AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i109_ecoli_mtub_100.orf -o109_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 cysM 23 cysteine synthase B, O-acetylserine sulfhydrolase B #2 BIME116 74 BIME #3 cysW 300 sulfate transport system permease W protein #4 cysP 300 thiosulfate binding protein #5 sbp 164 periplasmic sulfate-binding protein #6 subI 124 subI Motif number 1 ATTAAAAAGCCCGGATCGCGGGAAGCGCCTC 2 37 0 CCGGACGCGG 0.987147 -38 TGCAGCATGTCCGGATCGGCCAGATTCTGTA 3 45 0 CCGGACGGCC 0.985312 -256 ATCCGGACATGCTGCACGCCATCTGGCTGAC 3 60 1 GCTGCCGCCA 0.759492 -241 ACCAGGTTTACCGGTACGGCAATCAGCGCGA 3 99 0 CCGGTCGGCA 0.991332 -202 CCAGCAGAATGCCGAACACCAGGTTTACCGG 3 116 0 GCCGACACCA 0.848269 -185 GCGTCACCAGCCAGGCCAGCAGAATGCCGAA 3 131 0 CCAGGCAGCA 0.906626 -170 CTTTAACTTCCCTGGACGCCAGTTACTGCTG 3 163 1 CCTGGCGCCA 0.965161 -138 ATTCCGTTTGCCGTATCGCCGGTGGTTGCCG 3 206 1 CCGTACGCCG 0.96697 -95 AGCAAATACACCAGACCGGCAACCACCGGCG 3 222 0 CCAGACGGCA 0.982984 -79 GCTCTAACGGCCCGCTCGGCGGTTGGCTCGA 3 261 1 CCCGCCGGCG 0.994013 -40 TCATTTTGGCCCCGGGCAGTGCTCGAAATCC 4 82 1 CCCGGCAGTG 0.798234 -219 TCAGTTTGGACACGAACAGCGCGGAGAAACC 4 135 0 CACGACAGCG 0.819467 -166 TGACTCCCCACCCGTGCGCGGTCTGATGTGG 6 20 1 CCCGTCGCGG 0.96702 -105 GACAACGTTCCCGTAGCGGCGGAAAGGCGAT 6 78 0 CCGTACGGCG 0.977505 -47 TGGCGACCTTCCGGTGCGGGACTTTGGACAA 6 104 0 CCGGTCGGGA 0.970238 -21 ***** ***** Masking position 7 Map Score: 22.2534 Number of sites scoring better than the average of aligned sites = 4355 Number in coding regions = 4202 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 2 CCCGGATCGCGGGAAGCGCCTCCGGGCGTT 2 29 0 GGGAAGCGCC 0.935286 -46 GGCGCTTCCCGCGATCCGGGCTTTTTAATG 2 39 1 GCGATCCGGG 0.877151 -36 GTGCAGGCATTCAGCAAGGGGCTGA 3 6 1 GGCATTCAGC 0.972655 -295 CTGTAAAACCGGCATCAGCCCCTTGCTGAA 3 20 0 GGCATCAGCC 0.923537 -281 GGCCGATCCGGACATGCTGCACGCCATCTG 3 55 1 GACATGCTGC 0.865535 -246 CATGCTGCACGCCATCTGGCTGACGGTGAT 3 67 1 GCCATCTGGC 0.766368 -234 TTACCGGTACGGCAATCAGCGCGATCATCA 3 93 0 GGCAATCAGC 0.942524 -208 CCTGGTGTTCGGCATTCTGCTGGCCTGGCT 3 124 1 GGCATTCTGC 0.9635 -177 GCAACCACCGGCGATACGGCAAACGGAATG 3 205 0 GCGATACGGC 0.897766 -96 ACACCAGACCGGCAACCACCGGCGATACGG 3 216 0 GGCAACCACC 0.971036 -85 TGCTCGTCGAGCCAACCGCCGAGCGGGCCG 3 268 0 GCCAACCGCC 0.954942 -33 AGTTCAAGACGAAATCCTCCCCACAAATGC 4 28 0 GAAATCCTCC 0.73412 -273 AAAGGCGGAAGAAATCCGCCTCATATTGCT 5 31 0 GAAATCCGCC 