AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iphoB_tpal_opreg_300.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0074 300 sugar ABC transporter, periplasmic binding protein (y4oP) #2 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #3 TP0163 174 ABC transporter, periplasmic binding protein (troA) #4 TP0164 147 ABC transporter, ATP-binding protein (troB) #5 TP0802 45 T. pallidum predicted coding region TP0802 #6 TP0804 77 sugar ABC transporter, ATP-binding protein (ugpC) Motif number 1 GACATACACCGCACCCACACGCGTTTGCATTC 1 23 0 GCCCCCACGC 0.980618 -278 AACGGGGCAGATTCTCGTACGCTTTTCTCCCC 1 67 0 ATCTCTACGC 0.913757 -234 ACAGTTTGCTCCCCCTTCAACCTAACGGGGCA 1 90 0 CCCCTCAACC 0.85084 -211 ATCCACCGCGCGCATCGCACCCCATATCGATA 1 150 0 CGATCCACCC 0.817046 -151 CAATCGACGCACGCCCCTACGCAGTCCTACAA 1 212 0 ACCCCTACGC 0.981894 -89 GTCCGTTTTTCCCCTCACACCCCAGTCCTGAT 1 276 0 CCCTCCACCC 0.996559 -25 TCTTTTCTGCCCTCTCTTCCCCCAAGAAGAAG 2 18 0 CCCTCTCCCC 0.98485 -101 CATTCTGTTTCCGCTCATATCCAGCATCTTTT 2 44 0 CCCTCTATCC 0.969285 -75 GCACTCCCCCTCTTACGCTACCCAACGT 2 101 0 CCCTCTACGC 0.997628 -18 ATTTGATCTTCCTCGCATAAGCAGCTACAGTT 3 21 0 CCCGCTAAGC 0.954556 -154 ACCACCAACGGCTCTTCTACCCACTCAACTCT 4 21 0 GCCTTTACCC 0.939778 -127 TCACCGCTGACGGCTCTTACCCGATTGAGCGA 4 109 1 CGCTCTACCC 0.990382 -39 TTCCTCTCCATACCCTCGTGGGGGA 5 4 1 CTTCCTACCC 0.9463 -42 GGGGATGCCCCCCTGTGTACGCTTC 5 31 1 CCTGTTACGC 0.845071 -15 CAACACACTACTTTCCTTACGCAAACGGGAGG 6 24 0 CTTCCTACGC 0.939285 -54 ** *** ***** Masking position 12 Map Score: 22.624 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 874 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 TCGTACGCTTTTCTCCCCGTTGTCAACAAAG 1 54 0 TTCCCCCGTT 0.936321 -247 GCGTACGAGAATCTGCCCCGTTAGGTTGAAG 1 77 1 ATCGCCCCGT 0.707787 -224 ACGTACAGTTTGCTCCCCCTTCAACCTAACG 1 95 0 TGCCCCCCTT 0.993145 -206 CCGCGCGCATCGCACCCCATATCGATACGGG 1 146 0 CGCCCCCATA 0.850914 -155 CACCAATCGACGCACGCCCCTACGCAGTCCT 1 216 0 CGCCGCCCCT 0.982055 -85 CGTTTTTCCCCTCACACCCCAGTCCTGATAC 1 274 0 CTCCACCCCA 0.881574 -27 CCAGCATCTTTTCTGCCCTCTCTTCCCCCAA 2 25 0 TTCGCCCTCT 0.927133 -94 GCACTCCCCCTCTTACGCTACCCA 2 105 0 CTCCCCTCTT 0.943889 -14 CAGCTACAGTTGCGCCCTCTT 3 1 0 TGCCCCTCTT 0.969133 -174 GGCACTCTGGCGCGGACCTCTCGAGCTACAT 3 64 0 CGCGACCTCT 0.917828 -111 CCAACGGCTCTTCTACCCACTCAACTCTACA 4 18 0 TTCACCCACT 0.751654 -130 GCGGTGAGCGCGCCACCTCCTTCACTAATCA 4 85 0 CGCACCTCCT 0.933828 -63 GGAGGTGGCGCGCTCACCGCTGACGGCTCTT 4 96 1 CGCCACCGCT 0.97014 -52 ATACTGCTCCCTTCTTTTCGCTCAA 4 133 0 TGCCCCTTCT 0.962241 -15 TCGTGGGGGATGCCCCCCTGTGTACGCTTC 5 26 1 TGCCCCCTGT 0.978635 -20 AGTAGTGTGTTGCGCACCCGTGTTTCAAAAG 6 44 1 TGCCACCCGT 0.971035 -34 *** ******* Masking position 7 Map Score: 22.4374 Number of sites scoring better than the average of aligned sites = 1185 Number in coding regions = 1033 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 3 GTATCCACCGCGCGCATCGCACCCCATATC 1 154 0 CGCGCATCGC 0.95728 -147 CACCAATCGACGCACGCCCCTACGCAGTCC 1 217 0 CGCACGCCCC 0.963481 -84 CACGACACATAGCACCACACCAATCGACGC 1 234 0 AGCACCACAC 0.918384 -67 ACATCAAACCAGCACGACACATAGCACCAC 1 246 0 AGCACGACAC 0.967912 -55 CCCAACGTAACGCGCTCCACAGATAGAACA 2 79 0 CGCGCTCCAC 0.987063 -40 GGCACTCTGGCGCGGACCTCTCGAGCTACA 3 65 0 CGCGGACCTC 0.960921 -110 GCATCAAAGTAGCGGATCACGCAGGAAACG 3 129 0 AGCGGATCAC 0.966749 -46 GCTGCCGTACAGCCGACCACCAACGGCTCT 4 38 0 AGCCGACCAC 0.953465 -110 GTCAGCGGTGAGCGCGCCACCTCCTTCACT 4 90 0 AGCGCGCCAC 0.99577 -58 GAAACACGGGTGCGCAACACACTACTTTCC 6 40 0 TGCGCAACAC 0.958618 -38 ********** Masking position 3 Map Score: 12.8999 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 683 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 GCGCGGTGGATACGCTCCTTCTCGACTGAG 1 171 1 TACGCTCCTT 0.989069 -130 TCCTGCGTGATCCGCTACTTTGATGCATCA 3 133 1 TCCGCTACTT 0.887616 -42 GTGACACTCCTTGGGTGAATTT 3 163 0 GACACTCCTT 0.962676 -12 CACTCAACTCTACATTCCACG 4 2 0 TACATTCCAC 0.844544 -146 TTCCTCTCCATACCCTCGTGG 5 2 1 TCCTCTCCAT 0.944827 -44 CGCAACACACTACTTTCCTTACGCAAACGG 6 28 0 TACTTTCCTT 0.965898 -50 AGCGTTTACATTCCTTTTGAAACACG 6 62 0 TACATTCCTT 0.975953 -16 ********** Masking position 6 Map Score: 4.8331 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 113 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CCCCAAGAAGAAGAGACTTT 2 1 0 AAGAGACTTT 0.941561 -118 GTCCGCGCCAGAGTGCCGTTTTCTTTTCCT 3 78 1 GAGTGCCGTT 0.982909 -97 GGTACTGAAAAATTGACGTTTCCTGCGTGA 3 113 1 AATTGACGTT 0.918347 -62 GAGTGGGTAGAAGAGCCGTTGGTGGTCGGC 4 27 1 AAGAGCCGTT 0.993427 -121 TCAATCGGGTAAGAGCCGTCAGCGGTGAGC 4 107 0 AAGAGCCGTC 0.987833 -41 ********** Masking position 2 Map Score: 3.0842 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 20 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 GTAATCTTTGTTTTCCCGTATCGATATGGG 1 132 1 TTTTCCCGTA 0.914717 -169 CCTGTCCGTTTTTCCCCTCACACCCCAGTC 1 281 0 TTTCCCCTCA 0.990195 -20 TTCTGCCCTCTCTTCCCCCAAGAAGAAGAG 2 16 0 TCTTCCCCCA 0.932318 -103 CGTCATTCTGTTTCCGCTCATATCCAGCAT 2 49 0 TTTCCGCTCA 0.98578 -70 AGCATTTGATCTTCCTCGCATAAGCAGCTA 3 26 0 CTTCCTCGCA 0.909363 -149 TGCTCCCTTCTTTTCGCTCAATCGGGTAAG 4 124 0 TTTTCGCTCA 0.977822 -24 ********** Masking position 3 Map Score: 2.75197 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 84 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 CATGAGCACGTACAGTTTGCTCCCCCTTCAA 1 102 0 TACAGTTTCT 0.911291 -199 GGAAACAGAATGACGTGTTCTATCTGTGGAG 2 64 1 TGACGTGTCT 0.977056 -55 CGCGCCAGAGTGCCGTTTTCTTTTCCTGAAA 3 81 1 TGCCGTTTCT 0.995326 -94 ACTGAAAAATTGACGTTTCCTGCGTGATCCG 3 116 1 TGACGTTTCT 0.989532 -59 CAACACCACCTCCCGTTTGCGTAAGGAAAGT 6 16 1 TCCCGTTTCG 0.972821 -62 ******** ** Masking position 6 Map Score: 1.66299 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 33 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 CGCGTGTGGGTGCGGTGTATGTCTTTGTTG 1 32 1 TGCGGTGTAT 0.918057 -269 GTGCGATGCGCGCGGTGGATACGCTCCTTC 1 162 1 CGCGGTGGAT 0.995714 -139 TGCTATGTGTCGTGCTGGTTTGATGTATCA 1 250 1 CGTGCTGGTT 0.977091 -51 CTGTTCACGACGTGGTGATTAGTGAAGGAG 4 70 1 CGTGGTGATT 0.974225 -78 TCCATACCCTCGTGGGGGATGCCCCCCTGT 5 17 1 CGTGGGGGAT 0.989789 -29 ********** Masking position 10 Map Score: 2.85316 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 82 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 ********** No masking Map Score: -1.34049e-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 10 ********** No masking Map Score: -1.34049e-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: -1.34049e-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