AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_ecoli_reg_100.orf -o00760_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 lpxC 100 UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis #2 nadC 87 quinolinate phosphoribosyltransferase #3 ushA 217 UDP-sugar hydrolase (5'-nucleotidase) #4 pncB 265 nicotinate phosphoribosyltransferase #5 pntA 300 pyridine nucleotide transhydrogenase, alpha subunit #6 nadE 201 NAD synthetase, prefers NH3 over glutamine #7 gatZ 28 putative tagatose 6-phosphate kinase 1 #8 gatY 197 tagatose-bisphosphate aldolase 1 #9 agaZ 248 putative tagatose 6-phosphate kinase 2 #10 aceB 268 malate synthase A #11 aceA 29 isocitrate lyase #12 BIME206 22 BIME #13 aceK 27 isocitrate dehydrogenase kinase/phosphatase #14 deoC 257 2-deoxyribose-5-phosphate aldolase #15 deoA 83 thymidine phosphorylase #16 deoB 51 phosphopentomutase #17 deoD 56 purine-nucleoside phosphorylase Motif number 1 AATTTCTAATCTGGATGCAGATTTATCTTC 3 123 1 CTGGATGCAG 0.872899 -95 TTTATCTTCACCGGACGCAGACTTGTCTAT 3 144 1 CCGGACGCAG 0.984711 -74 TCAGTCTATTCCTGTTGCGTAAATCGCGCT 4 46 1 CCTGTTGCGT 0.787924 -220 CCTTAGAACGCCGGATAAAGACTGATAATT 5 63 0 CCGGATAAAG 0.872012 -238 TTGTGTGGCTCCTGACACAGGCAAACCATC 5 253 1 CCTGACACAG 0.90343 -48 TGTTTTTATGCCGGATGCGGTGTAAACATA 8 25 0 CCGGATGCGG 0.942375 -173 TTTATCTCACCATGACGCAGTATCAACTGA 9 182 1 CATGACGCAG 0.867237 -67 AATTTATTCACCTGCTGAGGTACGTTTCGG 10 82 0 CCTGCTGAGG 0.916083 -187 TTTTCGGATCCATGACGAGGAGCTGCACG 10 250 1 CATGACGAGG 0.867229 -19 ATTCTCTGCTCCTGATGAGGGCGCTAA 13 11 1 CCTGATGAGG 0.968257 -17 TCACTTTGATCCTGATGCGTTTGCCACCAC 14 66 1 CCTGATGCGT 0.969437 -192 TACCCGTAGGCCGGATAAGGCGTAGACGCA 15 21 1 CCGGATAAGG 0.908665 -63 GCGGCTTTTGCCGGATGCGTCTACGCCTTA 15 36 0 CCGGATGCGT 0.977093 -48 ********** Masking position 1 Map Score: 18.3415 Number of sites scoring better than the average of aligned sites = 2563 Number in coding regions = 2001 Number in noncoding regions = 562 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 TGAAAGCGGAGCCGTTTCGTTCACGGGCTTG 6 70 0 GCCGTTTCTT 0.965203 -132 GCTGTCGCTTGTCGTTTCAGTAGCAACGGGT 6 139 1 GTCGTTTCGT 0.985039 -63 AGGAAGTTTTGTCTTTTCTGTCTGGAGGGGT 6 178 1 GTCTTTTCGT 0.935628 -24 CTATCGGGAGGCCGTTTTTTTGCCTTTCACT 8 77 1 GCCGTTTTTT 0.910642 -121 TTTTCATATTGTCGTTTTTGTGATCGTTATC 8 118 1 GTCGTTTTGT 0.960302 -80 ATCCTGTCGTTTGTTTTCGATTTCAA 8 182 0 GTCGTTTGTT 0.929807 -16 TCGTAAAACTTTCGTTTCATTTCGTTTTGCC 9 22 1 TTCGTTTCTT 0.971555 -227 