AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_ctra_reg_100.orf -o00860_ctra_100.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 pfrA 187 Peptide Chain Releasing Factor (RF-1) #2 hemL 196 Glutamate-1-semialdehyde-2,1-aminomutase #3 rnc 108 Ribonuclease III #4 gltX 271 Glutamyl-tRNA Synthetase #5 hemZ 21 Ferrochetalase #6 fliY 45 Glutamine Binding Protein #7 CT488 88 hypothetical protein #8 glgC 192 Glucose-1-P Adenyltransferase #9 hemB 297 Porphobilinogen Synthase #10 hemA 300 Glutamyl tRNA Reductase #11 alaS 300 Alanyl tRNA Synthetase Motif number 1 TTATTAAAACAAAAAAAGCGGGGTGTTCGC 1 48 0 AAAAAAAGCG 0.959531 -140 AGTCAGATTCAAAAAGAGAGACTTATTAAA 1 70 0 AAAAAGAGAG 0.724731 -118 AGTATCTCTCTAACAAAGACCAGAGTGTAC 1 143 0 TAACAAAGAC 0.650346 -45 GATCGCATTAAAAAAAAGATGATGGATTCG 2 131 0 AAAAAAAGAT 0.845825 -66 TTTGTATTCTTAAAAAATAGTT 3 97 1 TAAAAAATAG 0.915529 -12 TTTTCAACAAAAAAAAAGCCCCCCTCCGGA 4 68 0 AAAAAAAGCC 0.909868 -204 TTTTTTTTGTTGAAAAAGAGCTCCGAAAAA 4 82 1 TGAAAAAGAG 0.943479 -190 CAGCTCGAAAAGAAAAATCCACTCT 7 6 0 AGAAAAATCC 0.729036 -83 GTGGTTGGCAAAATAAAGAGCTGATTCTTC 7 51 1 AAATAAAGAG 0.781343 -38 TTTAGATGTTTGAAAAATAAAAATTATCTA 8 72 0 TGAAAAATAA 0.649608 -121 ATTGCATGAATAATAAATCGATTTTATTTT 8 100 0 TAATAAATCG 0.458006 -93 AATAAATTATTAAAAAAGCCAGACAAACAA 8 140 0 TAAAAAAGCC 0.888623 -53 AAAATAATTTTAAAAAATAAATTATTAAAA 8 155 0 TAAAAAATAA 0.743173 -38 CCCGCCACCATAAAAAATAATTTTAAAAAA 8 168 0 TAAAAAATAA 0.743173 -25 TTATTTCGAGAGAAAAAGCTGTGAAAATAA 9 172 0 AGAAAAAGCT 0.716563 -126 TGCTCTCTTTAGAAAAATAATGTAAGGCGT 10 44 1 AGAAAAATAA 0.70111 -257 GAAAAACCGTTAAAAAAGGCGTTTCCACGG 10 143 0 TAAAAAAGGC 0.708469 -158 TAAAAATACGAAACAAAGAGAATGAGCCAA 10 241 1 AAACAAAGAG 0.846799 -60 CCCTTTCTAAAGAAAAAGATTGTATGCTTC 10 280 0 AGAAAAAGAT 0.778512 -21 AATAGGTGCATAAAAAATAGGGGATAGCAT 11 78 0 TAAAAAATAG 0.915529 -223 GGGGAGTTGATAAAAAATAGGTGCATAAAA 11 93 0 TAAAAAATAG 0.915529 -208 TGAGAGGTTAAGAAAAAGGGTTTTTTGGGG 11 119 0 AGAAAAAGGG 0.822285 -182 CAAAAAAAAGAAAAAAAGAGAGGAAAATTT 11 192 0 AAAAAAAGAG 0.970558 -109 GAATTTCGACAAAAAAATCGAAGAGAGGAA 11 234 0 AAAAAAATCG 0.907948 -67 TGGAGCGCTAAAAAAAAGAATTTCGACAAA 11 251 0 AAAAAAAGAA 0.89797 -50 ********** Masking position 5 Map Score: 25.8985 Number of sites scoring better than the average of aligned sites = 732 Number