AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_ctra_reg_100.orf -o02010_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 ytgA 300 Solute Protein Binding Family #2 glnP 206 ABC Amino Acid Transporter Permease #3 oppA_2 194 Oligopeptide binding protein permease #4 CT196 223 hypothetical protein #5 gcp_1 75 O-Sialoglycoprotein Endopeptidase #6 oppB_1 158 Oligopeptide Permease #7 oppC_1 31 Oligopeptide Permease #8 artJ 68 Arginine Binding Protein #9 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #10 yebL 300 Solute-binding protein #11 oppA_4 250 oligopeptide Binding Lipoprotein #12 fliY 45 Glutamine Binding Protein #13 CT488 88 hypothetical protein #14 glgC 192 Glucose-1-P Adenyltransferase #15 dppD 160 ABC Transport ATPase Motif number 1 ACGCGCTAGATTTTCCTTTTGGTTGAGGAT 1 54 1 TTTTCCTTTT 0.879554 -247 ATAAGCGAGGTTCTTTTTTTGGAGGGGGAG 1 115 1 TTCTTTTTTT 0.809341 -186 TAAAATAGAGTTTTTCTTATGATCCCATGT 1 170 1 TTTTTCTTAT 0.888662 -131 TGTACACGAGTTTTTATTTTTTTTCGAAAC 2 66 1 TTTTTATTTT 0.786247 -141 TTAGGAAAGGCTTTTTTTATAAGAACCTTT 2 133 1 CTTTTTTTAT 0.583287 -74 ATACTGGGCATTTTTTTCATAAAGGGGGTG 3 15 0 TTTTTTTCAT 0.723838 -180 ATTGTTAAGGTTTTTCTTTTTTTTATTGGT 3 64 1 TTTTTCTTTT 0.975287 -131 GCCAAAACTGTTTTTCTGTTACCAATAAAA 3 84 0 TTTTTCTGTT 0.833464 -111 CTTCTAAAAATTTTACTTTTACAAAGTTGA 4 23 1 TTTTACTTTT 0.825204 -201 AATGCTATTTCATTTCTTTTGCAAAAACTC 4 170 1 CATTTCTTTT 0.67164 -54 ATTCTTATTTTTTTTAAGAATCATG 8 6 1 TATTTTTTTT 0.567345 -63 ATTAAACGTTCTCTTCTCTTCAAGAGAAGA 9 15 1 CTCTTCTCTT 0.866398 -122 AAAAAACGCCCTCTTCTCTTGAAGAGAAGA 9 26 0 CTCTTCTCTT 0.866398 -111 GAAGAGGGCGTTTTTTTCATTGAAAAATCT 9 40 1 TTTTTTTCAT 0.723838 -97 CTTTCTATTTCTTTTCTCTTCCCTGTGTGT 9 68 1 CTTTTCTCTT 0.952863 -69 TTTTCCTTGTTTCTTCTCTTAACTCATGAA 9 109 0 TTCTTCTCTT 0.925368 -28 TTCGTACAATTTTTGCTTTTTCTTTAAAAA 10 103 1 TTTTGCTTTT 0.879554 -198 CAACTCTCTTTTTTTTTCTTAAAAGATTCT 11 37 1 TTTTTTTCTT 0.928363 -214 AAGAAAAGCTTTTTCCTCTTACAAACAAGA 11 123 0 TTTTCCTCTT 0.877328 -128 GAGGAAAAAGCTTTTCTTTTGCTATAATTC 11 135 1 CTTTTCTTTT 0.95379 -116 TGGATAAAAATTTTTCTCTTGAAT 12 32 1 TTTTTCTCTT 0.974779 -14 AGAGTGGATTTTTCTTTTCGAGCTGTTG 13 9 1 TTTTTCTTTT 0.975287 -80 AATTAGATAATTTTTATTTTTCAAACATCT 14 69 1 TTTTTATTTT 0.786247 -124 AATAAATCGATTTTATTTTTAGATGTTTGA 14 89 