AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_synecho_reg_300.orf -o099_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY14336 151 Synechocystis #2 RCY32451 300 Synechocystis #3 RCY49435 145 Synechocystis #4 RCY20029 74 Synechocystis #5 RCY51454 114 Synechocystis #6 RCY37955 185 Synechocystis #7 RCY30660 54 Synechocystis #8 RCY22672 300 Synechocystis #9 RCY39156 112 Synechocystis #10 RCY49018 300 Synechocystis Motif number 1 ACCGTTAATTTCAATTTCAATCAGCAGGCCATTGCTCAACTGA 1 31 0 TCCTGCACCT 0.993073 -121 GATTTTGGCATTCCGGTCTTTTCCCATACCCGTAGGTGGTCCT 1 75 1 TTCTCCACCT 0.995109 -77 GTCTGTTCAGTCGATTTCTTTCCCCATCCCCCTAGTATC 1 123 1 TCCTCCACCT 0.998661 -29 AATCTCGAACTCTCAAACTCTTCCCAAACCTATATTTTTGCTT 6 124 1 TCCTCCACCT 0.998661 -62 GGAAGGAAGATCAATGGCGATCGCCTCCCCACTCGGATATTTG 7 19 0 TCCTCCTCCT 0.993583 -36 GATCAACCTCTCCAGCCCTTTAACCAAACCTTTACTAGGGCTT 8 158 1 TCCTCCACCT 0.998661 -143 GTTGGACTATTTCACATCTGTGACCATGCCATTTTAATTATAA 10 45 1 TTCTCCACCT 0.995109 -256 ** * * *** ** * Masking position 11 Map Score: 13.6352 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 22 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 GTTAACCATAGCCGTTTTTTGACTTATTTT 2 39 0 GCCGTTTTTT 0.988329 -262 GGTAAGACGGGCCGTTTGCTGTCAATAAAG 2 186 0 GCCGTTTGCT 0.971054 -115 CTAGGGTTTTGCCGTTTTTTTAGGTCGATA 2 216 1 GCCGTTTTTT 0.988329 -85 AAGTCAATCTGCGGTTTTTCAAGCTCCCCT 3 21 1 GCGGTTTTTC 0.910309 -125 ACCTATTGCCTTTTCCTAGAGCCTGTT 3 129 0 GCCTTTTCCT 0.858207 -17 CGTTAATTTTCCCGTTTTCTCCGTTTACCA 4 31 1 CCCGTTTTCT 0.940623 -44 GGCTGTTTGAGCCGTTTCCCTGACTTGACA 6 38 1 GCCGTTTCCC 0.980741 -148 TATTCTTCGAGCCGTAATTCCAGTCTTTCA 8 86 0 GCCGTAATTC 0.77677 -215 GGTTGATCGTGCCGTATTTTTCGTCCCTAA 8 136 0 GCCGTATTTT 0.963978 -165 ********** Masking position 5 Map Score: 9.38269 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 317 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 AATAAAGCCAGAAACCTTACTGGTCCGTTCTAG 2 160 0 GAAACTACGG 0.888491 -141 CCCCGGTATTGGGAGATTTAGGGGGCAAATTAA 3 87 1 GGGAATTAGG 0.815985 -59 GGAGAAAACGGGAAAATTAACGATTAGGTATTG 4 20 0 GGAAATAAGA 0.966986 -55 ATGGGAAGGAAGATCAATGGCGATCGCCTC 7 35 0 GGAAATAAGG 0.98292 -20 AGTCTTTCAGGAAAAATTAATGGGACGGGACTC 8 62 0 GAAAATAAGG 0.985869 -239 ACAGGTTAACGAAAGCTAAATGGGCTATGATCT 9 53 1 GAAACTAAGG 0.971512 -60 ATTAAAGAGTGAAATATAAAAGACAATAATACT 10 90 0 GAAAATAAGA 0.972611 -211 AAGACACGAGGAAATATTAAAGAGTGAAATATA 10 105 0 GAAAATAAGA 0.972611 -196 AGATAATGGAGAGAAATGAATGATGGAACTCAA 10 160 1 GAGAATAAGA 0.945527 -141 **** ** ** ** Masking position 7 Map Score: 9.05642 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 