AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_tpal_reg_300.orf -o00251_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0218 300 sigma factor SigB regulation protein, putative #2 TP0220 28 anti-sigma F factor antagonist (spoIIAA-1) #3 TP0223 267 aspartate aminotransferase (tpaaT) #4 TP0406 190 glutamate racemase (murI) #5 TP0673 177 glutamyl-tRNA synthetase (gltX) #6 TP0736 233 hydrogenase, gamma chain (hydG) #7 TP0861 236 glucosamine-fructose-6-phosphate aminotransferase (glmS) #8 TP0862 134 peptidyl-prolyl cis-trans isomerase, FKBP-type, 22 kDa (fklB) Motif number 1 CAACTACGCTTTCTGCACGGTCGCGTGCGC 1 31 1 TTCTGCACGG 0.496882 -270 AAGCAACGGCGGATGGGCGTTTTCCCCTTC 1 84 0 GGATGGGCGT 0.862916 -217 CTACAGAAAGGGGCGCGTGGGGTAAAAGGA 1 136 1 GGGCGCGTGG 0.992133 -165 GATTATTCTCGCGTGCGTGGTGTTTCTTTC 1 164 1 GCGTGCGTGG 0.980269 -137 TCATCGTGATGGGTGCGTGTGCTATCTGAG 1 219 1 GGGTGCGTGT 0.978711 -82 TCATCCGTGTGGCTGCGCGGGCTTGTGTGC 3 43 1 GGCTGCGCGG 0.990115 -225 GACAGGGTCAGGGGGCGTGTCTACACTGTG 3 112 1 GGGGGCGTGT 0.989944 -156 ACCTCTCTGAAGGCGCGCGTGCGTTAAACG 3 150 1 AGGCGCGCGT 0.877281 -118 TCCTCTTGGTTTGCGCGCGTATTTTCCCCA 3 217 1 TTGCGCGCGT 0.631197 -51 CACAGAATGCAGAGGCGCGG 3 258 1 AGAGGCGCGG 0.938311 -10 TATAAGCTTTGCGCGCATGTTCGAACCCAC 4 72 0 GCGCGCATGT 0.789133 -119 AGCTTATACGGGCTGGACGGGTGTGGTGTC 4 94 1 GGCTGGACGG 0.930373 -97 TGAAGCGGCATCCTGCGTGGTAGGAAGGGG 5 47 1 TCCTGCGTGG 0.778595 -131 AGGGGAAGACAGGGAGGCGGTCACGGTGCA 5 72 1 AGGGAGGCGG 0.632264 -106 TGCGCCCCGGAGGGGGATGTGCGATAATCG 5 138 1 AGGGGGATGT 0.701497 -40 AGATATACGTGTCGGGGAGGTTTAC 6 6 0 GTCGGGGAGG 0.817263 -228 AAAAGCAGCGGTCGGCGCGTTAGTTGCCTT 6 118 1 GTCGGCGCGT 0.957313 -116 CCAAACTCTCGGAGGGATGGATGATAGTAC 6 197 0 GGAGGGATGG 0.907092 -37 TTTGGTCGAAGGAGGCATGGCT 6 222 1 GGAGGCATGG 0.953472 -12 AAGGCAACGGATGGGCATGGGATCGCCTGT 7 23 1 ATGGGCATGG 0.824303 -214 TCTCCCCTTGGGGGAGGTGGTGAGTCTCCC 7 84 1 GGGGAGGTGG 0.892138 -153 CTGGACCGTAGCCTGCGAGGCGGCTCGTGG 7 124 1 GCCTGCGAGG 0.835798 -113 TGGTTCCTACGCGTGCGTGTGTTCTGTGGG 7 170 1 GCGTGCGTGT 0.937181 -67 TGCCTGAAAAGTGGGTGTGGCTCAAGGAAG 8 22 1 GTGGGTGTGG 0.813928 -113 GACGTGTGAAGTACGGATGGGGTAGGCTGG 8 76 1 GTACGGATGG 0.567562 -59 GTCGCCTCGGGGCGGCGCGGATGAGCGCGC 8 