AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_synecho_reg_100.orf -o064_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 RCY10954 211 Synechocystis #2 RCY26047 35 Synechocystis #3 RCY44892 192 Synechocystis #4 RCY33884 213 Synechocystis #5 RCY44461 245 Synechocystis #6 RCY22265 286 Synechocystis #7 RCY39566 239 Synechocystis #8 RCY11341 81 Synechocystis #9 RCY10798 68 Synechocystis #10 RCY15876 126 Synechocystis #11 RCY45983 163 Synechocystis Motif number 1 GGCGATCGCCGTGGGGGGAAGCTCTCATCT 1 36 1 GTGGGGGGAA 0.965481 -176 CCCTCTCCGATTGGGGGCAAGGGCGGCGAA 2 12 0 TTGGGGGCAA 0.885929 -24 CTAGGAAAAAACAGGGGAAAGAATGCCCTT 3 76 0 ACAGGGGAAA 0.952273 -117 CGTCGCCTTTACAGCGGCAACGGTGTCGGG 3 107 1 ACAGCGGCAA 0.91807 -86 TATGGTCTGTAATGGGAGAAGCTTTAAACA 3 138 1 AATGGGAGAA 0.728364 -55 AATTACGATCAAAGGGGCAATAAATCCCTT 3 168 0 AAAGGGGCAA 0.916024 -25 CAACTAAGTTGCTGGGAAAATGTATTTGTC 4 39 1 GCTGGGAAAA 0.913985 -175 AAGGGACTTGGATGGGGAAATGGAACTTCA 4 73 1 GATGGGGAAA 0.942552 -141 GGCAGGGGAAATTAGTGAGTA 6 2 1 GCAGGGGAAA 0.980473 -285 ATACTGGAGTTTTGGGAAAACAGACTCTAA 6 179 1 TTTGGGAAAA 0.548271 -108 CAAGGCAAATTCAGGGGGAAAACTACCAGC 7 172 0 TCAGGGGGAA 0.97281 -68 GTATATCGTGATTGGGGCAAGGCAAATTCA 7 189 0 ATTGGGGCAA 0.938566 -51 GCAAATTTTGTCAGCGGCAATCAATAGCAA 9 29 1 TCAGCGGCAA 0.900943 -40 GTTCCTTGGGGTTGCGGGAAAACATTATAT 10 67 1 GTTGCGGGAA 0.929509 -60 CTTTGTTTCGGCAGGGGCAAGTTTAAACAT 10 102 0 GCAGGGGCAA 0.989637 -25 AGAGGACAGGGCGGGGAGAATGCAGTTGCT 11 40 1 GCGGGGAGAA 0.936318 -124 TGCTCAACTTCCTGCGGGAATACGGCCAGT 11 66 1 CCTGCGGGAA 0.843999 -98 TCAAAGGAAGGATGGGGGAATTCCGCCCCG 11 130 0 GATGGGGGAA 0.973152 -34 ********** Masking position 9 Map Score: 26.8618 Number of sites scoring better than the average of aligned sites = 3984 Number in coding regions = 3577 Number in noncoding regions = 407 Number of orfs with sites within 600 bp upstream = 410 Fraction of orfs with sites within 600 bp upstream = 0.0658529 Motif number 2 GCATAACGCTGGCGATCGCCGTGGGGGGAAGCTCTCAT 1 26 1 GCGCGTGGGG 0.908486 -186 CCATCTTATTGGCGAACGGCGGGAGTGAAAGAAGCCCT 1 70 0 GCGCGGGGGA 0.995196 -142 CGCAAAGTTGACCGCTCCCCAGGACGGACTAGCAATAT 5 146 0 ACGCAGGCGA 0.98742 -100 ACAATGGCTAGACGGGGGTTAGGTCCGATCATCAATGG 5 185 1 GCGTAGGCGA 0.993879 -61 GGGAAAAAAGACGCAAAGTAGGACAGAGTTAGACCAT 5 219 0 GCGTAGGCGA 0.993879 -27 GCTTGATTGGGTCAGTTTACAGGGCTGATCAGATCTGG 6 134 0 GCACAGGCGA 0.993879 -153 TATACTCAATGGCGACGATCAGGACAGAAAACCATT 7 214 1 GCGCAGGCGA 0.998789 -26 GTTTATGAAAGCCAGAGGACAGGGCGGGGAGAATGCAG 11 27 1 GCACAGGCGG 0.987557 -137 TAAATGTCAAGCCGTTCTGCGGGGCGGAATTCCCCCAT 11 111 1 GCGCGGGCGA 0.982328 -53 * ** **** * ** Masking position 3 Map Score: 17.0898 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 97 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 ATGAGAGCTTCCCCCCACGGCGATCGCCAG 