81 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 CTTTCCCCATCCCCCTAGTATC 1 140 1 CCCCCTAGTT 0.96143 -12 CGGCCCGTCTTACCCTAGGGTTTTGCCGTTT 2 202 1 TACCCTAGGT 0.885754 -99 TTTTTCAAGCTCCCCTAGTCTCCTCAGTTCG 3 35 1 TCCCCTAGTT 0.987798 -111 TGGATAAAGATCCCCCGGTATTGGGAGATTT 3 75 1 TCCCCCGGTT 0.992084 -71 ACCTGGGAAGTCCCTCGGTCTAGAACAACCC 5 38 1 TCCCTCGGTT 0.966429 -77 GGGCAAAAAGTCCCCTGGGCAGACGTTGTGG 8 20 1 TCCCCTGGGA 0.926447 -281 GAAGAATATATCCCTTGGTTTACAAATGTTA 8 108 1 TCCCTTGGTT 0.966994 -193 TTACTTCTCCGCCCCCAGGGTGGTCGATTGT 8 278 0 GCCCCCAGGT 0.956579 -23 ********* * Masking position 4 Map Score: 7.65258 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 589 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 TGAAATTAACGGTTGATTTTGGCATTCCGGTCT 1 61 1 GGTGATTTGC 0.983154 -91 AGCGAACAAGGGCTGACTGTTTCAACTGCACTA 2 269 1 GGTGACTGTC 0.90284 -32 GAAAAGCTTGGGTTGTTCTAGACCGAGGGACTT 5 45 0 GGTGTTCTGC 0.961911 -70 TTTACTTAGGGGCTGTTTGAGCCGTTTCCCTGA 6 28 1 GGTGTTTGGC 0.986839 -158 CTCCCCACTCGGATATTTGCGACTGAA 7 5 0 GGTATTTGGC 0.973341 -50 GGTTAATCGGGGCAAAAAGTCCC 8 1 1 GGTAATCGGC 0.982882 -300 GGGCTGGAGAGGTTGATCGTGCCGTATTTTTCG 8 143 0 GGTGATCGGC 0.993236 -158 GGGTCATTGCTCCCAACTCTGTG 9 100 0 GGTCATTGTC 0.888038 -13 TTTTCTCGAAGGGTAAGTTAGCCAAATCGACGG 10 240 1 GGTAAGTTGC 0.756287 -61 ** ****** * * Masking position 4 Map Score: 7.53151 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 220 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 AACTGATTAACTCCCCTTAAAATAAGTCAA 2 21 1 CTCCCCTTAA 0.948259 -280 CCCCCTAAATCTCCCAATACCGGGGGATCT 3 82 0 CTCCCAATAC 0.961917 -64 CTCTGCCATCAATACCTAATCG 4 3 1 CTGCCATCAA 0.915354 -72 TGGCGATCGCCTCCCCACTCGGATATTTGC 7 18 0 CTCCCCACTC 0.938542 -37 ATGGAGTCCCGTCCCATTAATTTTTCCTGA 8 59 1 GTCCCATTAA 0.839638 -242 TGTACTTAACCTCCCATCAATTTTGTCTAG 9 26 0 CTCCCATCAA 0.982533 -87 GGGTCATTGCTCCCAACTCTGTGCCATCG 9 94 0 CTCCCAACTC 0.957796 -19 ********** Masking position 2 Map Score: 3.36729 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 403 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 GGAGATTTAGGGGGCAAATTAAAACTTGGC 3 98 1 GGGGCAAATT 0.98165 -48 ACGGAGAAAACGGGAAAATTAACGATTAGG 4 25 0 CGGGAAAATT 0.840833 -50 TGAACCGGACAAATTAGTCATAGCT 4 60 0 CGGACAAATT 0.917425 -15 TTGACAATTACGGGCGAAATTTAAATCAAA 6 62 1 CGGGCGAAAT 0.974207 -124 GGTTAATCGGGGCAAAAAGTCCCCTGGG 8 9 1 GGGGCAAAAA 0.947012 -292 ACAAATGTTAGGGACGAAAAATACGGCACG 8 129 1 GGGACGAAAA 0.854811 -172 TCAACCAGCCGGGGCGACTTTAATATACAA 8 206 1 GGGGCGACTT 0.952101 -95 ********** Masking position 7 Map Score: 3.3368 Number of sites scoring better than the