AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_ctra_reg_300.orf -o00860_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 rl31 75 L31 Ribosomal Protein #2 pfrA 187 Peptide Chain Releasing Factor (RF-1) #3 hemL 196 Glutamate-1-semialdehyde-2,1-aminomutase #4 rnc 108 Ribonuclease III #5 gltX 271 Glutamyl-tRNA Synthetase #6 euo 300 CHLPS Euo Protein #7 hemZ 21 Ferrochetalase #8 fliY 45 Glutamine Binding Protein #9 CT488 88 hypothetical protein #10 glgC 192 Glucose-1-P Adenyltransferase #11 hemB 297 Porphobilinogen Synthase #12 hemA 300 Glutamyl tRNA Reductase #13 alaS 300 Alanyl tRNA Synthetase Motif number 1 ACTTATTAAAACAAAAAAAGCGGGGTGTTCG 2 49 0 AAAAAAAAGC 0.759379 -139 AAAGTCAGATTCAAAAAGAGAGACTTATTAA 2 71 0 TAAAAAGAGA 0.953539 -117 AGAGAAAACCTTAAAAATAACAACAGGTTAG 3 16 0 TAAAAATAAC 0.925142 -181 AGGATCGCATTAAAAAAAAGATGATGGATTC 3 132 0 TAAAAAAAGA 0.928259 -65 TTTGTATTCTTAAAAAATAGTT 4 97 1 TAAAAATAGT 0.927685 -12 CTTTTTCAACAAAAAAAAAGCCCCCCTCCGG 5 69 0 AAAAAAAAGC 0.759379 -203 TTTTTTTTGTTGAAAAAGAGCTCCGAAAAAC 5 82 1 TAAAAAGAGC 0.952616 -190 AAACTTTGTTTCAAAAATAGCATTTATTTTT 6 28 1 TAAAAATAGC 0.975089 -273 AAGCGGTTTGTTAAAAATAAATGCTATTTTT 6 40 0 TAAAAATAAA 0.926559 -261 TGCAAAATCCTTAAAAAGAGAAGGTAACATT 6 95 0 TAAAAAGAGA 0.953539 -206 GAGCGCTTACTGAAAAATTGCAAAATCCTTA 6 113 0 TAAAAATTGC 0.716287 -188 CCTCGTCCACTTAAAAATAAATCCTCTCATC 6 263 0 TAAAAATAAA 0.926559 -38 CCGTTTTTTGTCAAAATTAGATAATTTTTAT 10 55 1 TAAAATTAGA 0.720435 -138 TTTAGATGTTTGAAAAATAAAAATTATCTAA 10 71 0 TAAAAATAAA 0.926559 -122 AAAATAATTTTAAAAAATAAATTATTAAAAA 10 154 0 TAAAAATAAA 0.926559 -39 CCCGCCACCATAAAAAATAATTTTAAAAAAT 10 167 0 TAAAAATAAT 0.801997 -26 TGCTCTCTTTAGAAAAATAATGTAAGGCGTA 12 44 1 AAAAAATAAT 0.50212 -257 AATAGGTGCATAAAAAATAGGGGATAGCATA 13 77 0 TAAAAATAGG 0.932653 -224 GGGGAGTTGATAAAAAATAGGTGCATAAAAA 13 92 0 TAAAAATAGG 0.932653 -209 CAAAAAAAAGAAAAAAAGAGAGGAAAATTTT 13 191 0 AAAAAAGAGA 0.836337 -110 TTTGGAGCGCTAAAAAAAAGAATTTCGACAA 13 252 0 TAAAAAAAGA 0.928259 -49 * ********* Masking position 6 Map Score: 28.7156 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 226 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 GTTCGCCCCGCTTTTCTCTAGATAACAGAA 2 24 0 CTTTTCTCTA 0.807017 -164 TATTTTTAAGGTTTTCTCTCCTTACAACCG 3 28 1 GTTTTCTCTC 0.876034 -169 GTTTGACGCTTATTTCTCTCTAAGTGCAAG 3 