1 34 0 CCCCCCACGG 0.817351 -178 GCCGCCCTTGCCCCCAATCGGAGAGGGATC 2 15 1 CCCCCAATCG 0.975628 -21 GGGATTTATTGCCCCTTTGATCGTAATTGC 3 170 1 GCCCCTTTGA 0.947055 -23 AAGTTCCATTTCCCCATCCAAGTCCCTTGG 4 71 0 TCCCCATCCA 0.844906 -143 GAACTTCACCGCCCCATTCGAGCTTAATCT 4 95 1 GCCCCATTCG 0.99149 -119 GGCACATTATGCCCCTTTCTCGGCCGGCCG 6 41 1 GCCCCTTTCT 0.964095 -246 CCTGTAAACTGACCCAATCAAGCGACCGCA 6 149 1 GACCCAATCA 0.82929 -138 ACAGCAAAGCCCCCCTTTGTTTGTATTTGG 7 43 0 CCCCCTTTGT 0.888956 -197 AATTTGCCTTGCCCCAATCACGATATACTC 7 191 1 GCCCCAATCA 0.972194 -49 TGACCCATTGGTAAGGGTTTT 10 2 1 GACCCATTGG 0.892261 -125 GTTTAAACTTGCCCCTGCCGAAACAAAGCC 10 104 1 GCCCCTGCCG 0.937538 -23 GGGCGGAATTCCCCCATCCTTCCTTTGATG 11 132 1 CCCCCATCCT 0.956204 -32 ********** Masking position 5 Map Score: 11.708 Number of sites scoring better than the average of aligned sites = 1565 Number in coding regions = 1439 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 AGATGAGAGCTTCCCCCCACGGCGATCGCC 1 36 0 TTCCCCCCAC 0.837164 -176 ATCCCACCGTCTCCGCCATCTTATTGGCGA 1 93 0 CTCCGCCATC 0.890247 -119 GATATTAGAATTCAGCCAACACACCAATTT 5 47 0 TTCAGCCAAC 0.646936 -199 TCCGGGATCCTTCTGCCCAGAGATATTGCT 5 124 1 TTCTGCCCAG 0.981138 -122 GATATTGCTAGTCCGTCCTGGGGAGCGGTC 5 145 1 GTCCGTCCTG 0.923393 -101 AATGGTCTAACTCTGTCCTACTTTGCGTCT 5 218 1 CTCTGTCCTA 0.6935 -28 GCCAGATCTGATCAGCCCTGTAAACTGACC 6 133 1 ATCAGCCCTG 0.873071 -154 AATGGTTTTCTGTCCTGATCGTCGCCA 7 223 0 TTCTGTCCTG 0.966053 -17 GGTCTGCTTATTCTGTCCTGTAAGTGTTGT 8 21 1 TTCTGTCCTG 0.966053 -61 TTTTGGATAATTCTGCCCACCAAGGAAAAC 10 28 1 TTCTGCCCAC 0.968066 -99 ACTGCATTCTCCCCGCCCTGTCCTCTGGCT 11 36 0 CCCCGCCCTG 0.945048 -128 GATGGGGGAATTCCGCCCCGCAGAACGGCT 11 120 0 TTCCGCCCCG 0.973939 -44 ********** Masking position 7 Map Score: 8.53032 Number of sites scoring better than the average of aligned sites = 1303 Number in coding regions = 1145 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 5 GAGATATGCCATGGCCAAACTGCCAA 3 7 0 ATGGCCAAAC 0.804386 -186 CCCTAAAAAATAGCCCAAACAAAGGGCATT 3 55 1 TAGCCCAAAC 0.978225 -138 TTGTCCGTAGTATCCCAAAGATTAAGCTCG 4 113 0 TATCCCAAAG 0.89242 -101 AATATCAAAATTGCCCAATGGCGAACTTGA 5 71 1 TTGCCCAATG 0.915961 -175 AGAGTCTGTTTTCCCAAAACTCCAGTATTG 6 177 0 TTCCCAAAAC 0.893389 -110 AAAGAGAAGATTGCCAAAAGTTAGAGTCTG 6 199 0 TTGCCAAAAG 0.972369 -88 AAGTTTAGAGTTGCCCAAAGTCTAGAAAAT 7 114 0 TTGCCCAAAG 0.985743 -126 CCAGTCACCGTTGGCAAAACCTTAACAAAA 7 143 0 TTGGCAAAAC 0.929957 -97 TGGGCAGAATTATCCAAAACCCTTACCAAT 10 17 0 TATCCAAAAC 0.839484 -110 ********** Masking position 7 Map Score: 6.95075 Number of sites scoring better than the average of aligned sites = 1006 Number in coding regions = 887 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 6 GGCGGGAGTGAAAGAAGCCCTCCACAGATG 1 61 0 AAAGAAGCCC 0.873282 -151 