AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ipurR_ctra_opreg_300.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 CT035 300 Biotin Protein Ligase #2 clpB 300 Clp Protease ATPase #3 CT114 25 hypothetical protein #4 mgtE 300 Mg++ Transporter (CBS Domain) #5 dhnA 300 Predicted 1,6-Fructose biphosphate aldolase (dehydrin family) #6 ydaO 153 PP-Loop Superfamily ATPase #7 surE 100 SurE-like Acid Phosphatase #8 ubiA 111 4-hydroxybenzoate octaphenyltransferase #9 CT283 170 hypothetical protein #10 lplA_1 264 Lipoate Protein Ligase #11 glyA 300 Serine Hydroxymethyltransferase Motif number 1 AGAGTTGATAAAGCGTTTTTTTTGGTATAATGAGAAAAA 1 252 1 AAGCTTTTAA 0.97787 -49 TAATGAGAAAAAGCTTTTTGTAAGGCAAAGAG 1 279 1 AAGCTTTGAA 0.848572 -22 TAAAAGAGCTAAGATCATTTGATCACAGAAAACTACAGG 2 158 0 AAGACTTTAA 0.985138 -143 TCACTATAAAAAGATACTTTACAAACAGATACACTTAGG 4 55 0 AAGAATTTAA 0.919737 -246 ACTCTTAAACAAGAGTCCTTCACTATAAAAAGATACTTT 4 74 0 AAGATCTTAA 0.809415 -227 ACTATCTATTAAGAGACTTTTTTACGAAAACGACAAAAA 4 123 0 AAGAATTTAA 0.919737 -178 GACGACTTTTAAGAGTCTTTATATAAAGAACGGAGAAGG 4 210 1 AAGATTTTAA 0.969042 -91 CCCCGTTCTAAAGATCAGTTATATTAAAATAACCTTGGT 5 53 0 AAGACGTTAA 0.899939 -248 GACTCCAGGAAAGATCGTTTATCTTGAGGTTTTCTCCTA 5 149 1 AAGACTTTAG 0.973554 -152 CTTCTTTACAAAGCCCTTTTCTGTGCAAAAGAAT 6 6 0 AAGCCTTTAA 0.989427 -148 CTTTGTAAAGAAGCTCTTTTCTTTCTAAGACTTACCTGG 6 32 1 AAGCCTTTAG 0.98112 -122 AAGTACGTTGAAGTTCGTTTCAACGTACAGATAA 8 6 0 AAGTCTTTAA 0.912661 -106 ATTACAATACAAGATCTTTTACACCTATAATCCCATAAT 8 70 1 AAGACTTTAA 0.985138 -42 TGGGAGATTAAAGCACTTTTTATAGCAGACTTTTTTTAA 10 97 1 AAGCCTTTAA 0.989427 -168 AAATTTTTAGAAGCTTTTTTAGAGTCAGGCATTATTTAT 10 134 1 AAGCTTTTAG 0.960845 -131 AAGCTTTTTTCCTAGTAGGAAGCTTCTTG 11 1 1 AAGCTTTTAG 0.960845 -300 **** * *** * * Masking position 9 Map Score: 23.1326 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 83 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 TTACCAACTCTTTTTGTCTTTATCTGACTTTCG 1 40 0 TTTTTGTCTT 0.858597 -261 AAGCCTCTCTTTTTTCTCCTCTTCGTTTGAGGG 1 77 1 TTTTTCTCTT 0.970344 -224 TACAAAAAGCTTTTTCTCATTATACCAAAAAAA 1 268 0 TTTTTCTCTT 0.970344 -33 CAGCTAACTCTCTTCCCCTTACTGGCTATCCTA 2 69 0 TCTTCCCCTT 0.859547 -232 CTCGGAAGACTTTTTGTCGTTTTCGTAAAAAAG 4 113 1 TTTTTGTCTT 0.858597 -188 CAACATCCAATTTTTCTTCGTTTCTATTTTGCT 4 258 0 TTTTTCTTGT 0.878729 -43 AACTATTTTCTCTTTTTAATTTTTATT 5 5 1 ATTTTCTCTT 0.689418 -296 ACTCTGCGATTTTTCCCCGTTCTAAAGATCAGT 5 73 0 TTTTCCCCTT 0.874111 -228 AGATAAACGATCTTTCCTGGAGTCTTTAGTTAA 5 140 0 TCTTTCCTGT 0.657564 -161 TGTCTATAAATCTTTCTTAGCATGCAAACATTT 5 194 0 TCTTTCTTGT 0.864616 -107 GAAGCTCTTTTCTTTCTAAGACTTACCTGGATT 6 41 1 TCTTTCTAGT 0.66867 -113 ATCTTTAAAATTTCCCTCATGTTTACACTACAA 6 86 1 TTTCCCTCTT 0.927392 -68 