105 1 GGCGGCGCGG 0.995348 -30 ********** Masking position 9 Map Score: 36.1753 Number of sites scoring better than the average of aligned sites = 3335 Number in coding regions = 2955 Number in noncoding regions = 380 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 2 GCACGCGACCGTGCAGAAAGCGTAGTTGGAA 1 28 0 GTGCAGAAGC 0.852924 -273 TCCGCTAAGAGCGCACGCGACCGTGCAGAAA 1 40 0 GCGCACGCAC 0.972223 -261 TCCTTTTACCCCACGCGCCCCTTTCTGTAGC 1 135 0 CCACGCGCCC 0.879287 -166 TTCTCGTGTGTCGCAGGATGAGTTGGCTTCA 1 191 1 TCGCAGGAGA 0.795143 -110 AACTCAGATAGCACACGCACCCATCACGATG 1 220 0 GCACACGCCC 0.97396 -81 TAACCATTTGCCGCAGGAAGCTCATCCGTGT 3 22 1 CCGCAGGAGC 0.984774 -246 ACACAAGCCCGCGCAGCCACACGGATGAGCT 3 40 0 GCGCAGCCCA 0.648244 -228 CGACTTCAGAGCACACAAGCCCGCGCAGCCA 3 52 0 GCACACAACC 0.958261 -216 AGCGTTTAACGCACGCGCGCCTTCAGAGAGG 3 151 0 GCACGCGCCC 0.957846 -117 GGAGATAACAGCGCGTGCACCACCGTTCCTT 3 189 0 GCGCGTGCCC 0.906266 -79 GGGAAAATACGCGCGCAAACCAAGAGGAGAT 3 214 0 GCGCGCAACC 0.982235 -54 CGGGATTGTTGCACAGAATGCAGAGGCGCGG 3 247 1 GCACAGAAGC 0.964354 -21 GTTCGAACATGCGCGCAAAGCTTATACGGGC 4 76 1 GCGCGCAAGC 0.984883 -115 TCCCCAGGTCCTGCACACCGCATACATTGAC 4 121 0 CTGCACACGC 0.616907 -70 TTGAAAAATTTCACAGGAACCGTGTTATCCC 4 148 0 TCACAGGACC 0.911618 -43 GTGCAATCAACCGCGTGAAGCGGCATCCTGC 5 32 1 CCGCGTGAGC 0.808341 -146 CCTTCCTACCACGCAGGATGCCGCTTCACGC 5 44 0 ACGCAGGAGC 0.909137 -134 GGGCCGATTATCGCACATCCCCCTCCGGGGC 5 141 0 TCGCACATCC 0.743667 -37 ACCCTTCTCGGCGCCGATGGCGTTTTGCTTG 6 45 1 GCGCCGATGC 0.725941 -189 AATGAGGACTGCACGCAAAACCTGCCAGGAA 6 76 1 GCACGCAAAC 0.767039 -158 GGCAACTAACGCGCCGACCGCTGCTTTTCTC 6 115 0 GCGCCGACGC 0.944626 -119 TTCAGCTCTGTCGCACAAGGCAACTAACGCG 6 133 0 TCGCACAAGC 0.962442 -101 GAGAGTTTGGTCGAAGGAGGCATGGCT 6 217 1 TCGAAGGAGC 0.605704 -17 CTACGGTCCAGCGCACCAACAGGGAGACTCA 7 104 0 GCGCACCACA 0.680257 -133 ACGAGCCGCCTCGCAGGCTACGGTCCAGCGC 7 121 0 TCGCAGGCAC 0.893174 -116 ACACACGCACGCGTAGGAACCATTCTGACTC 7 161 0 GCGTAGGACC 0.90584 -76 AAACTCAAACCCACAGAACACACGCACGCGT 7 178 0 CCACAGAAAC 0.634691 -59 GGTGCGTACGATGCCTGAAAAGTG 8 4 1 GCGTACGAGC 0.912544 -131 ******** ** Masking position 2 Map Score: 34.068 Number of sites scoring better than the average of aligned sites = 5102 