CTGAGGTGCAAACAACGCCCTAGCGAAAGC 1 135 0 AACAACGCCC 0.949386 -77 TTAAACAAGCAGCAAAGTCGCTGAGGTGCA 1 155 0 AGCAAAGTCG 0.806582 -57 CCATCCCTAAAAAATAGCCCAAACAAAGGG 3 51 1 AAAATAGCCC 0.823002 -142 AAATAGCCCAAACAAAGGGCATTCTTTCCC 3 62 1 AACAAAGGGC 0.924427 -131 AGAAGCTTTAAACAAAGGGATTTATTGCCC 3 154 1 AACAAAGGGA 0.736692 -39 GGGAAAAAAGACGCAAAGTAGGA 5 233 0 AAAAAAGACG 0.709826 -13 GGCTGTTCTGAAAAAAGCCATTGCCACTCA 6 247 1 AAAAAAGCCA 0.893278 -40 TCGATAATACAGCAAAGCCCCCCTTTGTTT 7 51 0 AGCAAAGCCC 0.984223 -189 AGCAAAGGCCGGTCTGCTTA 8 1 1 AGCAAAGGCC 0.969834 -81 CCCCTGCCGAAACAAAGCCGTC 10 115 1 AACAAAGCCG 0.980891 -12 ********** Masking position 1 Map Score: 7.10559 Number of sites scoring better than the average of aligned sites = 852 Number in coding regions = 753 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 7 GGGATATAATCGGACAGGCTTTCGCTAGGGCG 1 118 1 CGGACGGCTT 0.969111 -94 AAACAGGGGAAAGAATGCCCTTTGTTTGGGCT 3 66 0 AAGAAGCCTT 0.79721 -127 CAATAGTCAACAGAAAACCTTCCCCTCAACTA 4 13 1 CAGAAACCTC 0.946347 -201 CTCCCCAGGACGGACTAGCAATATCTCTGGGC 5 138 0 CGGACAGCAT 0.793455 -108 ATGAGTCACTCAGAATAGCTTCTAGATTTGCT 6 80 1 CAGAAAGCTC 0.971612 -207 TGGCTTTTTTCAGAACAGCCTTAATCCATTTT 6 235 0 CAGAAAGCTT 0.983684 -52 ACGATCAGGACAGAAAACCATT 7 228 1 CAGAAACCTT 0.968894 -12 ACAGAATAAGCAGACCGGCCTTTGCT 8 5 0 CAGACGGCTT 0.98335 -77 TTCCGCCCCGCAGAACGGCTTGACATTTATCT 11 108 0 CAGAAGGCTG 0.959901 -56 ***** *** ** Masking position 4 Map Score: 6.39777 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 130 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 GGCATTCTTTCCCCTGTTTTTTCCTAGACG 3 79 1 CCCCTGTTTT 0.976791 -114 CGAACTTGATCCCCGGTTTAGCAAAGATTT 5 92 1 CCCCGGTTTA 0.941385 -154 TTTCCCAAAACTCCAGTATTGCGGTCGCTT 6 168 0 CTCCAGTATT 0.934833 -119 GGTAGTTTTCCCCCTGAATTTGCCTTGCCC 7 175 1 CCCCTGAATT 0.923603 -65 GGTTTCAGTCTCCAGATTTGTTGCTATTG 9 50 0 CTCCAGATTT 0.934833 -19 AGGAACATTTCTCCGGTTTTCCTTGGTGGG 10 43 0 CTCCGGTTTT 0.976416 -84 ********** Masking position 9 Map Score: 2.9428 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 227 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 9 ACAAGCAGCAAAGTCGCTGAGGTGCAAACAA 1 150 0 AAGTCGCTGG 0.979759 -62 AAGGGGCAATAAATCCCTTTGTTTAAAGCTT 3 156 0 AAATCCCTTG 0.889272 -37 CCCCTCAACTAAGTTGCTGGGAAAATGTATT 4 34 1 AAGTTGCTGG 0.978107 -180 TTCCCCATCCAAGTCCCTTGGCCGACAAATA 4 61 0 AAGTCCCTTG 0.953587 -153 TACTACGGACAAATTGCCGGGTTCGGATGTT 4 131 1 AAATTGCCGG 0.88248 -83 CAGATTAGTGAAATTGGTGTGTTGGCTGAAT 5 37 1 AAATTGGTGG 0.717313 -209 TTTCCCCCTGAATTTGCCTTGCCCCAATCAC 7 181 1 AATTTGCCTG 0.65079 -59 AACCGGAGAAATGTTCCTTGGGGTTGCGGGA 10 55 1 ATGTTCCTTG 0.727402 -72 AACCAAGTCGATTTGGGTTTATGAA 11 5 1 AAGTCGATTG 0.748468 -159 GCAGTTGCTCAACTTCCTGCGGGAATACGGC 11 61 1 AACTTCCTGG 0.873962 -103 ********* * Masking position 