AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_ctra_reg_300.orf -o00440_ctra_300.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 dhnA 300 Predicted 1,6-Fructose biphosphate aldolase (dehydrin family) #2 ydaO 153 PP-Loop Superfamily ATPase #3 surE 100 SurE-like Acid Phosphatase #4 ubiA 111 4-hydroxybenzoate octaphenyltransferase #5 CT355 300 hypothetical protein #6 CT421 300 hypothetical protein #7 CT421.1 184 hypothetical protein #8 CT423 132 (CBS Domain) #9 rsbV_1 188 Sigma Regulatory Factor #10 CT425 177 hypothetical protein #11 CT426 196 Fe-S oxidoreductase #12 ygcA 85 rRNA Methyltransferse #13 hctA 300 Histone-Like Developmental Protein Motif number 1 ATAAAAATTAAAAAGAGAAAATAGTT 1 3 0 AAAGAAAATG 0.627264 -298 ATTCTTTTGCACAGAAAAGGGCTTTGTAAAG 2 8 1 TAAGAAAAGG 0.989396 -146 AGGTAAGTCTTAGAAAGAAAAGAGCTTCTTTACA 2 35 0 TAAGAAAAGG 0.989396 -119 CAGAACACTTTTAACAAAAAAGCGTTATATCCTC 5 92 0 TAAAAAAAGG 0.967169 -209 GGCGGTAAGATCCAAAGAAAAAGGGGAGGAGGAA 5 229 1 TAAGAAAAAG 0.955355 -72 TTAAACGAGTTTCAAAGAAAAGGTGCATGTTAAG 6 200 0 TAAGAAAAGT 0.878965 -101 TTTGGAACGGTCTATAGAAGAGGGTTTTTCTCAC 6 243 0 TAAGAAGAGG 0.963665 -58 TTATCTTCTTTTTAAAAAGAAGGGAATTTAGTGG 7 23 1 TAAAAGAAGG 0.92508 -162 CATAGCTCTATTGAAAAAAAAACGGCGCTCTACT 7 67 1 TAAAAAAAAG 0.871075 -118 GGAAGGGATTTAAAAAGAAAATAGCAACTCTGCT 7 124 0 TAAGAAAATG 0.902999 -61 TATAGAGATTTCTAGAGGGAAGCGAAGACTT 8 8 0 TAAGGGAAGG 0.93919 -125 TACGCATCACTTGAAAAGAGAGCGAGTTGAAGGT 10 15 0 TAAAGAGAGG 0.767826 -163 ACAGAGGATCTTCAAAGAAAAGGCTATGTTACAC 10 84 0 TAAGAAAAGC 0.859231 -94 AAGCAAAATTTTTACAGATAAAGGACTTCCTGGT 10 129 1 TAAGATAAAG 0.632182 -49 CTGTTACTCCTATACTGAGAAGGGCTGTAGCGCA 11 50 0 TATGAGAAGG 0.82389 -147 AAAAGTGCCCTCTATAAAAAAGAGAAAGCGCTAA 12 15 0 TAAAAAAAGG 0.967169 -71 GGGATCAATGAGAAGAGGAAAGAGGGCCCTGTTG 12 51 0 AAAGGAAAGG 0.869472 -35 AAAAAAGAGAAGGGATCAATGAGA 12 72 0 AAAGAGAAGG 0.876078 -14 CTGAACCTTGTTTAGAAAAGAAAGAAAGGAGCTT 13 31 0 TAAAAAGAAG 0.6576 -270 TAGGGTTTCTTTTAATAGAAAGCGCTGAACCTTG 13 55 0 TATAGAAAGG 0.5819 -246 TTTTCCTCTGTTAATAGAAAAATTTTTTATAAAA 13 112 0 TAAGAAAAAT 0.624846 -189 * * ******* * Masking position 4 Map Score: 23.7882 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 293 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 