Number in coding regions = 4737 Number in noncoding regions = 365 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 TCTCAAGTAGGCTACAGAAAGGGGCGCGTGGGGT 1 125 1 GCCAGAAGGG 0.918298 -176 AGCCCGCGCAGCCACACGGATGAGCTTCCTGCGG 3 32 0 GCCACGATGG 0.979219 -236 TCGGGCTGTCGATTCACTGGGGTGCATAAATTGA 3 80 1 GACACGGGGG 0.965505 -188 CGCACGCGCGCCTTCAGAGAGGTCCATGTCTCAC 3 139 0 CCCAGGAGGC 0.86383 -129 AATACGCGCGCAAACCAAGAGGAGATAACAGCGC 3 206 0 CACCAGAGGG 0.900344 -62 GCTTATACGGGCTGGACGGGTGTGGTGTCAATGT 4 95 1 GCGACGGTGG 0.963649 -96 CCCCTTCCTACCACGCAGGATGCCGCTTCACGCG 5 43 0 CCGCAGATGC 0.702096 -135 GGTAGGAAGGGGAAGACAGGGAGGCGGTCACGGT 5 65 1 GGGACGGGAG 0.595027 -113 GAGGCGGTCACGGTGCATGAGGAGTGTAATTTTC 5 85 1 CGGCAGAGGG 0.851907 -93 AATTTTCAGGGCCTCACAGGGATGCTTGCGCCCC 5 112 1 GCCACGGGAG 0.941645 -66 AGGGATGCTTGCGCCCCGGAGGGGGATGTGCGAT 5 129 1 GCCCCGAGGG 0.990811 -49 CGCTCGCCCTCCCCGGGGGCCGATTATCGCA 5 157 0 CCCCCGGGGC 0.559935 -21 ATGGCGTTTTGCTTGAATGAGGACTGCACGCAAA 6 61 1 GCGAAGAGGC 0.94883 -173 AACCTGCCAGGAAACAATGATGAGAAAAGCAGCG 6 94 1 GACAAGATGG 0.788901 -140 AGACTCACCACCTCCCCCAAGGGGAGACCCGACG 7 77 0 CCCCCAAGGG 0.962428 -160 ACGGTCCAGCGCACCAACAGGGAGACTCACCACC 7 99 0 GCCAAAGGGG 0.961405 -138 TGCGTACGATGCCTGAAAAGTGGGTGTGGCTCAA 8 13 1 GCGAAAGTGG 0.771158 -122 GCTCATCCGCGCCGCCCCGAGGCGACCAGCCTAC 8 97 0 GCCCCGAGGG 0.995672 -38 GCGCGGATGAGCGCGCAAAAGGAGCG 8 119 1 GCGCAAAGGG 0.94796 -16 ** *** **** * Masking position 12 Map Score: 24.5834 Number of sites scoring better than the average of aligned sites = 1401 Number in coding regions = 1253 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 AAACGCCCATCCGCCGTTGCTTGAACTTTCAA 1 92 1 CCCGTTGCTT 0.994836 -209 CTACCGTTCCCTTTGTATGGCT 1 289 0 CCCGTTCCCT 0.994704 -12 AGCGCGTGCACCACCGTTCCTTCAAGAGCAGC 3 179 0 CCCGTTCCTT 0.991626 -89 ACTAACGCGCCGACCGCTGCTTTTCTCATCAT 6 110 0 CCCGCTGCTT 0.986001 -124 ATCCCATGCCCATCCGTTGCCTTGCTGCACAT 7 14 0 CCCGTTGCCT 0.996738 -223 TTGGTGCGCTGGACCGTAGCCTGCGAGGCGGC 7 116 1 GCCGTAGCCT 0.950921 -121 GGTGCGTACGATGCCTGAAAAGTGGG 8 5 1 CACGATGCCT 0.936891 -130 GATAGCTAATGCCCCGATCCTTCCTTGAGCCA 8 39 0 GCCGATCCTT 0.947987 -96 * ********* Masking position 12 Map Score: 12.3336 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 