AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iarcA_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 cydA 274 Cytochrome Oxidase Subunit I #2 sodM 131 Superoxide Dismutase (Mn) #3 lpdA 208 Lipoamide Dehydrogenase #4 sdhC 25 Succinate Dehydrogenase #5 CT593.1 221 hypothetical protein-possible frameshift with CT593 Motif number 1 TAACAACTGGTGACAGGGAAACGTGCATAGT 1 206 1 TGACAGGAAA 0.95098 -69 TTTTTGATTTGGAGAGCCAAAT 1 263 1 GGAGAGCAAA 0.979156 -12 GGATAGCTCTTGACAGTGAATATTTTATTGA 2 30 1 TGACAGGAAT 0.942281 -102 AGTGGTAGCAGGAGAGAAAAAATAGGAACGT 3 18 0 GGAGAGAAAA 0.990501 -191 AGCCTTTCTAGGAAAGGAAAAGAGAGGTCCT 3 107 0 GGAAAGAAAA 0.95976 -102 AGAAAGGCTTGGAAGGAGAATCCTCTTCCCT 3 129 1 GGAAGGGAAT 0.947508 -80 AACACTCATTGAAGAGGAAATGTT 3 195 1 GAAGAGAAAT 0.931124 -14 GGGAGAGAGAATTTTTTCTCTT 4 2 1 GGAGAGGAAT 0.99516 -24 CTGAAGAGAAAAAATTCTCTCTC 4 13 0 GAAGAGAAAA 0.9414 -13 GAACCATGAGGGACAGCGAATAAGGAGGCGT 5 122 1 GGACAGGAAT 0.990651 -100 GTTCATATGAGGAGGGAGATAGTACAAAAAT 5 151 1 GGAGGGGATA 0.922576 -71 ****** **** Masking position 3 Map Score: 17.6255 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 202 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 TGACTTCGGTTCATCCGTAATAAGTTTCAA 1 82 0 TCATCCGTAA 0.820567 -193 CTTCTTAAGACCTTCCTTGACTTCGGTTCA 1 99 0 CCTTCCTTGA 0.957489 -176 GGGATGAGTCCTTTCCCAAAGGCCTTCTTA 1 122 0 CTTTCCCAAA 0.929686 -153 GGGAAAGGACTCATCCCTAGTTTAGCTGGA 1 135 1 TCATCCCTAG 0.773953 -140 AGCCATCCTAAAAAATAAGGTT 2 120 0 CCATCCTAAA 0.965715 -12 CTCTCTTTTCCTTTCCTAGAAAGGCTTGGA 3 112 1 CTTTCCTAGA 0.802087 -97 AGGAGAATCCTCTTCCCTCAGATAATCATC 3 142 1 TCTTCCCTCA 0.944057 -67 TGGATCGTTGCAATCCTAAACACTCATTGA 3 177 1 CAATCCTAAA 0.734141 -32 TGAAAGGCTTCCATCCCTAATT 5 3 0 CCATCCCTAA 0.984086 -219 TGGTTCCTGCCCTTCCATAAAGAGCCCTCC 5 98 0 CCTTCCATAA 0.919135 -124 TCCTTATTCGCTGTCCCTCATGGTTCCTGC 5 118 0 CTGTCCCTCA 0.799509 -104 AGTACAAAAATCTTCCTACATTCGTTTCAT 5 171 1 TCTTCCTACA 0.884884 -51 ********** Masking position 4 Map Score: 9.91914 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 392 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 TCAGCAAAACAAGAAGCTGTACCAACTCCT 1 53 1 AAGAAGCTGT 0.716402 -222 AATAAGTTTCAAGGAGTTGGTACAGCTTCT 1 64 0 AAGGAGTTGG 0.784086 -211 ACCGAAGTCAAGGAAGGTCTTAAGAAGGCC 1 102 1 AGGAAGGTCT 0.757574 -173 GGAAGGTCTTAAGAAGGCCTTTGGGAAAGG 1 113 1 AAGAAGGCCT 0.966525 -162 CTAAACTAGGGATGAGTCCTTTCCCAAAGG 1 130 0 GATGAGTCCT 0.681439 -145 GTATTTTGTGGAAAAGGGCTGTTTTAACAA 1 182 1 GAAAAGGGCT 0.834056 -93 GTAGAAAATAGAGAAGGTGGCGAGGATAGT 2 90 1 GAGAAGGTGG 0.949624 -42 TCTCAATGAGGAGAAGTGGTAGCAGGAGAG 3 33 0 GAGAAGTGGT 0.951574 -176 GAAAGGAAAAGAGAGGTCCTTCAGACAAAT 3 97 0 GAGAGGTCCT 0.800926 -112 CATGATGTTTGAGGAGGGCTCTTTATGGAA 5 86 1 GAGGAGGGCT 0.986648 -136 GACAGCGAATAAGGAGGCGTTCATATGAGG 5 133 1 AAGGAGGCGT 0.965569 -89 GCGTTCATATGAGGAGGGAGATAGTACAAA 5 149 1 GAGGAGGGAG 0.842725 -73 ********** Masking