AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_ctra_reg_100.orf -o00340_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 yaeT 300 Omp85 Analog #3 CT242 68 (OmpH-Like Outer Membrane Protein) #4 lpxD 27 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase #5 CT355 300 hypothetical protein #6 CT426 196 Fe-S oxidoreductase #7 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #8 cutE 63 Apolipoprotein N-Acetyltransferase #9 yciA 135 Acyl-CoA Thioester Hydrolase #10 hisS 300 Histidyl tRNA Synthetase #11 ygcA 85 rRNA Methyltransferse #12 hctA 300 Histone-Like Developmental Protein Motif number 1 GCTAGTAGTTACAGAAAGAAGCTTTGTGAT 1 81 0 ACAGAAAGAA 0.687704 -51 AATATAGGAAGAAAAGAGAACAGAGAGAAC 2 95 0 GAAAAGAGAA 0.89623 -206 TGCTCTTCCCAGAAAGAGTAAGAATAAAAC 2 240 1 AGAAAGAGTA 0.70078 -61 AGACTTTTCTAGATAAAGGAAGTAATA 2 284 1 AGATAAAGGA 0.840729 -17 ATAACCAATAGGTGAAAGGAGAAGGATGCT 3 30 0 GGTGAAAGGA 0.622953 -39 CTTAAATATCGAAAAGAGGGGTAACTAAGA 5 20 0 GAAAAGAGGG 0.840377 -281 GCTTATATTCTAAAAAAGAACCTACCCTCG 5 165 0 TAAAAAAGAA 0.652505 -136 TAAGATCCAAAGAAAAAGGGGAGGAGGAAC 5 234 1 AGAAAAAGGG 0.927264 -67 AGACGAGTAGAAATAAAGAAGTCATGAAGG 6 18 0 AAATAAAGAA 0.792043 -179 GACTGCTGTCAGAAAAAGAAGTCTTGTCCC 6 143 1 AGAAAAAGAA 0.954365 -54 TTGCTAAAAAAAAAAAAGGATAATATACGG 7 59 1 AAAAAAAGGA 0.969619 -42 TCAAGATGAGAGAAAAAGAATCCCCTTAGA 8 17 0 AGAAAAAGAA 0.954365 -47 TATTAAGCTAAATGAAAGGAGTATTGACGA 10 29 0 AATGAAAGGA 0.795195 -272 TTTGCTGTGTAAAGAGAGGGAGTAGGGGTG 10 78 1 AAAGAGAGGG 0.882369 -223 AGGTGTGTCAAATAAAAGAAATAATAGAGA 10 145 1 AATAAAAGAA 0.807557 -156 TTCTTTGCGCAAAAAAAGAACTTTAAAAAG 10 235 1 AAAAAAAGAA 0.956418 -66 GCCCTCTATAAAAAAGAGAAAGCGCTAAAA 11 13 0 AAAAAGAGAA 0.95084 -73 AATGAGAAGAGGAAAGAGGGCCCTGTTGAT 11 49 0 GGAAAGAGGG 0.833809 -37 AAAAAAGAGAAGGGATCAATG 11 75 0 AAAAAGAGAA 0.95084 -11 TTTAGAAAAGAAAGAAAGGAGCTTGTTCTC 12 25 0 AAAGAAAGGA 0.953063 -276 ********** Masking position 5 Map Score: 20.5714 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 536 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 TGCTAGTGACCAGCACCCCCTCTGAGTTC 2 10 1 CCAGCACCCC 0.652118 -291 AAGAATAAAACTTCATCCCTAGCGCAGACT 2 259 1 CTTCATCCCT 0.75317 -42 AGGATGCTCTCCTTCTCCTTTCGGATT 3 8 0 CCTTCTCCTT 0.962636 -61 AGGAGAGCATCCTTCTCCTTTCACCTATTG 3 25 1 CCTTCTCCTT 0.962636 -44 CGGCTGGGTCCCTCCTCCCCTATAGCTTTT 5 127 1 CCTCCTCCCC 0.994346 -174 TGGGTGTTTGCCACATCTCTAGGGAGGCGG 5 204 1 CCACATCTCT 0.67426 -97 TTGGATCTTACCGCCTCCCTAGAGATGTGG 5 214 0 CCGCCTCCCT 0.986705 -87 TTGGGTTGTTCCTCCTCCCCTTTTTCTTTG 5 241 0 CCTCCTCCCC 0.994346 -60 GTCGCTGCGGCCACATCCTTTAGATAGGGG 6 116 0 CCACATCCTT 0.893795 -81 CAGGCCCACCTCTACTCCCCAGTCATCTCT 9 63 0 TCTACTCCCC 0.678265 -73 CATCCTCACCCCTACTCCCTCTCTTTACAC 10 84 0 CCTACTCCCT 0.974409 -217 CCACAATACGCCGCATCCTCACCCCTACTC 10 97 0 CCGCATCCTC 0.892045 -204 TACTCGAAAACCTGCTCCTTTTCTCTCTAT 10 168 0 CCTGCTCCTT 0.965292 -133 CTCATTGATCCCTTCTCTTTTTT 11 73 1 