AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -isoxS_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 zwf 300 Glucose-6-P Dehyrogenase #2 sodM 131 Superoxide Dismutase (Mn) #3 yhxB 151 Phosphomannomutase #4 CT296 108 hypothetical protein #5 nfo 172 Endonuclease IV #6 fumC 52 Fumarate Hydratase Motif number 1 AGAGAGAAATCTTTTTAGGCACATATTCGT 1 20 1 CTTTTTAGGC 0.987349 -281 CACATATTCGTTTTTTTGGTATTGTGGGCT 1 39 1 TTTTTTTGGT 0.783612 -262 AGAGTGTTAATTTTTTAAGAGAGAGCCCAC 1 62 0 TTTTTTAAGA 0.937322 -239 TTGTGTTGGGTTTGCTAGGCGACCTAAGTC 1 259 1 TTTGCTAGGC 0.909828 -42 AGTAACCTTATTTTTTAGGATGGCT 2 117 1 TTTTTTAGGA 0.976093 -15 GCCTATCCCACTTTCTAAGTTAAGCAAGTT 3 27 1 CTTTCTAAGT 0.738217 -125 AACTATTTTTTAAGAATACAAAATC 4 6 1 TTTTTTAAGA 0.937322 -103 TCAATCGGGTTTTTATAGGCGGAAATAATC 4 43 1 TTTTATAGGC 0.95155 -66 ACTCACTTATTTAGGCGAATAAACTC 4 93 0 TTATTTAGGC 0.940592 -16 TCTTTTTTTGTCTTTTAAGCCTTTTTAGGC 5 19 1 TCTTTTAAGC 0.895658 -154 TCTTTTAAGCCTTTTTAGGCCCTTTATACC 5 29 1 CTTTTTAGGC 0.987349 -144 ********** Masking position 6 Map Score: 13.6718 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 184 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 CATTACCAGCCTGTCCTCCCTGTATCGTGGT 1 135 1 CTTCCTCCCT 0.997035 -166 CTAGGAAGCTCTTTCCTGCTTTATACAATTT 1 195 1 CTTCCTGCTT 0.946334 -106 AATAAGGTTACTATCCTCGCCACCTTCTCTA 2 98 0 CTTCCTCGCC 0.9956 -34 TAGTCCCGTTTTGTCCTCGCTTGTATCTGTA 3 83 1 TTTCCTCGCT 0.977586 -69 CACTCTCCTCTTTTTTTGTCTTT 5 3 1 CTTCCTCTTT 0.958483 -170 ATAACTACCACTATTCTCGCTATTTATAGTT 5 93 1 CTTTCTCGCT 0.977586 -80 ATGCTCTCTTCCCCTATGATTCTT 6 39 0 CTTCTTCCCC 0.967049 -14 ** ******** Masking position 7 Map Score: 7.82265 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 3 GCCTAAAAAGATTTCTCTCTCATAAAACA 1 10 0 ATTTCTCTCT 0.739747 -291 CCTCGCCACCTTCTCTATTTTCTACAGGCT 2 85 0 TTCTCTATTT 0.969988 -47 TACGTCAGGCTTCTGTTTTTGTAAAAAACT 3 53 0 TTCTGTTTTT 0.88856 -99 CCTCGCTTGTATCTGTATTTGGTAGAGCGT 3 97 1 ATCTGTATTT 0.922069 -55 ACTCTCAAGATTTTGTATTCTTAAAAAATA 4 14 0 TTTTGTATTC 0.844044 -95 TCTCCTCTTTTTTTGTCTTTTAAGCCTTTT 5 14 1 TTTTGTCTTT 0.932026 -159 AGCCCGTTCTCTATCTAGTCATTCAT 5 157 0 TTCTCTATCT 0.948191 -16 TGAAGTCGTTTTTTCTATTTTT 6 3 0 TTTTCTATTT 0.953219 -50 ********** Masking position 6 Map Score: 4.69862 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 258 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 TTAAGAGAGAGCCCACAATACCAAAAAAACGAA 1 45 0 GCCCATACCA 0.985432 -256 AAGACTTTGGCCCCACATTACCAGCCTGTCCTC 1 120 1 CCCCATACCA 0.992439 -181 TCCTGTAGCACCAAAAATAACCACGATACAGGG 1 152 0 CCAAAAACCA 0.984599 -149 GCCTAGCAAACCCAACACAAACAAAGTTTTCGG 1 246 0 CCACAAAACA 0.92489 -55 AGTGGGATAGGCACAAAAATCCAAAGAA 3 6 0 GCCAAATCCA 0.869905 -146 AAACACTCATCCACGCTCTACCAAATACAGATA 3 106 0 CCCCTTACCA 0.953899 -46 AGACAACCTTCCGATCAGAACGAAACACTCATC 3 128 0 CCACAAACGA 0.948025 -24 ATTATTTCCGCCTATAAAAACCCGATTGACTCT 4 39 0 CCAAAAACCC 0.937253 -70 