0 TTTTATTTTT 0.612845 -104 AACCAAAATTTTTTGTTTTTTTCTAAGATT 15 97 1 TTTTGTTTTT 0.710021 -64 ********** Masking position 4 Map Score: 30.6896 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 566 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 CTCATCTCGAAGAGACAATTCTAAATAATTTTAACA 1 16 0 AAGATTAAAT 0.862869 -285 CGCTTATCGCAAAGATACTTTTAACAGAATGAATTT 1 86 0 AAGATTAACA 0.786824 -215 ATATTGAACGAAAGGTTCTTATAAAAAAAGCCTTTC 2 137 0 AAGGTTAAAA 0.865606 -70 GGATTGTACAAAAAACCATAGCAAAAAGCCAAAACT 3 105 0 AAAATAAAAA 0.862205 -90 AATTTAAAGTAGAGAGTTTTTGCAAAAGAAATGAAA 4 177 0 AAGATTCAAA 0.917407 -47 TAATTTAATAAAGGATTTCTAAAACAAACTC 7 8 1 AAAATTTAAA 0.655389 -24 GAAAAGAAATAGAAAGATTTTTCAATGAAAAAAACG 9 48 0 AAAATTCAAT 0.577338 -89 TCGCCGGCAAAAAGACAGTAGAAAGAATATTCTTAG 10 40 1 AAGATAAAGA 0.642215 -261 AAAGCTGGAGATAAAATCTTAAAAAACTAAGAATAT 10 66 0 AAAATTAAAA 0.959479 -235 AAGAAAAAGCAAAAATTGTACGAAAAAAGCTGGAGA 10 91 0 AAAATAAAAA 0.862205 -210 GGTTCAGAGCAGAGAAGCTTTAGAAAACGGGGTGAG 10 140 0 AAGATTGAAA 0.805582 -161 TAAGAAAAAAAAAGAGAGTTGAAAATTCAACTCTCT 11 22 0 AAGATTAAAT 0.86287 -229 GAGCTGGTATAGAGAATCTTTTAAGAAAAAAAAAGA 11 43 0 AAGATTAAGA 0.871673 -208 ACTTACTGAAAGAAATATTTCAAAAAATATTTAGGA 11 81 0 AAAATTAAAA 0.959479 -170 TGACAAAGGTAAAAGTGGTTGGCAAAATAAAGAGCT 13 37 1 AAAGTTCAAA 0.583019 -52 GATTTTATTTTTAGATGTTTGAAAAATAAAAATTAT 14 75 0 TAGATTAAAA 0.691842 -118 ATTTTAAAAAATAAATTATTAAAAAAGCCAGACAAA 14 143 0 AAAATTAAAA 0.959479 -50 CGCCACCATAAAAAATAATTTTAAAAAATAAATTAT 14 160 0 AAAATTAAAA 0.959479 -33 CATTTTTCTCAAAGACAATTAAAAAAGGCTTAT 15 8 0 AAGATTAAAA 0.972073 -153 TGTCTTTGAGAAAAATGCTCCCAAAATATACCTCCT 15 27 1 AAAATCAAAA 0.738133 -134 CTCGAGCGTGAAAAATCTTAGAAAAAAACAAAAAAT 15 104 0 AAAATAAAAA 0.862205 -57 * *** ** **** Masking position 9 Map Score: 21.2251 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 3 AGGAGCTCCCCCTCCAAAAAAAGAACCTCGC 1 119 0 CTCCAAAAAA 0.952424 -182 ACGACTTCTGTTTCGAAAAAAAATAAAAACT 2 74 0 TTCGAAAAAA 0.885415 -133 TAAAATCTTTTATCGAAAAAATTTTATACGA 2 101 0 TTCGAAAAAA 0.885415 -106 ACGAAAGGTTCTTATAAAAAAAGCCTTTCCT 2 135 0 CTATAAAAAA 0.740462 -72 TACAAAAAACCATAGCAAAAAGCCAAAACTG 3 104 0 CTAGCAAAAA 0.764152 -91 GCCAGGGGATTGTACAAAAAACCATAGCAAA 3 116 0 TTACAAAAAA 0.927513 -79 GATTAGTCGACTTAGAAATAAAACGGTTTTT 4 97 0 CTAGAAATAA 