TTTCAACACGTTTCCCTAATTTTGTCCATGGAG 6 126 0 TTTCCCTATT 0.617742 -28 ACTTGGTTTATTTTTCTTATTATTTTAAAAAGA 7 52 1 TTTTTCTTTT 0.929082 -49 GAGGGATCTCTTTCTCTCTTCGTAAAGGAATTC 9 113 1 TTTCTCTCTT 0.947637 -58 GTAGAAGTAGTTTTCCTTTTTTTTCTTAAAAGG 9 147 1 TTTTCCTTTT 0.902401 -24 GAGAAGTTGTTCTCTGTCTGTTTATTTAGAATG 10 221 1 TCTCTGTCGT 0.620805 -44 GCATCGTTTCTTTTTCTTATAGTTATAGTTAAA 11 141 1 TTTTTCTTTT 0.929082 -160 AAATAAATCCTCTTTCTCCTAGAAAGTTTAGAC 11 172 1 TCTTTCTCTA 0.661755 -129 CTCTACCCACTCTCCCTTATCCTTTATGGGAAT 11 224 0 TCTCCCTTTT 0.818422 -77 ******** * * Masking position 3 Map Score: 17.4814 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 514 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 CTGACTTTCGTTCTCGTAAGTCCTCTATTT 1 20 0 TTCTCGTAAG 0.905579 -281 GGCAATTATATTCCCATAAAGATTTTTCGT 1 137 1 TTCCCATAAA 0.933018 -164 CCATAAAGATTTTTCGTAAACAGTACCAAG 1 150 1 TTTTCGTAAA 0.946887 -151 TTTTAAACTATTTTCATAAATGGTTTGAAG 1 208 1 TTTTCATAAA 0.952712 -93 CTTTTTGTCGTTTTCGTAAAAAAGTCTCTT 4 122 1 TTTTCGTAAA 0.946887 -179 TCTCTTTCTCTCTTCGTAAAGGAATTCTGT 9 119 1 TCTTCGTAAA 0.836254 -52 TTTTCCTTTTTTTTCTTAAAAGGA 9 157 1 TTTTCTTAAA 0.807953 -14 AGTTGCATCATTATCATAAATGTCGTATAT 10 47 0 TTATCATAAA 0.865145 -218 ATGATGCAACTTTTCGTAAAGGGAAAGGAA 10 66 1 TTTTCGTAAA 0.946887 -199 ATGTAATATGTTTCCGTGAAATAAACGGGA 10 193 1 TTTCCGTGAA 0.785787 -72 CCCTAGTCGCTTACCATAAGGTGCTTTAAT 11 81 0 TTACCATAAG 0.598133 -220 AGTTTAGACTTTCTCATCAAAAGATTAGAT 11 196 1 TTCTCATCAA 0.765231 -105 AAAGATTAGATTCCCATAAAGGATAAGGGA 11 215 1 TTCCCATAAA 0.933018 -86 ********** Masking position 9 Map Score: 12.3425 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 88 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 CCTTTCGGGCTAAAGCTCCCTCAAACGAAGA 1 96 0 TAAGCTCCCT 0.899863 -205 TTGCCTTACAAAAAGCTTTTTCTCATTATAC 1 276 0 AAAGCTTTTT 0.785814 -25 CACAAACATAAACAGCTTCCTCTAAGGAGAG 2 13 0 AAAGCTTCCT 0.979858 -288 CAGCTAAATCATCAGCTCCTTGGTTAGGATA 2 45 1 ATAGCTCCTT 0.894848 -256 TTGATCAAGAAACAGCTAACTCTCTTCCCCT 2 83 0 AAAGCTAACT 0.765292 -218 CTTCACTATAAAAAGATACTTTACAAACAGA 4 65 0 AAAGATACTT 0.717397 -236 TTAGAAAGAAAAGAGCTTCTTTACAAAGCCC 6 29 0 AAAGCTTCTT 0.976443 -125 AAAAAGATCTAATAGCTCATTACGCAGGTTT 7 78 1 AAAGCTCATT 0.911646 -23 TTTCAGCAAGAAAAGCTCCTTCTGATTACAA 8 46 1 AAAGCTCCTT 0.985288 -66 CGAAGAGAGAAAGAGATCCCTCTAGAATATC 9 104 0 AAAGATCCCT 0.915107 -67 CTGACTCTAAAAAAGCTTCTAAAAATTTAAA 10 131 0 AAAGCTTCTA 0.829482 -134 GCAAAAGTCAAGAAGCTTCCTACTAGGAAAA 11 17 0 AGAGCTTCCT 0.901589 -284 ** ******** Masking position 4 Map Score: 10.4333 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 257 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 AAAGCTCCCTCAAACGAAGAGGAGAAAAAA 1 86 0 CAAACGAAGA 0.788083 -215 CAGAAGAAACGAAGCTTACAGTGCA 4 6 1 GAAACGAAGC 