AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -irpoH_ctra_opreg_100.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 groEL_1 37 HSP-60 #2 groES 171 10KDa Chaperonin #3 clpB 300 Clp Protease ATPase #4 clpC 264 ClpC Protease ATPase #5 dnaJ 28 Heat Shock Protein J #6 rs21 196 S21 Ribosomal Protein #7 lon 300 Lon ATP-dependent protease #8 proS 200 Prolyl tRNA Synthetase #9 hrcA 68 HTH Transcriptional Repressor #10 dnaK 25 HSP-70 #11 gapA 43 Glyceraldehyde-3-P Dehydrogenase #12 rs11 21 S11 Ribosomal Protein #13 rs13 55 S13 Ribosomal Protein #14 secY 22 Translocase #15 rl18 21 L18 Ribosomal Protein #16 rl6 27 L6 Ribosomal Protein #17 rl16 32 L16 Ribosomal Protein #18 rl2 23 L2 Ribosomal Protein #19 rl3 300 L3 Ribosomal Protein #20 rpoD 148 RNA Polymerase Sigma-66 #21 clpP_2 166 CLP Protease #22 CT793 62 hypothetical protein #23 ftsH 160 ATP-dependent zinc protease Motif number 1 TACAGTCAATAAAAGAGCTAAGATCATTTGATCACAGA 3 168 0 AAAAACTATT 0.902501 -133 AAAAAATCTTTGTTAGTGGTGTTTCGTC 5 3 1 AAAACTTAGT 0.89877 -26 TATAACCGTTAAAACCGTTTTAATTCAAAAATTAATTC 7 36 1 AAAACTTATA 0.799935 -265 ACTTTACTAAAAAAGCTCATTTATAATTCGATAAATAA 7 95 1 AAAACCAATT 0.937407 -206 GAAGTTGAATAGAAAAACTGTTATTTATCGAATTATAA 7 115 0 AGAAACTATT 0.68358 -186 TGCAATTGATAAAAACCCTGCTATACTTTCTCGTGTTA 7 160 1 AAAACCTATT 0.98479 -141 GATATACTACAAAATCGCAACAATTAGTGCATCTAACA 7 193 0 AAAACCAATT 0.937407 -108 CAACTAGTTCAAAATCCTTGGAAGAGCAAGGGTTGTGT 7 260 0 AAAACTTAGA 0.672524 -41 CAAAATTTGCAAAAACGCTTAAATTAATTTTAAGAAAC 8 24 1 AAAACCTATT 0.984782 -177 TAAGAACAAAAAAATCACAGAGATTGATCTAGAAACAC 8 120 1 AAAACCAATT 0.937407 -81 AGATTGATCTAGAAACACTCCTATGCTAAGATGCTCTT 8 140 1 AGAACCTATA 0.777543 -61 CAAAGCCTGAAAAATCGTTCTAGGTTTTACTAGTGGAG 19 38 0 AAAACTTGGT 0.789475 -263 AGCGTCAAGAAAAATCTCTTGTGTGGATGTCGCAGGTC 19 105 1 AAAACCTGTT 0.964757 -196 TAGGCCTAGAAAAACCCCTCCCGTCTTTTCTACTTATC 20 12 0 AAAACCTGTT 0.964676 -137 TTTTTATCTAAAAATCCCTAGATTTCTTGTTTTTCTTA 20 69 1 AAAACCTTTT 0.92245 -80 TGCGTGATCGAAAAAATTTTTTATTCGTAGTAGGGGAA 22 26 1 AAAAATTATT 0.711927 -37 TTGCTGAAAGAAAAACACTTCTTGTTTTTTATCTCTAT 23 47 1 AAAACCTTGT 0.850084 -114 **** * ** ** * Masking position 4 Map Score: 14.2829 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 237 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 2 GCCTCGTGGTCCGGCTTTGTTCCGCTACCAA 2 118 0 CCGCTTTGTT 0.987457 -54 TTTTTAGAGTCAGGCATTATTTATTTTATTA 