59 0 TATTTCTCTC 0.880621 -138 GGAAAGGAAACTTTTCTATCTTTATGAAAT 5 238 0 CTTTTCTATC 0.807017 -34 CCTTTCCACTCTATTCTCTCTTCCTAGTGT 6 147 0 CTATTCTCTC 0.650894 -154 TGGATAAAAATTTTTCTCTTGAAT 8 32 1 TTTTTCTCTT 0.956367 -14 AGAGTGGATTTTTCTTTTCGAGCTGTTG 9 9 1 TTTTTCTTTT 0.90219 -80 AAAGAGCTGATTCTTCTATCAAGCAAGAGG 9 65 1 TTCTTCTATC 0.855186 -24 CAGAAAAGAGTTCTTATCTCTATAAAGGGC 10 19 1 TTCTTATCTC 0.700544 -174 AATTAGATAATTTTTATTTTTCAAACATCT 10 69 1 TTTTTATTTT 0.446481 -124 TTTTCACAGCTTTTTCTCTCGAAATAACAA 11 175 1 TTTTTCTCTC 0.981162 -123 TATTAGTTTCTTCTTCTTTAAGGGGTGTGG 11 220 0 TTCTTCTTTA 0.71307 -78 TAAGGCGTAGTATTTCTTTTAGTCTTCTGT 12 66 1 TATTTCTTTT 0.566421 -235 TTTTTAACGGTTTTTCTATTTTCGTCTCCA 12 157 1 TTTTTCTATT 0.828723 -144 GATTGTATGCTTCTTCTCTCGGTTGGCTCA 12 263 0 TTCTTCTCTC 0.963966 -38 GCATACAATCTTTTTCTTTAGAAAGGGA 12 283 1 TTTTTCTTTA 0.828723 -18 TAAAACAAAATTTTCCTCTCTTTTTTTCTT 13 185 1 TTTTCCTCTC 0.853843 -116 TTCCTCTCTTTTTTTCTTTTTTTTGCTCAT 13 197 1 TTTTTCTTTT 0.90219 -104 ********** Masking position 4 Map Score: 17.5023 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 536 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 CTCACATAACAGAAGGGAGAGCATACCCGAACA 1 15 0 AGAGGGAGCA 0.893691 -61 TCTAGAGAAAAGCGGGGCGAACACCCCGCTTTT 2 32 1 AGGGGGAACA 0.981879 -156 TCTAACAAAGACCAGAGTGTACATTGGCAATCA 2 132 0 ACAGGGTACA 0.755838 -56 GGATTCGCAGACTGGAGAGGACTTGATTTCGAT 3 105 0 ACGGGGGACT 0.989493 -92 TAAGGGCACAGCAGGGGAGAGCTTGGGCCTCCT 5 28 1 GCGGGGAGCT 0.864638 -244 GAGAGAATAGAGTGGAAAGGGCTTGTCCGACTT 6 157 1 AGGGAGGGCT 0.888582 -144 TTTTAAGTGGACGAGGGAGGACTAAACAGTCGT 6 278 1 ACAGGGGACT 0.958895 -23 TATTTTTTATGGTGGCGGGGACAG 10 179 1 GGGGGGGACA 0.986614 -14 TTCTTCTTTAAGGGGTGTGGAAATTGTTTATAA 11 207 0 AGGGGGGAAA 0.967305 -91 ATCTTCTTCTAGGGGGGTGGAAACTTTCGATAA 11 263 1 AGGGGGGAAA 0.967305 -35 AAGCAGTGTGAGCGGTGAGGACTTGAGATACTA 12 102 1 AGGGGGGACT 0.99385 -199 ** ** * ***** Masking position 5 Map Score: 10.5086 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 58 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 GCCCCGCTTTTCTCTAGATAACAGAAAGTT 2 20 0 TCTCTAGATA 0.591488 -168 TACTCTAGTATCTCTCTAACAAAGACCAGA 2 149 0 TCTCTCTAAC 0.921609 -39 GACGCTTATTTCTCTCTAAGTGCAAGGCGG 3 55 0 TCTCTCTAAG 0.957435 -142 AAGCAGAGATCTCTGTAAAGATTGGGGAA 3 178 0 TCTCTGTAAA 0.910304 -19 GATAGAGCCTTCTCTGTAAGGGCACAGCAG 