AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i050_ecoli_mtub_300.orf -o050_ecoli_mtub_300.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 yaiM 93 putative esterase (EC 3.1.1.1) #2 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #3 yaiN 166 putative alpha helix chain #4 yeiG 257 putative esterase (EC 3.1.1.-). #5 adhB 98 adhB #6 Rv0767c 201 hypothetical protein Rv0767c #7 Rv1284 206 hypothetical protein Rv1284 #8 cysD 93 cysD #9 Rv1287 53 hypothetical protein Rv1287 #10 Rv1288 57 hypothetical protein Rv1288 #11 Rv3083 77 hypothetical protein Rv3083 #12 adhD 30 adhD Motif number 1 ATACTCTCCCCGGGCAGCCGTCCGGGGGATT 1 54 1 CGGCAGCCGT 0.725214 -40 CCCCGGATAGCGGGCGGCAGAAGGAA 3 6 0 CGGCGGCAGA 0.878094 -161 CCCGCTATCCGGGGCGGCCTTCCCTGCCGAT 3 23 1 GGGCGGCCTT 0.95851 -144 AGAGGAAAGGGGGGGGGGCTAATCGGCAGGG 3 44 0 GGGGGGGCTA 0.632884 -123 GTGACGCCTCCGCCCTGCGTGGGGGCAAAGT 4 31 1 CGCCTGCGTG 0.845173 -227 TGATTATTGTGCGTGAGGCGGCGCACATAAT 4 82 1 GCGGAGGCGG 0.844471 -176 TATTGTAATTGCCGCTGCCTTTCATCAGCAG 4 133 1 GCCCTGCCTT 0.797445 -125 GGCCGGAACGCCGACTGGCTGAGTGTAGGTC 5 27 0 CCGCTGGCTG 0.972055 -72 GTGGTCCCTAGCCTCGGCCGGAACGCCGACT 5 42 0 GCCCGGCCGG 0.967032 -57 CTTGCGGATACGGTCTCGATGAGGCAATATC 6 60 0 CGGCTCGATG 0.936716 -142 GACGGTGTAGCGGCCTTGCGGATACGGTCTC 6 74 0 CGGCTTGCGG 0.755037 -128 CCTGGTGCATCGGTCAGGACGGTGTAGCGGC 6 91 0 CGGCAGGACG 0.950503 -111 GGGACTGTCCGCGACGCGACGTGGCCCCTGG 6 117 0 GCGCGCGACG 0.856352 -85 TCGGATGGTCGCGGCAGGAGGCAAGCCAGTC 6 169 0 GCGCAGGAGG 0.92312 -33 CTGTCCCAATGCGACGCGGTGGTTGGGC 7 8 0 GCGCGCGGTG 0.773478 -199 ACGCCATCGCCGGGCTCGCTACCCTGTCCCA 7 31 0 CGGCTCGCTA 0.841094 -176 CATCAACCGGCGCGCTGGCGGCACGCCATCG 7 53 0 CGCCTGGCGG 0.547152 -154 CCGGTTGATGGGGTCACCCGTGATCCGGATG 7 74 1 GGGCACCCGT 0.88703 -133 CGGATGGTTCCGCTCGGGCCGATTCTGATGC 7 99 1 CGCCGGGCCG 0.972361 -108 TCGGGTATCGCGGTGTGGACTTTGCTACTCA 7 176 0 CGGGTGGACT 0.462623 -31 GCGGGCCTCCTCGGGTATCGCGG 7 194 0 GGGCTCCTCG 0.719342 -13 CTAGGCTGACGGCTCGGGCTG 8 1 0 GGCCGGGCTG 0.980282 -93 CAGCCTAGGGCGCACTGGCGCACCGGCAGCC 8 24 1 CGCCTGGCGC 0.771273 -70 CCCATCTCGGCGGGCTGCCGGTGCGCCAGTG 8 36 0 CGGCTGCCGG 0.508318 -58 CCGCCGAGATGGGGCTGCGTTGACAGCGATA 8 54 1 GGGCTGCGTT 0.805272 -40 GCCGGCCTGGTTGCTCTGCTGTC 9 3 1 CGGCTGGTTG 0.903471 -51 CCGCTTGCCAGGGACAGCAGAGCAACCAGGC 9 15 0 GGGCAGCAGA 0.826134 -39 