AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_ctra_reg_100.orf -o00310_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 htrB 131 Acyltransferase #2 sucA 300 Oxoglutarate Dehydrogenase #3 yaeT 300 Omp85 Analog #4 CT242 68 (OmpH-Like Outer Membrane Protein) #5 lpxD 27 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase #6 glyA 300 Serine Hydroxymethyltransferase #7 sohB 102 Protease #8 gidA 293 FAD-dependent oxidoreductase #9 cutE 63 Apolipoprotein N-Acetyltransferase #10 yciA 135 Acyl-CoA Thioester Hydrolase Motif number 1 TTACCCTTGGTAGGAAGCAAGTAAATTGGC 2 26 0 TAGGAAGCAA 0.877224 -275 ATTCGATACTTAAAAAAAAAGCAAAGTTTG 2 208 1 TAAAAAAAAA 0.673373 -93 CCTACAAATATAGGAAGAAAAGAGAACAGA 3 101 0 TAGGAAGAAA 0.98256 -200 CCCCACATATTAGGAAGAGACTACTCAAGA 3 173 0 TAGGAAGAGA 0.870245 -128 CCAGAAAGAGTAAGAATAAAACTTCATCCC 3 248 1 TAAGAATAAA 0.86011 -53 TATATTTTTATAGGAAAGAATT 4 57 1 TAGGAAAGAA 0.835018 -12 AGCTTCCTACTAGGAAAAAAGCTT 6 5 0 TAGGAAAAAA 0.975556 -296 ACTATAACTATAAGAAAAAGAAACGATGCT 6 140 0 TAAGAAAAAG 0.88944 -161 CTAAACTTTCTAGGAGAAAGAGGATTTATT 6 173 0 TAGGAGAAAG 0.840754 -128 TCTTGAGAAGAAAAGGACCTGGA 7 4 1 TGAGAAGAAA 0.955514 -99 TGTCAATTTTTGGGAATAAACTTGT 8 6 0 TGGGAATAAA 0.884145 -288 CACCAGGCGATGGGAAGAAGTTTACAATGG 8 37 0 TGGGAAGAAG 0.933757 -257 CGATACACTTTGAGAAGAAAACCTATGAGG 8 75 1 TGAGAAGAAA 0.955514 -219 CGTAAACCATTAAGAAGAAAACCATGTCAT 8 173 1 TAAGAAGAAA 0.968968 -121 TGTCATCTGTTAAGAAAAAACGAAGACTTA 8 197 1 TAAGAAAAAA 0.956745 -97 ACATTCAAGATGAGAGAAAAAGAATCCCCT 9 21 0 TGAGAGAAAA 0.846953 -43 AGTCTCGATATAGAAGAAAATCAAGAAATT 10 21 0 TAGAAGAAAA 0.575004 -115 ********** Masking position 5 Map Score: 23.0449 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 297 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 CCAAAATCTCTCCTGATCTATTTGTTTATGCC 2 92 0 TCCTTCTATT 0.936431 -209 AAGGATGCTCTCCTTCTCCTTTCGGATT 4 7 0 TCCTTCCTTT 0.985508 -62 AAGGAGAGCATCCTTCTCCTTTCACCTATTGG 4 24 1 TCCTTCCTTT 0.985508 -45 AAACGATGCTTCCAAGACCATTACCAAGCGCC 6 118 0 TCCAACCATT 0.858235 -183 TACCCACTCTCCCTTATCCTTTATGGGAATCT 6 222 0 CCCTTCCTTT 0.963099 -79 GCAGAGGCACTCTTTATCCTCTACCCACTCTC 6 243 0 TCTTTCCTCT 0.788186 -58 ATTTCCACCTCCACTGATTAAACCT 6 286 0 TCCATCCACT 0.967576 -15 AATACTATACTCCAGGTCCTTTTCTTCTCAAG 7 12 0 TCCATCCTTT 0.987777 -91 AGTATAGTATTCCAGGTCTTTTAATTTTTATT 7 33 1 TCCATCTTTT 0.967416 -70 GCCGATCTCTTCGACGTCTTTTTTTACGCTTA 8 240 0 TCGATCTTTT 0.793579 -54 GAGTTACAGGCCCACCTCTACTCCCCAGTCAT 10 67 0 CCCATCTACT 0.807983 -69 **** ****** Masking position 12 Map Score: 11.8367 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 173 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 CGTTTTATATAAAGAAGCTTTTACGTAGAGC 1 42 1 AAGAAGCTTT 0.933705 -90 GTAGTTACAGAAAGAAGCTTTGTGATCGAGA 