AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i162_ecoli_mtub_100.orf -o162_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 hemL 224 glutamate-1-semialdehyde aminotransferase (aminomutase) #2 hemB 136 5-aminolevulinate dehydratase = porphobilinogen synthase #3 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #4 hemC 300 porphobilinogen deaminase = hydroxymethylbilane synthase #5 mmpS2 173 mmpS2 #6 hemA 49 hemA #7 cysG 32 cysG #8 hemB 85 hemB #9 hemL 113 hemL #10 cysG2 276 cysG2 Motif number 1 TACTCCAAAAGGGGGCGCTCTCTTTTATTG 3 128 1 GGGGGCGCTC 0.940948 -86 TTCCGCCCATCGCGCGGACCTAGTGACCCT 5 147 0 CGCGCGGACC 0.989299 -27 TGTACACCGACACGCCGACCGAGCTGGCAT 8 43 1 CACGCCGACC 0.917743 -43 CGGCCAAAGGGGTGGCGACCCGCGGCGCCC 10 59 1 GGTGGCGACC 0.953065 -218 GGTGGCGACCCGCGGCGCCCGGTCCCCGCG 10 69 1 CGCGGCGCCC 0.999146 -208 CGATCGCAAGCGCGGGGACCGGGCGCCGCG 10 79 0 CGCGGGGACC 0.998623 -198 CATCAGGGCCAGTGGCGATCGCAAGCGCGG 10 94 0 AGTGGCGATC 0.983301 -183 TGGCCCTGATGGTGGCGACCCGCGGCGCCC 10 113 1 GGTGGCGACC 0.953065 -164 GGTGGCGACCCGCGGCGCCCGGTCCCCGCG 10 123 1 CGCGGCGCCC 0.999146 -154 CGATCGCAAGCGCGGGGACCGGGCGCCGCG 10 133 0 CGCGGGGACC 0.998623 -144 CATCAGGGCCAGTGGCGATCGCAAGCGCGG 10 148 0 AGTGGCGATC 0.983301 -129 TGGCCCTGATGGTGGCGACCCGCGGCGCCC 10 167 1 GGTGGCGACC 0.953065 -110 GGTGGCGACCCGCGGCGCCCGGTCCCCGCG 10 177 1 CGCGGCGCCC 0.999146 -100 CGATCGCAAGCGCGGGGACCGGGCGCCGCG 10 187 0 CGCGGGGACC 0.998623 -90 CATCAGGGCCAGTGGCGATCGCAAGCGCGG 10 202 0 AGTGGCGATC 0.983301 -75 TGGCCCTGATGGTGGCGACCCGCGGCGCCC 10 221 1 GGTGGCGACC 0.953065 -56 GGTGGCGACCCGCGGCGCCCGGTCCCCGCG 10 231 1 CGCGGCGCCC 0.999146 -46 CGATCGCAAGCGCGGGGACCGGGCGCCGCG 10 241 0 CGCGGGGACC 0.998623 -36 CGCCAAGCCTAGTGGCGATCGCAAGCGCGG 10 256 0 AGTGGCGATC 0.983301 -21 ********** Masking position 4 Map Score: 80.6923 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 325 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 AACCCTTAATGCTAGCGTTACCGTCCGCTATC 3 46 1 GCTGCGTACC 0.968856 -168 ATCAATAAAAGAGAGCGCCCCCTTTTGGAGTA 3 128 0 GAGGCGCCCC 0.731857 -86 TAGCGTCTACGCTAGCTAACGCAACGAGACAT 5 67 1 GCTGCTACGC 0.835202 -107 GACCCTTAGGCCTCCCGATACCTCCTGAAATG 5 121 0 CCTCCGTACC 0.835799 -53 TCGTAGCCGCGAGCGTACGCAAAATGCCAG 8 66 0 GCGGCGACGC 0.51172 -20 GCTTGATGCCGCGGCCGGTCCACGAGTTGGAT 9 18 0 GCGCCGTCCA 0.959643 -96 GCGACCCGCGGCGCCCGGTCCCCGCGCTTGCG 10 73 1 GCGCCGTCCC 0.840188 -204 CGGTCCCCGCGCTTGCGATCGCCACTGGCCCT 10 88 1 GCTGCGTCGC 0.767629 -189 GCGACCCGCGGCGCCCGGTCCCCGCGCTTGCG 10 127 1 GCGCCGTCCC 