in coding regions = 732 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 CGCCCCGCTTTTCTCTAGATAACAGAAAGT 1 21 0 TTCTCTAGAT 0.666803 -167 TTACTCTAGTATCTCTCTAACAAAGACCAG 1 150 0 ATCTCTCTAA 0.945911 -38 TGACGCTTATTTCTCTCTAAGTGCAAGGCG 2 56 0 TTCTCTCTAA 0.974758 -141 AAGCAGAGATCTCTGTAAAGATTGGGGA 2 179 0 ATCTCTGTAA 0.880659 -18 AGATAGAGCCTTCTCTGTAAGGGCACAGCA 4 11 1 TTCTCTGTAA 0.942183 -261 AGTCTCTTTAAATTCCTTGTT 5 11 0 GTCTCTTTAA 0.837397 -11 ATAAAAATTTTTCTCTTGAAT 6 35 1 TTCTCTTGAA 0.924061 -11 AAGAGTTCTTATCTCTATAAAGGGCATGGG 8 24 1 ATCTCTATAA 0.872368 -169 TCACAGCTTTTTCTCTCGAAATAACAATGT 9 178 1 TTCTCTCGAA 0.977917 -120 TTAGTCTTCTGTCTCACTAAGCAGTGTGAG 10 84 1 GTCTCACTAA 0.686188 -217 TACAATCTTTTTCTTTAGAAAGGGA 10 286 1 TTCTTTAGAA 0.683915 -15 AGATGTAGCTTTCTTTCGAACGAGGGTTGA 11 47 0 TTCTTTCGAA 0.860603 -254 ********** Masking position 9 Map Score: 12.1317 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 161 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 GAGACTTATTAAAACAAAAAAAGCGGGGTGT 1 52 0 AAAAAAAAAA 0.72776 -136 GGCGGTTGTAAGGAGAGAAAACCTTAAAAAT 2 29 0 AGGAAGAAAA 0.970693 -168 CTATTTTTTAAGAATACAAAATCTTGAGAGT 3 86 0 AGAAACAAAA 0.851034 -23 CCTGATTCATAGGACAGGAACCCGGGACGGG 4 201 1 AGGAAGGAAC 0.887078 -71 TCATTTCATAAAGATAGAAAAGTTTCCTTTC 4 236 1 AAGAAGAAAA 0.959957 -36 CTACTAACCCAGGAAAGGAAACTTTTCTATC 4 248 0 AGGAAGGAAA 0.978615 -24 GTCAACAGCTCGAAAAGAAAAATCCACTCT 7 10 0 CGAAAGAAAA 0.790847 -79 CACCCCTTAAAGAAGAAGAAACTAATAAATA 9 223 1 AGAAAAGAAA 0.836138 -75 TCTGGAGACGAAAATAGAAAAACCGTTAAAA 10 158 0 AAAAAGAAAA 0.94551 -143 TATTGGTATAAAAATACGAAACAAAGAGAAT 10 233 1 AAAAACGAAA 0.851034 -68 AAAAGAAAAAAAGAGAGGAAAATTTTGTTTT 11 186 0 AAGAAGGAAA 0.970693 -115 GGATGAGCAAAAAAAAGAAAAAAAGAGAGGA 11 198 0 AAAAAGAAAA 0.94551 -103 AAAAAAATCGAAGAGAGGAAGGGTAGGATGA 11 223 0 AAGAAGGAAG 0.850433 -78 **** ****** Masking position 6 Map Score: 12.7824 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 223 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 TTTTCTCTCCTTACAACCGCCTTGCACTTAGA 2 39 1 TACAACGCCT 0.734754 -158 GCGATCCTGGTATACACTTCCCTTTCCCCAAT 2 155 1 TTACACTCCC 0.792274 -42 GAAAAATTTTTATCCACCCACTATGATTACGC 6 16 0 TTCCACCACT 0.766511 -30 CTTTTACCTTTGTCAACAGCTCGAAAAGAAAA 7 20 0 TTCAACGCTC 0.967838 -69 TTCATAACTTTGTTCACAGCTTGTTTAAATTG 9 138 