1 76 0 AAGAAGCTTT 0.933705 -56 ACCAAGTAAGAATGGTGCTCTTCCCAGAAAG 3 225 1 AAGGTGCTCT 0.971624 -76 GTGAAAGGAGAAGGATGCTCTCCTTCTCCTT 4 18 0 AAGATGCTCT 0.962291 -51 TTTTTCCTAGTAGGAAGCTTCTTGACTTTTG 6 16 1 TAGAAGCTTC 0.88648 -285 TCGCTTACCATAAGGTGCTTTAATACCATTG 6 74 0 TAGGTGCTTT 0.935168 -227 GACTAGGGAAAATGGGGCGCTTGGTAATGGT 6 103 1 AAGGGGCGCT 0.910977 -198 AAGAAAAAGAAACGATGCTTCCAAGACCATT 6 128 0 AAGATGCTTC 0.962186 -173 TTTCTAGGAGAAAGAGGATTTATTTTAACTA 6 166 0 AAGAGGATTT 0.869604 -135 GTAACTTCTAAGGGGATTCTTTTTCTCTC 9 9 1 TAGGGGATTC 0.769292 -55 TAAAGGGGCTCCCTTACTAGCT 9 52 0 AAGGGGCTCC 0.9807 -12 ** ******** Masking position 2 Map Score: 9.39642 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 234 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 GAATTTTCTAAAAGTATCACCTTCAATCGATA 2 269 1 AAAGACACCT 0.957997 -32 TGCTAGTGACCAGCACCCCCTCTGAGTTCTC 3 10 1 CCAGACCCCT 0.956772 -291 AAAAGCCCGAAAAGCAACCCCTCTAGCAGGTT 3 47 0 AAAGACCCCT 0.989252 -254 TTTATCTAGAAAAGTCTGCGCTAGGGATGAAG 3 269 0 AAAGCGCGCT 0.932674 -32 AGACCATTACCAAGCGCCCCATTTTCCCTAGT 6 104 0 CAAGGCCCAT 0.814659 -197 TCGCCTGGTGAAAGCCGGCGATACACTTTGAG 8 57 1 AAAGCGCGAT 0.774334 -237 TGAGAACGGGCAAGCACCCGATCCTCATAGGT 8 95 0 CAAGACCGAT 0.892757 -199 AGTCTTTTGAAAAGACTCAGCTAATGCCTATG 8 125 0 AAAGCCAGCT 0.935065 -169 GATGAGAGAAAAAGAATCCCCTTAGAAGTTAC 9 11 0 AAAGACCCCT 0.989249 -53 GTAAGCTAGTAAGGGAGCCCCTTTA 9 49 1 AAGGACCCCT 0.932151 -15 TCTCAGAGTTACAGGCCCACCTCTACTCCCCA 10 72 0 ACAGCCACCT 0.904612 -64 **** * ***** Masking position 12 Map Score: 9.3748 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 188 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 GGCTAGTATGACTTTGCTAGTAGTTACAGA 1 96 0 ACTTTGCTAG 0.968048 -36 GATGCAGTTACCCTTGGTAGGAAGCAAGTA 2 33 0 CCCTTGGTAG 0.879381 -268 GATAAGCCAAGCTCTGCTAGCTTTTGTAAG 2 160 1 GCTCTGCTAG 0.925982 -141 TTCTCCCCCGAACCTGCTAGAGGGGTTGCT 3 37 1 AACCTGCTAG 0.92256 -264 CCTAGCGCAGACTTTTCTAGATAAAGGAAG 3 276 1 ACTTTTCTAG 0.89527 -25 ACGGCACTCCTCGGCTAGCTTCGCATG 5 10 0 CCTCGGCTAG 0.892418 -18 AGAAAGTCTAAACTTTCTAGGAGAAAGAGG 6 180 0 AACTTTCTAG 0.714678 -121 ATAAAGAGTGCCTCTGCAAGGTCTTGCAAG 6 258 1 CCTCTGCAAG 0.916173 -43 CACTGATTAAACCTTGCAAGACCTTGCAGA 6 270 0 ACCTTGCAAG 0.93463 -31 TAAAGGGGCTCCCTTACTAGCTTACATTCA 9 44 0 CCCTTACTAG 0.874552 -20 ATCACCCTTCTATATGAGTCTAA 10 123 0 ACCCTTCTAT 0.632243 -13 ********** Masking position 9 Map Score: 6.44173 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 159 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 GGAATTTTCTAAAAGTATCACCTTCAATCGAT 2 268 1 AAAAGATACC 0.981103 -33 AAAAAGCCCGAAAAGCAACCCCTCTAGCAGGT 3 48 0 AAAAGAACCC 0.928653 -253 CTTTATCTAGAAAAGTCTGCGCTAGGGATGAA 3 270 0 AAAAGCTCGC 0.969648 -31 TCTTTCCTATAAAAATATAACCAATAGGTGAA 