AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -itrpR_bsub_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 cysK 75 cysteine synthetase A #10 pabB 166 para-aminobenzoate synthase (subunit A) #11 trpE 215 anthranilate synthase #12 aroB 61 3-dehydroquinate synthase #13 aroF 69 chorismate synthase #14 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #15 ndk 115 nucleoside diphosphate kinase #16 gerCA 162 heptaprenyl diphosphate synthase component I #17 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #18 mtrA 187 GTP cyclohydrolase I #19 hbs 300 non-specific DNA-binding protein HBsu Motif number 1 ATAACAGGTGGGAGATGAGAGGA 1 288 1 GGGATGAAGA 0.878682 -13 AATTTCTTCTGGCGAAGATGGGAATATATGAAT 2 28 1 GGGAAGAGGA 0.976689 -57 GGGTTGAAAGTGTTAGGATATGAATATCTTTAA 4 53 1 TGTAGGAAGA 0.805119 -51 ACCTGCTCATTGTGAGGAGGACATT 4 89 1 TGGAGGAGCA 0.979625 -15 GTGCTTACTGTGGGAGGAGGTAAGGA 5 82 1 TGGAGGAGAA 0.983049 -16 GAAGATGGCATGAGAGGATAAAATACTATATAA 11 163 0 TGGAGGAAAA 0.958412 -53 GCAAGGAGAATGAGAAGATGGCATGAGAGGATA 11 176 0 TGGAAGAGCA 0.961937 -40 GAGAAAATGTGGAGAATATGAGAAAACTGTCGA 12 29 1 GGGAATAGGA 0.750387 -33 AAAGCGTTAATGCGATGAAGGGAGAAGAAGTC 13 48 1 TGGATGAGGA 0.973049 -22 GGGGCTTTTCTGTGAAGAAATAAAGTGTATGTA 18 42 0 TGGAAGAAAA 0.923762 -146 CAGAAAAAAATGAGAGCAAGTAAGAGAAAGACA 19 196 0 TGGAGCAGAA 0.860481 -105 CAGACTGAACTGTGAAGAAATGATAATAAACGA 19 244 1 TGGAAGAAGA 0.970571 -57 TGTATCCTTTTGGGAGGAGGTGAAAGGC 19 283 1 TGGAGGAGGA 0.993705 -18 ** ***** * ** Masking position 8 Map Score: 16.566 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 209 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 TCTTGCAGAAGCCGATTTTTTTCATTTTTAG 1 130 1 GCGATTTTTT 0.967356 -171 CTCACAATGAGCAGGTATTTTAAAGATATTC 4 74 0 GCGGTATTTT 0.894556 -30 GCGTCAGCCGGCAGTTTTTTTAGAAAGAAAG 6 15 0 GCGTTTTTTT 0.987797 -180 GCTGACGCTGGCAGTTTTTTTATGTAAATGA 6 38 1 GCGTTTTTTT 0.987797 -157 CACTTCCTACGCGGTTTCTTTCATAAATCAA 7 49 0 GCGTTTCTTT 0.938439 -37 GCTCTTTAGCGGGTTTTTAATTTGAGAAA 8 9 1 GCGGTTTTTA 0.903799 -38 CGGTTCGCCGGGAGTTTTTTTATATTTCGTG 10 27 1 GGGTTTTTTT 0.904335 -140 ATATAACGCCGCCGGTTTTTGTTCTGTTTTG 14 43 1 GCGGTTTTTG 0.932996 -194 CAGCTGAAAAGCTGATTTTTTTATTGAAACA 14 152 1 GCGATTTTTT 0.967356 -85 TCCCAGTCTCGCTGTCTTTTTGTCCTAGTAT 14 208 0 GCGTCTTTTT 0.938439 -29 TCCTCAGAGTGCAGTTTTTCTTAAAAAGCCG 19 159 1 GCGTTTTTCT 0.938439 -142 ** ******** Masking