5 12 1 TCTCTGTAAG 0.904684 -260 TGTTACCTTCTCTTTTTAAGGATTTTGCAA 6 97 1 TCTTTTTAAG 0.695056 -204 AGTCTCTTTAAATTCCTTGTT 7 10 0 TCTCTTTAAA 0.903853 -12 TAAAAATTTTTCTCTTGAAT 8 36 1 TCTCTTGAAT 0.67187 -10 AGAGTTCTTATCTCTATAAAGGGCATGGGT 10 25 1 TCTCTATAAA 0.924402 -168 CACAGCTTTTTCTCTCGAAATAACAATGTT 11 179 1 TCTCTCGAAA 0.966817 -119 AGTTATGCTCTCTTTAGAAAAATAATGTAA 12 39 1 TCTTTAGAAA 0.793996 -262 TAGTCTTCTGTCTCACTAAGCAGTGTGAGC 12 85 1 TCTCACTAAG 0.688845 -216 ACAATCTTTTTCTTTAGAAAGGGA 12 287 1 TCTTTAGAAA 0.793996 -14 GATGTAGCTTTCTTTCGAACGAGGGTTGAA 13 46 0 TCTTTCGAAC 0.787417 -255 ********** Masking position 8 Map Score: 11.4392 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 225 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 TCTTAGTATGTGAAAATCTCACATAACAGA 1 35 0 TGAAAATCTC 0.713112 -41 AAAAGAGCTCCGAAAAACTCGTTATTTTAG 5 95 1 CGAAAAACTC 0.953758 -177 TTGTAAAAAACTTTACAAAACTT 6 4 1 TAAAAAACTT 0.914415 -297 TAAAAAACTTTACAAAACTTTGTTTCAAAA 6 14 1 TACAAAACTT 0.627582 -287 ATTTTCCCAACAAAAAACTTATTAATCAAG 6 68 0 CAAAAAACTT 0.952069 -233 CCACACATAACAAAACACTCAAAGTTTTTC 11 41 1 CAAAACACTC 0.761475 -257 AGCTTTTTGCTGAAAAACTTTGAGTGTTTT 11 52 0 TGAAAAACTT 0.915876 -246 AGTTTTTCAGCAAAAAGCTTGTTGAAAAAC 11 63 1 CAAAAAGCTT 0.789059 -235 AAAAGCTTGTTGAAAAACTTGATGACCACC 11 75 1 TGAAAAACTT 0.915876 -223 TTCTCTGCATTGAAAAAATTTTGTAGTCTG 12 185 0 TGAAAAAATT 0.684296 -116 AAGAGAGTCTCAAAAATATTGGTATAAAAA 12 217 1 CAAAAATATT 0.469787 -84 ATCAACTCCCCAAAAAACCCTTTTTCTTAA 13 112 1 CAAAAAACCC 0.761475 -189 AGAATTTCGACAAAAAAATCGAAGAGAGGA 13 235 0 CAAAAAAATC 0.801181 -66 ********** Masking position 5 Map Score: 7.46457 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 236 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 TTTAATAAGTCTCTCTTTTTGAATCTGACT 2 70 1 CTCTCTTTTT 0.940503 -118 CCACTCTATTCTCTCTTCCTAGTGTAGCGA 6 142 0 CTCTCTTCCT 0.984265 -159 AAAATAAATCCTCTCATCTTGGCCTGTCTT 6 251 0 CTCTCATCTT 0.961844 -50 ATTTTTGAGACTCTCTTCGTTCTCTGCATT 12 204 0 CTCTCTTCGT 0.984265 -97 CTATCGCGCCCTCTCATCCACGTAAGAGGC 13 11 1 CTCTCATCCA 0.922108 -290 CAAAATTTTCCTCTCTTTTTTTCTTTTTTT 13 190 1 CTCTCTTTTT 0.940503 -111 CCTACCCTTCCTCTCTTCGATTTTTTTGTC 13 227 1 CTCTCTTCGA 0.964555 -74 ********** Masking position 4 Map Score: 8.16107 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 110 