57 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 TCCGCTAAGAGCGCACGCGACCGTGCAGAAA 1 40 0 GCCACGCGAC 0.649136 -261 AAGAAACACCACGCACGCGAGAATAATCCTT 1 161 0 ACCACGCGAG 0.660172 -140 GCCCGCGCAGCCACACGGATGAGCTTCCTGC 3 34 0 CCCACGGATG 0.690247 -234 GTCAATTTATGCACCCCAGTGAATCGACAGC 3 84 0 GCCCCCAGTG 0.659173 -184 AGACACGCCCCCTGACCCTGTCAATTTATGC 3 103 0 CCGACCCTGT 0.377137 -165 CGCGTATTTTCCCCACGGGATTGTTGCACAG 3 232 1 CCCACGGGAT 0.933057 -36 ATGTTCGAACCCACACCGTATTGCTCTACGT 4 55 0 CCCACCGTAT 0.913522 -136 CCACACCCGTCCAGCCCGTATAAGCTTTGCG 4 89 0 CCGCCCGTAT 0.836531 -102 CCCAGGTCCTGCACACCGCATACATTGACAC 4 119 0 GCCACCGCAT 0.908929 -72 AGGGATGCTTGCGCCCCGGAGGGGGATGTGC 5 129 1 GCCCCCGGAG 0.990113 -49 CGCTCGCCCTCCCCGGGGGCCGATTATC 5 160 0 CCCCCCGGGG 0.972991 -18 CAACTAACGCGCCGACCGCTGCTTTTCTCAT 6 113 0 GCGACCGCTG 0.797098 -121 AGACTCACCACCTCCCCCAAGGGGAGACCCG 7 80 0 CCCCCCCAAG 0.911278 -157 TGTTGGTGCGCTGGACCGTAGCCTGCGAGGC 7 114 1 CTGACCGTAG 0.434033 -123 AAGCCACGAGCCGCCTCGCAGGCTACGGTCC 7 126 0 CCCCTCGCAG 0.712161 -111 CAGTGCAAAAGCACACGGGAGAACGTTAAAC 7 205 0 GCCACGGGAG 0.974022 -32 GCTCATCCGCGCCGCCCCGAGGCGACCAGCC 8 100 0 GCGCCCCGAG 0.951907 -35 ** ******** Masking position 6 Map Score: 11.2566 Number of sites scoring better than the average of aligned sites = 1308 Number in coding regions = 1162 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 6 ATGGGCGTTTTCCCCTTCCTCTTGAGAAAT 1 72 0 TCCCCTTCCT 0.97758 -229 AACGCCCATCCGCCGTTGCTTGAACTTTCA 1 93 1 CGCCGTTGCT 0.953749 -208 CTACCGTTCCCTTTGTATGGC 1 290 0 TACCGTTCCC 0.962331 -11 GCGCGTGCACCACCGTTCCTTCAAGAGCAG 3 180 0 CACCGTTCCT 0.99141 -88 CTGGGGATAACACGGTTCCTGTGAAATTTT 4 145 1 CACGGTTCCT 0.950254 -46 CTCCCTGTCTTCCCCTTCCTACCACGCAGG 5 58 0 TCCCCTTCCT 0.97758 -120 CGCTCGCCCTCCCCGGGGGCCGAT 5 164 0 CGCCCTCCCC 0.920115 -14 ATAGCTAATGCCCCGATCCTTCCTTGAGCC 8 40 0 CCCCGATCCT 0.97017 -95 ********** Masking position 3 Map Score: 7.44722 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 142 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 AAAGGTATTGGTGCGTATTCCAA 1 4 1 GGTATTGGTG 0.599747 -297 CATCGTGATGGGTGCGTGTGCTATCTGAGT 1 220 1 GGTGCGTGTG 0.939701 -81 TAAAAGACAACGTGTTTTTGAAGCAGCCAT 1 