average of aligned sites = 792 Number in coding regions = 704 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 8 GATTTTGGCATTCCGGTCTTTTCCCATACC 1 75 1 TTCCGGTCTT 0.942646 -77 TAAAAAAAATTTCGTGTTTTAAATTAACAA 2 110 1 TTCGTGTTTT 0.768745 -191 ACCAGTAAGGTTTCTGGCTTTATTGACAGC 2 169 1 TTTCTGGCTT 0.935232 -132 ATCGTTAATTTTCCCGTTTTCTCCGTTTAC 4 29 1 TTCCCGTTTT 0.893224 -46 ATGGTTCTCTCTGTTTTACTCTGTCAA 5 8 1 TCTCTGTTTT 0.860818 -107 CCGAGGGACTTCCCAGGTTTGACAGAGTAA 5 26 0 TCCCAGGTTT 0.889463 -89 TTGAGCCGTTTCCCTGACTTGACAATTACG 6 44 1 TCCCTGACTT 0.901447 -142 CGAGCCGTAATTCCAGTCTTTCAGGAAAAA 8 79 0 TTCCAGTCTT 0.951349 -222 TCTTTTCTTTTTTCTGGCTTGCATCCAGAT 10 134 1 TTTCTGGCTT 0.935232 -167 ********** Masking position 9 Map Score: 3.34996 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 453 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 9 CATAGCCGTTTTTTGACTTATTTTAAGGGG 2 33 0 TTTTGACTTA 0.836639 -268 TTTTTGCTGCAATTATTTTT 6 1 1 TTTTTGCTGC 0.937071 -185 GCTGCAATTATTTTTACTTAGGGGCTGTTT 6 16 1 TTTTTACTTA 0.933362 -170 CAAACCTATATTTTTGCTTATTCTCCTAGG 6 148 1 TTTTTGCTTA 0.95588 -38 GTCCCATTAATTTTTCCTGAAAGACTGGAA 8 69 1 TTTTTCCTGA 0.947262 -232 GGAACTCAATTTTTTCCTTCGAAATCAGAA 10 184 1 TTTTTCCTTC 0.947262 -117 ********** Masking position 4 Map Score: 1.46156 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 227 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 10 CCAAAATCAACCGTTAATTTCAATTTCAAT 1 53 0 CCGTTAATTT 0.951861 -99 ATAGTCTGTTCAGTCGATTTCTTTCCCCAT 1 120 1 CAGTCGATTT 0.961451 -32 GGGAGTTAATCAGTTGATTAAGTCG 2 6 0 CAGTTGATTA 0.80325 -295 TTTCCCAAAAAAGTCGATTAACTTTTGGTT 2 66 0 AAGTCGATTA 0.464932 -235 CAATACCTAATCGTTAATTTTCCCGTTTTC 4 20 1 TCGTTAATTT 0.688277 -55 TGGATTAAGCCAGTCAGTTTAAAAGACGAA 6 96 1 CAGTCAGTTT 0.82208 -90 GAGTCCCGTCCCATTAATTTTTCCTGAAAG 8 62 1 CCATTAATTT 0.795437 -239 ACTTAACCTCCCATCAATTTTGTCTAGTTC 9 23 0 CCATCAATTT 0.884056 -90 AGTTTAATTACCGTCGATTTGGCTAACTTA 10 253 0 CCGTCGATTT 0.980376 -48 ********** Masking position 4 Map Score: 3.39062 Number of sites scoring better than the average of aligned sites = 816 Number in coding regions = 719 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 11 ACCAATTCTCCATGGAGCGGTCAGTTGAG 1 9 1 TCCTGGAGCG 0.9066 -143 CTATTGCCTTTTCCTAGAGCCTGTTTGCCAA 3 123 0 TTCTAGAGCC 0.9648 -23 TGTGGCATTGTTCATGGAGTCCCGTCCCATT 8 46 1 TTCTGGAGTC 0.961921 -255 AAGGGATATATTCTTCGAGCCGTAATTCCAG 8 93 0 TTCTCGAGCC 0.993057 -208 GCTGGAGAGGTTGATCGTGCCGTATTTTTCG 8 143 0 TTGTCGTGCC 0.922853 -158 AATTCATCGAGGGAACTAGACAA 9 3 1 TTCTCGAGGG 0.944877 -110 TCTTTAATATTTCCTCGTGTCTTTTCTTTTT 10 115 1 TTCTCGTGTC 