0 TTTCACGCTT 0.939451 -160 ATGAACATTATTTTCACAGCTTTTTCTCTCGA 9 165 1 TTTCACGCTT 0.939451 -133 TTATAAACAATTTCCACACCCCTTAAAGAAGA 9 207 1 TTCCACCCCC 0.990204 -91 TTATCGAAAGTTTCCACCCCCCTAGAAGAAGA 9 264 0 TTCCACCCCC 0.990204 -34 GTATCTCAAGTCCTCACCGCTCACACTGCTTA 10 101 0 TCTCACGCTC 0.865864 -200 AAAAAAGGCGTTTCCACGGCTTAATCTTAGTA 10 130 0 TTCCACGCTT 0.976868 -171 ACCTATTTTTTATCAACTCCCCAAAAAACCCT 11 101 1 TTCAACCCCC 0.97024 -200 AAACCCTTTTTCTTAACCTCTCAATTTATCCC 11 126 1 TTTAACTCTC 0.716614 -175 * ***** **** Masking position 6 Map Score: 9.0874 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 106 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 GGCAATCAATTTTTGGGGAACACTAGACTT 1 110 0 TTTTGGGGAA 0.964525 -78 ACTCACTTATTTAGGCGAATAAACTCGAA 3 10 1 TTTAGGCGAA 0.876456 -99 GGGGCTTTTTTTTTGTTGAAAAAGAGCTCC 4 76 1 TTTTGTTGAA 0.954227 -196 GTTATTTTAGTTTTGTTAAAGTCGCCAAGA 4 115 1 TTTTGTTAAA 0.826043 -157 TGGGTCCGTTTTTTGTCAAAATTAGATAAT 8 50 1 TTTTGTCAAA 0.882217 -143 TCAACAAGCTTTTTGCTGAAAAACTTTGAG 9 58 0 TTTTGCTGAA 0.902611 -240 AAAAAGGGTTTTTTGGGGAGTTGATAAAAA 11 107 0 TTTTGGGGAG 0.878391 -194 TCTTCGATTTTTTTGTCGAAATTCTTTTTT 11 240 1 TTTTGTCGAA 0.970409 -61 ********** Masking position 9 Map Score: 4.55136 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 78 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 AGATTCAAAAAGAGAGACTTATTAAAACAAAAAAAG 1 60 0 AGAGAGAAAA 0.952567 -128 GGTCTTTGTTAGAGAGATACTAGAGTAAAGGCAGAA 1 152 1 AGAGAGATAT 0.912139 -36 CCTTGCACTTAGAGAGAAATAAGCGTCAAACATACA 2 58 1 AGAGAGAACT 0.982498 -139 TTGTTGAAAAAGAGCTCCGAAAAACTCGTTATTTTA 4 88 1 AGAGCTCAAT 0.565892 -184 AAACGATACCAGAGAGATTCATTCTTGGCGACTTTA 4 131 0 AGAGAGAACT 0.982498 -141 TGCCCTTTATAGAGATAAGAACTCTTTTCTGACTCG 8 14 0 AGAGATAACT 0.925332 -179 ATTGTTATTTCGAGAGAAAAAGCTGTGAAAATAATG 9 170 0 CGAGAGAATT 0.830419 -128 GAAGATTCGTAGAGATATTTATTAGTTTCTTCTTCT 9 233 0 AGAGATAAAT 0.951808 -65 ATTTTTCTAAAGAGAGCATAACTATTAGCTGATTGT 10 26 0 AGAGAGCAAT 0.971752 -275 CACACTGCTTAGTGAGACAGAAGACTAAAAGAAATA 10 76 0 AGTGAGAAAT 0.91213 -225 CAGAGAACGAAGAGAGTCTCAAAAATATTGGTATAA 10 208 1 AGAGAGTAAT 0.926535 -93 ATGAGCCAACCGAGAGAAGAAGCATACAATCTTTTT 10 262 1 CGAGAGAAAA 0.874371 -39 ******* * * * Masking position 4 Map Score: 7.80073 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 113 