GTCTTTAGTTAAGATCTTTGAGAAGGTGAG 1 122 0 AAGATCTTTG 0.867849 -179 GACTCCAGGAAAGATCGTTTATCTTGAGGT 1 149 1 AAGATCGTTT 0.873871 -152 TCGAAGATGCTCCTATTTTAAAT 1 288 0 AAGATGCTCC 0.65489 -13 CTTCTTTACAAAGCCCTTTTCTGTGCAAAA 2 15 0 AAGCCCTTTT 0.795996 -139 CTTTGTAAAGAAGCTCTTTTCTTTCTAAGA 2 32 1 AAGCTCTTTT 0.963963 -122 AATGAGCTATTAGATCTTTTTAAAATAATA 3 69 0 TAGATCTTTT 0.634323 -32 TCAGCAAGAAAAGCTCCTTCTGATTACAAT 4 48 1 AAGCTCCTTC 0.974445 -64 ATTACAATACAAGATCTTTTACACCTATAA 4 70 1 AAGATCTTTT 0.94987 -42 TTTAGAATATAAGCTGCTTTGTTTGGGTGT 5 181 1 AAGCTGCTTT 0.951846 -120 CAGAGGACTGAAGATCCTTGTGTCGTCGGT 6 97 0 AAGATCCTTG 0.948833 -204 ATAACCCAACAAGATCCTTCTGCCTTCCTG 7 162 0 AAGATCCTTC 0.9643 -23 TCACGATCAAAAGCACCTTTTCGTAATCTC 9 92 0 AAGCACCTTT 0.881436 -97 CTTTTCTTTGAAGATCCTCTGTAAAGCATG 10 96 1 AAGATCCTCT 0.934914 -82 ACAAGAGAACAAGCTCCTTTCTTTCTTTTC 13 21 1 AAGCTCCTTT 0.986934 -280 ATGTCAAATAAAGCTGCTTTAGGATCCTTA 13 179 1 AAGCTGCTTT 0.951846 -122 ********** Masking position 2 Map Score: 20.4589 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 233 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 3 AACTATTTTCTCTTTTTAATT 1 2 1 ACTATTTTCT 0.562307 -299 CTGCGATTTTTCCCCGTTCTAAAGATCAGT 1 73 0 TCCCCGTTCT 0.718807 -228 AGAGTGTGTTGCGCTTTTTTGGGTTTTCAC 1 255 1 GCGCTTTTTT 0.828312 -46 TCGAAGATGCTCCTATTTTAAATATGGT 1 283 0 GCTCCTATTT 0.550984 -18 TCTTTACAAAGCCCTTTTCTGTGCAAAAGA 2 13 0 GCCCTTTTCT 0.960957 -141 TTGTAAAGAAGCTCTTTTCTTTCTAAGACT 2 34 1 GCTCTTTTCT 0.938583 -120 GCTCTTAGTTACCCCTCTTTTCGATATTTA 5 18 1 ACCCCTCTTT 0.708957 -283 TGAGGATATAACGCTTTTTTGTTAAAAGTG 5 91 1 ACGCTTTTTT 0.725218 -210 TTGTTCCTCCTCCCCTTTTTCTTTGGATCT 5 236 0 TCCCCTTTTT 0.868233 -65 CGTGAGAAAAACCCTCTTCTATAGACCGTT 6 242 1 ACCCTCTTCT 0.811201 -59 CCCACTAAATTCCCTTCTTTTTAAAAAGAA 7 28 0 TCCCTTCTTT 0.676837 -157 GAATAGTAGAGCGCCGTTTTTTTTTCAATA 7 75 0 GCGCCGTTTT 0.514828 -110 CAGCAGAGTTGCTATTTTCTTTTTAAATCC 7 123 1 GCTATTTTCT 0.701353 -62 CTTTTCGTAATCTCCCTTCTACTATGGCTA 9 76 0 TCTCCCTTCT 0.698064 -113 CCTTCAACTCGCTCTCTTTTCAAGTGATGC 10 16 1 GCTCTCTTTT 0.733611 -162 TACTAGGAAGACCCCTATCTAAAGGATGTG 11 105 1 ACCCCTATCT 0.656888 -92 TTTAGCGCTTTCTCTTTTTTATAGAGGGCA 12 14 1 TCTCTTTTTT 0.802961 -72 TTCTCATTGATCCCTTCTCTTTTTT 12 71 1 TCCCTTCTCT 0.787635 -15 