4 106 0 CAGCATTATT 0.737089 -159 CTTTTTATAGCAGACTTTTTTTAAATTTTTA 4 143 0 CAGCTTTTTT 0.970745 -122 CAAATCAAAACCGACTTTACTAAAAAAGCTC 7 82 1 CCGCTTTACT 0.966467 -219 AACGATTTTTCAGGCTTTGTTTTTGCGATTT 19 57 1 CAGCTTTGTT 0.975652 -244 TGCCCATTCGCCGCCTTTGTTTGCTTTAAGG 19 152 1 CCGCTTTGTT 0.987457 -149 CTTTAAGGAGCCGCGTTTTCTTTGTCGTGGA 19 175 1 CCGGTTTTCT 0.886536 -126 AAAACCCCTCCCGTCTTTTCTACTTATCC 20 9 0 CCGCTTTTCT 0.981743 -140 ATCTGATCAACAGGCTTTTTTTTATCTAAAA 20 51 1 CAGCTTTTTT 0.970745 -98 *** ******* Masking position 7 Map Score: 11.4055 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 60 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 3 TCGAAACTACTCTCTTTGATCAAGAAACAGCTAAC 3 94 0 TCTGATCAAA 0.985289 -207 TCAAAGAGAGTAGTTTCGATCAAGATCGATTTCTA 3 110 1 TTTGATCAAA 0.86783 -191 TGCCTGTAGTTTTCTGTGATCAAATGATCTTAGCT 3 156 1 TCTGATCAAT 0.913482 -145 GGCTTGCCAATCACATCGATCAATAAAGCAGACCT 3 230 0 TCAGATCAAA 0.949026 -71 AGAAAACCGTCTCCACTGGTCAAGAATTTTAGCGC 9 27 0 CCAGGTCAAA 0.896621 -42 GTAATATAAGCATCTTAGGTCAAAAATTGTTATTT 13 12 0 CCTGGTCAAA 0.968945 -44 TTTCTAGGCCTAAATCTGATCAACAGGCTTTTTTT 20 38 1 TATGATCAAA 0.86783 -111 GTCAAGCGTTTTCCTGCGATCAAAA 21 1 0 TCTGATCAAA 0.985289 -166 TGTTTAAGTGTCTCTTGGGTCAAGCGTTTTCCTGC 21 19 0 TCTGGTCAAC 0.944302 -148 GGGTCTTTCTTTTCTAGGGTCAAGAGTAGCCATAA 21 98 1 TCTGGTCAAA 0.986406 -69 * ** ****** * Masking position 10 Map Score: 9.73033 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 15 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 4 GAACGTTCAGAGGAAGAACGATAGCAAAGT 2 69 0 AGGAAGAACG 0.925104 -103 AGCCAGTAAGGGGAAGAGAGTTAGCTGTTT 3 75 1 GGGAAGAGAG 0.914136 -226 TTTTATTGACTGTAAGAGAATTAAGCTGTA 3 192 1 TGTAAGAGAA 0.844396 -109 TCAAAATCCTTGGAAGAGCAAGGGTTGTGT 7 260 0 TGGAAGAGCA 0.98726 -41 TTGTTTCGTGTGGAAGAGCATCTTAGCATA 8 161 0 TGGAAGAGCA 0.98726 -40 TAAAGAAGGAAGAGAAGAATAAC 18 7 1 AGGAAGAGAA 0.962252 -17 GGAGCTTCCTTGGAAGAAAACTTATAACGC 19 12 0 TGGAAGAAAA 0.953998 -289 CCCTCCATCCTGCAAGAGCGATTTCCACGA 19 199 0 TGCAAGAGCG 0.901304 -102 ATGATTTGAGAGGAAGCACACAT 21 154 1 AGGAAGCACA 0.783451 -13 AGCAGATTGCTGAAAGAAAAACACTTCTTG 23 41 1 TGAAAGAAAA 0.698415 -120 ********** Masking position 5 Map Score: 6.6004 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 240 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 5 GGGAAGAGAGTTAGCTGTTTCTTGATCAAAGAG 3 85 1 TTTGTTTCTT 0.950255 -216 