0.840188 -150 CGGTCCCCGCGCTTGCGATCGCCACTGGCCCT 10 142 1 GCTGCGTCGC 0.767629 -135 GCGACCCGCGGCGCCCGGTCCCCGCGCTTGCG 10 181 1 GCGCCGTCCC 0.840188 -96 CGGTCCCCGCGCTTGCGATCGCCACTGGCCCT 10 196 1 GCTGCGTCGC 0.767629 -81 GCGACCCGCGGCGCCCGGTCCCCGCGCTTGCG 10 235 1 GCGCCGTCCC 0.840188 -42 CGGTCCCCGCGCTTGCGATCGCCACTAGGCTT 10 250 1 GCTGCGTCGC 0.767629 -27 *** *** **** Masking position 6 Map Score: 46.2633 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 330 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 3 TACCACTTTTCGCGCCTGGTTTTTTTAGTTTCA 4 45 1 CCGCCGGTTT 0.762094 -256 TGACATCACTCTGGCAAGGATGTTAGGATGGAC 4 273 1 CGGCAGGTGT 0.968842 -28 ACCGGTACGCGCAAAGCTGGGTACGTGAAA 5 8 1 CCGCAAGTGG 0.832572 -166 GTCGAGGGAGCTGGCCAGGTGGTGCTGCC 6 31 1 CGGCCGGGGT 0.993204 -19 GCACGCTCACCTGACGAGGGTGGGCCA 8 5 0 CGACGGGTGG 0.981025 -81 CACCGACACGCCGACCGAGCTGGCATTTTGCGT 8 47 1 CGACCAGTGG 0.942101 -39 GTTGAGCGACCTGGGCAGGCTGGAACACTAGTC 9 88 1 CGGGCGGTGG 0.984533 -26 CTGCGAATTTCCGGCCCGGCTTTTCGCAGTGCC 10 12 0 CGGCCGGTTT 0.946865 -265 GCGCGGGGACCGGGCGCCGCGGGTCGCCACCCC 10 67 0 CGGCGCGGGG 0.973925 -210 GCGATCGCCACTGGCCCTGATGGTGGCGACCCG 10 102 1 CGGCCTGTGG 0.996 -175 GCGCGGGGACCGGGCGCCGCGGGTCGCCACCAT 10 121 0 CGGCGCGGGG 0.973925 -156 GCGATCGCCACTGGCCCTGATGGTGGCGACCCG 10 156 1 CGGCCTGTGG 0.996 -121 GCGCGGGGACCGGGCGCCGCGGGTCGCCACCAT 10 175 0 CGGCGCGGGG 0.973925 -102 GCGATCGCCACTGGCCCTGATGGTGGCGACCCG 10 210 1 CGGCCTGTGG 0.996 -67 GCGCGGGGACCGGGCGCCGCGGGTCGCCACCAT 10 229 0 CGGCGCGGGG 0.973925 -48 * **** ** *** Masking position 9 Map Score: 39.1354 Number of sites scoring better than the average of aligned sites = 1100 Number in coding regions = 1066 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 GGTTTGCGCAGGCGTCTACGTTTCACCACA 4 239 1 GGCGTCTACG 0.82701 -62 TGTCAACGGTAGCGTCTACGCTAGCTAACG 5 58 1 AGCGTCTACG 0.48558 -116 GAGGCCTAAGGGTCACTAGGTCCGCGCGAT 5 139 1 GGTCACTAGG 0.603877 -35 CGCATGAAGAAGTGACTGGGAGTGACAATC 7 13 1 AGTGACTGGG 0.535026 -20 TGCGTACGCTCGCGGCTACGA 8 75 1 CGCGGCTACG 0.822912 -11 GCAAACCTCTGGTGGCTGCGGCAAACTCTT 9 48 1 GGTGGCTGCG 0.897533 -66 CGGCACTGCGAAAAGCCGGG 10 1 1 CGGCACTGCG 0.984715 -276 GCGAATGTAACGCCACTGCGAATTTCCGGC 10 30 0 CGCCACTGCG 0.983975 -247 CGCGGGGACCGGGCGCCGCGGGTCGCCACC 10 69 0 GGGCGCCGCG 0.948742 -208 GCCCGGTCCCCGCGCTTGCGATCGCCACTG 10 85 1 CGCGCTTGCG 0.93215 -192 CGCTTGCGATCGCCACTGGCCCTGATGGTG 10 97 1 CGCCACTGGC 0.925027 -180 CGCGGGGACCGGGCGCCGCGGGTCGCCACC 10 123 0 GGGCGCCGCG 0.948742 -154 GCCCGGTCCCCGCGCTTGCGATCGCCACTG 