0.907235 -134 CGCACGGGTGGGGAGTCAGCGACAACA 6 8 0 GGGAGTCAGC 0.792623 -117 ********** Masking position 4 Map Score: 12.1796 Number of sites scoring better than the average of aligned sites = 4835 Number in coding regions = 4581 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 3 GTGCAGGCATTCAGCAAGGGGCTGATGCC 3 10 1 TTCAGCAAGG 0.930168 -291 GATCATCACCGTCAGCCAGATGGCGTGCAG 3 71 0 GTCAGCCAGA 0.947018 -230 GTTAAAGCGCGTCACCAGCCAGGCCAGCAG 3 140 0 GTCACCAGCC 0.956397 -161 GTCCAGTAGCGTCAGCAGTAACTGGCGTCC 3 176 0 GTCAGCAGTA 0.972983 -125 TTGAACTAAGTTCACCAGGCTATTTTATTT 4 51 1 TTCACCAGGC 0.955279 -250 AAGAACTTGGTTCAACAGGCGTAATTGTTG 4 169 0 TTCAACAGGC 0.886773 -132 AGCGCACTTTGTCAGCAATATGAGGCGGAT 5 18 1 GTCAGCAATA 0.965666 -147 CGGGTGGGGAGTCAGCGACAACA 6 4 0 GTCAGCGACA 0.945035 -121 TCCTGCAATGTTCAGCGATCGCCTTTCCGC 6 61 1 TTCAGCGATC 0.927841 -64 ********** Masking position 4 Map Score: 5.69403 Number of sites scoring better than the average of aligned sites = 1879 Number in coding regions = 1767 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 TCCCGCGATCCGGGCTTTTTAATGGCAAGGTTT 2 45 1 CGCTTTTAAT 0.9887 -30 CGGTGGTTGCCGGTCTGGTGTATTTGCTGTTCT 3 225 1 CGCTGTGTAT 0.921245 -76 CTAAGTTCACCAGGCTATTTTATTTGTCATTTT 4 56 1 CGCTTTTTAT 0.9887 -245 TATAAATTTAATGACTTTCTAATAGCCATCATA 4 268 0 AGCTTCTAAT 0.918176 -33 CGGATTTCTTCCGCCTTTTTAATCCCTCAACAT 5 43 1 CGCTTTTAAT 0.9887 -122 CGCCCGACTCTCTTATGTTGTGTTGT 5 149 0 CGCTTCTTAT 0.986401 -16 * * ** ****** Masking position 6 Map Score: 3.61308 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 32 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 AGGGGCTGATGCCGGTTTTACAGAATCTGGC 3 27 1 GCCGGTTTAC 0.784107 -274 ATGCCGAACACCAGGTTTACCGGTACGGCAA 3 108 0 CCAGGTTACC 0.941719 -193 GGCGTCCAGGGAAGTTAAAGCGCGTCACCAG 3 152 0 GAAGTTAAGC 0.784144 -149 TCCCTGGACGCCAGTTACTGCTGACGCTACT 3 171 1 CCAGTTATGC 0.931997 -130 CGCCGAGCGGGCCGTTAGAGCCGTAGAACAG 3 251 0 GCCGTTAAGC 0.897525 -50 AATTTGCAGGTTATGCTCGTCGAGCC 3 285 0 GCAGGTTTGC 0.981085 -16 CATTTTGGCCCCGGGCAGTGCTCGAAATCCT 4 83 1 CCGGGCATGC 0.819578 -218 TGTGTACGCTCCGGTTTCTCCGCGCTGTTCG 4 123 1 CCGGTTTTCC 0.917059 -178 GGTATATAAAACCGTTACTCCTTTCACGTCC 4 229 1 ACCGTTATCC 0.564993 -72 CTGACAAAGTGCGCTTTGTCCA 5 2 0 GCGCTTTTCC 0.832604 -163 CATATACCCGCAAGTTATAGCCAATCTTTTT 5 73 1 CAAGTTAAGC 0.697169 -92 AAGCGTGCCAGAAGGTTAACCAAACATTAAA 5 110 0 GAAGGTTACC 0.868595 -55 