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 AATAAGTCTCTCTTTTTGAATCTGACTTTT 2 73 1 TCTTTTTGAA 0.878444 -115 AACTTTTCTATCTTTATGAAATGAACACCC 5 230 0 TCTTTATGAA 0.725694 -42 TTAACAAACCGCTTGATTAATAAGTTTTTT 6 57 1 GCTTGATTAA 0.876685 -244 TGTAGCGAGCGCTTACTGAAAAATTGCAAA 6 120 0 GCTTACTGAA 0.838984 -181 TTAGAGCTATGCTTATTGAATCTCTAAGTC 6 185 0 GCTTATTGAA 0.94424 -116 TGTTTGTCTGGCTTTTTTAATAATTTATTT 10 141 1 GCTTTTTTAA 0.941457 -52 TCAGCAAAAAGCTTGTTGAAAAACTTGATG 11 69 1 GCTTGTTGAA 0.97446 -229 TTTGTTCACAGCTTGTTTAAATTGTTTAGA 11 132 0 GCTTGTTTAA 0.951028 -166 CGTGGAAACGCCTTTTTTAACGGTTTTTCT 12 144 1 CCTTTTTTAA 0.755596 -157 ********** Masking position 4 Map Score: 5.42539 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 88 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 AATTTTTGGGGAACACTAGACTTTACTCTG 2 103 0 GAACACTAGA 0.913716 -85 GCAGACTGGAGAGGACTTGATTTCGATCTC 3 102 0 GAGGACTTGA 0.969822 -95 GTGGACGAGGGAGGACTAAACAGTCGT 6 284 1 GAGGACTAAA 0.974446 -17 TAGTGAGACAGAAGACTAAAAGAAATACTA 12 73 0 GAAGACTAAA 0.92798 -228 TGTGAGCGGTGAGGACTTGAGATACTAAGA 12 108 1 GAGGACTTGA 0.969822 -193 AGCTTGTTTGGAGCGCTAAAAAAAAGAATT 13 259 0 GAGCGCTAAA 0.879338 -42 ********** Masking position 7 Map Score: 2.50727 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 10 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 TTATGTGAGATTTTCACATACTAAGATAGT 1 39 1 TTTTCACATA 0.291475 -37 TAAAGTCTAGTGTTCCCCAAAAATTGATTG 2 108 1 TGTTCCCCAA 0.382468 -80 GCTTTTTTTTTGTTGAAAAAGAGCTCCGAA 5 79 1 TGTTGAAAAA 0.562901 -193 GTTATTTTAGTTTTGTTAAAGTCGCCAAGA 5 115 1 TTTTGTTAAA 0.452246 -157 CAAAGCCCTATGTTCCTAAACGATACCAGA 5 154 0 TGTTCCTAAA 0.764151 -118 TACAAAACTTTGTTTCAAAAATAGCATTTA 6 24 1 TGTTTCAAAA 0.469349 -277 TAGCATTTATTTTTAACAAACCGCTTGATT 6 45 1 TTTTAACAAA 0.467649 -256 GAAGGTAACATTTTCCCAACAAAAAACTTA 6 77 0 TTTTCCCAAC 0.885772 -224 CTTTTCGAGCTGTTGACAAAGGTAAAAGTG 9 24 1 TGTTGACAAA 0.831628 -65 CAGCTCTTTATTTTGCCAACCACTTTTACC 9 44 0 TTTTGCCAAC 0.824767 -45 AATTATCTAATTTTGACAAAAAACGGACCC 10 51 0 TTTTGACAAA 0.788035 -142 ATAATTTTTATTTTTCAAACATCTAAAAAT 10 75 1 TTTTTCAAAC 0.470712 -118 GCAAAAAGCTTGTTGAAAAACTTGATGACC 11 72 1 TGTTGAAAAA 0.562901 -226 GATGACCACCTGTTTACAAATAGGCATAAC 11 95 1 TGTTTACAAA 0.781447 -203 CATAACCTTTTGTTCTAAACAATTTAAACA 11 119 1 TGTTCTAAAC 0.586916 -179 TTCATAACTTTGTTCACAGCTTGTTTAAAT 