10 139 1 CGCGCTTGCG 0.93215 -138 CGCTTGCGATCGCCACTGGCCCTGATGGTG 10 151 1 CGCCACTGGC 0.925027 -126 CGCGGGGACCGGGCGCCGCGGGTCGCCACC 10 177 0 GGGCGCCGCG 0.948742 -100 GCCCGGTCCCCGCGCTTGCGATCGCCACTG 10 193 1 CGCGCTTGCG 0.93215 -84 CGCTTGCGATCGCCACTGGCCCTGATGGTG 10 205 1 CGCCACTGGC 0.925027 -72 CGCGGGGACCGGGCGCCGCGGGTCGCCACC 10 231 0 GGGCGCCGCG 0.948742 -46 GCCCGGTCCCCGCGCTTGCGATCGCCACTA 10 247 1 CGCGCTTGCG 0.93215 -30 CGCTTGCGATCGCCACTAGGCTTGGCGG 10 259 1 CGCCACTAGG 0.934439 -18 ********** Masking position 2 Map Score: 34.9886 Number of sites scoring better than the average of aligned sites = 5769 Number in coding regions = 5449 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 5 AAGTTAAATACTCGTCAAACATCAGGCTGC 1 148 0 CTCGTCAAAC 0.859744 -77 CGCGACAACTTTCGTAAAACATCCCTACCC 2 102 1 TTCGTAAAAC 0.76957 -35 GTCTGCGGGAAATAATACCAACG 3 201 0 TGCGGGAAAT 0.947775 -13 CATTCGGGATATTTCGTATGTC 4 3 1 TTCGGGATAT 0.680342 -298 CCATTTTTTCGTCGTGAAACTAAAAAAACC 4 62 0 GTCGTGAAAC 0.977708 -239 TTATTACAACGGCGTGAAACGCCTGTCAGG 4 185 1 GGCGTGAAAC 0.979389 -116 TGTCAGTGTTGTGGTGAAACGTAGACGCCT 4 248 0 GTGGTGAAAC 0.836652 -53 CAAAGCTGGGTACGTGAAATCCTGAATTCT 5 22 1 TACGTGAAAT 0.788068 -152 CTCCCGATACCTCCTGAAATGTCCTAACGT 5 112 0 CTCCTGAAAT 0.741748 -62 CTCTGGTGGCTGCGGCAAACTCTTACACCC 9 54 1 TGCGGCAAAC 0.902245 -60 CGAAAAGCCGGGCCGGAAATTCGCAGTGGC 10 19 1 GGCCGGAAAT 0.847741 -258 ********** Masking position 7 Map Score: 4.19504 Number of sites scoring better than the average of aligned sites = 1433 Number in coding regions = 1343 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 GAAGAGAATGGAAGAGAGGCCAGGACATCTTTTTAA 2 56 0 GGAGGCCGGC 0.997782 -81 TACTGGGGTAGTCGAGGGAGCTGGCCAGGTGGTGCT 6 21 1 GGAGGGCGGC 0.976082 -29 ACCCTCGTCAGGTGAGCGTGCGTGTCTGTACACCGA 8 17 1 GGAGGGCTGC 0.977394 -69 ACACCGACACGCCGACCGAGCTGGCATTTTGCGTAC 8 46 1 GGACGGCGGA 0.913158 -40 CATCCAACTCGTGGACCGGCCGCGGCATCAAGCAAA 9 17 1 GGACGCCCGC 0.945483 -97 ACACCCTGTAGTTGAGCGACCTGGGCAGGCTGGAAC 9 78 1 GGAGGCCGGC 0.997361 -36 GGCGATCGCAAGCGCGGGGACCGGGCGCCGCGGGTC 10 75 0 AGCGGACGGC 0.994209 -202 GGCGATCGCAAGCGCGGGGACCGGGCGCCGCGGGTC 10 129 0 AGCGGACGGC 0.994209 -148 GGCGATCGCAAGCGCGGGGACCGGGCGCCGCGGGTC 10 183 0 AGCGGACGGC 0.994209 -94 GGCGATCGCAAGCGCGGGGACCGGGCGCCGCGGGTC 10 237 0 AGCGGACGGC 0.994209 -40 * *** * ** ** * Masking position 11 Map Score: 22.6315 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 133 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 TAGACCATTTTTTCGTCGTGAAACTAAAAA 