4 44 0 AAAAAATACC 0.870704 -25 AAGTCTTTTGAAAAGACTCAGCTAATGCCTAT 8 126 0 AAAAGCTAGC 0.963577 -168 GAGTCTTTTCAAAAGACTTACCAATTATTCCT 8 139 1 AAAAGCTACC 0.9843 -155 AGATGAGAGAAAAAGAATCCCCTTAGAAGTTA 9 12 0 AAAAGATCCC 0.9843 -52 ***** ** *** Masking position 4 Map Score: 5.56586 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 28 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 CTTTGTGATCGAGACAGGCTCTACGTAAAA 1 60 0 GAGACAGGCT 0.961044 -72 GATCAGGAGAGATTTTGGCTAATAAAATAC 2 106 1 GATTTTGGCT 0.873041 -195 AAAGCTAGCAGAGCTTGGCTTATCAGTTGA 2 154 0 GAGCTTGGCT 0.973932 -147 GGACGCCTATGAGATTGGCTTCTGACCAAG 3 201 1 GAGATTGGCT 0.990308 -100 AAGGATAAGGGAGAGTGGGTAGAGGATAAA 6 233 1 GAGAGTGGGT 0.942146 -68 AGACGTCGAAGAGATCGGCATAAAAATAGA 8 253 1 GAGATCGGCA 0.905267 -41 GACTAGTCAAGATAGAGGCTATTAGACTCA 10 102 1 GATAGAGGCT 0.925291 -34 ********** Masking position 2 Map Score: 3.11656 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 8 TGTGTTCCGTAAGGCTAGTATGACTTTGCT 1 108 0 AAGGCTAGTA 0.918163 -24 AAGAAGTCAGGAGGCTAGGGTATTCGATAC 2 187 1 GAGGCTAGGG 0.967726 -114 CTATATTTGTAGGGCTAGTCAAATTATCCT 3 118 1 AGGGCTAGTC 0.844439 -183 ATATTAGGAAGAGACTACTCAAGACCTATC 3 167 0 GAGACTACTC 0.953484 -134 CTTATGGTAAGCGACTAGGGAAAATGGGGC 6 91 1 GCGACTAGGG 0.853304 -210 CTTCTATATCGAGACTACTATCCATTACAG 10 35 1 GAGACTACTA 0.928821 -101 CTGTAACTCTGAGACTAGTCAAGATAGAGG 10 90 1 GAGACTAGTC 0.979849 -46 AGTCAAGATAGAGGCTATTAGACTCATATA 10 106 1 GAGGCTATTA 0.883565 -30 ********** Masking position 7 Map Score: 2.16029 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 9 TTTGCTCTGTCTGAGCAAAAGATGCAGTTA 2 53 0 CTGAGCAAAA 0.972883 -248 TTTGCTCAGACAGAGCAAAAAGTGAGCAGG 2 64 1 CAGAGCAAAA 0.980938 -237 AGAAAATTCCCATAGCAAAATTTTTATTTT 2 248 0 CATAGCAAAA 0.949639 -53 ATCATATTCTTACAGCAAAAGTCAAGAAGC 6 32 0 TACAGCAAAA 0.907907 -269 TTTAGACTTTCTCATCAAAAGATTAGATTC 6 198 1 CTCATCAAAA 0.873133 -103 ********** Masking position 4 Map Score: 1.01459 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 61 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 10 TGCTAGTGACCAGCACCCCCTCTGAGTTC 3 10 1 CCAGCACCCC 0.992831 -291 AGACCATTACCAAGCGCCCCATTTTCCCTA 6 106 0 CAAGCGCCCC 0.992152 -195 AAACTTCTTCCCATCGCCTGGTGAAAGCCG 8 44 1 CCATCGCCTG 0.930304 -250 TGAGAACGGGCAAGCACCCGATCCTCATAG 8 97 0 CAAGCACCCG 0.988282 -197 ********** Masking position 3 Map Score: 0.118913 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 4 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 ********** No masking Map Score: -1.2126e-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 12 ********** No masking Map Score: -1.2126e-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: -1.2126e-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