AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_ecoli_reg_100.orf -o00450_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 selD 116 selenophosphate synthase, H(2)Se added to acrylyl-tRNA #2 metG 101 methionine tRNA synthetase #3 cysK 184 cysteine synthase A, O-acetylserine sulfhydrolase A #4 yfeK 104 orf, hypothetical protein #5 b2420 32 orf, hypothetical protein #6 cysM 23 cysteine synthase B, O-acetylserine sulfhydrolase B #7 BIME116 74 BIME #8 cysW 300 sulfate transport system permease W protein #9 cysD 251 ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 #10 cysJ 300 sulfite reductase (NADPH), flavoprotein beta subunit #11 metK 55 methionine adenosyltransferase 1 (AdoMet synthetase); methyl and propylamine donor, corepressor of met genes #12 metC 103 cystathionine beta-lyase (beta-cystathionase) #13 ggt 119 gamma-glutamyltranspeptidase #14 selA 97 selenocysteine synthase: L-seryl-tRNA (Ser) selenium transferase #15 yibF 227 putative S-transferase #16 metB 276 cystathionine gamma-synthase Motif number 1 GAATTCCTGCGCCTTTGCTCACAATCCAGACAGTTTCGCGACAAT 1 13 0 GCTCCACGTT 0.979986 -104 GGCCTGTCCTTAACTGTATGAAATTGGGATACAACA 3 159 0 GCTCACAGTG 0.966883 -26 ATGGCGTGCAGCATGTCCGGATCGGCCAGATTCTGTAAAACCGGC 8 37 0 GCTCTCCGTG 0.939159 -264 ACGGCAATCAGCGCGATCATCACCGTCAGCCAGATGGCGTGCAGC 8 70 0 GCCCACCGAT 0.92938 -231 AAGTTAAAGCGCGTCACCAGCCAGGCCAGCAGAATGCCGAACACC 8 127 0 GCTCCACGAT 0.901849 -174 CTGGTGACGCGCTTTAACTTCCCTGGACGCCAGTTACTGCTGACG 8 152 1 GCTCCCAGTT 0.992916 -149 CTGTTCTACGGCTCTAACGGCCCGCTCGGCGGTTGGCTCGACGAG 8 251 1 GCCCCCCGTG 0.986169 -50 CGAAAAAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCG 10 7 0 GCTCACAGTT 0.984483 -294 TCTTCAGGATGCGCCCGCGAATATTCATGCTAGTTTAGACATCCA 12 44 1 GCCCTAAGTT 0.878284 -60 GCTGATCAAGGCCCTCTCACACGGAGAAGGGCGTTTAACATAACC 14 53 0 GCCCCGAGTT 0.942883 -45 GCCCTTTTTCCCATCACCAGGCCATACTGATATTTTTCCTCGCAC 15 181 1 CCTCCCCGTT 0.938907 -47 TCACGGTAACGCCTGTACGGTAAACTATGCGGGTTTACGGTCAGT 16 69 0 GCTCAAAGTT 0.948016 -208 AAAATTATATGCATTATCACGCCGACAGGTGCATTACACGATGTC 16 112 0 GCTCCCAGTT 0.992916 -165 TTTGGGATTTGCTCAATCTATACGCAAAGAAGTTTAGATGTCCAG 16 165 1 GCCCACAGTT 0.982966 -112 ** * * ** * * ** Masking position 8 Map Score: 18.2253 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 588 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 TAATTGTCGCGAAACTGTCTGGATTGTGAGC 1 9 1 GCACTGTCTG 0.860656 -108 ATATTCTTCAGGTAAACTATCAGCTG 2 4 0 GGACTATCAG 0.918694 -98 ACCGTTTGTGTGAAACAGGGGTGGCTTATGCCG 3 33 1 TGCAGGGGTG 0.507966 -152 CATGCAAGATGGAATAAGGGGCGGCATAAGCCA 3 54 0 GGAAGGGGCG 0.869624 -131 AGTTTCGGTTGGATTACGATGAGGATCATCGGC 4 27 0 GGACGATGAG 0.899712 -78 CCAGATGGCGTGCAGCATGTCCGGATCGGCCAG 8 53 0 TGCATGTCCG 0.609245 -248 CACGCCATCTGGCTGACGGTGATGATCGCGCTG 8 74 1 GGACGGTGAT 0.689585 -227 TCGGCATTCTGCTGGCCTGGCTGGTGACGCGCT 8 132 1 GCCCTGGCTG 0.791405 -169 TATCGCCGGTGGTTGCCGGTCTGGTGTATTTGC 8 219 1 GGCCGGTCTG 0.982113 -82 AGGTTAACGGGGCAAACGGTGTGGATTAAAGAC 10 207 0 GGACGGTGTG 0.97144 -94 AAGCTGTTTCTGCGCCCTGTCAGCGCCCATAAA 10 255 0 TGCCTGTCAG 0.87809 -46 AGGAAACCTGGCTGATCAAGGCCC 14 84 0 GGCCTGGCTG 0.96339 -14 CCTGGTGATGGGAAAAAGGGCAGAAAATGTTGA 15 169 0 GGAAGGGCAG 0.950622 -59 CTTTGTGCGAGGAAAAATATCAGTATGGCCTGG 15 197 0 GGAATATCAG 0.796134 -31 AAACTATGCGGGTTTACGGTCAGTACCCACATC 16 60 0 GGACGGTCAG 0.987802 -217 ACGCCTGTACGGTAAACTATGCGGGTTTACGGT 16 73 0 GGACTATGCG 0.796533 -204 GGGCTTTGTCGGTGAAATGTCAGGCACCAGAGT 16 239 0 GGAATGTCAG 0.951218 -38 ** ******** Masking position 13 Map Score: 12.7215 Number of sites scoring better than the average of aligned sites = 3449 Number in coding regions = 3257 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 3 ATGAAATTGGGATACAACAGGTAGCATACC 3 148 0 GATACAACAG 0.960584 -37 AATCGGCTATCACAAAACAAGGATAAGGTA 4 80 1 CACAAAACAA 0.797623 -25 CTGCCGCTGCGCTAAAACAATTTCAAATCT 9 60 1 GCTAAAACAA 0.857889 -192 CGATAAAACCGCCGTAGAGTA 10 2 1 GATAAAACCG 0.922828 -299 TAGATAATGCGAAAAAACAGCCTTTCCGGT 10 31 0 GAAAAAACAG 0.909174 -270 CAATCATTAAGATAAATCAGCGATTTTGCG 10 75 0 GATAAATCAG 0.899344 -226 AAAGACTATTGCTAAAACAGGTTAGTCGAT 10 153 1 GCTAAAACAG 0.960584 -148 TGTCAGCGCCCATAAAACAGAAGAGAAGGT 10 241 0 CATAAAACAG 0.973687 -60 AGAAAATCCACACAACAGTTTGAGCTAA 11 9 1 CACACAACAG 0.859287 -47 GAAGAATTGGCATAAAGCAGAAAATTTTCG 12 19 0 CATAAAGCAG 0.885283 -85 CAAATAACCCGATAAAACAAGGATGAGAA 15 10 0 GATAAAACAA 0.940224 -218 ********** Masking position 6 Map Score: 9.51415 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 386 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 TTGAGTGAATGTTAAACGCCCGGAGGCGCT 7 15 1 GTTAAACGCC 0.957625 -60 TCAGCCCCTTGCTGAATGCCTGCAC 8 6 0 GCTGAATGCC 0.98998 -295 ATCCGGACATGCTGCACGCCATCTGGCTGA 8 60 1 GCTGCACGCC 0.987306 -241 TGATGATCGCGCTGATTGCCGTACCGGTAA 8 93 1 GCTGATTGCC 0.946531 -208 AGCCAGGCCAGCAGAATGCCGAACACCAGG 8 124 0 GCAGAATGCC 0.946542 -177 CTTTAACTTCCCTGGACGCCAGTTACTGCT 8 163 1 CCTGGACGCC 0.964933 -138 TTCAAATCTTCCTAAACGCCCGAAATCCGG 9 81 1 CCTAAACGCC 0.972189 -171 CCGTGGTTATGTTAAACGCCCTTCTCCGTG 14 49 1 GTTAAACGCC 0.957625 -49 ********** Masking position 8 Map Score: 8.96362 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 648 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 TGCGCCTTTGCTCACAATCCAGACAGTTTC 1 21 0 CTCACAATCC 0.749904 -96 GGTATGGTAACCCTCATTCCGTGAAGTGAT 1 72 0 CCCTCATTCC 