0.731098 -127 TTACTCCGTGCGTAGAAAAGATTCTCTCTTT 6 20 1 CTAGAAAAGA 0.752559 -139 CAACATGATTCTTAAAAAAAATAAGAAT 8 8 0 CTAAAAAAAA 0.740462 -61 AAACTACTACTCTCCAAACAACTCGGCTATC 10 11 1 TTCCAAACAA 0.830166 -290 AAGCAAAAATTGTACGAAAAAAGCTGGAGAT 10 90 0 TTACGAAAAA 0.618714 -211 AATGGCTTGTCTTCCAAACAATTTCATTCTT 10 225 0 CTCCAAACAA 0.917474 -76 TCAACTCTCTTTTAGAAAAAA 11 1 0 TTAGAAAAAA 0.918255 -250 GCTTTTTCCTCTTACAAACAAGATGATCGAC 11 115 0 CTACAAACAA 0.941731 -136 TTATCTAATTTTGACAAAAAACGGACCCATG 14 48 0 TGACAAAAAA 0.749142 -145 TTAAAAAAGCCAGACAAACAAAACTGTAATT 14 130 0 CGACAAACAA 0.790442 -63 CGTGAAAAATCTTAGAAAAAAACAAAAAATT 15 103 0 CTAGAAAAAA 0.962333 -58 * ********* Masking position 7 Map Score: 14.2487 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 178 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 TTGTATCCTTTAAAATAGAGTTTTTCTTAT 1 160 1 TAAAATAGAG 0.717634 -141 AAAGGTTCTTATAAAAAAAGCCTTTCCTAA 2 133 0 ATAAAAAAAG 0.464556 -74 GCCCAGTATCCTATAGAGAGGTTGAATAAT 3 36 1 CTATAGAGAG 0.694767 -159 CTGTTACCAATAAAAAAAAGAAAAACCTTA 3 69 0 TAAAAAAAAG 0.694577 -126 AATTAATTTAAAGTAGAGAGTTTTTGCAAA 4 187 0 AAGTAGAGAG 0.798207 -37 AGCGAACACTTAAAAAAGAGGGAAACATTT 5 56 0 TAAAAAAGAG 0.911519 -20 TCTCCGCATTTTAAAGAGAGAATCTTTTCT 6 33 0 TTAAAGAGAG 0.879617 -126 AAGAGAAAAGAAATAGAAAGATTTTTCAAT 9 58 0 AAATAGAAAG 0.734319 -79 TATCGCCGGCAAAAAGACAGTAGAAAGAAT 10 38 1 AAAAAGACAG 0.777879 -263 TTTTTTCTAAAAGAGAGTTGAATTTTC 11 8 1 TAAAAGAGAG 0.957911 -243 TTTAAGAAAAAAAAAGAGAGTTGAAAATTC 11 30 0 AAAAAGAGAG 0.964343 -221 GTGGTTGGCAAAATAAAGAGCTGATTCTTC 13 51 1 AAATAAAGAG 0.850015 -38 AGGCGAGTCAGAAAAGAGTTCTTATCTC 14 9 1 CAGAAAAGAG 0.686529 -184 ********** Masking position 5 Map Score: 6.56579 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 401 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 CTATCGCCACATGGGATCATAAGAAAAACTC 1 177 0 ATGGGTCATA 0.889844 -124 TTTTGTCCTTAGGGGATCGTATACTTTTTCA 1 245 1 AGGGGTCGTA 0.992285 -56 TTTTTCATAAAGGGGGTGATAA 3 2 0 AGGGGTGATA 0.984197 -193 TTACCTGGCCAGGGGATTGTACAAAAAACCA 3 123 0 AGGGGTTGTA 0.970037 -72 TTATTAAACCAGCGGTTGATATTTCTTGATT 4 124 0 AGCGGTGATA 0.934553 -100 TTTTGGAAGGAGAGGATCGTATCATGAGATT 5 28 0 AGAGGTCGTA 0.95215 -48 ATATTTAGGAAGGAGCTGGTATAGAGAATCT 11 60 0 AGGAGTGGTA 0.943452 -191 ***** ***** Masking