AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_synecho_reg_100.orf -o071_synecho_100.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 RCY43837 121 Synechocystis #2 RCY31101 143 Synechocystis #3 RCY07805 300 Synechocystis #4 RCY01566 145 Synechocystis #5 RCY23220 69 Synechocystis #6 RCY06784 29 Synechocystis #7 RCY29543 100 Synechocystis #8 RCY50255 220 Synechocystis #9 RCY34011 64 Synechocystis #10 RCY02550 36 Synechocystis #11 RCY26220 201 Synechocystis #12 RCY36788 79 Synechocystis #13 RCY23507 77 Synechocystis #14 RCY44672 300 Synechocystis Motif number 1 ACTTGCTTGCGGAACTTGCACAATTGGCAG 1 22 1 GGAACTTGCA 0.644171 -100 CAAATCCTTTGGGGATTGGCCATGGGACTA 2 17 1 GGGGATTGGC 0.947147 -127 GATTGGCCATGGGACTATGGCAAAATATGT 2 30 1 GGGACTATGG 0.898235 -114 AAAGGAAGGTGGGATTGGGATCATCTCCCT 2 103 0 GGGATTGGGA 0.877515 -41 CTTAAAAAGGGGGACTTTCGACGTTGATTC 3 16 0 GGGACTTTCG 0.902231 -285 TTTTTAAGCCGGAGCTTTAGTGAGGAGATT 3 38 1 GGAGCTTTAG 0.692649 -263 GCTTTAGTGAGGAGATTTGGGGGGATAAAT 3 51 1 GGAGATTTGG 0.893445 -250 TCAAAGGGACGGGGATAGACCCAAAATTAT 3 122 0 GGGGATAGAC 0.453603 -179 TTATTTACCTGGAAATTGGAAATTCTGTCA 3 209 1 GGAAATTGGA 0.847973 -92 CTTATTTTACGGGGTTAGGGCGGCCTTTCC 3 247 0 GGGGTTAGGG 0.900794 -54 CCATCAGCGGGGGATTTTCC 5 1 0 GGGATTTTCC 0.871653 -69 CCCCGCTGATGGGATTGTGGCAAAATGCTA 5 19 1 GGGATTGTGG 0.938497 -51 AAATTTCCTGGGGATTTTAGGTTGAATAGT 7 76 0 GGGATTTTAG 0.893644 -25 AAAATCCCCAGGAAATTTGCCCT 7 88 1 GGAAATTTGC 0.873332 -13 CCAGACCGGTGGAATTTTACCCCAATGGCC 8 28 0 GGAATTTTAC 0.702598 -193 ACTCTAGTGAGGAATTTTGCAAAATGCAAG 8 136 0 GGAATTTTGC 0.921662 -85 TCCGCTTCTAGGGATTGGGAGCCAGGGGA 12 10 0 GGGATTGGGA 0.877515 -70 CAGTCAGGAAGGGAATTGGGAAAGTTTTAT 13 55 0 GGGAATTGGG 0.974159 -23 TTACTCTGTTGGGATTTTGAGCGA 14 5 0 GGGATTTTGA 0.936939 -296 GCTGGCCGGAGGAGCTTGGGCAACAAAATT 14 195 1 GGAGCTTGGG 0.937179 -106 ********** Masking position 6 Map Score: 22.3386 Number of sites scoring better than the average of aligned sites = 4085 Number in coding regions = 3584 Number in noncoding regions = 501 Number of orfs with sites within 600 bp upstream = 437 Fraction of orfs with sites within 600 bp upstream = 0.0701895 Motif number 2 AAAACCTTTGCCAACATTGAAA 1 110 0 AAACCTTTCC 0.769994 -12 ACCTATGCTGAAATCATTACCCGGTCAAAGG 3 145 0 AAATCATTCC 0.777429 -156 CTTAGCCTAAAAAATTTTACCTATGCTGAAA 3 163 0 AAAATTTTCC 0.942811 -138 AATACGAGAAAACTAATTGCCCCTTATTTTA 3 268 0 AACTAATTCC 0.736584 -33 TTGCTTCCCTAGCATTTTGCCACAATCCCAT 5 27 0 AGCATTTTCC 0.921267 -43 AGCCTATTTCAACAATTTTCCTAAAATTTAG 7 24 1 AACAATTTCC 0.94398 -77 CCTAAAATTTAGAACATTTCCATCTGTTTAT 7 43 1 AGAACATTCC 0.925921 -58 AAAATCCCCAGGAAATTTGCCCT 7 88 1 GGAAATTTCC 0.518064 -13 CCAGACCGGTGGAATTTTACCCCAATGGCCA 8 27 0 GGAATTTTCC 0.79502 -194 TAGTCGACAGAACAATTCTCCTATGTAACCT 9 23 0 AACAATTCCC 0.683031 -42 AGATGTAACTTATTTCCTGTCAATTTA 11 7 1 AACTTATTCC 0.670109 -195 TAGCATTTCCAGAATATTTCCAGAAAATTAC 11 178 1 AGAATATTCC 0.903119 -24 GAATATTTCCAGAAAATTACCAT 11 189 1 AGAAAATTCC 0.929882 -13 ACCCGACCATAAAACTTTCCCAATTCCCTTC 13 47 1 AAAACTTTCC 0.955006 -31 TCAAAAGTGAAAAAATTTCCCCGTGAATCCA 14 138 0 AAAAATTTCC 0.957786 -163 TCTTAGCCGCAAAAATATCCCTTGCATTGAC 14 271 1 AAAAATATCC 0.660086 -30 ******** ** Masking position 10 Map Score: 15.6322 Number of sites scoring better than the average of aligned sites = 1020 Number in coding regions = 859 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 TTGCGGAACTTGCACAATTGGCAGAAGTTT 1 28 1 TGCACAATTG 0.742247 -94 CCATGGCCAATCCCCAAAGGATTTGCTCAA 2 12 0 TCCCCAAAGG 0.958428 -132 GGAAAATCCCCCGCTGATGGGATTGT 5 7 1 TCCCCCGCTG 0.845441 -63 AGAAGGCGATCGCCGGTGGCCATTGGGGT 8 10 1 TCGCCGGTGG 0.973629 -211 GTGGAATTTTACCCCAATGGCCACCGGCGA 8 20 0 ACCCCAATGG 0.894184 -201 TCACTAACTTTGCACGACTGGGCCCTAACC 8 57 0 TGCACGACTG 0.657239 -164 AATGCAAGCTTGCCCGGCGGGCATGGTAGG 8 114 0 TGCCCGGCGG 0.982479 -107 TTAACGCCGTTGCCCAATGGAGTGATCTAG 11 47 1 TGCCCAATGG 0.981365 -155 ACCATGCCGATCGCCAGTGGTCTATAAATA 11 114 1 TCGCCAGTGG 0.975912 -88 CTGTATTAGCTCCCCAATAGCTGTTACAAA 13 14 1 TCCCCAATAG 0.877335 -64 TCGTAATCACTCCACAGTGGATTCACGGGG 14 121 1 TCCACAGTGG 0.962655 -180 TTAGAGTGGCTGGCCGGAGGAGCTTGGGCA 14 187 1 TGGCCGGAGG 0.896323 -114 ********** Masking position 5 Map Score: 11.2478 Number of sites scoring better than the average of aligned sites = 2546 Number in coding regions = 2370 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 4 GCAAGGCTTATTGTTGGTTGCTCTGTCCGTTCCAGGGAGA 2 70 1 TTTTGCCCGT 0.982495 -74 CAATCCCACCTTCCTTTTTGTCCTAGCCTAGCCTGCCC 2 116 1 TTTTGCCCTA 0.909812 -28 TAGGGAAGCAATTGTTGTAGGGCGGGCCTTGCT 5 47 1 ATTAGCCCTT 0.906443 -23 ATCTTAAACGATTGTTTTTGCCCTTGCCATAGATTTTT 8 193 1 ATTTGCCCAT 0.981112 -28 ACTGCATTGATTCTAACTAGATCACTCCATTGGGCAACGG 11 