265 1 CGTGTTTTTG 0.918478 -36 CGGTGTTTGTGTAACCATTTG 3 2 1 GGTGTTTGTG 0.9621 -266 GAAGCTCATCCGTGTGGCTGCGCGGGCTTG 3 38 1 CGTGTGGCTG 0.884204 -230 TGTGGCTGCGCGGGCTTGTGTGCTCTGAAG 3 50 1 CGGGCTTGTG 0.887173 -218 GCCGTGTATGTGTGTTGACGTA 4 3 1 CGTGTATGTG 0.947484 -188 TCATAAAAAACCTGTCTGTGCAATCAACCG 5 15 1 CCTGTCTGTG 0.939045 -163 AACAGATATACGTGTCGGGGAGGTTTAC 6 9 0 CGTGTCGGGG 0.953352 -225 GGTGAGTCTCCCTGTTGGTGCGCTGGACCG 7 102 1 CCTGTTGGTG 0.928212 -135 CGAGGCGGCTCGTGGCTTGGTTGAGTCAGA 7 139 1 CGTGGCTTGG 0.472078 -98 GGTTCCTACGCGTGCGTGTGTTCTGTGGGT 7 171 1 CGTGCGTGTG 0.978211 -66 ********** Masking position 10 Map Score: 9.07156 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 654 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 ACGCGACCGTGCAGAAAGCGTAGTTGGAATA 1 26 0 GCAGAAGCGT 0.961026 -275 AGAAATCTCCGCTAAGAGCGCACGCGACCGT 1 47 0 GCTAAGGCGC 0.849402 -254 GTAGGCTACAGAAAGGGGCGCGTGGGGTAAA 1 131 1 GAAAGGGCGC 0.879979 -170 CTCGTGTGTCGCAGGATGAGTTGGCTTCATC 1 193 1 GCAGGAGAGT 0.913964 -108 GCTTCATCGTGATGGGTGCGTGTGCTATCTG 1 216 1 GATGGGGCGT 0.964467 -85 TGAGGAAAAGTTCGGGAGCGCCGT 2 15 1 TTCGGGGCGC 0.666309 -14 ACCATTTGCCGCAGGAAGCTCATCCGTGTGG 3 24 1 GCAGGAGCTC 0.867023 -244 ATTGACAGGGTCAGGGGGCGTGTCTACACTG 3 109 1 TCAGGGGCGT 0.939938 -159 CATGGACCTCTCTGAAGGCGCGCGTGCGTTA 3 145 1 TCTGAAGCGC 0.844942 -123 GCTTATACGGGCTGGACGGGTGTGGTGTCAA 4 95 1 GCTGGAGGGT 0.819045 -96 CGGCCCCCGGGGAGGGCGAGCG 5 166 1 GGAGGGGAGC 0.819103 -12 CCTTCTCGGCGCCGATGGCGTTTTGCTTGAA 6 47 1 GCCGATGCGT 0.758821 -187 GAGTTTGGTCGAAGGAGGCATGGCT 6 219 1 GAAGGAGCAT 0.586326 -15 GGGGAGACCCGACGAACGAGCAAGGTAACCC 7 60 0 GACGAAGAGC 0.698069 -177 GGGCGGCGCGGATGAGCGCGCAAAAGGAGCG 8 114 1 GATGAGGCGC 0.954297 -21 ****** **** Masking position 8 Map Score: 7.78518 Number of sites scoring better than the average of aligned sites = 2497 Number in coding regions = 2312 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 9 ********** No masking Map Score: 4.00336e-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 10 ********** No masking Map Score: 4.00336e-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 11 ********** No masking Map Score: 4.00336e-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