0.931389 -45 CTTATGCCGCCCCTTATTCCATCTTGCATG 3 57 1 CCCTTATTCC 0.921376 -128 GATGATCCTCATCGTAATCCAACCGAAACT 4 30 1 ATCGTAATCC 0.8695 -75 GATCTCTATCCATACGTGGTG 6 13 0 ATCTCTATCC 0.644378 -11 GGAGGCGCTTCCCGCGATCCGGGCTTTTTA 7 36 1 CCCGCGATCC 0.956189 -39 GATTGCCGTACCGGTAAACCTGGTGTTCGG 8 106 1 CCGGTAAACC 0.716501 -195 TTCCTAAACGCCCGAAATCCGGTGCCTTAA 9 89 1 CCCGAAATCC 0.93528 -163 GTTATTAGTTATCGCTATCCCGTCTTTAAT 10 186 1 ATCGCTATCC 0.800123 -115 CACCGTTTGCCCCGTTAACCTTACCTTCTC 10 219 1 CCCGTTAACC 0.930688 -82 CTGGGGTTGCCCCTTAATCTCTGGAGAATA 13 97 1 CCCTTAATCT 0.706245 -23 ACATTTTCTGCCCTTTTTCCCATCACCAGG 15 172 1 CCCTTTTTCC 0.858716 -56 GTGGGTACTGACCGTAAACCCGCATAGTTT 16 63 1 ACCGTAAACC 0.881541 -214 ********** Masking position 9 Map Score: 5.123 Number of sites scoring better than the average of aligned sites = 1244 Number in coding regions = 1124 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 6 CCGGATCGCGGGAAGCGCCTCCGGGCGTTT 7 28 0 GGAAGCGCCT 0.985604 -47 CAATTCTTCAGGATGCGCCCGCGAATATTC 12 40 1 GGATGCGCCC 0.977022 -64 GCTTAGCTGGGGTTGCCCCTTAATCTCTGG 13 91 1 GGTTGCCCCT 0.975587 -29 AAATCTGTAGGGTTTCGCCTGTCAGCAGAC 15 39 0 GGTTTCGCCT 0.972575 -189 ACGATGTCACGGTAACGCCTGTACGGTAAA 16 90 0 GGTAACGCCT 0.961164 -187 ********** Masking position 6 Map Score: 2.20739 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 99 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TCTACCGGTTATTTTGTAAACCGTTTGTGTGA 3 14 1 ATTTGTAAAC 0.915336 -171 GGAAGTAAGGATTTAGCATATCTATATACAGA 3 100 0 ATTAGCATAC 0.871764 -85 GGCGTTTAACATTCACTCAACCTA 7 3 0 ATTACTCAAC 0.797403 -72 GATCGGCCAGATTCTGTAAAACCGGCATCAGC 8 31 0 ATTTGTAAAC 0.915404 -270 CGGAATAACGATTTGGCAAAGCTAATATCAAA 9 125 0 ATTGGCAAAC 0.936797 -127 GTTTTTTCGCATTATCTAAAACGACTTTGTTG 10 43 1 ATTTCTAAAC 0.827634 -258 AAACAAATGAATTTAGCCAATCATTAAGATAA 10 90 0 ATTAGCCAAC 0.954055 -211 AGCGATAACTAATAACCAAATCGACTAACCTG 10 170 0 AATACCAAAC 0.771757 -131 GTTATGTTCCAGTAAGCAAAGCTGTTTCTGCG 10 274 0 AGTAGCAAAC 0.918667 -27 TTGCGTATAGATTGAGCAAATCCCAAATAGCC 16 160 0 ATTAGCAAAC 0.979732 -117 *** ****** * Masking position 3 Map Score: 3.69833 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 181 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 ACCTGAAGAATATAGAGAAGTACTTACTTAACA 2 24 1 TATGAAGTAC 0.960998 -78 CCCTTTTCACTATTAAGAAGTAATGCCTACT 2 81 1 TATGAAGTAA 0.973416 -21 AGCATATCTATATACAGAAGGGAAATAATGACA 3 85 0 TATGAAGGGA 0.943119 -100 GCTCAGAGAATATGCGGAAGTAAGGATTTAGCA 3 114 0 TATGAAGTAA 0.973416 -71 GCAAAGCTAATATCAAAAAGTGCTTAAGGCACC 9 109 0 TATAAAGTGC 0.818942 -143 AAAATAGCGGTATTGCAAAGGAACGGTT 9 234 1 TATAAAGGAA 0.870494 -18 ATATGTGATTTATTTGGAAGTAACAAACCATCA 15 139 1 TATGAAGTAA 