TCTAATCAAGTTTTTTGCCTGTAGTTTTCTGTG 3 141 1 TTTGCCTGTA 0.766919 -160 GGAGAAGTTGTTCTCTGTCTGTTTATTTAGAAT 4 33 0 TTTGTCTGTT 0.9549 -232 TTCAAGAGTTTTGTTTACTTGTTTGGTAATTTT 6 38 1 TTTACTTGTT 0.719229 -159 GTTATACAACTTAAGTATCTCTTGAAGCCTAAA 6 86 1 TTTATCTCTT 0.930307 -111 GATGTTTCTTTTGTTTGTTTCTTAAAATTAATT 8 45 0 TTTGTTTCTT 0.950255 -156 TTCTTAATAACTTGATGTTTCTTTTGTTTGTTT 8 58 0 CTTGTTTCTT 0.782486 -143 CTAGTTCAGATTCTTTATTTCTTAATAACTTGA 8 76 0 TTTATTTCTT 0.875285 -125 AATTCTATGTTTAAGTGTCTCTTGGGTCAAGCG 21 28 0 TTTGTCTCTT 0.973214 -139 ACACTTCTTGTTTTTTATCTCTATAATTAGAGG 23 61 1 TTTATCTCTA 0.768093 -100 TATTGAATAATTATCTGCCTGTTTGATTAGCAT 23 125 1 TTTGCCTGTT 0.929879 -36 ** ******** Masking position 6 Map Score: 6.04199 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 82 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 6 ACTACTCTCTTTGATCAAGAAACAGCTAAC 3 94 0 TTGATCAAGA 0.700117 -207 TCTCTGTCTGTTTATTTAGAATGGTTATAG 4 25 0 TTTATTTAGA 0.88625 -240 TAACACCACTTTTATTTAGGCTTCAAGAGA 6 103 0 TTTATTTAGG 0.676337 -94 CGTAATTGGTTTTATTTAATAACGCGCGCC 6 163 0 TTTATTTAAT 0.505387 -34 TCCTAGATTGATTTAGACAAAGGATTA 7 8 1 TTGATTTAGA 0.926408 -293 GAATTAATTTTTGAATTAAAACGGTTTTAA 7 44 0 TTGAATTAAA 0.577851 -257 TCCAAGGATTTTGAACTAGTTGCCCAAGGA 7 276 1 TTGAACTAGT 0.860408 -25 CTTATTGGATTTTAACTAGTTCAGATTCTT 8 94 0 TTTAACTAGT 0.793825 -107 ATCACAGAGATTGATCTAGAAACACTCCTA 8 133 1 TTGATCTAGA 0.952731 -68 CAGGCTTTTTTTTATCTAAAAATCCCTAGA 20 61 1 TTTATCTAAA 0.733126 -88 TAGGTGTATTTTGAATTAGATGGGGTCTTT 21 76 1 TTGAATTAGA 0.86673 -91 AGCTTTATCTAGTATTGCGTGAT 22 4 1 TTTATCTAGT 0.881305 -59 ********** Masking position 4 Map Score: 6.43725 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 116 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 7 ATGGTTATAGATATTTATTGAATA 4 3 0 ATATTTTGAA 0.808993 -262 CTTCTCCCGTTTATTTCACGGAAACATATTAC 4 59 1 TTATTTAGGA 0.750973 -206 GACTTTTTTTAAATTTTTAGAAGCTTTTTTAG 4 130 0 AAATTTTGAA 0.861127 -135 ACTTGTTTGGTAATTTTTATAATTCAAAGAAG 6 54 1 TAATTTTTAA 0.660879 -143 CGACAGCGAATTAATTTTTGAATTAAAACGGT 7 49 0 TTAATTTGAA 0.681925 -252 AGAAAAACTGTTATTTATCGAATTATAAATGA 7 111 0 TTATTTTGAA 0.9384 -190 ACGCTTAAATTAATTTTAAGAAACAAACAAAA 8 38 1 TAATTTAGAA 0.861115 -163 ATTGAACACCTAATTTCTAGGATAA 10 4 0 TAATTTTGGA 0.940767 -22 TGATGCTAATTTTTCGAAAACACTGACT 11 7 1 TAATTTTGAA 0.957094 -37 TAATTTTTAGGAGAGAGTGTT 12 1 1 TAATTTTGGA 0.940767 -21 ****** * *** Masking