AAGAGAACAAGCTCCTTTCTTTCTTTTCTA 13 23 1 GCTCCTTTCT 0.93881 -278 AATTCATGCAACCATTTTCTAGAATCTAGG 13 209 0 ACCATTTTCT 0.67417 -92 GTTGTTTTAAACTATTTTTTTCAGTTTTAA 13 262 0 ACTATTTTTT 0.42045 -39 ********** Masking position 8 Map Score: 16.7348 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 570 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 CAGTTATATTAAAATAACCTTGGTGTTCAA 1 47 0 AAAATAACCT 0.942676 -254 GCAAATCTTTAAAATTTCCCTCATGTTTAC 2 82 1 AAAATTTCCC 0.80137 -72 AATAATAAGAAAAATAAACCAAGTATTATG 3 46 0 AAAATAAACC 0.76341 -55 TATATTCTAAAAAAGAACCTACCCTCGTCC 5 162 0 AAAAGAACCT 0.938947 -139 GTTTTTAGGTAGAAAAACCTTAAGAATTTT 5 269 0 AGAAAAACCT 0.854235 -32 GTATTTCTCTAGAATAGCCCCGTGTATGGC 6 148 0 AGAATAGCCC 0.862963 -153 GCTATTCTAGAGAAATACCCGCTTTAAATC 6 160 1 AGAAATACCC 0.81747 -141 AAACTCGTTTAAAAATTCCTCGTGAGAAAA 6 222 1 AAAAATTCCT 0.56546 -79 ATTCCTCGTGAGAAAAACCCTCTTCTATAG 6 236 1 AGAAAAACCC 0.914626 -65 AAAATAACCCAACAAGATCC 7 175 0 AAAATAACCC 0.967805 -10 TATCACGATCAAAAGCACCTTTTCGTAATC 9 94 0 AAAAGCACCT 0.743339 -95 CCCTGTTGATAAAAGTGCCCTCTATAAAAA 12 29 0 AAAAGTGCCC 0.802879 -57 GCTTTCTATTAAAAGAAACCCTATTCAGAC 13 66 1 AAAAGAAACC 0.751097 -235 TAACAGAGGAAAAATAACCTATTGATAAAC 13 133 1 AAAATAACCT 0.942676 -168 GAAAAAATATCCTCTAGTTGTTG 13 288 0 AAAATATCCT 0.840743 -13 ********** Masking position 4 Map Score: 12.6698 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 197 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 AAAAGCTATAGGGGAGGAGGGACCCAGCCG 5 127 0 GGGGAGGAGG 0.990316 -174 CCACATCTCTAGGGAGGCGGTAAGATCCAA 5 214 1 AGGGAGGCGG 0.994871 -87 CAAAGAAAAAGGGGAGGAGGAACAACCCAA 5 241 1 GGGGAGGAGG 0.990316 -60 CTTCCCATTCAGGAAGGCAGAAGGATCTTG 7 153 1 AGGAAGGCAG 0.91023 -32 AGATTTCTAGAGGGAAGCGAAGACTT 8 7 0 AGGGAAGCGA 0.91023 -126 CAATGAGAAGAGGAAAGAGGGCCCTGTTGA 12 50 0 AGGAAAGAGG 0.933707 -36 ********** Masking position 5 Map Score: 4.98748 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 39 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 AGATTTAAATAAAAATTTGTATTAATCATA 3 20 1 AAAAATTTGT 0.588522 -81 GAAAAACCTTAAGAATTTTGGGTTGTTCCT 5 258 0 AAGAATTTTG 0.87384 -43 TTTTCTCACGAGGAATTTTTAAACGAGTTT 6 222 0 AGGAATTTTT 0.782028 -79 CTATATCGATAAAAATTTTTATCGTAACAT 8 37 1 AAAAATTTTT 0.498991 -96 