AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 atpC 23 ATP synthase (subunit epsilon) #2 atpD 25 ATP synthase (subunit beta) #3 atpG 76 ATP synthase (subunit gamma) #4 atpF 162 ATP synthase (subunit b) #5 atpE 45 ATP synthase (subunit c) #6 atpI 300 ATP synthase (subunit i) Motif number 1 GAGAGAAAAAGAGAACCTTTTTCTCTCATCA 3 20 0 GAAACCTTTT 0.995166 -57 AGATTTCACCACCTTTTCTCTTCATCT 3 60 0 CACACCTTTT 0.946898 -17 ATCATTCCAAGAGAACCTTCGCCATTGCTTT 4 46 1 GAAACCTTCG 0.977081 -117 TATCCAAACGGATAACATTTTAAAGGAGGAA 5 18 1 GAAACATTTT 0.963908 -28 CATTTTAAAGGAGGAACTTTTTC 5 33 1 GAGAACTTTT 0.956788 -13 TGAAAGCTATGAAAACCTTCTCATAATACCC 6 62 0 GAAACCTTCT 0.992834 -239 ACCCTTAGTAGAAGACCTTTTTTGACCGGCA 6 217 0 GAGACCTTTT 0.994175 -84 ** ******** Masking position 5 Map Score: 10.2295 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 124 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 AACCTTTTTCTCTCATCAGCATTCGAG 3 8 0 TCTCATCAGC 0.978912 -69 CACCTTTTCTCTTCATCTGCGTAAAAAGAG 3 48 0 CTTCATCTGC 0.972174 -29 ACTTGTCTCTTTTCAGCCGGCAAGGCGGGA 4 91 0 TTTCAGCCGG 0.984658 -72 TTCTTTGCTGATCCAGCAGCCGCACTTGTC 4 114 0 ATCCAGCAGC 0.907682 -49 CGGCAACTCCCTTCTGCAGGTTTTTCTTTG 4 137 0 CTTCTGCAGG 0.885094 -26 TCATTATAGTCCTCATCCTCAATGTAAATC 6 90 1 CCTCATCCTC 0.897298 -211 AGGGATGCTGTTTCATTCGCTTAAATAAAT 6 145 0 TTTCATTCGC 0.936716 -156 CGAAAAAATCATTCATCCGCAAGCCTTGCA 6 174 0 ATTCATCCGC 0.987793 -127 TACATTATTTTTTCATCAGGAGACAGATAA 6 278 1 TTTCATCAGG 0.980003 -23 ********** Masking position 4 Map Score: 8.95157 Number of sites scoring better than the average of aligned sites = 2345 Number in coding regions = 2221 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 GCTTTTACCCTCCTAGGACCA 1 13 0 CTTTTACCCT 0.933841 -11 CGCTATCCCTCCTGACAAAA 2 16 0 CGCTATCCCT 0.931298 -10 AAAAGAGAACCTTTTTCTCTCATCAGCATT 3 15 0 CTTTTTCTCT 0.978529 -62 AAAAGGTTCTCTTTTTCTCTCTTTTTACGC 3 30 1 CTTTTTCTCT 0.978529 -47 GATTTCACCACCTTTTCTCTTCATCTGCGT 3 56 0 CCTTTTCTCT 0.943388 -21 TTCGCCATTGCTTTATGTCTGATAAGCATC 4 63 1 CTTTATGTCT 0.920803 -100 ATAAGCATCCCGCCTTGCCGGCTGAAAAGA 4 84 1 CGCCTTGCCG 0.868784 -79 CGAACAGGCCCGTTTTGCCGGTCAAAAAAG 6 202 1 CGTTTTGCCG 0.98313 -99 TTAACCGCTGATTTTTGCCGTATCCAAGCT 6 247 1 ATTTTTGCCG 0.853915 -54 ********** Masking position 9 Map Score: 7.87634 Number of sites scoring better than the average of aligned sites = 1336 Number in coding regions = 1157 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 4 TTTTTCTCTCATCAGCATTCGAG 3 3 0 ATCAGCATCG 0.985743 -74 AAAAATGGCGAAGATCATTCCAAGAGAACCT 4 33 1 AAGATCATCC 0.843165 -130 TTTATGTCTGATAAGCATCCCGCCTTGCCGG 4 74 1 ATAAGCATCC 0.962047 -89 TGAAAACCTTCTCATAATACCCTCGTTTAGC 6 53 0 CTCATAATCC 0.944828 -248 TGTAAATCCTCTCAGCAAACCCGTATTATGA 6 112 1 CTCAGCAACC 0.98594 -189 TAAATAAATCCTCATAATACGGGTTTGCTGA 6 123 0 CTCATAATCG 0.858314 -178 AAGCGAATGAAACAGCATCCCTGCAAGGCTT 6 153 1 AACAGCATCC 0.986215 -148 AAAATCATTCATCCGCAAGCCTTGCAGGGAT 6 169 0 ATCCGCAACC 0.950005 -132 ******** ** Masking position 7 Map Score: 6.40012 Number of sites scoring better than the average of aligned sites = 1052 Number in coding regions = 952 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 CTCGAATGCTGATGAGAGAAAAAG 3 5 1 AATGCTGATG 0.963296 -72 ATGAACTAAAAATGGCGAAGATCATTCCAA 4 26 1 AATGGCGAAG 0.995473 -137 GACATAAAGCAATGGCGAAGGTTCTCTTGG 4 52 0 AATGGCGAAG 0.995473 -111 ********** Masking position 8 Map Score: 1.11177 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 71 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 GCTTTTACCCTCCTAGGACCAGA 1 7 0 CCCTCCTAGG 0.940799 -17 TGATAAGCATCCCGCCTTGCCGGCTGAAAA 4 82 1 CCCGCCTTGC 0.997615 -81 TCATAATACCCTCGTTTAGCATACAATAGC 6 43 0 CTCGTTTAGC 0.935393 -258 CATTCATCCGCAAGCCTTGCAGGGATGCTG 6 165 0 CAAGCCTTGC 0.952789 -136 TTCGAACAGGCCCGTTTTGCCGGTCAAAAA 6 200 1 CCCGTTTTGC 0.988012 -101 ********** Masking position 7 Map Score: 1.7976 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 267 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ********** No masking Map Score: -2.67574e-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 8 ********** No masking Map Score: -2.67574e-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 9 ********** No masking Map Score: -2.67574e-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