0.986074 -295 GAGCAAAATAGAAACGAAGAAAAATTGGAT 4 257 1 GAAACGAAGA 0.950845 -44 AAAGGGCTTTGTAAAGAAGCTCTTTTCTTT 6 26 1 GTAAAGAAGC 0.937249 -128 TTCCCTTTACGAAAAGTTGCATCATTATCA 10 61 0 GAAAAGTTGC 0.75595 -204 TACAGCAAAAGTCAAGAAGCTTCCTACTAG 11 22 0 GTCAAGAAGC 0.821295 -279 ATAAGAAAAAGAAACGATGCTTCCAAGACC 11 131 0 GAAACGATGC 0.968196 -170 ********** Masking position 4 Map Score: 2.20363 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 72 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 TTTATTGACTGTAAGAGAATTAAGCTGTAT 2 193 1 GTAAGAGAAT 0.935653 -108 GGACTCTTGTTTAAGAGTCTCGGAAGACTT 4 95 1 TTAAGAGTCT 0.949834 -206 AGACTATCTATTAAGAGACTTTTTTACGAA 4 134 0 TTAAGAGACT 0.935653 -167 TAGACGACTTTTAAGAGTCTTTATATAAAG 4 208 1 TTAAGAGTCT 0.949834 -93 TACTTGTTGCGTAAGATTATTATCAAGTTT 9 68 0 GTAAGATTAT 0.745455 -103 GACTTTTGCTGTAAGAATATGATCAACTGA 11 39 1 GTAAGAATAT 0.745487 -262 GCACCTTATGGTAAGCGACTAGGGAAAATG 11 87 1 GTAAGCGACT 0.902351 -214 ********** Masking position 4 Map Score: 1.93303 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 AAATTACTAAAATAGAGGACTTACGAG 1 8 1 TAAAATAGAG 0.887847 -293 AAAGAGTTGGTAAAAAAAAGCCTCTCTTTT 1 60 1 TAAAAAAAAG 0.943761 -241 ACGAAGAGGAGAAAAAAGAGAGGCTTTTTT 1 73 0 GAAAAAAGAG 0.84381 -228 CTCTTTGCCTTACAAAAAGCTTTTTCTCA 1 282 0 TTACAAAAAG 0.647989 -19 CCGAGACTCTTAAACAAGAGTCCTTCACTA 4 88 0 TAAACAAGAG 0.84381 -213 AGAATAAAAATTAAAAAGAGAAAATAGTT 5 10 0 TTAAAAAGAG 0.916155 -291 CTCAAAGATCTTAACTAAAGACTCCAGGAA 5 130 1 TTAACTAAAG 0.610642 -171 TCTTATTATTTTAAAAAGATCTAATAGCTC 7 66 1 TTAAAAAGAT 0.685079 -35 TCCTTTTAAGAAAAAAAAGGAAAACTACT 9 152 0 GAAAAAAAAG 0.841313 -19 TTCTAAAAATTTAAAAAAAGTCTGCTATAA 10 116 0 TTAAAAAAAG 0.914698 -149 AGTGATCTAATAAAATAAATAATGCCTGAC 10 157 0 TAAAATAAAT 0.607331 -108 ACTATAACTATAAGAAAAAGAAACGATGCT 11 140 0 TAAGAAAAAG 0.742324 -161 TAGTTATAGTTAAAATAAATCCTCTTTCTC 11 160 1 TAAAATAAAT 0.607331 -141 ********** Masking position 7 Map Score: 6.46374 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 329 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 AGGACTTACGAGAACGAAAGTCAGATAAAG 1 26 1 AGAACGAAAG 0.919281 -275 AGTCAGATAAAGACAAAAAGAGTTGGTAAA 1 44 1 AGACAAAAAG 0.762662 -257 AGGGAGCTTTAGCCCGAAAGGACCATTACA 1 106 1 AGCCCGAAAG 0.976574 -195 TGGTTAGGATAGCCAGTAAGGGGAAGAGAG 2 65 1 AGCCAGTAAG 0.771843 -236 GCGAGACTTTAGACCGAATGTGTCGCTAAT 4 179 1 AGACCGAATG 0.96972 -122 ACTCTCCGTCAGAGCGGATGCGACATGGCA 5 230 0 AGAGCGGATG 0.806131 -71 TCATGGACAAAGACCGAAGGGAGGATCTGT 9 38 0 AGACCGAAGG 0.964181 -133 TCCTTTACGAAGAGAGAAAGAGATCCCTCT 9 112 0 AGAGAGAAAG 0.923911 -59 ********** Masking position 8 Map Score: 2.75302 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 54 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 