AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00730_ecoli_reg_100.orf -o00730_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ybaD 90 orf, hypothetical protein #2 ribH 88 riboflavin synthase, beta chain #3 thiL 77 thiamin-monophosphate kinase #4 thiM 222 hydoxyethylthiazole kinase #5 thiC 232 thiamin biosynthesis, pyrimidine moiety #6 aceB 268 malate synthase A #7 aceA 29 isocitrate lyase #8 BIME206 22 BIME #9 aceK 27 isocitrate dehydrogenase kinase/phosphatase Motif number 1 TCTATTTTACCCTGAACTGACGATACAACA 1 41 0 CCTGAACTGA 0.869852 -50 ACGGCGTCCTGACCAGGTGGTTAACGG 1 74 0 CCTGACCAGG 0.552234 -17 CATAATATTTCGTGCGCTGCTTCCCTTTCG 2 21 0 CGTGCGCTGC 0.954042 -68 ACGTTATGCCTCAGCAGGTAAAAAAGAA 3 60 0 CCTCAGCAGG 0.631852 -18 GTTTACAACGCGTGCGCTGGACATTACCAT 4 47 1 CGTGCGCTGG 0.925854 -176 ACATTACCATCCTCCTCTGCGATTTATCAT 4 67 1 CCTCCTCTGC 0.95452 -156 ACCCGTATCACCTGATCTGGATAATGCCAG 4 144 1 CCTGATCTGG 0.582141 -79 CCGTGACTTCCCTACGCTGGCATTATCCAG 4 160 0 CCTACGCTGG 0.910044 -63 GTAAATTACGCGTTAACAGCGCAGAAC 5 8 0 CGTTAACAGC 0.714412 -225 TGTCGGAGTGCCTTAACTGGCTGAGACCGT 5 69 1 CCTTAACTGG 0.964518 -164 ATCCGCGGAACCTGATCAGGCTAATACCTG 5 108 1 CCTGATCAGG 0.49996 -125 ACTCTTGTTCCCTTCGCAGGTATTAGCCTG 5 124 0 CCTTCGCAGG 0.563115 -109 CCGAAACGTACCTCAGCAGGTGAATAAATT 6 82 1 CCTCAGCAGG 0.631852 -187 TTAGCGCCCTCATCAGGAGCAGAGAAT 9 11 0 CCTCATCAGG 0.619189 -17 ********** Masking position 3 Map Score: 31.3457 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 644 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 TATCTCAAAAGCGTTGCGCCTTTGTTGTATCGT 1 19 1 GCGTGCCTTT 0.975764 -72 TGGCCCCGCAGGGGGGCGGATTTTAGCATAATA 2 44 0 GGGGGCGTTT 0.986509 -45 CCGCCCCCCTGCGGGGCCATACTCGAACCCGAA 2 58 1 GCGGGCAACT 0.935763 -31 CAAACGACTCGGGGTGCCCTTCTGCGTGAAGGC 4 103 1 GGGGGCCTCT 0.993053 -120 TGCCCCATTTGCGGGGCTAATTTCTTGTCGGAG 5 44 1 GCGGGCATTT 0.991153 -189 GCCTTAACTGGCTGAGACCGTTTATTCGGGATC 5 78 1 GCTGGACTTT 0.963642 -155 CATCGCCCCTGCGGCGATCGTCTCTTGCTTCAT 5 167 1 GCGGGACTCT 0.991073 -66 ACGAAGGATCGTTGTGCTCTTTTCGTTCAGCAC 6 203 0 GTTGGCCTTT 0.956636 -66 TTCGTTCACAGTGGGGAAGTTTTCGGATCCATG 6 231 1 GTGGGAGTTT 0.93937 -38 **** ** * *** Masking position 13 Map Score: 10.3234 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 491 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 GAGTATGGCCCCGCAGGGGGGCGGATTTTA 2 52 0 CCGCAGGGGG 0.994007 -37 ATACTCGAACCCGAAGGAAGAAA 2 76 1 CCGAAGGAAG 0.839925 -13 CGTTATGCCTCAGCAGGTAAAAAAGAAAAG 3 57 0 CAGCAGGTAA 0.923072 -21 CGATGATAAATCGCAGAGGAGGATGGTAAT 4 69 0 TCGCAGAGGA 0.794353 -154 CTTCACGTTATGGCAGGAGCAAACT 4 208 1 TGGCAGGAGC 0.917791 -15 CTTGTTCCCTTCGCAGGTATTAGCCTGATC 5 121 0 TCGCAGGTAT 0.803476 -112 GAGACGATCGCCGCAGGGGCGATGCGATAG 5 161 0 CCGCAGGGGC 0.996916 -72 AAAAAGGCACCCGAAGGTGCCTGAGGTAAG 6 47 0 CCGAAGGTGC 0.978871 -222 AAACGTACCTCAGCAGGTGAATAAATTTTA 6 85 1 CAGCAGGTGA 0.977025 -184 TTAGCGCCCTCATCAGGAGCAGAGAAT 9 8 0 CATCAGGAGC 0.854927 -20 ********** Masking position 5 Map Score: 9.06405 Number of sites scoring better than the average of aligned sites = 2829 Number in coding regions = 2646 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 4 TTACCCTGAACTGACGATACAACAAAGGCGCA 1 33 0 CTGGATACAA 0.719503 -58 CGGCTCGAAAGGGAAGCAGCGCACGAAATATT 2 16 1 GGGGCAGCGC 0.946614 -73 TATCCAGGCCGGTAGATTCACGGAAGACCGT 3 10 1 CGGGATTCAC 