CCCTGCCGATGGCTCTGGCGG 10 1 0 GGCCTGGCGG 0.98497 -57 GCCATCGGCAGGGCCTGCCTGAGCCAGGTGC 10 19 1 GGGCTGCCTG 0.962162 -39 TTATCATTTTCCGACAGGAGGTG 11 3 0 CCGCAGGAGG 0.942859 -75 TTGACACTTTGCGACAGCCTTTTATCATTTT 11 24 0 GCGCAGCCTT 0.863092 -54 TGGTGGAGGACCCCCGCCACGTATTGACACT 11 47 0 CCCCGCCACG 0.640071 -31 GTTCTAGAAAGGGACACCACG 12 20 1 GGGCACCACG 0.87549 -11 *** ******* Masking position 5 Map Score: 47.258 Number of sites scoring better than the average of aligned sites = 15026 Number in coding regions = 14388 Number in noncoding regions = 638 Number of orfs with sites within 600 bp upstream = 503 Fraction of orfs with sites within 600 bp upstream = 0.0807902 Motif number 2 TTAAGAACCCCCGCCTGAAGTGGACGGGGTAAA 1 22 0 CCGCCTAGGG 0.946214 -72 CAGGGTTAATCCCCCGGACGGCTGCCCGGGGAG 1 59 0 CCCCCGCGCT 0.848652 -35 CCTTCTGCCGCCCGCTATCCGGGGCGGCCTTCC 3 13 1 CCCGCTCCGG 0.987963 -154 CTATCCGGGGCGGCCTTCCCTGCCGATTAGCCC 3 27 1 CGGCCTCCGC 0.909447 -140 ATTAGCCCCCCCCCCTTTCCTCTTTGTTTTCCG 3 52 1 CCCCCTCCCT 0.982108 -115 TGTTTTCCGACCACATTCACCGGATAAATTTTA 3 76 1 CCACATACGG 0.478504 -91 CAATGCATACCCCCCTATAGTATATAACACTGG 3 113 0 CCCCCTAGAT 0.872706 -54 TATAGAATACCCCCCTATAGTATATTGC 3 149 1 CCCCCTAGAT 0.872706 -18 TGTGACGCCTCCGCCCTGCGTGGGGGCAAAGTT 4 30 1 CCGCCCCGGG 0.920642 -228 ATTATGTGCGCCGCCTCACGCACAATAATCAGG 4 80 0 CCGCCTCGAC 0.894228 -178 ACGCCCTAGCGCCGTTGACCTACA 5 2 1 CGCCCTCGCG 0.980659 -97 GACGGTGTAGCGGCCTTGCGGATACGGTCTCGA 6 72 0 CGGCCTCGAT 0.907287 -130 GCCGCTACACCGTCCTGACCGATGCACCAGGGG 6 91 1 CGTCCTCCAT 0.620462 -111 GCACCAGGGGCCACGTCGCGTCGCGGACAGTCC 6 114 1 CCACGTCGCG 0.469242 -88 GACTGGCTTGCCTCCTGCCGCGACCATCCGATA 6 169 1 CCTCCTCGGA 0.772341 -33 CATCGCCGGGCTCGCTACCCTGTCCCAATGCGA 7 25 0 CTCGCTCCGT 0.691573 -182 GCTGGCGGCACGCCATCGCCGGGCTCGCTACCC 7 38 0 CGCCATCCGG 0.95423 -169 CATCAACCGGCGCGCTGGCGGCACGCCATCGCC 7 51 0 CGCGCTCGCA 0.748856 -156 TCACGGGTGACCCCATCAACCGGCGCGCTGGCG 7 64 0 CCCCATACGG 0.872047 -143 GCGGAACCATCCGGATCACGGGTGACCCCATCA 7 79 0 CCGGATCGGT 0.872995 -128 ATTTTAACAACCGGTTACCCAGTTTTCACGCAT 7 126 0 CCGGTTCCGT 0.549968 -81 AAGTCCACACCGCGATACCCGAGGAGGCCCGC 7 185 1 CGCGATCCAG 0.748905 -22 GTCAACGCAGCCCCATCTCGGCGGGCTGCCGGT 8 45 0 CCCCATCGCG 0.966977 -49 GATTGTGCCACCCGCTTGCCAGGGACAGCAGAG 9 24 0 CCCGCTCCGG 0.988252 -30 ****** ** ** Masking position 1 Map Score: 29.7278 Number