AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ifruR_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 CT203 213 hypothetical protein #2 ybhI 29 Dicarboxylate Translocator #3 CT330 208 hypothetical protein #4 pykF 96 Pyruvate Kinase #5 ptsH 136 PTS Phosphocarrier Protein Hpr #6 CT646 100 hypothetical protein #7 pgk 127 Phosphoglycerate Kinase Motif number 1 CTCTTTGTTAATGCTTTTTTTTGTCATAAAT 1 32 1 AGCTTTTTTT 0.97463 -182 ACGTCTTTAGAAGCTTCTCTTGCCTTGTATG 3 87 1 AGCTTCTCTT 0.987807 -122 GTATAGTTGAAGGCTTCTTTCATTTCGGATA 4 34 1 AGCTTCTTTC 0.881003 -63 GAAAAAAAGTACGCTTTTCTTCTCTTTAGCT 5 24 1 AGCTTTTCTT 0.989927 -113 TAAACCCTTAGAGCTTCTTTTCAAAGCTAAA 5 48 0 GGCTTCTTTT 0.96315 -89 TTTATAATTAATGTTTTTCTTGAAAAAGATG 6 24 1 AGTTTTTCTT 0.980401 -77 CTTGAAAAAGATGTTTTTATTTTTTAAAATG 6 42 1 AGTTTTTATT 0.885566 -59 TTAGCGTTTTTCTTTATCTTTTTA 6 87 0 GGTTTTTCTT 0.976337 -14 ATAAAGGCTTGAGTTTTCCTTTGCTTAGGCC 7 74 1 GGTTTTCCTT 0.906016 -54 * ********* Masking position 6 Map Score: 11.213 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 259 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 2 CGAACTGTTATCTTTTGCGTGTCAACTTAA 1 85 1 TCTTTTGCGT 0.913308 -129 AACTTAATGTTGTTTAGATTCGCCTTGTCT 1 108 1 TGTTTAGATT 0.935461 -106 GGAAAAAATCTCTTTTGAAGACGCTATGAA 3 17 1 TCTTTTGAAG 0.837041 -192 ACCAACCACGTCTTTAGAAGCTTCTCTTGC 3 80 1 TCTTTAGAAG 0.812118 -129 GCTTTTCTTCTCTTTAGCTTTGAAAAGAAG 5 36 1 TCTTTAGCTT 0.970912 -101 ATTATCGTATTCTTTTGATTGGATTTAGCT 5 78 1 TCTTTTGATT 0.967274 -59 TAAAAAACTCTGTTTATAATTAATGTTTTT 6 12 1 TGTTTATAAT 0.706859 -89 TTATAATTAATGTTTTTCTTGAAAAAGATG 6 25 1 TGTTTTTCTT 0.894652 -76 TTGAAAAAGATGTTTTTATTTTTTAAAATG 6 43 1 TGTTTTTATT 0.863541 -58 TTAGCGTTTTTCTTTATCTTTTTAAAATGA 6 81 0 TCTTTATCTT 0.924604 -20 GCTTGAGTTTTCCTTTGCTTAGGCCTATAA 7 80 1 TCCTTTGCTT 0.881931 -48 ********** Masking position 5 Map Score: 10.6811 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 380 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 TGGAGCTCGGAGTCTAAGCAGACAAGGCGA 1 127 0 AGTCTAAGCA 0.968343 -87 CGAGCTCCATGGTCGTTGCTCTGCTACGGC 1 148 1 GGTCGTTGCT 0.909524 -66 AAAACGAGCAGGCCGTAGCAGAGCAACGAC 1 159 0 GGCCGTAGCA 0.991549 -55 GCATTCAAGAAGTCGAAGCACGTATTAAAC 3 154 1 AGTCGAAGCA 0.985744 -55 TTTTCTTATAGGCCTAAGCAAAGGAAAACT 7 85 0 GGCCTAAGCA 0.985961 -43 ********** Masking position 4 Map Score: 3.13767 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 4 ATCTATAATAGCGTTGCACGCTCTCGAACT 1 61 1 GCGTTGCACG 0.984438 -153 GTTTAGATTCGCCTTGTCTGCTTAGACTCC 1 119 1 GCCTTGTCTG 0.987175 -95 TACGGCCTGCTCGTTTTCTGAGAGTCCTTC 1 172 1 TCGTTTTCTG 0.82122 -42 ACCTTCAAGCCTTTCACGGAAGGAAGGA 1 196 0 GCCTTTCACG 