TAACCTTCTGGCACGCTTTGCTCATCACAAC 5 123 1 GCACGCTTGC 0.811194 -42 GCCGCTACGGGAACGTTGTCCAAAGTCCCGC 6 89 1 GAACGTTTCC 0.767651 -36 ******* *** Masking position 11 Map Score: 6.56354 Number of sites scoring better than the average of aligned sites = 7033 Number in coding regions = 6695 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 325 Fraction of orfs with sites within 600 bp upstream = 0.0522004 Motif number 6 CACCAGGTTTACCGGTACGGCAATCAGCGC 3 101 0 ACCGGTACGG 0.950019 -200 CGATACGGCAAACGGAATGTCCAGTAGCGT 3 194 0 AACGGAATGT 0.800693 -107 CAGCAAATACACCAGACCGGCAACCACCGG 3 224 0 ACCAGACCGG 0.965411 -77 GCGCGGAGAAACCGGAGCGTACACATAGTA 4 118 0 ACCGGAGCGT 0.984999 -183 CTTCCAAATCACCAAACGGTATATAAAACC 4 212 1 ACCAAACGGT 0.778312 -89 AGCAAAGCGTGCCAGAAGGTTAACCAAACA 5 115 0 GCCAGAAGGT 0.936853 -50 TTCCGCCGCTACGGGAACGTTGTCCAAAGT 6 85 1 ACGGGAACGT 0.967992 -40 AAAGTCCCGCACCGGAAGGTCGCCA 6 110 1 ACCGGAAGGT 0.989165 -15 ********** Masking position 9 Map Score: 5.24858 Number of sites scoring better than the average of aligned sites = 1111 Number in coding regions = 1041 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 TCTCTATCCATACGTGGTGTT 1 2 0 TACGTGGTGT 0.958762 -22 TAGGTTGAGTGAATGTTAAA 2 1 1 TAGGTTGAGT 0.968613 -74 CTTGCGGGTATATGTTGAGGGATTAAAAAG 5 57 0 TATGTTGAGG 0.959515 -108 CCGACTCTCTTATGTTGTGTTGTGATGAGC 5 142 0 TATGTTGTGT 0.973486 -23 TGCGCGGTCTGATGTGGAGTTCGTGAGTCC 6 34 1 GATGTGGAGT 0.962384 -91 ********** Masking position 5 Map Score: 1.36916 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 21 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 TGGTGACGCGCTTTAACTTCCCTGGACGCCA 3 153 1 CTTAACTTCC 0.984171 -148 GTAGCGTCAGCAGTAACTGGCGTCCAGGGAA 3 170 0 CATAACTGGC 0.943048 -131 TGTTCTACGGCTCTAACGGCCCGCTCGGCGG 3 252 1 CTTAACGGCC 0.987813 -49 CTTATTCCCTTTTCAACTTCCAAATCACCAA 4 196 1 TTCAACTTCC 0.88482 -105 GCCATCATATTTATAACGGACGTGAAAGGAG 4 246 0 TTTAACGGAC 0.873312 -55 AAAAGATTGGCTATAACTTGCGGGTATATGT 5 72 0 CTTAACTTGC 0.977109 -93 ** ******** Masking position 6 Map Score: 0.443495 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 256 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 ********** No masking Map Score: -7.43638e-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: -7.43638e-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: -7.43638e-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