position 6 Map Score: 7.6842 Number of sites scoring better than the average of aligned sites = 608 Number in coding regions = 607 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 4 GCCCTTTTCCACAAAATACTTTGCCATTAA 1 171 0 ACAAAATACT 0.958685 -104 TATATACTAAAAAGAATACTAGAAGTTTTT 1 238 1 AAAGAATACT 0.906446 -37 TCTCCAAATCAAAAACTTCTAGTATTCTTT 1 248 0 AAAAACTTCT 0.932399 -27 CTGAAGAGAAAAAATTCTCTCTCCC 4 8 0 AAAAAATTCT 0.968144 -18 GGGAGATAGTACAAAAATCTTCCTACATTC 5 164 1 ACAAAAATCT 0.90998 -58 ********** Masking position 5 Map Score: 0.928272 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 5 TTGTTTTGCTGAAAATAATGAAAACACTTC 1 35 0 GAAAATAATG 0.941877 -240 CTAGCCTGTAGAAAATAGAGAAGGTGGCGA 2 83 1 GAAAATAGAG 0.972913 -49 TAGCAGGAGAGAAAAAATAGGAACGTAAGA 3 14 0 GAAAAAATAG 0.881906 -195 TCTAGGAAAGGAAAAGAGAGGTCCTTCAGA 3 102 0 GAAAAGAGAG 0.982319 -107 ATCATATAATGAAACGAATGTAGGAAGATT 5 179 0 GAAACGAATG 0.918646 -43 ********** Masking position 4 Map Score: 0.753694 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 108 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 6 CTTCAACTGCTAGGGTTATCTTATATAG 1 9 0 TAGGGTTATC 0.856977 -266 TGATAATCTAGAGGGATCTATCTAGCTAGC 2 58 1 GAGGGATCTA 0.979368 -74 GTATTTGTCTGAAGGACCTCTCTTTTCCTT 3 95 1 GAAGGACCTC 0.864933 -114 TCTGAGGGAAGAGGATTCTCCTTCCAAGCC 3 134 0 GAGGATTCTC 0.81393 -75 ATCCATATGAGATGATTATCTGAGGGAAGA 3 152 0 GATGATTATC 0.57256 -57 CCTTTCAGTTGAGGGATATAGCTGCTGTTT 5 26 1 GAGGGATATA 0.975239 -196 GATGTTTGAGGAGGGCTCTTTATGGAAGGG 5 89 1 GAGGGCTCTT 0.869642 -133 CAGGAACCATGAGGGACAGCGAATAAGGAG 5 119 1 GAGGGACAGC 0.928187 -103 TTCATATGAGGAGGGAGATAGTACAAAAAT 5 152 1 GAGGGAGATA 0.924085 -70 ********** Masking position 2 Map Score: 4.16706 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 255 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 CCACATCTTTACGTACTGATG 2 2 0 ACGTACTGAT 0.951667 -130 CACTCTTACGTTCCTATTTTTTCTCTC 3 8 1 ACGTTCCTAT 0.89475 -201 CTGTTTGTTAACGTCGCGATTAAGTGCGCT 5 50 1 ACGTCGCGAT 0.985018 -172 CCCTCCTCAAACATCATGATGAACAGCGCA 5 74 0 ACATCATGAT 0.897318 -148 ACATCCCGATACGGAATGAA 5 212 0 ACATCCCGAT 0.987378 -10 ********** Masking position 4 Map Score: 0.39954 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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 GGTACAGCTTCTTGTTTTGCTGAAAATAATGA 1 44 0 CTGTTTGCTG 0.99442 -231 GGACTCATCCCTAGTTTAGCTGGAAGACAGTT 1 141 1 CTGTTTGCTG 0.994151 -134 ATATACTATGCACGTTTCCCTGTCACCAGTTG 1 209 0 CAGTTTCCTG 0.977782 -66 AGGGATCTATCTAGCTAGCCTGTAGAAAATAG 2 69 1 CTGCTACCTG 0.929238 -63 ** **** **** Masking position 6 Map Score: 0.214598 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 9 ********** No masking Map Score: 8.62189e-13 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: 8.62189e-13 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: 8.62189e-13 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