53 0 TTTAGCCCAT 0.985446 -149 TACCGTAGTATTCTCCCTAGATTGTGCCATATTCTCCGCT 12 34 0 TTTAGTCCAT 0.912523 -46 CCAATAGCTGTTACAAATTGACCCGACCATAAAACTTTCC 13 27 1 TTTTGCCCAT 0.991368 -51 AAAAGTACTTTTGCGCATTGTACTCACCAGCTTGACAGCC 14 81 0 TTTTGCCCAG 0.96407 -220 GGGAAATTTTTTCACTTTTGAACAATCCATTCAGACTAGT 14 148 1 TTTTGCCCAT 0.991367 -153 CGGCTAAGAGGTGAAATTAGCTCATTCCAATTTTAAATAG 14 240 0 GTTAGCCCAA 0.833293 -61 AGCCGCAAAAATATCCCTTGCATTGACCGTCAATTT 14 275 1 ATTTGTCCGT 0.796579 -26 ** *** * **** Masking position 8 Map Score: 9.4481 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 218 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 GCAAGCAAGTAGAGCCAGGAA 1 2 0 AGAGCCAGGA 0.951107 -120 CTTATTTTACGGGGTTAGGGCGGCCTTTCC 3 247 0 GGGGTTAGGG 0.884083 -54 AGGAACCAGGGGCAAAAAAGC 4 2 1 GGAACCAGGG 0.947896 -144 ATTATTTGCAAGAGTTAAGGTTAACAT 4 129 1 AGAGTTAAGG 0.733354 -17 ATTGTGGCAAAATGCTAGGGAAGCAATTGT 5 32 1 AATGCTAGGG 0.784201 -38 ACAACACCAATGCCAGGGTTGGAGTTCC 6 12 0 AATGCCAGGG 0.873605 -18 ATTCCTCACTAGAGTTAGGGAAGCTGAAGA 8 151 1 AGAGTTAGGG 0.972149 -70 CTAGGGATTGGGAGCCAGGGGA 12 3 0 GGAGCCAGGG 0.991603 -77 GGACAGTCAGGAAGGGAATTGG 13 66 0 ACAGTCAGGA 0.757003 -12 GCAGAACAAGACAATCAGGGCTGTCAAGCT 14 63 1 ACAATCAGGG 0.757003 -238 GCTGGCCGGAGGAGCTTGGGCAACAAAATT 14 195 1 GGAGCTTGGG 0.887499 -106 ********** Masking position 9 Map Score: 7.76188 Number of sites scoring better than the average of aligned sites = 1773 Number in coding regions = 1537 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 6 CACTACTGAACCTTTGACAGTTCGCTCTTT 1 83 1 CCTTTGACAG 0.971342 -39 ATTGTTGGTTGCTCTGTCCGTTCCAGGGAG 2 79 1 GCTCTGTCCG 0.947694 -65 TATCCCCGTCCCTTTGACCGGGTAATGATT 3 135 1 CCTTTGACCG 0.994378 -166 TCCCCGTCCACATTTGACCGTAAAGGAGCA 10 11 1 CATTTGACCG 0.964741 -26 TCTTGTTCTGCCTTTGTCTGGGCTACCATT 14 44 0 CCTTTGTCTG 0.947826 -257 AATATCCCTTGCATTGACCGTCAATTT 14 284 1 GCATTGACCG 0.957998 -17 ********** Masking position 5 Map Score: 4.42187 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 205 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CAATAGTGGGAGGACTGATCCCGTTTAAAAC 4 37 1 AGGATGATCC 0.950724 -109 GATATAAGGCTGGATTTATCAACGAATTTCA 8 84 0 TGGATTATCA 0.88434 -137 CTGGAATGCTCCTTTACGGTCA 10 25 0 TGGATGCTCC 0.970699 -12 CGTTGCCCAATGGAGTGATCTAGTTAGAATC 11 54 1 TGGATGATCT 0.979502 -148 ATTAACCAACTGCATTGATTCTAACTAGATC 11 70 