of sites scoring better than the average of aligned sites = 3529 Number in coding regions = 3198 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 282 Fraction of orfs with sites within 600 bp upstream = 0.0452939 Motif number 3 CCCCCGCCTGAAGTGGACGGGGTAAACCTGC 1 17 0 AAGTGACGGG 0.413113 -77 ATCCCCCGGACGGCTGCCCGGGGAGAGTATT 1 53 0 CGGCTCCCGG 0.82065 -41 CTTCTGCCGCCCGCTATCCGGGGCGGCCTTC 3 14 1 CCGCTTCCGG 0.865879 -153 AAAGGGGGGGGGGCTAATCGGCAGGGAAGGC 3 39 0 GGGCTATCGG 0.741044 -128 AAAATTTATCCGGTGAATGTGGTCGGAAAAC 3 77 0 CGGTGATGTG 0.704295 -90 TGTAGGTCAACGGCGCTAGGGCGT 5 4 0 CGGCGTAGGG 0.970218 -95 CTCAGCCAGTCGGCGTTCCGGCCGAGGCTAG 5 35 1 CGGCGTCCGG 0.992714 -64 TCGGTCAGGACGGTGTAGCGGCCTTGCGGAT 6 82 0 CGGTGAGCGG 0.943618 -120 ACGTGGCCCCTGGTGCATCGGTCAGGACGGT 6 99 0 TGGTGATCGG 0.869802 -103 CAATGCGACGCGGTGGTTGGGC 7 2 0 CGGTGTTGGG 0.972513 -205 GTAGCGAGCCCGGCGATGGCGTGCCGCCAGC 7 40 1 CGGCGTGGCG 0.851724 -167 GCCAGCGCGCCGGTTGATGGGGTCACCCGTG 7 65 1 CGGTTATGGG 0.939372 -142 CGGAACCATCCGGATCACGGGTGACCCCATC 7 80 0 CGGATACGGG 0.925887 -127 GCGTGAAAACTGGGTAACCGGTTGTTAAAAT 7 128 1 TGGGTACCGG 0.610123 -79 TAGGGCGCACTGGCGCACCGGCAGCCCGCCG 8 29 1 TGGCGACCGG 0.968891 -65 CGGCAGCCCGCCGAGATGGGGCTGCGTTGAC 8 47 1 CCGAGTGGGG 0.677894 -47 GCTGCGTTGACAGCGATAGGGAAGCCTGGTT 8 67 1 CAGCGTAGGG 0.777724 -27 ***** ***** Masking position 3 Map Score: 16.4614 Number of sites scoring better than the average of aligned sites = 3934 Number in coding regions = 3787 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 GACGGGGTAAACCTGCGGGAAA 1 2 0 ACCTGCGGAA 0.958841 -92 GGGCGGCCTTCCCTGCCGATTAGCCCCCCCC 3 34 1 CCCTGCGATT 0.934305 -133 GAGGCGTCACACCTGCAGGAGAAATCATAA 4 10 0 ACCTGCGGAG 0.984473 -248 GACGCCTCCGCCCTGCGTGGGGGCAAAGTTA 4 33 1 CCCTGCTGGG 0.799336 -225 ATGTTTTAACATCTGCTGATGAAAGGCAGCG 4 145 0 ATCTGCGATG 0.782085 -113 GGTCCCTAGCCTCGGCCGGAACGCCGACTGG 5 40 0 CTCGGCGGAA 0.778512 -59 GGTGTAGCGGCCTTGCGGATACGGTCTCGAT 6 71 0 CCTTGCGATA 0.676464 -131 GCGACGTGGCCCCTGGTGCATCGGTCAGGAC 6 102 0 CCCTGGGCAT 0.535106 -100 AGTCTGCTAAACATGCAGCTAACATGGGACT 6 142 0 ACATGCGCTA 0.496445 -60 ATCGGATGGTCGCGGCAGGAGGCAAGCCAGT 6 170 0 CGCGGCGGAG 0.936709 -32 CATCTCGGCGGGCTGCCGGTGCGCCAGTGCG 8 34 0 GGCTGCGGTG 0.871907 -60 CTCAGGCAGGCCCTGCCGATGGCTCTGGCGG 10 11 0 CCCTGCGATG 0.98634 -47 GGGTCCTCCACCATGCTGGAGCC 11 65 