0.973416 -89 *** ******* Masking position 8 Map Score: 1.94126 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 26 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 GGACATCTCCTGTCAATGCAATCCG 1 102 0 TCTCCTGTCA 0.945661 -15 TTAATTTTTTCTCCTTGCCGATGATCCTC 4 10 1 TCTCCTTGCC 0.943892 -95 TGTTCGGCATTCTGCTGGCCTGGCTGGTGA 8 129 1 TCTGCTGGCC 0.990888 -172 AGTCGAAACATCTGATGGCAAGAAAATAGC 9 212 1 TCTGATGGCA 0.914513 -40 CGCGATATGTCCTCCTGACCCATCTCACGT 14 13 1 CCTCCTGACC 0.946372 -85 GGGTTATTTGTCTGCTGACAGGCGAAACCC 15 30 1 TCTGCTGACA 0.96844 -198 ********** Masking position 6 Map Score: 1.26873 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 479 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 CAATCTACCGGTTATTTTGTAAACC 3 2 1 ATCTAGGTAT 0.967484 -183 AATTTGCAGGTTATGCTCGTCGAG 8 287 0 ATTTGGGTAT 0.980728 -14 GCGGTAAAAAAATTTGCATGGTATTTAAGGACTC 9 14 0 ATTTGTGTAT 0.868432 -238 GAAGCGAGTAAACTTAAAGGATATCTTCAGAGGA 13 20 0 ACTTAGGTAT 0.883468 -100 CTTTCTTATAAATCTGTAGGGTTTCGCCTGTCAG 15 44 0 ATCTGGGTTT 0.927314 -184 TAATTATTTCACTCTGATGGATATCTCACTTCAG 15 79 0 ATCTGGGTAT 0.983988 -149 AATGCATATAATTTTAACGGCTATTTGGGATTTG 16 142 1 ATTTAGGTAT 0.960997 -135 * **** ** *** Masking position 1 Map Score: 0.831339 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 85 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 GATACAACAGGTAGCATACCCGCTCAGAGA 3 138 0 GTAGCATACC 0.916817 -47 AGGTTACAAACCTTGCCATTAA 7 63 0 GTTACAAACC 0.980431 -12 TTAATTCAGAGTTATATACCAGGCTTAGCT 13 69 1 GTTATATACC 0.858349 -51 CCCATCTCACGTTACAATCCGTGGTTATGT 14 31 1 GTTACAATCC 0.938516 -67 TTATTTGGAAGTAACAAACCATCAACATTT 15 148 1 GTAACAAACC 0.97226 -80 ********** Masking position 6 Map Score: 0.258626 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 40 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 TGAATTACCTTATCCTTGTTTTGTGATAG 4 86 0 CTATCCTTGT 0.975291 -19 CAGCAAGGGGCTGATGCCGGTTTTACAGAAT 8 22 1 CTATGCCGGT 0.890105 -279 AAAGCTGTTTCTGCGCCCTGTCAGCGCCCAT 10 258 0 CTCGCCCTGT 0.966981 -43 GCAACCCCAGCTAAGCCTGGTATATAACTCT 13 76 0 CTAGCCTGGT 0.964433 -44 GTTAAACGCCCTTCTCCGTGTGAGAGGGCCT 14 59 1 CTCTCCGTGT 0.950483 -39 TTCTCATCCTTGTTTTATCGGGT 15 3 1 CTATCCTTGT 0.975291 -225 ** ******** Masking position 2 Map Score: 0.206263 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 99 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 ********** No masking Map Score: 4.00279e-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 14 ********** No masking Map Score: 4.00279e-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 15 ********** No masking Map Score: 4.00279e-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