position 9 Map Score: 16.0755 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 294 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 ATGGTGCAAACTGCAGAGCCTATGCT 4 7 1 CAAACTGCAG 0.959978 -97 ATCTCGGAAGCAGGCTGCCGA 5 2 0 CAGGCTGCCG 0.906661 -96 TCTTTCTAAAAAAACTGCCGGCTGACGCTG 6 18 1 AAAACTGCCG 0.989059 -177 TTTACATAAAAAAACTGCCAGCGTCAGCCG 6 36 0 AAAACTGCCA 0.939857 -159 GATGATTGTAAAAGCCGCAGCTGAGCCAAT 6 68 0 AAAGCCGCAG 0.849606 -127 AAAAAGCCAAAACTCCCGGTTCGCCGGG 10 9 1 AAAACTCCCG 0.951048 -158 GAAATATAAAAAAACTCCCGGCGAACCGGG 10 25 0 AAAACTCCCG 0.951048 -142 AGAATATGAGAAAACTGTCGAGGGAATTTT 12 41 1 AAAACTGTCG 0.866421 -21 GGCAACATATAACGCCGCCGGTTTTTGTTC 14 37 1 AACGCCGCCG 0.916457 -200 AGGTCTGATGCACACTGCCATTCAACCCTT 14 98 0 CACACTGCCA 0.889526 -139 TATAGGCTTTCACACTGCACACCGAAATCG 15 71 0 CACACTGCAC 0.800686 -45 CTTTTTAAGAAAAACTGCACTCTGAGGAAT 19 157 0 AAAACTGCAC 0.88632 -144 ********** Masking position 2 Map Score: 10.649 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 923 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 4 TCATCCTAACAAATCGGTTTCTCTTGCAGA 1 109 1 AAATCGGTTT 0.760511 -192 AAAATGAAAAAAATCGGCTTCTGCAAGAGA 1 128 0 AAATCGGCTT 0.954348 -173 ATACATTGCGTAAACAGCTTGGTAAAGGGG 3 58 1 TAAACAGCTT 0.753716 -31 TCTTAACCCTAAAAGGGCTGGAATTGATTT 7 26 1 AAAAGGGCTG 0.94263 -60 TAATTTGAGAAAAGGGGCTGAAAGCAGGT 8 28 1 AAAGGGGCTG 0.952019 -19 TTAAAGTGAATAAAGGGTTGAATGGCAGTG 14 86 1 TAAAGGGTTG 0.598791 -151 CAACGATCTAAAATCAGCTGAAAAGCTGAT 14 138 1 AAATCAGCTG 0.829182 -99 TTCAATAAAAAAATCAGCTTTTCAGCTGAT 14 150 0 AAATCAGCTT 0.83846 -87 AGCCCCTTAGAAAGGGGCTTTTCTGTGAAG 18 58 0 AAAGGGGCTT 0.954986 -130 AGCCCCTTTCTAAGGGGCTTTTCATATTTC 18 69 1 TAAGGGGCTT 0.925977 -119 GAAAGACAATTAAACGGCTTTTTAAGAAAA 19 174 0 TAAACGGCTT 0.925116 -127 ********** Masking position 3 Map Score: 9.64241 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 869 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 GTTGTTAGTGAAAAAAGTGAATTTCTCTTCCA 10 94 0 AAAAGTGAAT 0.983489 -73 AAAGGTTTACATTAAAGTGAATAAAGGGTTGA 14 75 1 AAAAGTGAAT 0.983078 -162 TTGTTTTATCAGGAAATTGTATTGTTTCAATA 14 173 0 AAAATTGTAT 0.770768 -64 AGATTAAGAAATAAATGTGAATTTGGGGACAA 16 130 1 AAATGTGAAT 0.925177 -33 TCTGTGAAGAAATAAAGTGTATGTAAGCTAGA 18 35 0 AAAAGTGTAT 0.962842 -153 CCCCGCTAAAAGCAAAGTGAATGCCCTGTCAG 18 114 0 AAAAGTGAAT 0.983496 -74 ATGTTTGTCCAACAAAGTGAAGAATTTCTGTA 