TTCTGATAATGCAATAACTACCACTATTCTCGC 5 80 1 GCAAATACCA 0.963954 -93 ** * ** ***** Masking position 2 Map Score: 7.52793 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 91 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 CCACAATACCAAAAAAACGAATATGTGCCTAA 1 34 0 AAAAAAGAAT 0.778063 -267 TCTCTCTTAAAAAATTAACACTCTATACTAGG 1 68 1 AAAATACACT 0.964084 -233 ATCTTGGAAGAAATTAAAGACTTTGGCCCCAC 1 104 1 AAATAAGACT 0.877915 -197 TGTAGCACCAAAAATAACCACGATACAGGGAG 1 150 0 AAAAAACACG 0.96225 -151 ACAATTTAACAAAGGAAGGACGTCTATCCGAA 1 219 1 AAAGAAGACG 0.820877 -82 GATTATCAATAAAATATTCACTGTCAAGAGCT 2 34 0 AAAAATCACT 0.892949 -98 CTTCCGATCAGAACGAAACACTCATCCACGCT 3 122 0 GAACAACACT 0.871304 -30 GCATTATCAGAAAAATATCACTAGCCGTTATT 5 60 0 AAAATACACT 0.964084 -113 TGATAATGCAATAACTACCACTATTCTCGCTA 5 83 1 ATAATACACT 0.790663 -90 AAAAATAGAAAAAACGACTTCATGAAGGA 6 8 1 GAAAAAGACT 0.945217 -45 **** ** **** Masking position 3 Map Score: 5.12321 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 117 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 AAGAGAGAGCCCACAATACCAAAAAAACGA 1 46 0 CCACAATACC 0.990972 -255 TTAATTTCTTCCAAGATACAACCTAGTATA 1 91 0 CCAAGATACA 0.965069 -210 GACTTTGGCCCCACATTACCAGCCTGTCCT 1 122 1 CCACATTACC 0.977499 -179 CCAAAAATAACCACGATACAGGGAGGACAG 1 145 0 CCACGATACA 0.990972 -156 ********** Masking position 7 Map Score: 2.7293 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 7 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 CTAAAAAGATTTCTCTCTCATAAAACA 1 5 0 TTTCTCATAA 0.767612 -296 TCTTAAAAAATTAACACTCTATACTAGGTTGTA 1 72 1 TTACTCTATA 0.728319 -229 CAATAAAATATTCACTGTCAAGAGCTATCCACA 2 27 0 TTACTCAAGA 0.978617 -105 GAATATTTTATTGATAATCTAGAGGGATCTATC 2 47 1 TTATTCTAGA 0.825365 -85 AAAAACCCGATTGACTCTCAAGATTTTGTATTC 4 24 0 TTACTCAAGA 0.978617 -85 ATTTATAGTTTCTTTAATCAAGAACCTCTGGCA 5 114 1 TCTTTCAAGA 0.879821 -59 CCTCTGGCAATCTTCTATCATGAATGACTAGAT 5 138 1 TCTCTCATGA 0.959817 -35 AGCCCGTTCTCTATCTAGTCATTCATGAT 5 154 0 TTTCTCTAGT 0.823418 -19 CCCCTATGATTCTTCCTTCATGAAGTCGTTTTT 6 20 0 TCTCTCATGA 0.959817 -33 ** ** ****** Masking position 8 Map Score: 3.98866 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 187 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 GTTATTTTTGGTGCTACAGGAGACTTGACC 1 164 1 GTGCTACAGG 0.980454 -137 AGGAAAGAGCTTCCTAGAGGTCAAGTCTCC 1 182 0 TTCCTAGAGG 0.983616 -119 TGTGTTGGGTTTGCTAGGCGACCTAAGTCT 1 260 1 TTGCTAGGCG 0.953999 -41 CCTTCTCTATTTTCTACAGGCTAGCTAGAT 2 77 0 TTTCTACAGG 0.96554 -55 TGATAGAAGATTGCCAGAGGTTCTTGATTA 5 128 0 TTGCCAGAGG 0.986498 -45 ********** Masking position 6 Map Score: 1.26249 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 68 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: -1.58208e-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: -1.58208e-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: -1.58208e-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