GTGGTCCTGAAAAAATTTTTGGTGTAACAT 10 63 1 AAAAATTTTT 0.498991 -115 CTTTATCTGTAAAAATTTTGCTTTCGCATG 10 122 0 AAAAATTTTG 0.64066 -56 TAGTTTTATAAAAAATTTTTCTATTAACAG 13 109 1 AAAAATTTTT 0.498991 -192 ********** Masking position 5 Map Score: 4.29439 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 103 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 TTTATCTTGAGGTTTTCTCCTACGAAATAAATG 1 166 1 GGTTTTCCAC 0.974926 -135 CGCTTTTTTGGGTTTTCACCATATTTAAAATAG 1 266 1 GGTTTACCTA 0.559746 -35 GTGTTCTGACGGCTGGGTCCCTCCTCCCCTATA 5 118 1 GGTGGTCCTC 0.949024 -183 TGCTTTGTTTGGGTGTTTGCCACATCTCTAGGG 5 195 1 GGTGTTGCAC 0.848342 -106 CTTTTTCTTTGGATCTTACCGCCTCCCTAGAGA 5 219 0 GGTCTACCCC 0.948376 -82 TAAGAATTTTGGGTTGTTCCTCCTCCCCTTTTT 5 246 0 GGTTGTCCCC 0.960178 -55 GTTCGATCCCGGCTCTGGCCATCCCATGAGTAT 6 66 0 GGTCTGCCTC 0.934197 -235 GCCAGAGCCGGGATCGAACCGACGACACAAGGA 6 80 1 GGTCGACCAC 0.929679 -221 CTATAGAAGAGGGTTTTTCTCACGAGGAATTTT 6 233 0 GGTTTTCTAC 0.736143 -68 AGAGCTATGAGTCTGGTTCCCACTAAATTCCCT 7 43 0 GTTGGTCCAC 0.714511 -142 TACAGGAGCTGGCTTTTTCGCCCCTCATC 8 114 1 GGTTTTCGCC 0.876794 -19 TACTGAGAAGGGCTGTAGCGCAACAGACGAGTA 11 39 0 GGTGTGCGAA 0.579475 -158 TGTTTTGATAGGGTCTTTCCTACTAGGAAGACC 11 85 1 GGTCTTCCAC 0.980414 -112 CCTATCTAAAGGATGTGGCCGCAGCGACTGCTG 11 118 1 GGTGTGCCCA 0.868152 -79 ** *** *** ** Masking position 4 Map Score: 6.60923 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 108 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 ACGGAGAGTGTGTTGCGCTTTTTTGGGTTTT 1 251 1 TTTGCGCTTT 0.751691 -50 TGAGGGAAATTTTAAAGATTTGCGAATTAGA 2 74 0 TTAAAGATTT 0.745199 -80 GGCTTGAGGATATAACGCTTTTTTGTTAAAA 5 87 1 TTAACGCTTT 0.785889 -214 AATTTAGAGAGTTCTCCGTCAAA 6 3 1 TTAGAGAGTT 0.946677 -298 GCTAATGGCGTTTAGAGAGTTTTGACGGAGA 6 23 0 TTAGAGAGTT 0.946677 -278 AACCCTCTTCTATAGACCGTTCCAAAAACGC 6 251 1 TTAGACCGTT 0.735612 -50 TTTTTATCGATATAGAGATTTCTAGAGGGAA 8 21 0 TTAGAGATTT 0.94996 -112 GGACAACAGCTACAGAGAGTGTGATTTACTA 9 36 0 TCAGAGAGTG 0.723385 -153 TGCACTATATTCTAGAGATTGCACGAAAAGG 9 131 0 TTAGAGATTG 0.879314 -58 TATTTTAGCGCTTTCTCTTTTTTA 12 4 1 TTAGCGCTTT 0.959718 -82 CTAAACAAGGTTCAGCGCTTTCTATTAAAAG 13 50 1 TCAGCGCTTT 0.90142 -251 * ********* Masking position 10 Map Score: 4.39288 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 119 