19 127 0 AAAAGTGAAG 0.948285 -174 * ********* Masking position 5 Map Score: 6.03224 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 34 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ATCGGCTTCTGCAAGAGAAACCGATTTGTT 1 116 0 GCAAGAGAAA 0.881755 -185 TAAAAAGTAAAGTAGAGAAACTATTCAAAA 6 162 1 AGTAGAGAAA 0.922103 -33 TGTTATTCTTGGAAGAGAAATTCACTTTTT 10 85 1 GGAAGAGAAA 0.974867 -82 AAGCAATGTTGTTAGTGAAAAAAGTGAATT 10 103 0 GTTAGTGAAA 0.834988 -64 AATGAGTTGAGTTAGAGAATAGGGTAGCAG 11 61 1 GTTAGAGAAT 0.89039 -155 AGAATAGGGTAGCAGAGAATGAGTTTAGTT 11 76 1 AGCAGAGAAT 0.760354 -140 AATTGACCGCATTAGAGAAAATGTGGAGAA 12 15 1 ATTAGAGAAA 0.834757 -47 ATCAATCCGGGGCGGAGAAATTTCTTAATA 15 21 0 GGCGGAGAAA 0.952698 -95 ATAATGATGGGGTGGAGAAT 15 106 1 GGTGGAGAAT 0.922613 -10 ATGAGAGCAAGTAAGAGAAAGACAATTAAA 19 190 0 GTAAGAGAAA 0.943031 -111 CCTTTTGGGAGGAGGTGAAAGGC 19 288 1 GGAGGTGAAA 0.85771 -13 ********** Masking position 8 Map Score: 7.54055 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 476 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 7 TATTGTTACCTTCTTTTGACAAAATCCTAT 1 226 1 TTCTTTTGAC 0.908298 -75 TAAATCAAATTTCTTCTGGCGAAGATGGGA 2 21 1 TTCTTCTGGC 0.96649 -64 AAAGAAAGACTTCTTTTGGGTAGAATAAAC 11 121 0 TTCTTTTGGG 0.984621 -95 AAAGAAGTCTTTCTTTTGGGTTTATTTGTT 11 135 1 TTCTTTTGGG 0.984621 -81 TGCTCTCACTCCTTATGGCAAGGAGAATG 11 197 0 TCCTTATGGC 0.941527 -19 ACTGAATGTATCCTTTTGGGAGGAGGTGAA 19 277 1 TCCTTTTGGG 0.981504 -24 ********** Masking position 5 Map Score: 4.67021 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 86 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TTTCTAAAAAAACTGCCGGCTGACGCTGGC 6 20 1 AACTGCCGGC 0.995715 -175 TACATAAAAAAACTGCCAGCGTCAGCCGGC 6 34 0 AACTGCCAGC 0.978111 -161 AAAAAGCCAAAACTCCCGGTTCGCCGGGAG 10 11 1 AACTCCCGGT 0.968363 -156 AATATAAAAAAACTCCCGGCGAACCGGGAG 10 23 0 AACTCCCGGC 0.993788 -144 ACAGAACAAAAACCGGCGGCGTTATATGTT 14 40 0 AACCGGCGGC 0.96756 -197 ********** Masking position 2 Map Score: 4.50898 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 79 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 TCTAAAAATGAAAAAAATCGGCTTCTGCAAGAG 1 129 0 AAAAAAGGCT 0.775055 -172 TGCTTTCGCTATAATGACAGGCAACGAATATAA 1 259 1 AAATGAGGCA 0.886464 -42 GCCGGGTACGACAATCAAAGGCAAGTGGAATGG 3 17 1 AAATCAGGCA 0.938083 -72 CAAGCAAAGAAGAAGCATAGGCTCTGCAGTTTG 4 17 0 AAAGCAGGCT 0.989834 -87 