11 140 0 TGTTCACAGC 0.777511 -158 GTGAAAATAATGTTCATAACTTTGTTCACA 11 152 0 TGTTCATAAC 0.812658 -146 ATGAACATTATTTTCACAGCTTTTTCTCTC 11 165 1 TTTTCACAGC 0.732552 -133 GTGTGGAAATTGTTTATAACATTGTTATTT 11 196 0 TGTTTATAAC 0.656032 -102 TAGCTGATTGTTTTCTCAGAAATTAT 12 7 0 TTTTCTCAGA 0.523911 -294 CCTTACATTATTTTTCTAAAGAGAGCATAA 12 41 0 TTTTTCTAAA 0.521093 -260 TGCACCTATTTTTTATCAACTCCCCAAAAA 13 98 1 TTTTATCAAC 0.3669 -203 AAAAAACCCTTTTTCTTAACCTCTCAATTT 13 123 1 TTTTCTTAAC 0.635408 -178 TCCTTAACACTTTTTATAAAACAAAATTTT 13 169 1 TTTTTATAAA 0.534707 -132 TCGAAATTCTTTTTTTTAGCGCTCCAAACA 13 255 1 TTTTTTTAGC 0.20504 -46 ********** Masking position 4 Map Score: 7.77231 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 541 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 CAAAATCACTATCTTAGTATGTGAAAATCTCA 1 44 0 ATCTTAGTGT 0.91997 -32 GGCGGAAATAATCTTAAAGTCTATAGTACTTT 4 38 0 ATCTTAATCT 0.743148 -71 GACTCTCAAGATTTTGTATTCTTAAAAAATAG 4 85 1 ATTTTGTTCT 0.859738 -24 AAATCCTCTCATCTTGGCCTGTCTTGTGAATA 6 244 0 ATCTTGGTGT 0.9576 -57 CCACGGCTTAATCTTAGTATCTCAAGTCCTCA 12 117 0 ATCTTAGTCT 0.937883 -184 CATTGAAAAAATTTTGTAGTCTGGAGACGAAA 12 176 0 ATTTTGTTCT 0.859738 -125 AGAAAGCTACATCTTATGCTATCCCCTATTTT 13 63 1 ATCTTATTAT 0.762836 -238 AGAGAGGAAAATTTTGTTTTATAAAAAGTGTT 13 174 0 ATTTTGTTAT 0.674391 -127 ACAAGCTTACATCTTGGCTTGTTCTAATT 13 282 1 ATCTTGGTGT 0.9576 -19 ******* *** Masking position 5 Map Score: 1.5712 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 56 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 TTGACAACCCCAAAATCACT 1 66 0 TTGACAACCC 0.852997 -10 AAAAGCGGGGCGAACACCCCGCTTTTTTTG 2 39 1 CGAACACCCC 0.97097 -149 CTTTATGAAATGAACACCCCGTCCCGGGTT 5 219 0 TGAACACCCC 0.955098 -53 ATCTCTAAGTCGGACAAGCCCTTTCCACTC 6 166 0 CGGACAAGCC 0.977744 -135 GAACTCTTTTCTGACTCGCCT 10 2 0 CTGACTCGCC 0.837098 -191 GATTAAGCCGTGGAAACGCCTTTTTTAACG 12 136 1 TGGAAACGCC 0.882141 -165 AATTAGAACAAGCCAAGATGTAAG 13 287 0 AGAACAAGCC 0.842612 -14 ********** Masking position 4 Map Score: 0.666644 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 37 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: 5.14676e-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: 5.14676e-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: 5.14676e-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