0.976132 -18 AGCTTCTCTTGCCTTGTATGAAGAGGCTGA 3 98 1 GCCTTGTATG 0.989344 -111 AGTATTCTTCCCTGTACGTGTAAAAACA 5 119 0 TCCCTGTACG 0.947472 -18 ********** Masking position 5 Map Score: 2.45562 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 61 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 GTGAGTCTCGCATTCAAGAAGTCGAAGCAC 3 145 1 CATTCAAGAA 0.949671 -64 TCATTTCGGATATTCTAGAAGATATTCTAC 4 53 1 TATTCTAGAA 0.957207 -44 AGCGTACTTTTTTTCTAAAACTAGCCTT 5 9 0 TTTTCTAAAA 0.863283 -128 AAAAACATCTTTTTCAAGAAAAACATTAAT 6 30 0 TTTTCAAGAA 0.857753 -71 GAAGAGCGCTCATTTTAAAAAATAAAAACA 6 53 0 CATTTTAAAA 0.882903 -48 GAGCGCTCTTCATTTTAAAAAGATAAAGAA 6 72 1 CATTTTAAAA 0.882903 -29 ********** Masking position 4 Map Score: 1.63244 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 166 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 CATTAACAAAGAGCTACAGGATAACGATAGAT 1 13 0 GAGTCAGGAT 0.989014 -201 ATCTATAATAGCGTTGCACGCTCTCGAACTGT 1 61 1 GCGTCACGCT 0.954679 -153 CTTAGACTCCGAGCTCCATGGTCGTTGCTCTG 1 139 1 GAGTCATGGT 0.935484 -75 ATATTTTGTATAGTTGAAGGCTTCTTTCATTT 4 27 1 TAGTAAGGCT 0.977573 -70 ATGTGGCACTGAGATAAAGGCTTGAGTTTTCC 7 61 1 GAGTAAGGCT 0.992308 -67 TAAGAAAATTTAGGTTAAGGATCAGATAAGC 7 107 1 TAGTAAGGAT 0.950851 -21 *** * ****** Masking position 5 Map Score: 1.37111 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 59 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 ********** No masking Map Score: -1.69577e-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 8 AGAGCGTGCAACGCTATTATAGATTTATGACAAAAA 1 49 0 ACGCTATATT 0.962066 -165 ATAGCGTTGCACGCTCTCGAACTGTTATCTTTTGCG 1 68 1 ACGCTGAATT 0.923023 -146 GGAAGGAAGGACTCTCAGAAAACGAGCAGGCCGTAG 1 171 0 ACTCTAAAAG 0.738473 -43 TCTTTTGAAGACGCTATGAAACGTTTGGAAGAGATC 3 27 1 ACGCTAAATT 0.984535 -182 AAGGCAAGAGAAGCTTCTAAAGACGTGGTTGGTTGA 3 77 0 AAGCTAAAGT 0.708698 -132 TGAATGCGAGACTCACATATACGCATTAATTGATCA 3 125 0 ACTCAATAAT 0.778618 -84 GAAGCCTTCAACTATACAAAATATTTAGCAACCGCA 4 15 0 ACTATAAATT 0.891334 -82 AAGATATTCTACTCACTAATACCGGTATCCCGATTT 4 71 1 ACTCAATAGT 0.844882 -26 TCAAAAGAATACGATAATAAACCCTTAGAGCTTCTT 5 60 0 ACGATAAATT 0.916568 -77 ATGAAGAATCACTCAGACAAAACATTTTTAGTCTGC 7 27 0 ACTCAAAATT 0.964962 -101 TTCATGTGGCACTGAGATAAAGGCTTGAGTTTTCCT 7 58 1 ACTGAAAATT 0.801654 -70 ***** *** ** Masking position 11 Map Score: 1.70233 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 9 ********** No masking Map Score: -1.69577e-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 10 ********** No masking Map Score: -1.69577e-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: -1.69577e-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