GCAAGCTACTCTCGTTTCAGTGACTTTCATT 9 102 1 CTCGTTTCGT 0.958839 -147 ACCATTATCTTTCGTTTTATTTTTATCTCAC 9 161 1 TTCGTTTTTT 0.926192 -88 ATATTAATCTTTCGTTTTGTTTCAGTTGATA 9 202 0 TTCGTTTTTT 0.926192 -47 GATCGTTGTGCTCTTTTCGTTCAGCACAACT 10 199 0 CTCTTTTCTT 0.862085 -70 CTTCTTTTCCTTTTATGCCGAA 14 2 1 TTCTTTTCTT 0.882902 -256 ******** ** Masking position 6 Map Score: 15.4214 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 154 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 TAAACTGGCCCGCCGAATGTATAGTACACTT 1 48 1 CGCCAATGTA 0.946086 -53 CGTATTATCTCGCCAAATTACCTATCCAACC 1 80 0 CGCCAATTAC 0.946895 -21 GAAGTCTCAACGCCGAATACAGAATTTCTAA 3 101 1 CGCCAATACA 0.946086 -117 TTGCGTAAATCGCGCTATGCAGAATCTTCAT 4 60 1 CGCGTATGCA 0.80358 -206 TAACATACACCGCGTAATGCCATCGACCAGA 4 128 1 CGCGAATGCC 0.97272 -138 ACCCCGATCACACCATATGCCACCTTTCTGG 4 154 0 CACCTATGCC 0.808967 -112 TGCGAGTTCACGCCGAAATACTGATTTTTGG 5 130 1 CGCCAAATAC 0.90242 -171 TGTGATCTAGCGCCAAAAATCAGTATTTCGG 5 142 0 CGCCAAAATC 0.90242 -159 TAGTAACAAACGCCCTATAACGTACTGAAAA 5 180 0 CGCCTATAAC 0.863749 -121 CTTGAAAAAGCGCCCAATGTATTCCAGGCTT 6 43 0 CGCCAATGTA 0.946086 -159 TAGACGCATCCGGCAAAAGCCGCCTCATACT 15 43 1 CGGCAAAGCC 0.901536 -41 GTCAACGCTCCGCCCAAATCCA 17 2 0 CGCCAAATCC 0.965774 -55 **** ****** Masking position 7 Map Score: 8.61204 Number of sites scoring better than the average of aligned sites = 1286 Number in coding regions = 1191 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 AGTAGCGTCCTCGTACAGGAGCGTTTAGTACA 4 236 0 TCGTCAGAGC 0.974491 -30 AAGTAGTGATTCGTGCCGGGGCGATGTCTCGT 5 11 1 TCGTCCGGGC 0.975015 -290 CAGTATTTCGGCGTGAACTCGCAAAATATTAA 5 121 0 GCGTAATCGC 0.840338 -180 AACATTTAGCTCGTACATGAGCAGCTTGTGTG 5 228 1 TCGTCAGAGC 0.974491 -73 CGGAGCCGTTTCGTTCACGGGCTTGAAAAAGC 6 63 0 TCGTCAGGGC 0.994048 -139 GTTTTTTCCTTGTTAAATGGCAGGTGCG 7 8 0 TTGTAATGGC 0.765132 -21 TAATAGAAAGGCGTTAATAGGCAAAACGAAAT 9 40 0 GCGTAAAGGC 0.915478 -209 AGAGTAGCTTGCGTCAATGGGCAAGGTGGGCT 9 82 0 GCGTAAGGGC 0.985935 -167 TCACGAAACTTCTTACAATGGCGCATCACCTT 14 31 0 TCTTCATGGC 0.864873 -227 **** ** **** Masking position 4 Map Score: 6.68776 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 341 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 CTTTGTGCTAAACTGGCCCGCCGAATGTATAGT 1 40 1 ACTCCCGCCG 0.993398 -61 TCGCCAAATTACCTATCCAACCGAAGTGTACTA 1 69 0 ACTCCAACCG 0.904317 -32 TTCCAGGCTTATCTAACACGCTGATAAACAAGA 6 20 0 ACTCACGCTG 0.966676 -182 TTTAACCACCATTCAGCCCGCTGTCGCTTGTCG 6 120 1 