4 Map Score: 2.50214 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 339 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 ACTACTTAGAAATCAATTCCC 1 201 1 AATCATTCCC 0.882665 -11 ATGTCGTCCCAATCCATCCCTAAAAAATAGC 3 38 1 AATCATCCCT 0.791748 -155 AACAAAGGGCATTCTTTCCCCTGTTTTTTCC 3 72 1 ATTCTTCCCC 0.882956 -121 TCCCATTACAGACCATACCCCGACACCGTTG 3 124 0 GACCTACCCC 0.969476 -69 AGTCAACAGAAAACCTTCCCCTCAACTAAGT 4 17 1 AAACTTCCCC 0.966369 -197 ACGCAAAGTTGACCGCTCCCCAGGACGGACT 5 154 0 GACCCTCCCC 0.956782 -92 TTGATGATCGGACCTAACCCCCGTCTAGCCA 5 189 0 GACCAACCCC 0.962658 -57 CAATTTCACCAATCTTTTCCCC 6 275 1 AATCTTTCCC 0.90261 -12 ACACAACTATAACCTAACCCCAAATACAAAC 7 24 1 AACCAACCCC 0.973123 -216 GAGAATGTTTAAACTTGCCCCTGCCGAAACA 10 98 1 AAACTGCCCC 0.89839 -29 **** ****** Masking position 4 Map Score: 7.90841 Number of sites scoring better than the average of aligned sites = 959 Number in coding regions = 862 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 11 GACGTCGCCTTTACAGCGGCAACGGTGTCG 3 105 1 TTACAGCGGC 0.964056 -88 GACTCATCCGTTTGAGCGGCCGGCCGAGAA 6 57 0 TTTGAGCGGC 0.988062 -230 TAGAAGCTATTCTGAGTGACTCATCCGTTT 6 74 0 TCTGAGTGAC 0.880527 -213 GATTGGTGAAATTGAGTGGCAATGGCTTTT 6 259 0 ATTGAGTGGC 0.934335 -28 AACAAAAAGTTTAGAGTTGCCCAAAGTCTA 7 120 0 TTAGAGTTGC 0.872242 -120 AAGCAAATTTTGTCAGCGGCAATCAATAGC 9 27 1 TGTCAGCGGC 0.940237 -42 ATCAGAGTGGCTCATCAAAGG 11 153 0 TCAGAGTGGC 0.977597 -11 ********** Masking position 5 Map Score: 3.13773 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 190 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 CACCGCCCCATTCGAGCTTAATCTTTGGGA 4 101 1 TTCGAGCTTA 0.925445 -113 GTTGGCATTATTTGAGATTTGAGAACC 5 8 0 TTTGAGATTT 0.694989 -238 TCAGAATAGCTTCTAGATTTGCTCATTTTT 6 89 1 TTCTAGATTT 0.946712 -198 ATACTTAATTTTCTAGACTTTGGGCAACTC 7 107 1 TTCTAGACTT 0.936422 -133 ATCTGTTAAATTCTAGCTTTTGGTCT 8 66 1 TTCTAGCTTT 0.965441 -16 ACATTTATCTTTCTAGCCTATCACTGGCCG 11 88 0 TTCTAGCCTA 0.925445 -76 ********** Masking position 5 Map Score: 1.38434 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 78 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 ATTATATCCCACCGTCTCCGCCATCTTATT 1 98 0 ACCGTCTCCG 0.981703 -114 AGATCCCTCTCCGATTGGGGGCA 2 23 0 TCCCTCTCCG 0.96412 -13 CAGACCATACCCCGACACCGTTGCCGCTGT 3 117 0 CCCGACACCG 0.968792 -76 AAACTACCAGCCAGTCACCGTTGGCAAAAC 7 153 0 CCAGTCACCG 0.978415 -87 GGTTTCAGTCTCCAGATTTGTTGC 9 55 0 TCAGTCTCCA 0.88946 -14 ********** Masking position 6 Map Score: 0.101739 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 233 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 ********** No masking Map Score: 1.71484e-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 15 ********** No masking Map Score: 1.71484e-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