CCTTCTCTTT 0.74952 -13 ********** Masking position 7 Map Score: 18.7113 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 220 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 CTTTATATAAAACGCTGTTTCAGTTGAAAA 1 26 0 AACGCTGTTT 0.946807 -106 GCTCTACGTAAAAGCTTCTTTATATAAAAC 1 43 0 AAAGCTTCTT 0.96029 -89 TCTCGATCACAAAGCTTCTTTCTGTAACTA 1 76 1 AAAGCTTCTT 0.96029 -56 AAGGAGAAGGAGAGCATCCTTCTCCTTTCA 3 18 1 AGAGCATCCT 0.797896 -51 TTGAGGATATAACGCTTTTTTGTTAAAAGT 5 90 1 AACGCTTTTT 0.942625 -211 ACACCCAAACAAAGCAGCTTATATTCTAAA 5 181 0 AAAGCAGCTT 0.879271 -120 TATAGGAGTAACAGCTGTTTTGATAGGGTC 6 70 1 ACAGCTGTTT 0.834855 -127 TATTTTAGCGCTTTCTCTTTTTTATA 11 7 1 AGCGCTTTCT 0.906092 -79 AACAAGGTTCAGCGCTTTCTATTAAAAGAA 12 53 1 AGCGCTTTCT 0.906092 -248 GATGTCAAATAAAGCTGCTTTAGGATCCTT 12 178 1 AAAGCTGCTT 0.963235 -123 ********** Masking position 1 Map Score: 8.6788 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 262 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 CCTGCTAGAGGGGTTGCTTTTCGGGCTTTTT 2 49 1 GGGTTCTTTT 0.971602 -252 GTTGCTTTTCGGGCTTTTTTTCGTTGTTTTC 2 61 1 GGGCTTTTTT 0.865542 -240 TCTGACGGCTGGGTCCCTCCTCCCCTATAGC 5 122 1 GGGTCCTCCT 0.948521 -179 GGACGAGGGTAGGTTCTTTTTTAGAATATAA 5 162 1 AGGTTTTTTT 0.885592 -139 TAAGAATTTTGGGTTGTTCCTCCTCCCCTTT 5 248 0 GGGTTTTCCT 0.940799 -53 TGTTTTGATAGGGTCTTTCCTACTAGGAAGA 6 85 1 GGGTCTTCCT 0.928837 -112 CCTTTAGATAGGGGTCTTCCTAGTAGGAAAG 6 99 0 GGGGTTTCCT 0.948468 -98 GATAATATACGGGGTCTCTTTGTCAGGGTTT 7 77 1 GGGGTTCTTT 0.882863 -24 AACTTCTAAGGGGATTCTTTTTCTCTCATCT 8 13 1 GGGATCTTTT 0.915339 -51 TAAAGGGGCTCCCTTACTAGCTTAC 8 49 0 GGGGCCCCTT 0.904578 -15 TTTTTTATAGAGGGCACTTTTATCAACAGGG 11 28 1 AGGGCCTTTT 0.912254 -58 TTTTATCAACAGGGCCCTCTTTCCTCTTCTC 11 45 1 AGGGCCTCTT 0.918549 -41 GGTCTGAATAGGGTTTCTTTTAATAGAAAGC 12 66 0 GGGTTCTTTT 0.971602 -235 GTTTATCAATAGGTTATTTTTCCTCTGTTAA 12 132 0 AGGTTTTTTT 0.885592 -169 CAACAACTAGAGGATATTTTTTC 12 288 1 AGGATTTTTT 0.709816 -13 ***** ***** Masking position 11 Map Score: 17.1381 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 209 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 AGCAAAGTCATACTAGCCTTACGGAACACA 1 108 1 TACTAGCCTT 0.907478 -24 AGGATAATTTGACTAGCCCTACAAATATAG 2 118 0 GACTAGCCCT 0.934249 -183 GATAGGTCTTGAGTAGTCTCTTCCTAATAT 2 167 1 GAGTAGTCTC 0.979895 -134 CTGTAATGGATAGTAGTCTCGATATAGAAG 9 35 0 TAGTAGTCTC 0.95118 -101 CCTCTATCTTGACTAGTCTCAGAGTTACAG 9 90 0 GACTAGTCTC 0.98495 -46 TATATGAGTCTAATAGCCTCTATCTTGACT 9 106 0 TAATAGCCTC 0.827831 -30 GCAGGTTTTCGAGTAGTCCTGAAAACTCTT 10 183 1 GAGTAGTCCT 0.916919 -118 TGTATAACCGGACTATTCTCACGAAAAATG 10 279 0 GACTATTCTC 0.879464 -22 ********** Masking position 5 Map Score: 5.41898 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 46 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 AAAACGCTGTTTCAGTTGAAAAACGCTCATCA 1 16 0 TTCAGTGAAA 0.784377 -116 GCCCTACAAATATAGGAAGAAAAGAGAACAGA 2 101 0 TATAGAAGAA 0.864486 -200 