AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -ipdhR_synecho_opreg_100.orf -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 1651827 181 hypothetical protein #2 phdD 86 dihydrolipoamide dehydrogenase #3 merA 300 mercuric reductase #4 odhB 210 dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex Motif number 1 TTCCCCCCTGGCGATCGGGT 1 1 1 TTCCCCCCTG 0.976422 -181 ACCTGCAGTATTGCTCCCCAAGCTTGGCCG 1 51 0 TTGCTCCCCA 0.959529 -131 GGCCCGATTCTAACACCCCATCAAAGTTTG 1 135 0 TAACACCCCA 0.897837 -47 CTCTGGAAAGTTGACCCCCGTCCTGGCGAT 2 27 0 TTGACCCCCG 0.986049 -60 GAGGTTGCCCTTAACCCCTAAACTAAAGTC 2 54 1 TTAACCCCTA 0.927679 -33 GACTAGGTATTTATCCCCCTAAATCTCCTC 3 72 1 TTATCCCCCT 0.969444 -229 TTTACGGCAGTTCCCCCCTTCTCAAGGGGG 3 130 1 TTCCCCCCTT 0.971666 -171 TAATCCCCCCTAGCCCCCCTTGAGAAGGGG 3 144 0 TAGCCCCCCT 0.99339 -157 TTTGGCTGTTTAATCCCCCCTAGCCCCCCT 3 154 0 TAATCCCCCC 0.923238 -147 GCTCCTTAACTAACCCCCCGGCAGAAATCT 4 110 1 TAACCCCCCG 0.992956 -101 AAATCTCTTGTAGATCCCTTGGAATACAGC 4 175 0 TAGATCCCTT 0.757763 -36 ********** Masking position 1 Map Score: 14.8816 Number of sites scoring better than the average of aligned sites = 2245 Number in coding regions = 1921 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 2 ACAAAGACCCGATCGCCAGGGGGGAA 1 7 0 GATCGCCAGG 0.996012 -175 CTGCAGTATTGCTCCCCAAGCTTGGCCGAG 1 49 0 GCTCCCCAAG 0.98435 -133 TGAGCGTTTGGAGCCCCAGGCC 1 170 1 GAGCCCCAGG 0.993328 -12 GACAATGGGCGATCGCCAGGACGGGGGTCA 2 16 1 GATCGCCAGG 0.996012 -71 ATCCCCCCTAGCCCCCCTTGAGAAGGGGGG 3 142 0 GCCCCCCTTG 0.948542 -159 TCCTTTGGGCGATCGCCTAGATGGTCGAAA 4 77 1 GATCGCCTAG 0.981284 -134 CTCCTTAACTAACCCCCCGGCAGAAATCTG 4 111 1 AACCCCCCGG 0.932356 -100 ATCTCTTGTAGATCCCTTGGAATACAGCGG 4 173 0 GATCCCTTGG 0.97216 -38 ********** Masking position 6 Map Score: 13.0904 Number of sites scoring better than the average of aligned sites = 1682 Number in coding regions = 1543 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 TGGCCGAGCCGGCAGTTTCCACAAAGACCC 1 27 0 GGCAGTTTCC 0.992281 -155 ATCAAAGTTTGGCATTTTCACTGTTTTTCC 1 116 0 GGCATTTTCA 0.966599 -66 CTAAAGTCTTGACAGATTGAG 2 76 1 GACAGATTGA 0.886724 -11 AGAATTTTACGGCAGTTCCCCCCTTCTCAA 3 125 1 GGCAGTTCCC 0.985435 -176 GTTGATTTATGACAAATTCCTCAATGAGCT 3 208 0 GACAAATTCC 0.923967 -93 GGCAGTTTGCTATTTTCTTG 4 1 1 GGCAGTTTGC 0.992502 -210 AACCCATTTTGACATTTTCCTTTGGGCGAT 4 60 1 GACATTTTCC 0.980168 -151 ********** Masking position 4 Map Score: 10.1437 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 494 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 TAACGGTTTAGACTACCAGGGAGAAGGAAAAA 1 91 1 GATACAGGGA 0.98036 -91 CAGGGAGAAGGAAAAACAGTGAAAATGCCAAA 1 107 1 GAAACAGTGA 0.866212 -75 TCGAAGACAATGGGCGATCGCCAGGAC 2 6 1 GAAAGGGCGA 0.983102 -81 CGCTTTCTTAGATAACGATGGATACGTGAATG 3 26 0 GAAAGATGGA 0.938814 -275 TTAGTGAGGAGATTTAGGGGGATAAATACCTA 3 75 0 GATTGGGGGA 0.981895 -226 AGCCCCCCTTGAGAAGGGGGGAACTGCCGTAA 3 131 0 GAAAGGGGGA 0.996706 -170 TCTCAAGGGGGGCTAGGGGGGATTAAACAGCC 3 149 1 GGTAGGGGGA 0.987712 -152 AGATCCCTTGGAATACAGCGGATTAGGACTGC 4 162 0 GATAAGCGGA 0.900003 -49 ** ** ****** Masking position 12 Map Score: 6.38063 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 516 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 GCCTGGGGCTCCAAACGCTCAAATGTGGCC 1 161 0 CCAAACGCTC 0.967541 -21 TATTTATCCCCCTAAATCTCCTCACTAAAG 3 79 1 CCTAAATCTC 0.982986 -222 AAATCTCCTCACTAAAGCTCCGGCTTAAAA 3 92 1 ACTAAAGCTC 0.933574 -209 ACAGCCAAAACCCAACTTTCCAAATATGCT 3 175 1 CCCAACTTTC 0.888878 -126 TCCAAATATGCTCTAAGCTCATTGAGGAAT 3 193 1 CTCTAAGCTC 0.891013 -108 GGTTTTATCTCTTAAATCTCTTGTAGATCC 4 188 0 CTTAAATCTC 0.951273 -23 ********** Masking position 5 Map Score: 1.59211 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 367 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 CTAAACCGTTATTTTTGCTTCACCTGCAGT 1 72 0 ATTTTTGCTT 0.950138 -110 CATTTTCACTGTTTTTCCTTCTCCCTGGTA 1 104 0 GTTTTTCCTT 0.95364 -78 TTGTTTTTTCATTTACATTCACG 3 4 1 TTTTTTCATT 0.900958 -297 TGAATCTTAAGTTGTTGATTTATGACAAAT 3 221 0 GTTGTTGATT 0.953637 -80 ATTCTAAATAATTTTTCATTAAACAATTAA 3 276 1 ATTTTTCATT 0.958301 -25 ATCCAGATCCATTGTTGATCAGTCAAGAAA 4 24 0 ATTGTTGATC 0.874481 -187 ********** Masking position 5 Map Score: 1.517 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 317 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 7 CCAAACGCTCAAATGTGGCCCGATTCTAACACCCC 1 146 0 AAATGCCATT 0.925083 -36 GAATTGAATTAAATTTTGGAGTATTAATCTGAATC 3 245 0 AAATTAGATT 0.978874 -56 GTTTAATGAAAAATTATTTAGAATTGAATTAAATT 3 265 0 AAATTAGATT 0.978862 -36 GAAAATGTCAAAATGGGTTAGGATTATCCAGATCC 4 44 0 AAATGAGATT 0.99038 -167 CCCCCGGCAGAAATCTGATAGAATTTGAACGGTCT 4 124 1 AAATGAGATT 0.97035 -87 **** * ** *** Masking position 4 Map Score: 0.547755 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 TGGCGATCGCCCATTGTCTTCGA 2 4 0 CCATTGTCTT 0.919202 -83 GGAAAGTTGACCCCCGTCCTGGCGATCGCC 2 23 0 CCCCCGTCCT 0.981579 -64 TAATTTTCAAACGCTTTCTTAGATAACGAT 3 39 0 ACGCTTTCTT 0.909252 -262 GGGGATAAATACCTAGTCTTGTAATTTTCA 3 60 0 ACCTAGTCTT 0.843017 -241 ACGGCAGTTCCCCCCTTCTCAAGGGGGGCT 3 133 1 CCCCCTTCTC 0.849495 -168 ACCCATTTTGACATTTTCCTTTGGGCGATC 4 61 1 ACATTTTCCT 0.630151 -150 GAACGGTCTTCCGCAGTCCTAATCCGCTGT 4 150 1 CCGCAGTCCT 0.97179 -61 CAGTCCTAATCCGCTGTATTCCAAGGGATC 4 163 1 CCGCTGTATT 0.879849 -48 ********** Masking position 7 Map Score: 0.605328 Number of sites scoring better than the average of aligned sites = 1667 Number in coding regions = 1469 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 9 ********** No masking Map Score: 1.75747e-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: 1.75747e-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: 1.75747e-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