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 GTAAGGAGAGAAAACCTTAAAAATAACAAC 2 23 0 AAAACCTTAA 0.814827 -174 ATAGGCGGAAATAATCTTAAAGTCTATAGT 3 43 0 ATAATCTTAA 0.750507 -66 TTAAGAATACAAAATCTTGAGAGTCAATCG 3 80 0 AAAATCTTGA 0.943511 -29 ATTCAAGAGAAAAATTTTTATCCACCCACT 6 26 0 AAAATTTTTA 0.773067 -20 TCAAAATTAGATAATTTTTATTTTTCAAAC 8 65 1 ATAATTTTTA 0.685317 -128 ACCATAAAAAATAATTTTAAAAAATAAATT 8 162 0 ATAATTTTAA 0.685413 -31 TTTTTGCTGAAAAACTTTGAGTGTTTTGTT 9 49 0 AAAACTTTGA 0.918754 -249 TTTTTCAGCAAAAAGCTTGTTGAAAAACTT 9 65 1 AAAAGCTTGT 0.71868 -233 AAGCTTGTTGAAAAACTTGATGACCACCTG 9 77 1 AAAAACTTGA 0.749269 -221 ACAAATAGGCATAACCTTTTGTTCTAAACA 9 110 1 ATAACCTTTT 0.628031 -188 AATAATGTTCATAACTTTGTTCACAGCTTG 9 147 0 ATAACTTTGT 0.821495 -151 CTGCATTGAAAAAATTTTGTAGTCTGGAGA 10 181 0 AAAATTTTGT 0.884878 -120 AAAAGAGAGGAAAATTTTGTTTTATAAAAA 11 179 0 AAAATTTTGT 0.884878 -122 ********** Masking position 4 Map Score: 4.77509 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 238 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 8 CGAACACCCCGCTTTTTTTGTTTTAATAAGT 1 49 1 GCTTTTTTGT 0.75747 -139 GAAACCTCTTGCTTGATAGAAGAATCAGCTC 7 68 0 GCTTGATGAA 0.921245 -21 TGTTTGTCTGGCTTTTTTAATAATTTATTTT 8 141 1 GCTTTTTAAT 0.791076 -52 AGGCTAATCTGCTTTATAGGAGTTTTCTT 9 9 0 GCTTTATGGA 0.83082 -289 TCAGCAAAAAGCTTGTTGAAAAACTTGATGA 9 69 1 GCTTGTTAAA 0.959253 -229 TTTGTTCACAGCTTGTTTAAATTGTTTAGAA 9 131 0 GCTTGTTAAA 0.959253 -167 CCGTGGAAACGCCTTTTTTAACGGTTTTTCT 10 143 1 GCCTTTTTAA 0.736812 -158 CAAGATGTAAGCTTGTTTGGAGCGCTAAAAA 11 267 0 GCTTGTTGGA 0.968287 -34 TTACATCTTGGCTTGTTCTAATT 11 288 1 GCTTGTTTAA 0.959253 -13 ******* *** Masking position 7 Map Score: 3.44597 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 129 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 TGAATCTGACTTTTCAGAGTAAAGTCTAGT 1 89 1 TTTTCAGAGT 0.863503 -99 GAACGACTTCTTCTGCCTTTACTCTAGT 1 170 0 TCTTCTGCCT 0.912483 -18 AATCAAGTCCTCTCCAGTCTGCGAATCCAT 2 110 1 TCTCCAGTCT 0.918492 -87 GAATACAAAATCTTGAGAGTCAATCGGGTT 3 76 0 TCTTGAGAGT 0.85132 -33 ATAAGAACTCTTTTCTGACTCGCCT 8 6 0 TTTTCTGACT 0.917669 -187 TTTCTTTTAGTCTTCTGTCTCACTAAGCAG 10 78 1 TCTTCTGTCT 0.925399 -223 TCTATTTTCGTCTCCAGACTACAAAATTTT 10 171 1 TCTCCAGACT 0.962829 -130 ATACCAATATTTTTGAGACTCTCTTCGTTC 10 212 0 TTTTGAGACT 0.863503 -89 ********** Masking position 3 Map Score: 3.1065 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 80 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 AAAGCGGGGCGAACACCCCGCTTTTTTTGT 1 40 1 GAACACCCCG 0.958655 -148 TTTCCGCCTATAAAAACCCGATTGACTCTC 3 62 1 TAAAAACCCG 0.881302 -47 AAAGAGCTCCGAAAAACTCGTTATTTTAGT 4 96 1 GAAAAACTCG 0.955296 -176 TTTATGAAATGAACACCCCGTCCCGGGTTC 4 218 0 GAACACCCCG 0.958655 -54 AGCTCGAAAAGAAAAATCCACTCT 7 5 0 GAAAAATCCA 0.669469 -84 AAGAAAACTCCTATAAAGCAGA 9 3 1 GAAAACTCCT 0.825925 -295 GCTTTTTGCTGAAAAACTTTGAGTGTTTTG 9 51 0 GAAAAACTTT 0.681706 -247 AAAGCTTGTTGAAAAACTTGATGACCACCT 9 76 1 GAAAAACTTG 0.807985 -222 GACGAAAATAGAAAAACCGTTAAAAAAGGC 10 153 0 GAAAAACCGT 0.864499 -148 TCAACTCCCCAAAAAACCCTTTTTCTTAAC 11 113 1 AAAAAACCCT 0.790754 -188 ********** Masking position 5 Map Score: 3.21281 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 152 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 11 CTCCGGAATTCCGGAGGAGGCCCAAGCTCT 4 45 0 CCGGAGGAGG 0.994221 -227 CTCCGGAATTCCGGAGGGGGGCTTTTTTTT 4 59 1 CCGGAGGGGG 0.99625 -213 GACAGGAACCCGGGACGGGGTGTTCATTTC 4 213 1 CGGGACGGGG 0.990056 -59 TAGCTTTCTTTCGAACGAGGGTTGAAGGAA 11 42 0 TCGAACGAGG 0.916189 -259 ********** Masking position 5 Map Score: 0.491126 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 11 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 TTTCTCTCTAAGTGCAAGGCGGTTGTAAGG 2 47 0 AGTGCAAGGC 0.941615 -150 CTGTAAAGATTGGGGAAAGGGAAGTGTATA 2 165 0 TGGGGAAAGG 0.869043 -32 CTTCTCTGTAAGGGCACAGCAGGGGAGAGC 4 20 1 AGGGCACAGC 0.904399 -252 AGGGCACAGCAGGGGAGAGCTTGGGCCTCC 4 30 1 AGGGGAGAGC 0.948338 -242 CAAAGGTAAAAGTGGTTGGCAAAATAAAGA 7 40 1 AGTGGTTGGC 0.88365 -49 ATCTCTATAAAGGGCATGGGTCCGTTTTTT 8 34 1 AGGGCATGGG 0.942294 -159 TTTTGTTATGTGTGGTAGGCTAATCTGCTT 9 26 0 TGTGGTAGGC 0.757579 -272 CATAAAAAATAGGGGATAGCATAAGATGTA 11 70 0 AGGGGATAGC 0.969035 -231 AAAATCGAAGAGAGGAAGGGTAGGATGAGC 11 221 0 AGAGGAAGGG 0.86455 -80 ********** Masking position 4 Map Score: 2.72457 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 134 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: 3.98858e-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: 3.98858e-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: 3.98858e-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