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 9 TTTTTAATTTTTATTCTGCACACATTGAAC 1 23 1 TTATTCTGCA 0.82823 -278 ACAAAGCCCTTTTCTGTGCAAAAGAAT 2 8 0 TTTCTGTGCA 0.742143 -146 TCAACGTACTTTTTTCAGCAAGAAAAGCTC 4 34 1 TTTTTCAGCA 0.925289 -78 CAAAAATGTATTTTTCTGGAATTTTTTCAC 5 49 0 TTTTTCTGGA 0.949749 -252 GCATTACAAGTTATAGAGGATTTAGCTATA 6 280 1 TTATAGAGGA 0.588942 -21 GCCTCGAGTCTTTTTGTGGACTCTCCCAAT 8 75 1 TTTTTGTGGA 0.938493 -58 CAATAATTTCTTTTACAGGAGCTGGCTTTT 8 101 1 TTTTACAGGA 0.848851 -32 ATTTCATGCCTTTTCGTGCAATCTCTAGAA 9 123 1 TTTTCGTGCA 0.791248 -66 CACCAAAAATTTTTTCAGGACCACACAACT 10 57 0 TTTTTCAGGA 0.938803 -121 ********** Masking position 2 Map Score: 2.92709 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 150 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 GACGGAGAGTGTGTTGCGCTTTTTTGGGTT 1 250 1 GTGTTGCGCT 0.981645 -51 GTGTTTTGCTCTTAGTTACCCC 5 3 1 GTTTTGCTCT 0.955442 -298 CTAGAATATAGTGCAGCTCTTCTAACTACT 9 147 1 GTGCAGCTCT 0.930467 -42 TTCTACTCGTCTGTTGCGCTACAGCCCTTC 11 36 1 CTGTTGCGCT 0.924599 -161 CAGTTTGTGAGTTTTGCTTTTCACGGGGAC 11 168 0 GTTTTGCTTT 0.735542 -29 TATTTTAGCGCTTTCTCTTTTT 12 3 1 TTTTAGCGCT 0.840297 -83 TCTAAACAAGGTTCAGCGCTTTCTATTAAA 13 49 1 GTTCAGCGCT 0.958135 -252 ********** Masking position 2 Map Score: 1.79048 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 41 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 TTTCTTTACCTCACCTTCTCAAAGATCTTA 1 113 1 TCACCTTCTC 0.847976 -188 AGCAAGAAAAGCTCCTTCTGATTACAATAC 4 50 1 GCTCCTTCTG 0.97061 -62 GAGGACTGAAGATCCTTGTGTCGTCGGTTC 6 95 0 GATCCTTGTG 0.916511 -206 TTCTTAACATGCACCTTTTCTTTGAAACTC 6 198 1 GCACCTTTTC 0.950213 -103 AACCCAACAAGATCCTTCTGCCTTCCTGAA 7 160 0 GATCCTTCTG 0.941143 -25 ACGATCAAAAGCACCTTTTCGTAATCTCCC 9 90 0 GCACCTTTTC 0.950213 -99 AGAAAGCGCTGAACCTTGTTTAGAAAAGAA 13 43 0 GAACCTTGTT 0.782502 -258 ********** Masking position 6 Map Score: 1.63314 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 128 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 12 ********** No masking Map Score: -6.3285e-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 13 ********** No masking Map Score: -6.3285e-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: -6.3285e-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