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 CGCTGCCTAAGTGTATCTGTTTGTAAAGTA 4 50 1 GTGTATCTGT 0.924566 -251 TAATACCTCAGACTATCTATTAAGAGACTT 4 143 0 GACTATCTAT 0.878707 -158 CGACTTTTAAGAGTCTTTATATAAAGAACG 4 212 1 GAGTCTTTAT 0.796073 -89 AATAGGGAGGGAGGATCTGTACAGATCCTC 6 18 1 GAGGATCTGT 0.98736 -153 AGACCGAAGGGAGGATCTGTACAGATCCTC 6 28 0 GAGGATCTGT 0.98736 -143 CTAGGAGAAAGAGGATTTATTTTAACTATA 7 164 0 GAGGATTTAT 0.943781 -137 ********** Masking position 6 Map Score: 1.89789 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 AACTACTCTCTTTGATCAAGAAACAGCTAAC 2 94 0 TTGATCAAGA 0.976448 -207 AGAGAGTAGTTTCGATCAAGATCGATTTCTA 2 114 1 TCGATCAAGA 0.927326 -187 AAGATCGATTTCTAATCAAGTTTTTTGCCTG 2 131 1 TTAATCAAGT 0.911873 -170 TGTAGTTTTCTGTGATCAAATGATCTTAGCT 2 160 1 TTGATCAAAT 0.948041 -141 TGCGTAAGATTATTATCAAGTTTTCATGGAC 6 60 0 TTTATCAAGT 0.911872 -111 GCTGTAAGAATATGATCAACTGAAGCTGCAA 7 46 1 TTGATCAACT 0.938785 -255 GTTTAGACTTTCTCATCAAAAGATTAGATTC 7 197 1 TTCATCAAAA 0.799172 -104 * ********* Masking position 5 Map Score: 1.46562 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 33 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 AGAAGGGCTATTTACTGTTTTGAGTAAAGA 1 178 1 TTTACTGTTT 0.900389 -123 GGGAAGAGAGTTAGCTGTTTCTTGATCAAA 2 85 1 TTAGCTGTTT 0.972909 -216 TCAAATGATCTTAGCTCTTTTATTGACTGT 2 175 1 TTAGCTCTTT 0.972906 -126 TCGTTTCTATTTTGCTCTTTCACGCCCTTC 4 244 0 TTTGCTCTTT 0.972909 -57 ********** Masking position 6 Map Score: 0.446552 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 36 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 ACTACAGGCAAAAAACTTGATTAGAAATCG 2 136 0 AAAAACTTGA 0.807949 -165 TTTGATCACAGAAAACTACAGGCAAAAAAC 2 150 0 GAAAACTACA 0.978643 -151 ACTTTTTTACGAAAACGACAAAAAGTCTTC 4 117 0 GAAAACGACA 0.953795 -184 CTTTGTCCATGAAAACTTGATAATAATCTT 6 56 1 GAAAACTTGA 0.956435 -115 GAAAAAAAAGGAAAACTACTTCTACAGAAT 6 142 0 GAAAACTACT 0.933011 -29 ********** Masking position 5 Map Score: 0.154432 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 36 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 AATTGCCCTGTAATGGTCCTTTCGGGCTAA 1 114 0 TAATGGTCCT 0.974242 -187 AAATAGCCCTTCTTGGTACTGTTTACGAAA 1 161 0 TCTTGGTACT 0.919975 -140 CTAGAATATCTCATGGTACTTGTTGCGTAA 6 84 0 TCATGGTACT 0.974242 -87 ACTGAAGCTGCAATGGTATTAAAGCACCTT 7 64 1 CAATGGTATT 0.875082 -237 GGGCGCTTGGTAATGGTCTTGGAAGCATCG 7 117 1 TAATGGTCTT 0.943779 -184 ********** Masking position 4 Map Score: 0.0822963 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 10 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: -4.66526e-13 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: -4.66526e-13 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: -4.66526e-13 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