ATCCCCGCTG 0.899253 -82 ACTTCCTTAAAGCTAACCCGTTGCTACTGAAAC 6 152 0 ACTCCCGTTG 0.983873 -50 ATGCAAGCCCACCTTGCCCATTGACGCAAGCTA 9 77 1 ACTCCCATTG 0.967255 -172 TGGATCCGAAAACTTCCCCACTGTGAACGAAGG 10 229 0 ACTCCCACTG 0.990849 -40 * ** ******* Masking position 1 Map Score: 3.28609 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 233 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 GTAGCAATAAAGGCGTTTGTACCTGAAAAGATG 4 88 0 AGCGTTTGCC 0.979929 -178 CCTCGTACAGGAGCGTTTAGTACAATAAACATC 4 227 0 GGCGTTTAAC 0.974434 -39 CGGCGTTCTAAGGTGTTTATCCCACTATCACGG 5 80 1 AGTGTTTACC 0.950979 -221 GTACGTTATAGGGCGTTTGTTACTAATTTATTT 5 186 1 GGCGTTTGAC 0.969172 -115 GCACTGCCACGTATGTTTACACCGCATCCGGCA 8 14 1 GATGTTTACC 0.788873 -184 CAAAGTGCGCGTGTTTTTATGCCGGATGCGGTG 8 33 0 GGTTTTTACC 0.788872 -165 TTTGATCCTGATGCGTTTGCCACCACTGACGCA 14 70 1 AGCGTTTGAC 0.941181 -188 CTTTTGCCGGATGCGTCTACGCCTTATCCGGCC 15 29 0 AGCGTCTACC 0.932567 -55 GATTTGGGCGGAGCGTTGACTCCGCCTTTGTTA 17 13 1 GGCGTTGACC 0.964503 -44 * ******* ** Masking position 6 Map Score: 3.85565 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 448 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 TATGTGGTGCTAATACCCGGTTCAGAGTAGCATGTTTCT 2 25 1 TACGTTCAAA 0.986695 -63 TCATACTATTTTTCAACACGTTGAAATCAGGTCAGGGAG 3 183 1 TACGTTGAAA 0.963286 -35 TCGCAATTTATTGAACCCCGATCACACCATATGCCACCT 4 160 0 TACGATCAAA 0.964477 -106 ATACTGATTTTTGGCGCTAGATCACAGGCATAATTTTCA 5 147 1 TCCGATCAAC 0.803289 -154 ATAATGGTTTTCTGATCTGATTCACAAAAGAAACATAAT 9 130 0 TACATTCAAA 0.892265 -119 TTTCCTCTCCAGTTCAGATTACTGCGATATT 9 228 0 TCCGTTCAAA 0.976411 -21 TAAAAATACTTGATAACTTGTTGATAACAATATGAATAA 10 112 0 TACGTTGAAA 0.962949 -157 ATCACTGTAATGCGATCTGGTTCAAATAATTCACTTTCA 14 109 0 TACGTTCAAA 0.986696 -149 * * * ***** * * Masking position 14 Map Score: 2.83047 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 GCAGGATCTCCTTATATGTGGTGCTAATACCCG 2 11 1 CTTATGTGTG 0.989565 -77 AAAGAATGATCTTATTTGTGATTATTACCAGAC 3 41 1 CTTATGTGTT 0.969737 -177 CGGACGCAGACTTGTCTATGATGTCGCGTCATA 3 155 1 CTTGTATGTG 0.937753 -63 GCAAGGTGGGCTTGCATTTGCTTAATAGAAAGG 9 61 0 CTTGTTTGTT 0.835812 -188 AATGAGTAGTCTTAGTTGTGCTGAACGAAAAGA 10 186 1 CTTATGTGTG 0.989565 -83 AGTAGATTTCCTTAATTGTGATGTGTATCGAAG 14 159 1 CTTATGTGTG 0.98956 -99 **** **** ** Masking position 7 Map Score: 2.44568 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 2 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 CACCACATATAAGGAGATCCTGC 2 1 0 AGGAGACTGC 0.877794 -87 CGCGACATCATAGACAAGTCTGCGTCCGGTGAA 3 150 0 TGACAACTGC 0.682492 -68 GAAAAATAGTATGACGCGACATCATAGACAAGT 3 164 0 AGACGCCATC 0.960121 -54 ACCTGAAAAGATGAAGATTCTGCATAGCGCGAT 4 68 0 AGAAGACTGC 0.897389 -198 CTCCTGTACGAGGACGCTACTGCGCACCT 4 247 1 AGACGCCTGC 0.98276 -19 ACGGTCGGGTAAAACGAGACATCGCCCCGGCAC 5 23 0 AAACGACATC 0.851926 -278 TCGCAAAATATTAACGATTCAGCCGTGATAGTG 5 102 0 TAACGACAGC 0.778688 -199 TGGAATACATTGGGCGCTTTTTCAAGCCCGTGA 6 48 1 TGGCGCTTTC 0.544088 -154 CCAGACAGAAAAGACAAAACTTCCTTAAAGCTA 6 170 0 AGACAACTTC 0.778509 -32 TTATCTCACCATGACGCAGTATCAACTGAAACA 9 183 1 AGACGCTATC 0.721003 -66 AGTCGATCGTTAAGCGATTCAGCACCTTACCTC 10 22 1 TAGCGACAGC 0.74292 -247 CGAAAAGAGCACAACGATCCTTCGTTCACAGTG 10 211 1 AAACGACTTC 0.894612 -58 CCACATAACTATGGAGCATCTGCAC 11 15 1 AGGAGCCTGC 0.886261 -15 ACTTCTTACAATGGCGCATCACCTTCGGCATAA 14 23 0 AGGCGCCACC 0.840054 -235 CAAAGTGAACATCACGAAACTTCTTACAATGGC 14 41 0 ACACGACTTC 0.792705 -217 * ***** **** Masking position 13 Map Score: 5.9872 Number of sites scoring better than the average of aligned sites = 2910 Number in coding regions = 2707 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 10 ATAATCACAAATAAGATCATTCTTTACATC 3 36 0 ATAAGATCAT 0.819373 -182 ACACGTTGAAATCAGGTCAGGGAGAGAAGT 3 198 1 ATCAGGTCAG 0.976757 -20 TCTTTTGTGAATCAGATCAGAAAACCATTA 9 138 1 ATCAGATCAG 0.986228 -111 AATTTAAATGATCAGATCAGTATACCG 16 8 0 ATCAGATCAG 0.986228 -44 ********** Masking position 4 Map Score: 1.06224 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 25 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TTCCTTCAGACGACGCATACAGGTATGTTA 3 74 0 CGACGCATAC 0.971778 -144 GAAGTCTCAACGCCGAATACAGAATTTCTA 3 101 1 CGCCGAATAC 0.931637 -117 TCTATGATGTCGCGTCATACTATTTTTCAA 3 169 1 CGCGTCATAC 0.964984 -49 AATTGCGAAACAAGGTATACTCCAGCAGTT 4 191 1 CAAGGTATAC 0.570856 -75 TGGTGGTTAAAACGTCATACAGGAATCCTC 6 101 0 AACGTCATAC 0.640096 -101 CGTATGTTTACACCGCATCCGGCATAAAAA 8 23 1 CACCGCATCC 0.965989 -175 GATGCGTCTACGCCTTATCCGGCCTACGGG 15 23 0 CGCCTTATCC 0.909818 -61 GATAAGGCGTAGACGCATCCGGCAAAAGCC 15 34 1 AGACGCATCC 0.848305 -50 CGGCAAAAGCCGCCTCATACTCTTTTCCTC 15 53 1 CGCCTCATAC 0.981643 -31 ********** Masking position 7 Map Score: 4.49387 Number of sites scoring better than the average of aligned sites = 1473 Number in coding regions = 954 Number in noncoding regions = 519 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 12 CGCGTCATACTATTTTTCAACACGTTGAAATCAG 3 179 1 TTTTTCAACG 0.891686 -39 