0 TGCATGATTC 0.802984 -132 GAATCCACTGTGGAGTGATTACGAAAAAGTA 14 114 0 TGGATGATTA 0.939979 -187 CTAGTCTGAATGGATTGTTCAAAAGTGAAAA 14 156 0 TGGATGTTCA 0.93426 -145 TATTTAAAATTGGAATGAGCTAATTTCACCT 14 241 1 TGGATGAGCT 0.926961 -60 **** ****** Masking position 4 Map Score: 2.90877 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 171 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 GTTGAGCAAATCCTTTGGGGATTGGCCATGGGACT 2 9 1 AATTTGGAGG 0.854605 -135 GACTATGGCAAAATATGTGAGGCTCAGAGCAAGGCTT 2 42 1 AAATTGGCAG 0.988841 -102 AAAGTGTTTGAAAAGTGCGAGGCTAGGTATTTATCCC 3 72 0 AAATCGGCGG 0.982552 -229 AGCATAGGTAAAATTTTTTAGGCTAAGTATGGACAAT 3 167 1 AAATTGGCAG 0.988841 -134 AAAAATCTATGGCAAGGGCAAAAACAA 8 204 0 AAATTGGCGG 0.994566 -17 GGGAATTGGGAAAGTTTTATGGTCGGGTCAATTTGTA 13 38 0 AAATTGGTGG 0.965884 -40 AATGCAAGGGATATTTTTGCGGCTAAGAGGTGAAATT 14 262 0 ATATTGGCAG 0.948443 -39 *** * * *** ** Masking position 1 Map Score: 3.34591 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 75 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 AAGCCTTGCTCTGAGCCTCACATATTTTGC 2 49 0 CTGAGCCTCA 0.972874 -95 TCCTTTTTGTCCTAGCCTAGCCTGCCC 2 127 1 CCTAGCCTAG 0.976237 -17 GGGATAAATACCTAGCCTCGCACTTTTCAA 3 72 1 CCTAGCCTCG 0.989332 -229 ATTGTCCATACTTAGCCTAAAAAATTTTAC 3 174 0 CTTAGCCTAA 0.972465 -127 AATTTCACCTCTTAGCCGCAAAAATATCCC 14 262 1 CTTAGCCGCA 0.972874 -39 ********** Masking position 4 Map Score: 2.57688 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 13 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 CCGTAGAATCAACGTCGAAAGTC 3 1 1 CCGTAGATCC 0.983538 -300 GCGGCCTTTCCCGTGGGAATGACAGAATTTCCA 3 225 0 CCGTGGAATC 0.953295 -76 TAACCCAGACCGGTGGAATTTTACCCCAATGGC 8 29 0 CGGTGGATTA 0.811734 -192 GAAGAGTAGTCCGTCGGATCTTAAACGATTGTT 8 176 1 CCGTCGATCA 0.889084 -45 TTGGGTAATTCCGTAGCATTTCCAGAATATTTC 11 165 1 CCGTAGATTC 0.990611 -37 GGTGTTGTTACCGTAGTATTCTCCCTAGATTGT 12 49 0 CCGTAGATTC 0.990611 -31 CCGCTGTATTAGCTCCCCAATAG 13 1 1 CCGCTGATTC 0.951355 -77 GCAAAAATATCCCTTGCATTGACCGTCAATTT 14 279 1 CCCTTGATTC 0.924166 -22 ****** *** * Masking position 8 Map Score: 2.6739 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 251 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 GGGCAGGCTAGGCTAGGACAAAAA 2 130 0 CGGCTAGGCT 0.936388 -14 AGATCTGAATCAGGTCTGAGTTTTAAACGGG 4 56 0 CGGTCTGAGT 0.930775 -90 TGTTGTAGGGCGGGCCTTGCT 