position 1 Map Score: 4.02616 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 27 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 6 ATACAAGCCTCCTGTAAGGAGCTCCCCCTCC 1 135 0 CCTGTAAGAG 0.956053 -166 TATCCCCTATCCTGTCATTAGTATCACAAGA 2 186 0 CCTGTCATAG 0.861441 -21 GCGGAGAGGTCTTGTCTAGAGAGTGTTAAAT 6 56 1 CTTGTCTGAG 0.972124 -103 ACGTTCTCTTCTCTTCAAGAGAAGAGGGCGT 9 20 1 CTCTTCAGAG 0.724723 -117 GTATGATTTGCTGTTCATGAGTTAAGAGAAG 9 96 1 CTGTTCAGAG 0.901865 -41 TAGGAAGGAGCTGGTATAGAGAATCTTTTAA 11 55 0 CTGGTATGAG 0.902111 -196 GTATTCTAGACCTGTCTTGAGACTTTTTGGT 11 201 1 CCTGTCTGAG 0.982355 -50 GGACCCATGCCCTTTATAGAGATAAGAACTC 14 26 0 CCTTTATGAG 0.894807 -167 ******* *** Masking position 10 Map Score: 2.51596 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 48 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 CTCCTTACAGGAGGCTTGTATCCTTTAAAAT 1 145 1 GAGGCTGTAT 0.976303 -156 TTTGTCCTTAGGGGATCGTATACTTTTTCAA 1 246 1 GGGGATGTAT 0.988505 -55 TACCTGGCCAGGGGATTGTACAAAAAACCAT 3 122 0 GGGGATGTAC 0.974835 -73 TTTGGAAGGAGAGGATCGTATCATGAGATTG 5 27 0 GAGGATGTAT 0.974467 -49 TATTTAGGAAGGAGCTGGTATAGAGAATCTT 11 59 0 GGAGCTGTAT 0.946775 -192 ****** **** Masking position 6 Map Score: 1.78711 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 9 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 CCCTAAGGACAAAAACCAACCGATATTTCT 1 229 0 AAAAACCAAC 0.936679 -72 AACCATAGCAAAAAGCCAAAACTGTTTTTC 3 98 0 AAAAGCCAAA 0.973365 -97 GGATTGTACAAAAAACCATAGCAAAAAGCC 3 111 0 AAAAACCATA 0.862689 -84 CTGGTTTAATAAAACCCAACTAGTTATAAT 4 143 1 AAAACCCAAC 0.924606 -81 TTTTTAAAGAAAAAGCAAAAATTGTACGAA 10 103 0 AAAAGCAAAA 0.877993 -198 ACTAGAATTCAAAACCCAGATTGATAAGAG 11 172 1 AAAACCCAGA 0.934241 -79 AAATTATTAAAAAAGCCAGACAAACAAAAC 14 137 0 AAAAGCCAGA 0.953905 -56 AGAATGTACTAAGAACCAAAATTTTTTGTT 15 84 1 AAGAACCAAA 0.876095 -77 AATCTTAGAAAAAAACAAAAAATTTTGGTT 15 97 0 AAAAACAAAA 0.856304 -64 ********** Masking position 4 Map Score: 6.42365 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 53 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 GATCCCATGTGGCGATAGGCCGGGTCTAGCG 1 190 1 GGCGATAGCC 0.995961 -111 TTCTACTATCGGCGCTAGACCCGGCCTATCG 1 202 0 GGCGCTAGCC 0.994218 -99 GAATCATGTTGGGTATAGTCCCTGCCGTTAG 8 28 1 GGGTATAGCC 0.941278 -41 