1 CCATGCGGAG 0.964681 -13 ****** **** Masking position 5 Map Score: 6.40465 Number of sites scoring better than the average of aligned sites = 4319 Number in coding regions = 4092 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 5 GACGGCTGCCCGGGGAGAGTATTAAGAACC 1 46 0 CGGGGAGAGT 0.938432 -48 ATAAAATTTATCCGGTGAATGTGGTCGGAA 3 80 0 TCCGGTGAAT 0.785566 -87 CAATAATTATCGCTGTGAATACTGGATTAT 4 108 0 CGCTGTGAAT 0.98354 -150 TTATTCAATGTGCTGTGAGTAACTTTCACT 4 193 0 TGCTGTGAGT 0.974668 -65 GTCCAATCGATGATGAGAGTCGGAGAAGTT 6 22 0 TGATGAGAGT 0.821951 -180 CACGTCGCGTCGCGGACAGTCCCATGTTAG 6 125 1 CGCGGACAGT 0.960238 -77 AGATCGACGCCGCGGTGAATTTTAACAACC 7 147 0 CGCGGTGAAT 0.987168 -60 ACCGCGGCGTCGATCTGAGTAGCAAAGTCC 7 161 1 CGATCTGAGT 0.795985 -46 GCTTCCCTATCGCTGTCAACGCAGCCCCAT 8 62 0 CGCTGTCAAC 0.809612 -32 ********** Masking position 8 Map Score: 3.84249 Number of sites scoring better than the average of aligned sites = 1176 Number in coding regions = 1075 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 CAGTCATTATCTCAGGGTTAATCCCCC 1 77 0 GCATCTCAGG 0.786919 -17 GCCGCCTCACGCACAATAATCAGGCTGTAAATCAG 4 69 0 GACAATCAGC 0.926925 -189 TAGCGCCGTTGACCTACACTCAGCCAGTCGGCGTT 5 17 1 GCCACTCACC 0.976828 -82 TCGCTACCCTGTCCCAATGCGACGCGGTGGTTGGG 7 12 0 GCCAGCGAGC 0.928764 -195 GTTCCGCTCGGGCCGATTCTGATGCGTGAAAACTG 7 105 1 GCCACTGAGC 0.994004 -102 GCGCCAGTGCGCCCTAGGCTGACGGCTCGGGCTG 8 10 0 GCCACTGAGG 0.989042 -84 CAAGCGGGTGGCACAATCCTGAAGC 9 39 1 GACACTGAGC 0.990027 -15 TCCTTCGGTTGCACCTGGCTCAGGCAGGCCCTGCC 10 25 0 GACTCTCAGC 0.963191 -33 * ** * **** ** Masking position 12 Map Score: 3.21597 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 280 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 AATGCATACCCCCCTATAGTATATAACACT 3 115 0 CCCCTATAGT 0.991642 -52 ATAGAATACCCCCCTATAGTATATTGC 3 150 1 CCCCTATAGT 0.991642 -17 GCCCATAGAGTTCTAGAAAGG 12 2 1 CCCATAGAGT 0.973324 -29 ********** Masking position 6 Map Score: 1.1966 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 0 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 ********** No masking Map Score: -3.12396e-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 9 ********** No masking Map Score: -3.12396e-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: -3.12396e-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