position 6 Map Score: 4.38692 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 74 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 8 AAAAAATCTTTGTTAGTGGTGTTTCGTC 5 10 1 TTGGGTTTCT 0.991887 -19 TTATATTACTTTAAGGGAGGCCCTTCGT 13 38 1 TTGGGCTTCT 0.99023 -18 GTTCTAGGTTTTACTAGTGGAGCTTCCTTGGAAGAAAA 19 22 0 TTGGGCTTCT 0.99023 -279 TTTTGCGATTTTTGGTGTGGGATTTCTTAGCGTCAAGA 19 77 1 TTGGGTTTCT 0.991887 -224 GTATTTTGAATTAGATGGGGTCTTTCTTTTCTAGGGTC 21 81 1 TTGGGTTTCT 0.991887 -86 AATCATTTGGTTACAGGTGTGCTTACGTTATGGCTACT 21 122 0 TTGGTTTACT 0.823513 -45 ** * ** **** * Masking position 14 Map Score: 3.17844 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 16 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 AGTGTTTTCCTTTTGGGACA 6 1 1 AGTGTTTTCC 0.981504 -196 AATTAATTTAAGCGTTTTTGCAAATTTTGT 8 23 0 AGCGTTTTTG 0.959387 -178 CCAGGTAGTCAGTGTTTTCGAAAAATTAGC 11 15 0 AGTGTTTTCG 0.975846 -29 ATCCTGCAAGAGCGATTTCCACGACAAAGA 19 193 0 AGCGATTTCC 0.93009 -108 TCTTGGGTCAAGCGTTTTCCTGCGATCAAA 21 12 0 AGCGTTTTCC 0.984635 -155 TAGTGTTTTTGGGGCTGCCCT 23 2 1 AGTGTTTTTG 0.951366 -159 AAAAACAAGAAGTGTTTTTCTTTCAGCAAT 23 46 0 AGTGTTTTTC 0.962538 -115 ********** Masking position 1 Map Score: 9.66916 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 GCCAACTGCTAAACCAGTTGCAAAAAAGCGAGGA 2 36 1 AAACCATCAA 0.956682 -136 ACCTTTTATCACACCTGTTACAAAGGCTATCAAT 3 273 0 ACACCTTCAA 0.983442 -28 GACGAAACACCACTAACAAAGATTTTTT 5 9 0 ACACCATCAA 0.978547 -20 TTATTAAATAAAACCAATTACGTATTAAGGTTAT 6 171 1 AAACCATCTA 0.820949 -26 TAACGGTTATAATCCTTTGTCTAAATCAATCTAG 7 13 0 AATCCTTCAA 0.856532 -288 GTGCCTAATTACACTTTTAGCAAACGGCCATGCC 19 227 0 ACACTTTCAA 0.88511 -74 TAACGTAAGCACACCTGTAACCAAATGATTTGAG 21 130 1 ACACCTTCAA 0.983442 -37 ****** * * ** Masking position 1 Map Score: 2.01075 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 11 ACTACAGGCAAAAAACTTGATTAGAAATCG 3 136 0 AAAAACTTGA 0.940048 -165 AAAAACCTGAATGGCAAGGT 4 255 0 AAAAACCTGA 0.901938 -10 GGAGATTTAAAAACAAAATTTGCAAAAA 8 9 1 AAAAACAAAA 0.725901 -192 TTTATTTCTTAATAACTTGATGTTTCTTTT 8 66 0 AATAACTTGA 0.764999 -135 CTCCACTAGTAAAACCTAGAACGATTTTTC 19 38 1 AAAACCTAGA 0.862682 -263 TTATCTTAAGAAAAACAAGAAATCTAGGGA 20 83 0 AAAAACAAGA 0.953309 -66 TATAGAGATAAAAAACAAGAAGTGTTTTTC 23 56 0 AAAAACAAGA 0.953309 -105 ********** Masking position 4 Map Score: 1.61667 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 53 