TATAGTCCCTGCCGTTAGACCATTGAGTCGG 8 41 1 GCCGTTAGCC 0.970676 -28 TCTTTTTGCCGGCGATAGCCGAGTTGTTTGG 10 24 0 GGCGATAGCG 0.988186 -277 ******** ** Masking position 6 Map Score: 1.26444 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 3 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 TAGTTGTTAAAATTATTTAGAATTGTCTCT 1 12 1 AATTATTTAG 0.861335 -289 AGTCGTATAAAATTTTTTCGATAAAAGATT 2 99 1 AATTTTTTCG 0.839252 -108 TGTAAAAGTAAAATTTTTAGAAGGTTAGAA 4 16 0 AAATTTTTAG 0.94896 -208 TTCACATATAAATTTTTTAGTAATATGGGG 10 174 0 AATTTTTTAG 0.934549 -127 ATATTTCAAAAAATATTTAGGAAGGAGCTG 11 73 0 AAATATTTAG 0.889967 -178 TTCAAGAGAAAAATTTTTATCCACCCACTA 12 25 0 AAATTTTTAT 0.706884 -21 CTAAGAACCAAAATTTTTTGTTTTTTTCTA 15 92 1 AAATTTTTTG 0.821007 -69 ********** Masking position 2 Map Score: 2.60616 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 55 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: -3.72792e-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: -3.72792e-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 GGCTTGTATCCTTTAAAATAGAGTTTTTCT 1 157 1 CTTTAAAATA 0.580005 -144 CGGGGACATACTTTGAAAAAGTATACGATC 1 259 0 CTTTGAAAAA 0.966296 -42 TTATCACCCCCTTTATGAAAAAAATGCCCA 3 11 1 CTTTATGAAA 0.631141 -184 TGTTGTAGTACTTTCAATAACGTCAATTAC 3 150 0 CTTTCAATAA 0.719598 -45 ATGGCTTCAACTTTGTAAAAGTAAAATTTT 4 29 0 CTTTGTAAAA 0.843274 -195 CAACATGATTCTTAAAAAAAATAAGAAT 8 9 0 CTTAAAAAAA 0.723619 -60 GCGTTTTTTTCATTGAAAAATCTTTCTATT 9 47 1 CATTGAAAAA 0.724266 -90 TTTGCTTTTTCTTTAAAAAACTGTTCCTCA 10 114 1 CTTTAAAAAA 0.937643 -187 AGCAGAGAAGCTTTAGAAAACGGGGTGAGG 10 139 0 CTTTAGAAAA 0.703523 -162 ATTCAACTCTCTTTTAGAAAAAA 11 4 0 CTTTTAGAAA 0.692256 -247 TGAAAGAAATATTTCAAAAAATATTTAGGA 11 81 0 ATTTCAAAAA 0.473635 -170 TGAAATATTTCTTTCAGTAAGTCGATCATC 11 95 1 CTTTCAGTAA 0.608031 -156 ATTTTTAGATGTTTGAAAAATAAAAATTAT 14 75 0 GTTTGAAAAA 0.721328 -118 TTTTAATTGTCTTTGAGAAAAATGCTCCCA 15 20 1 CTTTGAGAAA 0.945485 -141 CGTGAAAAATCTTAGAAAAAAACAAAAAAT 15 104 0 CTTAGAAAAA 0.83277 -57 ********** Masking position 10 Map Score: 7.9473 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 275 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: -3.72792e-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: -3.72792e-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