0.933562 -68 CTGCCATAACGTGAAGAAGCAATGACCTGGTG 4 192 0 GTGGAAGCAA 0.963767 -31 GATCGCCGCAGGGGCGATGCGATAGCAGATTA 5 154 0 GGGGATGCGA 0.983515 -79 TGTCAGACGACGGATGAAGCAAGAGACGATCG 5 181 0 CGGGAAGCAA 0.9622 -52 CTGAGGTAAGGTGCTGAATCGCTTAACGATCG 6 25 0 GTGGAATCGC 0.894104 -244 GATCCATGACGAGGAGCTGCACG 6 256 1 GAGGCTGCAC 0.756203 -13 GTGCAGATGCTCCATAGTTATG 7 18 0 GTGGATGCTC 0.800046 -12 *** ******* Masking position 10 Map Score: 3.98481 Number of sites scoring better than the average of aligned sites = 1264 Number in coding regions = 1188 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TATCTCAAAAGCGTTGCGCCTTTGTTGTAT 1 19 1 GCGTTGCGCC 0.967015 -72 ACGTTATGCCTCAGCAGGTA 3 68 0 ACGTTATGCC 0.968675 -10 ACCAAACGACTCGGGGTGCCCTTCTGCGTG 4 101 1 TCGGGGTGCC 0.981146 -122 TTGCTTCTTCACGTTATGGCAGGAGCAAAC 4 202 1 ACGTTATGGC 0.856007 -21 TAATTTCTTGTCGGAGTGCCTTAACTGGCT 5 61 1 TCGGAGTGCC 0.972308 -172 TGAGTAGTCTTAGTTGTGCTGAACGAAAAG 6 188 1 TAGTTGTGCT 0.882129 -81 GAACGAAGGATCGTTGTGCTCTTTTCGTTC 6 208 0 TCGTTGTGCT 0.982963 -61 ********** Masking position 3 Map Score: 3.22153 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 872 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 GCGTCCTGACCAGGTGGTTAACGGAAATCTAT 1 66 0 CAGGGTTAAC 0.915568 -25 TTTTTACCTGCTGAGGCATAACGT 3 64 1 CTGACATAAC 0.827743 -14 AACGCGTGCGCTGGACATTACCATCCTCCTCT 4 53 1 CTGGATTACC 0.976435 -170 TGCGTGAAGGCTGAGAAATACCCGTATCACCT 4 125 1 CTGAAATACC 0.962715 -98 ATCACCTGATCTGGATAATGCCAGCGTAGGGA 4 150 1 CTGGAATGCC 0.968391 -73 AGTGCCTTAACTGGCTGAGACCGTTTATTCGG 5 75 1 CTGGGAGACC 0.967772 -158 GGAACCTGATCAGGCTAATACCTGCGAAGGGA 5 114 1 CAGGAATACC 0.98567 -119 CGTACCTCAGCAGGTGAATAAATTTTATTCAT 6 88 1 CAGGAATAAA 0.774375 -181 TACTTGATAACTTGTTGATAACAATATGAATA 6 113 0 CTTGGATAAC 0.865084 -156 **** ****** Masking position 1 Map Score: 4.25106 Number of sites scoring better than the average of aligned sites = 1607 Number in coding regions = 1538 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 CAACGCTTTTGAGATAAAGGATCG 1 1 0 GGATAAATCG 0.966126 -90 GAAAAGGCCGGCGATCATGGAACGGTCTTCCGTG 3 29 0 GGATATAACG 0.984117 -49 TTTATTAACGCGATTGTAAAACTGCCGTTTTTC 4 10 1 GGATGTAACT 0.937783 -213 TCGTTTGGTTGCGATGATAAATCGCAGAGGAGGA 4 76 0 GGATATATCG 0.991424 -147 CGCCCCTGCGGCGATCGTCTCTTGCTTCATCCGT 5 170 1 GGATGTCTTG 0.911371 -63 TCTTCTGTGATAGTCGATCGTTAAGCGATT 6 7 1 GGATGTATCG 0.994529 -262 * *** ** **** Masking position 5 Map Score: 1.68988 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 155 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 GGGTTCGAGTATGGCCCCGCAGGGGGGCGG 2 58 0 ATGGCCCCGC 0.965801 -31 GTAAAAAAGAAAAGGCCGGCGATCATGGAA 3 41 0 AAAGGCCGGC 0.965392 -37 CTTCACGCAGAAGGGCACCCCGAGTCGTTT 4 104 0 AAGGGCACCC 0.977683 -119 CGACAAGAAATTAGCCCCGCAAATGGGGCA 5 44 0 TTAGCCCCGC 0.948113 -189 CTCAGCCAGTTAAGGCACTCCGACAAGAAA 5 64 0 TAAGGCACTC 0.912539 -169 CGGAAATAAAAAAGGCACCCGAAGGTGCCT 6 55 0 AAAGGCACCC 0.981524 -214 ********** Masking position 6 Map Score: 1.45293 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 204 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 ********** No masking Map Score: -1.39023e-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: -1.39023e-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: -1.39023e-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