0.954598 -186 *** ******* Masking position 5 Map Score: 2.6121 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 92 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 GCGGTCAGTTGAGCAATGGCCTGCTGATTG 1 27 1 GAGCAATGGC 0.991363 -125 CCCCATCAGCGAACAAGGGCTGACTGTTTC 2 262 1 GAACAAGGGC 0.980263 -39 GGGTTTGGGGGGCCAGGGCCTAGGAGAAT 6 167 0 GGGCCAGGGC 0.964656 -19 TGGGAAGGAAGATCAATGGCGATCGCCTCC 7 34 0 GATCAATGGC 0.946688 -21 GGGACTCCATGAACAATGCCACAACGTCTG 8 39 0 GAACAATGCC 0.857546 -262 AACCTTCAACCAGCCGGGGCGACTTTAATA 8 201 1 CAGCCGGGGC 0.906435 -100 ACAGAGTTGGGAGCAATGACCC 9 101 1 GAGCAATGAC 0.937063 -12 GAACACAACAGCAAGCGCACTAACTAGA 10 283 0 CAGCAAGCGC 0.914244 -18 ********** Masking position 4 Map Score: 5.3921 Number of sites scoring better than the average of aligned sites = 855 Number in coding regions = 785 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 13 TAATAACGGAAAAGCTTGGGTTGTTCTAGA 5 56 0 AAAGCTTGGG 0.952536 -59 AATTTAAATCAAAGCTCTGGATTAAGCCAG 6 79 1 AAAGCTCTGG 0.978488 -107 AAGCAAAAATATAGGTTTGGGAAGAGTTTG 6 137 0 ATAGGTTTGG 0.943445 -49 AGGTTTGGTTAAAGGGCTGGAGAGGTTGAT 8 159 0 AAAGGGCTGG 0.974165 -142 AAGCCCTAGTAAAGGTTTGGTTAAAGGGCT 8 171 0 AAAGGTTTGG 0.982106 -130 CATACAAGAGAGAGCGTTGGACTATTTCAC 10 30 1 AGAGCGTTGG 0.95348 -271 ********** Masking position 3 Map Score: 3.85732 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 161 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 ACCGGGGGATCTTTATCCAGTTTCTTCCCG 3 64 0 CTTTATCCAG 0.96265 -82 CCGTTTTCTCCGTTTACCAGCTATGACTAA 4 42 1 CGTTTACCAG 0.961965 -33 CTGTTTGAGCCGTTTCCCTGACTTGACAAT 6 40 1 CGTTTCCCTG 0.832121 -146 AACTGACTGGCTTAATCCAGAGCTTTGATT 6 85 0 CTTAATCCAG 0.864203 -101 CTCTCCAGCCCTTTAACCAAACCTTTACTA 8 165 1 CTTTAACCAA 0.861972 -136 AGGGCTTAACCTTCAACCAGCCGGGGCGAC 8 194 1 CTTCAACCAG 0.94623 -107 ATTTAGCTTTCGTTAACCTGTACTTAACCT 9 44 0 CGTTAACCTG 0.961967 -69 ********** Masking position 3 Map Score: 2.34923 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 258 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 AAGAAATCGACTGAACAGACTATTTAGGAC 1 113 0 CTGAACAGAC 0.941828 -39 ACTAGGGGAGCTTGAAAAACCGCAGATTGA 3 24 0 CTTGAAAAAC 0.708291 -122 TCTTCCCGAACTGAGGAGACTAGGGGAGCT 3 42 0 CTGAGGAGAC 0.947017 -104 CAAATTAAAACTTGGCAAACAGGCTCTAGG 3 112 1 CTTGGCAAAC 0.941796 -34 TCTGTCAAACCTGGGAAGTCCCTCGGTCTA 5 30 1 CTGGGAAGTC 0.93949 -85 AAAAAGTCCCCTGGGCAGACGTTGTGGCAT 8 24 1 CTGGGCAGAC 0.992997 -277 ********** Masking position 7 Map Score: 0.560682 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 274 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207