5 59 1 CGGCCTTGCT 0.978461 -11 AACTCCAACCCTGGCATTGGTGTTGT 6 14 1 CGGCATTGGT 0.956285 -16 TAAAATTCCACCGGTCTGGGTTAGGGCCCAG 8 39 1 CGGTCTGGGT 0.988625 -182 TTCCTCGGCACTGGCTTGGGTAATTCCGTAG 11 150 1 CGGCTTGGGT 0.991316 -52 * ********* Masking position 11 Map Score: 2.267 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 336 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 GCCATAGTCCCATGGCCAATCCCCAAAGGAT 2 20 0 CATGGCCATC 0.777697 -124 GGAGATGATCCCAATCCCACCTTCCTTTTTG 2 105 1 CCAATCCACC 0.815778 -39 TTTGTCCTAGCCTAGCCTGCCC 2 132 1 CCTAGCCGCC 0.973036 -12 GTTAGGGCGGCCTTTCCCGTGGGAATGACAG 3 233 0 CCTTTCCGTG 0.829478 -68 AGCAAGGCCCGCCCTACAACAAT 5 57 0 CAAGGCCGCC 0.972498 -13 ACAACACCAATGCCAGGGTTGGAGTTCC 6 12 0 CAATGCCGGG 0.848191 -18 GGGCCCTAACCCAGACCGGTGGAATTTTACC 8 37 0 CCAGACCGTG 0.880356 -184 TTATATCCTACCATGCCCGCCGGGCAAGCTT 8 108 1 CCATGCCGCC 0.990456 -113 CCTACTGTTACCATGCCGATCGCCAGTGGTC 11 105 1 CCATGCCATC 0.957884 -97 ACGGAATTACCCAAGCCAGTGCCGAGGAACG 11 148 0 CCAAGCCGTG 0.976578 -54 ******* *** Masking position 6 Map Score: 5.53859 Number of sites scoring better than the average of aligned sites = 1556 Number in coding regions = 1471 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 13 AAAAAAGCAGCAACAATAGTGGGAGGACTG 4 24 1 CAACAATAGT 0.950369 -122 GCCCGCCCTACAACAATTGCTTCCCTAGCA 5 44 0 CAACAATTGC 0.973298 -26 GAAATAGGCTCAACAATCGCAAA 7 4 0 CAACAATCGC 0.982573 -97 GAGCCTATTTCAACAATTTTCCTAAAATTT 7 23 1 CAACAATTTT 0.866137 -78 GCAAGGGCAAAAACAATCGTTTAAGATCCG 8 190 0 AAACAATCGT 0.909161 -31 ********** Masking position 5 Map Score: 0.631586 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 173 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 AGGTCTGAGTTTTAAACGGGATCAGTCCTC 4 46 0 TTTAAACGGG 0.955393 -100 AAATACTTGCTTTAAACAGTTTAGATCTGA 4 79 0 TTTAAACAGT 0.942627 -67 AAAGCAAGTATTTAAACGGTACTTTAAATA 4 96 1 TTTAAACGGT 0.931604 -50 TAAACGGTACTTTAAATAAGAATTATTTGC 4 108 1 TTTAAATAAG 0.717637 -38 AGGAAAATTGTTGAAATAGGCTCAACAATC 7 16 0 TTGAAATAGG 0.857294 -85 TCATTCCAATTTTAAATAGTAGGATGGAAT 14 229 0 TTTAAATAGT 0.912652 -72 ********** Masking position 5 Map Score: 0.448312 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 91 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 ********** No masking Map Score: 6.53943e-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