CCTATCCAATTACAATAGAGAATCGAGGATAA 2 141 0 TACAAAGAAA 0.539504 -160 GTTATATTTTTATAGGAAAGAATT 3 55 1 TATAGAAAAA 0.919427 -14 CTTTTCGATATTTAAGTGAAAAAATTCCAGAA 5 34 1 TTTAATGAAA 0.698546 -267 TCAGAACACTTTTAACAAAAAAGCGTTATATC 5 95 0 TTTAAAAAAA 0.829257 -206 TAGGTTCTTTTTTAGAATATAAGCTGCTTTGT 5 171 1 TTTAGATAAA 0.820389 -130 ATTTGTAGTTTTTAGGTAGAAAAACCTTAAGA 5 274 0 TTTAGTAGAA 0.813883 -27 CTTTTTTTTTTTTAGCAAGCAAGCGATATCAA 7 45 0 TTTAGAAGAA 0.924811 -56 GTAGTCTCGATATAGAAGAAAATCAAGAAATT 9 21 0 TATAGAGAAA 0.938701 -115 CTTAATAGCTTTTAGAAGACAATACGTTTGCT 10 52 1 TTTAGAGAAA 0.96724 -249 CTGAACCTTGTTTAGAAAAGAAAGAAAGGAGC 12 33 0 TTTAGAAAAA 0.956522 -268 ***** *** ** Masking position 4 Map Score: 5.27069 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 219 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 7 CGTTGTTTTCAAAGTTCTCTCTGTTCTCTTT 2 82 1 AAGTTCTCTC 0.933179 -219 CCAAGTAAGAATGGTGCTCTTCCCAGAAAGA 2 226 1 AGGTGCTCTT 0.958853 -75 TGAAAGGAGAAGGATGCTCTCCTTCTCCTTT 3 17 0 AGATGCTCTC 0.881195 -52 GTTCTGACGGCTGGGTCCCTCCTCCCCTATA 5 120 1 CGGGTCCCTC 0.89531 -181 CATCCTTTAGATAGGGGTCTTCCTAGTAGGA 6 102 0 AAGGGGTCTT 0.865022 -95 GGATAATATACGGGGTCTCTTTGTCAGGGTT 7 76 1 CGGGTCTCTT 0.76982 -25 TAAAGGGGCTCCCTTACTAGCTT 8 51 0 AGGGGCTCCC 0.958363 -13 TCTGTAATGGATAGTAGTCTCGATATAGAAG 9 35 0 AAGTAGTCTC 0.682829 -101 TTGGTGTAACATGGTGGTCTCGTTCTTTGCG 10 213 1 AGGTGGTCTC 0.973452 -88 CCTGTTGATAAAAGTGCCCTCTATAAAAAAG 11 27 0 AAGTGCCCTC 0.968744 -59 ACTTTTATCAACAGGGCCCTCTTTCCTCTTC 11 43 1 AAGGGCCCTC 0.976519 -43 * ********* Masking position 9 Map Score: 5.84159 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 137 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 8 TGTTTCAGTTGAAAAACGCTCATCATAGCA 1 11 0 GAAAAACGCT 0.948906 -121 AGGGGAGGAGGAACAACCCAAAATTCTTAA 5 250 1 GAACAACCCA 0.927615 -51 TTTTTAGGTAGAAAAACCTTAAGAATTTTG 5 268 0 GAAAAACCTT 0.910042 -33 TTCCTAGTAGGAAAGACCCTATCAAAACAG 6 84 0 GAAAGACCCT 0.959856 -113 CCCGTGAAAAGCAAAACTCACAAACTGATA 6 171 1 GCAAAACTCA 0.847742 -26 GCAAAACCCTGACAAAGAGA 7 91 0 GCAAAACCCT 0.981888 -10 ********** Masking position 6 Map Score: 0.470502 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 9 TCTATTGTAATTGGATAGGTCTTGAGTAGT 2 154 1 TTGGATAGGT 0.940075 -147 TAACAGCTGTTTTGATAGGGTCTTTCCTAC 6 78 1 TTTGATAGGG 0.953715 -119 GCCACATCCTTTAGATAGGGGTCTTCCTAG 6 107 0 TTAGATAGGG 0.953715 -90 TGCATAGGGTCTGAATAGGGTTTCTTTTAA 12 74 0 CTGAATAGGG 0.956976 -227 AAACTATGTGCTGCATAGGGTCTGAATAGG 12 85 0 CTGCATAGGG 0.970559 -216 ********** Masking position 5 Map Score: 0.17558 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 21 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 ********** No masking Map Score: -4.23951e-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 11 ********** No masking Map Score: -4.23951e-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: -4.23951e-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