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 CCAACTGCTAAACCAGTTGCAAAAAAGCGAGGA 2 37 1 AACATGCAAA 0.81451 -135 CCTTTTATCACACCTGTTACAAAGGCTATCAAT 3 273 0 CACTTACAAA 0.906424 -28 GACGAAACACCACTAACAAAGATTTTTT 5 9 0 CACATACAAA 0.93413 -20 GGGTTTTTATCAATTGCAGCAAAGAGAAGTTGA 7 145 0 CAATCGCAAA 0.753412 -156 GATTTAAAAACAAAATTTGCAAAAACGCTTAAA 8 14 1 CAAATGCAAA 0.955455 -187 AATCCCACACCAAAAATCGCAAAAACAAAGCCT 19 68 0 CAAATGCAAA 0.955455 -233 TGCCTAATTACACTTTTAGCAAACGGCCATGCC 19 227 0 CACTTGCAAA 0.971696 -74 TACCTTATCACACAACTTGACAACGCTTCACAG 19 271 0 CACATGACAA 0.757663 -30 TTTCTAGGGTCAAGAGTAGCCATAACGTAAGCA 21 108 1 CAAATGCCAT 0.682426 -59 AACGTAAGCACACCTGTAACCAAATGATTTGAG 21 131 1 CACTTACCAA 0.873367 -36 *** * * ***** Masking position 2 Map Score: 1.94952 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 97 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 TTATGTTTGTGTCAGCTAAATCATCAGCTC 3 33 1 GTCAGCTAAA 0.894641 -268 TGGATATGAGGTCTGCTTTATTGATCGATG 3 222 1 GTCTGCTTTA 0.965682 -79 TTTAAAAAAAGTCTGCTATAAAAAGTGCTT 4 149 1 GTCTGCTATA 0.975797 -116 CGCCGCCTTTGTTTGCTTTAAGGAGCCGCG 19 160 1 GTTTGCTTTA 0.925863 -141 GGGCATGGCCGTTTGCTAAAAGTGTAATTA 19 226 1 GTTTGCTAAA 0.925428 -75 ********** Masking position 7 Map Score: 0.987436 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 CAGACAGAGAACAACTTCTCCCGTTTATTT 4 45 1 ACAACTTCTC 0.975826 -220 TGATAATGATGCAACTTTTCGTAAAGGGAA 4 195 0 GCAACTTTTC 0.938599 -70 TTTTGGGACAACAACTTTTCAAGAGTTTTG 6 21 1 ACAACTTTTC 0.963092 -176 GTTTTTCTATTCAACTTCTCTTTGCTGCAA 7 135 1 TCAACTTCTC 0.941093 -166 ACCTTATCACACAACTTGACAACGCTTCAC 19 273 0 ACAACTTGAC 0.869569 -28 ********** Masking position 6 Map Score: 0.660635 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 20 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 AATTAATTTTTGAATTAAAACGGTTTTAAC 7 43 0 TGAATTAAAA 0.766944 -258 TCGCTGTCGCCAAATCAAAACCGACTTTAC 7 72 1 CAAATCAAAA 0.910585 -229 TGTTATTTATCGAATTATAAATGAGCTTTT 7 105 0 CGAATTATAA 0.840437 -196 CAAATTAAAAGATTAGGACG 16 1 1 CAAATTAAAA 0.924721 -27 GCTGACAAATTAAAACTAAGGAAAA 20 134 0 CAAATTAAAA 0.924721 -15 AATACACCTACGCATCAAAATGATGAATTC 21 56 0 CGCATCAAAA 0.866165 -111 TCCCCTACTACGAATAAAAAATTTTTTCGA 22 33 0 CGAATAAAAA 0.885206 -30 ********** Masking position 4 Map Score: 0.971494 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 41 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