4 66 0 TTTCGTCGTG 0.807112 -235 TAAAATGAGGTCTGGCAGTGGATCCTGACA 4 208 0 TCTGGCAGTG 0.979694 -93 TAATCGGATGTCTCGTTGCGTTAGCTAGCG 5 76 0 TCTCGTTGCG 0.480586 -98 TGAAGAAGTGACTGGGAGTGACAATC 7 17 1 ACTGGGAGTG 0.892822 -16 CAACTCGTGGACCGGCCGCGGCATCAAGCA 9 21 1 ACCGGCCGCG 0.940618 -93 CGGCCCGGCTTTTCGCAGTGCCG 10 4 0 TTTCGCAGTG 0.911736 -273 CGGGCCGGAAATTCGCAGTGGCGTTACATT 10 27 1 ATTCGCAGTG 0.92467 -250 TCGCCACCCCTTTGGCCGCGAATGTAACGC 10 47 0 TTTGGCCGCG 0.962983 -230 TGCGATCGCCACTGGCCCTGATGGTGGCGA 10 101 1 ACTGGCCCTG 0.981248 -176 TGCGATCGCCACTGGCCCTGATGGTGGCGA 10 155 1 ACTGGCCCTG 0.981248 -122 TGCGATCGCCACTGGCCCTGATGGTGGCGA 10 209 1 ACTGGCCCTG 0.981248 -68 ********** Masking position 5 Map Score: 11.948 Number of sites scoring better than the average of aligned sites = 1723 Number in coding regions = 1646 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 CGTCCGCTATCGTCTATGTTCAAGTTGTCT 3 67 1 CGTCTATGTT 0.930587 -147 AGACTAACCCTATCAACGTTGGTATTATTT 3 185 1 TATCAACGTT 0.847308 -29 ATATTTCGTATGTCAAAGGTAACCGTTACC 4 19 1 TGTCAAAGGT 0.871735 -282 TTTGCGCAGGCGTCTACGTTTCACCACAAC 4 241 1 CGTCTACGTT 0.975415 -60 GCCAGAGTGATGTCAGTGTTGTGGTGAAAC 4 258 0 TGTCAGTGTT 0.816448 -43 TTCTTCAGCCTGTCAACGGTAGCGTCTACG 5 48 1 TGTCAACGGT 0.972578 -126 TCAACGGTAGCGTCTACGCTAGCTAACGCA 5 60 1 CGTCTACGCT 0.947015 -114 ********** Masking position 3 Map Score: 1.52744 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 305 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 9 ********** No masking Map Score: 2.53196e-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 GTACTGGTGCAATCCTGATTTCTTAGAGTA 1 116 0 AATCCTGATT 0.935464 -109 GGAGGGTTCCTGATTCGTAGAAAAA 1 210 0 GTTCCTGATT 0.932954 -15 ATATAAAATTATTGCTGTTTCTATTAAAAA 2 33 1 ATTGCTGTTT 0.851007 -104 TGATCTTACGCATCCTGTATGATGCAAGCA 3 156 1 CATCCTGTAT 0.789404 -58 AATTTAACACCTTGCTGATTGACCGTAAAG 4 106 1 CTTGCTGATT 0.915854 -195 TTCTCTGTAAATTCCTTATTACAACGGCGT 4 170 1 ATTCCTTATT 0.801103 -131 GGGTACGTGAAATCCTGAATTCTTCAGCCT 5 29 1 AATCCTGAAT 0.882608 -145 ********** Masking position 6 Map Score: 0.728152 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 446 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 11 ********** No masking Map Score: 2.53196e-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 12 ********** No masking Map Score: 2.53196e-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 13 ********** No masking Map Score: 2.53196e-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