ATCACAGGCATAATTTTCAGTACGTTATAGGGCG 5 167 1 TATTTCAACG 0.910252 -134 CTTCCATCGGTTTTATTGATGATGGTTTGCCTGT 5 269 0 TTTTTGAATG 0.836865 -32 ACTCCTCGAATAATTTTCATATTGTCGTTTTTGT 8 105 1 TATTTCATTG 0.96234 -93 CTCGTTTCAGTGACTTTCATTATGTTTCTTTTGT 9 112 1 TACTTCAATG 0.846418 -137 GGTGAATAAATTTTATTCATATTGTTATCAACAA 10 100 1 TTTTTCATTG 0.954022 -169 AAATGGAAATTGTTTTTGATTTTGCATTTTAAAT 10 155 1 TTTTTGATTG 0.86339 -114 AGAAGTTTCGTGATGTTCACTTTGATCCTGATGC 14 50 1 TATTTCATTG 0.962354 -208 TTGTCGCCAATAAAATTCACCTTGCGAGTTTGTT 14 220 0 TAATTCATTG 0.820828 -38 * ** **** *** Masking position 7 Map Score: 1.23519 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 150 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ACTATACATTCGGCGGGCCAGTTTAGCACAA 1 42 0 CGGCGGGCAG 0.975474 -59 TAGTACACTTCGGTTGGATAGGTAATTTGGC 1 69 1 CGGTTGGTAG 0.896762 -32 TCTTGTTTATCAGCGTGTTAGATAAGCCTGG 6 20 1 CAGCGTGTAG 0.879273 -182 GTTTCAGTAGCAACGGGTTAGCTTTAAGGAA 6 152 1 CAACGGGTAG 0.964522 -50 AACGGCCTCCCGATAGGGAAGCCGTAGCAAA 8 62 0 CGATAGGAAG 0.807907 -136 TAGCTTGCGTCAATGGGCAAGGTGGGCTTGC 9 79 0 CAATGGGAAG 0.95747 -170 CCTTCGTTCACAGTGGGGAAGTTTTCGGATC 10 229 1 CAGTGGGAAG 0.978946 -40 ******* *** Masking position 10 Map Score: 0.148269 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 290 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 ACCCGGTTCAGAGTAGCATGTTTCTACCTT 2 39 1 GAGTAGCATG 0.978421 -49 GCTCGTACATGAGCAGCTTGTGTGGCTCCT 5 236 1 GAGCAGCTTG 0.985942 -65 ACTGAAACGAGAGTAGCTTGCGTCAATGGG 9 93 0 GAGTAGCTTG 0.978421 -156 CCATGACGAGGAGCTGCACG 10 259 1 GAGCTGCACG 0.942135 -10 ********** Masking position 2 Map Score: 0.140684 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 41 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 GTTAAAACTCCAGATAGCTAACGAATC 2 71 0 ACTCCAGAAG 0.875482 -17 GTTGAGACTTCCTTCAGACGACGCATACAGG 3 81 0 CCTTCAGAGA 0.774963 -137 GTAATGCCATCGACCAGAAAGGTGGCATATG 4 141 1 CGACCAGAAG 0.805108 -125 TGAACCCCTCCAGACAGAAAAGACAAA 6 185 0 CCTCCAGAAG 0.981826 -17 AAAAAAACGGCCTCCCGATAGGGAAGCCGTA 8 67 0 CCTCCCGAAG 0.981371 -131 AATAAAAAAGGCACCCGAAGGTGCCTGAGGT 10 50 0 GCACCCGAGG 0.926542 -219 ACCACCACATAACTATGGAGCA 11 2 1 CCACCACAAA 0.677758 -28 ATTCTCTGCTCCTGATGAGGGCGCTAA 13 8 1 GCTCCTGAGA 0.75605 -20 GGTAACCTCCCGAGGAAAAGAGTATG 15 68 0 CCTCCCGAGA 0.972065 -16 ******** ** Masking position 8 Map Score: 1.20092 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 599 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826