CGATTTCTAATCAAGTTTTTTGCCTGTAGT 2 136 1 TCAAGTTTTT 0.841767 -165 GTTTTTTGCCTGTAGTTTTCTGTGATCAAA 2 150 1 TGTAGTTTTC 0.895147 -151 GAAGACTTTTTGTCGTTTTCGTAAAAAAGT 4 117 1 TGTCGTTTTC 0.757375 -184 TCGTTTATCTTGAGGTTTTCTCCTACGAAA 5 163 1 TGAGGTTTTC 0.960433 -138 AGCTCATTACGCAGGTTTTT 7 91 1 GCAGGTTTTT 0.849607 -10 GTAATCAGAAGGAGCTTTTCTTGCTGAAAA 8 45 0 GGAGCTTTTC 0.842613 -67 AAGATTATTATCAAGTTTTCATGGACAAAG 9 56 0 TCAAGTTTTC 0.949632 -115 ATTCTGTAGAAGTAGTTTTCCTTTTTTTTC 9 142 1 AGTAGTTTTC 0.639299 -29 ACCTTGCCATTCAGGTTTTT 10 1 0 TCAGGTTTTT 0.872594 -264 TGATAATGATGCAACTTTTCGTAAAGGGAA 10 61 1 GCAACTTTTC 0.806134 -204 ********** Masking position 6 Map Score: 2.53475 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 122 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 GACCCTAAATTATTTTGCACTGTAAGCTTC 4 21 0 TATTTTGCAC 0.979417 -280 TCTTCGTTTCTATTTTGCTCTTTCACGCCC 4 247 0 TATTTTGCTC 0.935327 -54 TTTTAATTTTTATTCTGCACACATTGAACA 5 24 1 TATTCTGCAC 0.955427 -277 ATTCTTTTGCACAGAAAAGGGC 6 3 1 TCTTTTGCAC 0.980904 -151 CAATACAAGATCTTTTACACCTATAATCCC 8 74 1 TCTTTTACAC 0.907774 -38 ********** Masking position 6 Map Score: 2.45397 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 6 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 TACTTTACAAACAGATACACTTAGGCAGCGA 4 49 0 ACAGATCACT 0.92389 -252 TTCACTATAAAAAGATACTTTACAAACAGAT 4 64 0 AAAGATCTTT 0.700855 -237 GGGAAAAATCGCAGAGTCTTTCATTTTCTTT 5 89 1 GCAGAGCTTT 0.835421 -212 ATGCGACATGGCAGATTGTCTATAAATCTTT 5 212 0 GCAGATGTCT 0.87775 -89 TCGAAGATGCTCCTATTTTAAAT 5 288 0 GAAGATCTCC 0.928833 -13 AGGGCTTTGTAAAGAAGCTCTTTTCTTTCTA 6 28 1 AAAGAACTCT 0.717802 -126 GAGGATCTGTACAGATCCTCCCTCCCTATTA 9 17 0 ACAGATCTCC 0.969139 -154 GAGGATCTGTACAGATCCTCCCTTCGGTCTT 9 28 1 ACAGATCTCC 0.969139 -143 GCAAGACCTTGCAGAGGCACTCTTTATCCTC 11 254 0 GCAGAGCACT 0.898481 -47 ****** **** Masking position 5 Map Score: 1.93227 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 210 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 TCGATGTGATTGGCAAGCCTTCTCAGAATT 2 246 1 TGGCAAGCCT 0.911498 -55 ACAAAAAGTCTTCCGAGACTCTTAAACAAG 4 100 0 TTCCGAGACT 0.965763 -201 GTATTAGATTTGGCGAGACTTTAGACCGAA 4 167 1 TGGCGAGACT 0.958985 -134 GCTCTTTTCTTTCTAAGACTTACCTGGATT 6 44 1 TTCTAAGACT 0.840352 -110 GAAACGATGCTTCCAAGACCATTACCAAGC 11 121 0 TTCCAAGACC 0.965763 -180 TGATTAAACCTTGCAAGACCTTGCAGAGGC 11 267 0 TTGCAAGACC 0.965763 -34 ********** Masking position 6 Map Score: 0.56684 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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: 8.76972e-14 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: 8.76972e-14 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: 8.76972e-14 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