TTTTTTTATGTAAATGATTGGCTCAGCTGCGGC 6 52 1 TAATGAGGCT 0.799933 -143 AATACCATACACGATCAGCGGCTCATTTGTAAA 6 117 0 AGATCAGGCT 0.974518 -78 CTATACATACATAATGATGGGGTGGAGAAT 15 96 1 AAATGAGGGT 0.802945 -20 CCCCGCTGTTAAAAGCAAATGCTCGCAAACAGC 16 20 1 AAAGCATGCT 0.884693 -143 TAGCATAAAAAAAAGAATTGGCTGTATCCTCCC 16 53 0 AAAGAAGGCT 0.95703 -110 TTCATATTTCAAGAGCATGGGCTTCCTGACAGG 18 89 1 AGAGCAGGCT 0.983868 -99 TAAATCCTTGACGAGCAAGGGATTGACGCTTTA 19 56 1 AGAGCAGGAT 0.841981 -245 * ***** **** Masking position 7 Map Score: 4.71332 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 579 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 ATGGTGCAAACTGCAGAGCCTATGCTTCTT 4 11 1 CTGCAGAGCC 0.975677 -93 GTAAAAGCCGCAGCTGAGCCAATCATTTAC 6 61 0 CAGCTGAGCC 0.911416 -134 GATTTGTTTACAAATGAGCCGCTGATCGTG 6 111 1 CAAATGAGCC 0.863924 -84 TGAAAATAAGCAACAGAGCCGGCAACATAT 14 17 1 CAACAGAGCC 0.943091 -220 CTAAAATCAGCTGAAAAGCTGATTTTTTTA 14 145 1 CTGAAAAGCT 0.787375 -92 TATTTCTTCACAGAAAAGCCCCTTTCTAAG 18 53 1 CAGAAAAGCC 0.968414 -135 CTCTTGAAATATGAAAAGCCCCTTAGAAAG 18 74 0 ATGAAAAGCC 0.896263 -114 AGTAACACATATAAAAAGCCATATCAAGCA 19 92 0 ATAAAAAGCC 0.814728 -209 GCAGTTTTTCTTAAAAAGCCGTTTAATTGT 19 169 1 TTAAAAAGCC 0.713779 -132 ********** Masking position 7 Map Score: 3.62115 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 693 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 AAAGAAGGTAACAATACCAAAGAAATCTTC 1 212 0 ACAATACCAA 0.872635 -89 TCCATTGGCCCCTTTACCAAGCTGTTTACG 3 66 0 CCTTTACCAA 0.842818 -23 GAAAATCATTCCAATACAAACAATAACCAT 5 30 0 CCAATACAAA 0.962042 -68 CAAACATTCTACAATACCATACACGATCAG 6 132 0 ACAATACCAT 0.782326 -63 TACTAAACCTCCTATACACTTCCTACGCGG 7 66 0 CCTATACACT 0.741347 -20 ATACATAATACCAATACAAATAGTCGGAAA 9 42 1 CCAATACAAA 0.962042 -34 TTAATGTAAACCTTTACAAAACAGAACAAA 14 60 0 CCTTTACAAA 0.86668 -177 TTTTATTGAAACAATACAATTTCCTGATAA 14 170 1 ACAATACAAT 0.813337 -67 AGTGTGAAAGCCTATACATACATAATGATG 15 85 1 CCTATACATA 0.786624 -31 ********** Masking position 5 Map Score: 3.24764 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 167 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 TATTCTCCAGGAGGAATGAAT 2 74 1 GAGGAATGAT 0.967393 -11 TCAAAGGCAAGTGGAATGGAAACACTTATAC 3 31 1 GTGGAATGAA 0.920178 -58 ATTGTTTGTATTGGAATGATTTTCTATGGTA 5 36 1 TTGGAATGTT 0.871561 -62 GTATGGTATTGTAGAATGTTTGTAAAAAGTA 6 140 1 GTAGAATGTT 0.890029 -55 CTTTTAGGGTTAAGAATGGATCAACGATGT 7 10 0 TAAGAATGAT 0.649261 -76 CCATGTCTGCGACGAATGTTATTCTTGGAAG 10 69 1 GACGAATGTA 0.871833 -98 AAAGAAAATAGAGGAATGATACAA 10 153 1 GAGGAATGTA 0.967392 -14 ACTGCACTCTGAGGAATGTTTGTCCAACAAA 19 143 0 GAGGAATGTT 0.979421 -158 ******** ** Masking position 6 Map Score: 2.67427 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 162 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 13 CCCGTACGGGATTCGAACCCGTGTTACCGC 1 79 0 ATTCGAACCC 0.881981 -222 TATCCTAACACTTTCAACCCCTCCAAGCAA 4 43 0 CTTTCAACCC 0.982118 -61 TCATAAATCAATTCCAGCCCTTTTAGGGTT 7 30 0 ATTCCAGCCC 0.965992 -56 ACCTGCTTTCAGCCCCTTTTCTCAA 8 32 0 CTTTCAGCCC 0.983413 -15 TGCACACTGCCATTCAACCCTTTATTCACT 14 90 0 CATTCAACCC 0.94348 -147 ********** Masking position 6 Map Score: 0.484015 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 39 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 CGCTTCCGTATAAATCAAATTTCTTCTGG 2 10 1 ATAAATCAAA 0.389099 -75 GGTTTCTTTCATAAATCAATTCCAGCCCTT 7 38 0 ATAAATCAAT 0.833621 -48 GTTTTTAATTGTAAAGCAATGTTGTTAGTG 10 116 0 GTAAAGCAAT 0.91754 -51 AAGAGTGTGTATAAAGCAATTAGAATGAGT 11 38 1 ATAAAGCAAT 0.94671 -178 TATTGTTTCAATAAAAAAATCAGCTTTTCA 14 156 0 ATAAAAAAAT 0.596503 -81 TTTTGTAGATATTAAGAAATTTCTCCGCCC 15 12 1 ATTAAGAAAT 0.874057 -104 CTTTCTGATAATTAATCAATCCGGGGCGGA 15 35 0 ATTAATCAAT 0.722399 -81 TCATACATAGATTAAGAAATAAATGTGAAT 16 122 1 ATTAAGAAAT 0.874057 -41 GGGCTTTTCTGTGAAGAAATAAAGTGTATG 18 44 0 GTGAAGAAAT 0.824416 -144 GTTACTCTACATACAGAAATTCTTCACTTT 19 116 1 ATACAGAAAT 0.713719 -185 AGACTGAACTGTGAAGAAATGATAATAAAC 19 245 1 GTGAAGAAAT 0.824416 -56 ********** Masking position 5 Map Score: 2.58142 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 498 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 15 AGCCGATTTTTTTCATTTTTAGACAACATT 1 139 1 TTTCATTTTT 0.955177 -162 GTTTCTCTACTTTACTTTTTACAAACATTC 6 153 0 TTTACTTTTT 0.748987 -42 ATTCCTCTATTTTCTTTTTTACTTGTTTTT 10 140 0 TTTCTTTTTT 0.936995 -27 GATACAGCCAATTCTTTTTTTTATGCTATA 16 58 1 ATTCTTTTTT 0.755351 -105 CTAAGGGGCTTTTCATATTTCAAGAGCATG 18 78 1 TTTCATATTT 0.815637 -110 TATTCCTTTTTTTCCTTTTTTCATCC 19 7 0 TTTCCTTTTT 0.95834 -294 TCTTACTTGCTCTCATTTTTTTCTGAGACA 19 204 1 TCTCATTTTT 0.867673 -97 ********** Masking position 6 Map Score: 0.868773 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 508 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987