AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i263_hypothetical_synecho_reg_300.orf -o263_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 RCY05387 284 Synechocystis #2 RCY20297 90 Synechocystis #3 RCY31385 125 Synechocystis #4 RCY08522 85 Synechocystis Motif number 1 TCTCTGTAGACAATCGTAGGCGGTTAAACTTT 1 11 0 CAATGAGGCG 0.723343 -274 TGGGTAGAAGGAACCACAACGGGAATATGCGG 1 79 1 GAACAAACGG 0.646068 -206 CCGGTGGTGGCCCCCAGGGCCGTATGGGGCAA 1 136 0 CCCCAGGCCG 0.992488 -149 GCCCTGGGGGCCACCACCGGGGATAGTATGAA 1 148 1 CCACACGGGG 0.589266 -137 AGCAGTGGTTGACCTATGAGCGAAATTAAACT 1 263 0 GACCAGAGCG 0.958977 -22 GCTCCTGGTGCCCCGATGACGGGCC 2 4 0 CCCCAGACGG 0.763528 -87 GTCATCGGGGCACCAGGAGCCGTGTTAGGATG 2 16 1 CACCGAGCCG 0.979639 -75 TTGGGATGCGCCTCCACGGCCGAATATTTCCT 2 52 1 CCTCAGGCCG 0.980241 -39 GTTTTAGCCACCCTTAGGAGCGCTAAAAATAG 3 12 0 CCCTAGAGCG 0.949763 -114 GGCCGAAACCCACCGATCGCCGTTTTTTATGC 3 47 0 CACCACGCCG 0.989265 -79 AAACCCCAGACAACAAACGGCGGGCCGAAACC 3 69 0 CAACACGGCG 0.986015 -57 **** * ***** Masking position 12 Map Score: 13.2835 Number of sites scoring better than the average of aligned sites = 3084 Number in coding regions = 2918 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 2 GGGCCGTATGGGGCAAGTTGAGGTCAGCAA 1 122 0 GGGCAAGTTG 0.892542 -163 ACGGCCCTGGGGGCCACCACCGGGGATAGT 1 145 1 GGGCCACCAC 0.993477 -140 GAAAGCATGGGGTCAACTACACCGATTCCC 1 222 1 GGTCAACTAC 0.984045 -63 TTCGCTCATAGGTCAACCACTGCT 1 271 1 GGTCAACCAC 0.986538 -14 GCCCGTCATCGGGGCACCAGGAGCCGTGTT 2 12 1 GGGGCACCAG 0.986107 -79 AGTTTGGGATGCGCCTCCACGGCCGAATAT 2 49 1 GCGCCTCCAC 0.929976 -42 TTGGAGACTGGGGCTAGTAGTAAATTTTCC 3 101 1 GGGCTAGTAG 0.96117 -25 AATATTCCCAGGGGTTCTAGCTACACTAGA 4 15 1 GGGGTTCTAG 0.886794 -71 ATTAGGATTCGGTCAACTCCAAAAAACGAT 4 66 0 GGTCAACTCC 0.941253 -20 ********** Masking position 1 Map Score: 8.95152 Number of sites scoring better than the average of aligned sites = 1917 Number in coding regions = 1801 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 3 AAAGTTTAACCGCCTACGATTGTCTACA 1 8 1 AACCCCTACG 0.870009 -277 TCCTTCTACCCAAAGCCAACCAAATTCGCTA 1 60 0 CAAACCAACC 0.858198 -225 TGGGTAGAAGGAACCACAACGGGAATATGCG 1 79 1 GAACACAACG 0.965641 -206 CGGCCCTGGGGGCCACCACCGGGGATAGTAT 1 146 1 GGCCCCACCG 0.99432 -139 AGCATGGGGTCAACTACACCGATTCCCAAGT 1 225 1 CAACACACCG 0.971379 -60 GTTTGGGATGCGCCTCCACGGCCGAATATTT 2 50 1 CGCCCCACGG 0.956632 -41 ACGGCGGGCCGAAACCCACCGATCGCCGTTT 3 54 0 GAAACCACCG 0.987044 -72 AAAAACCCCAGACAACAAACGGCGGGCCGAA 3 72 0 GACACAAACG 0.894819 -54 **** ****** Masking position 8 Map Score: 2.9762 Number of sites scoring better than the average of aligned sites = 3215 Number in coding regions = 3080 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 4 CAAAGCCAACCAAATTCGCTAACATGAATG 1 51 0 CAAATTCGCT 0.955836 -234 AGGAAAACCGCATATTCCCGTTGTGGTTCC 1 88 0 CATATTCCCG 0.889207 -197 TAATTAAGTTTAATTTCGCTCATAGGTCAA 1 257 1 TAATTTCGCT 0.809625 -28 TCCACGGCCGAATATTTCCTGTGCAAACTT 2 64 1 AATATTTCCT 0.927275 -27 TTTCCTGTGCAAACTTCCCTTAG 2 78 1 AAACTTCCCT 0.977469 -13 AGGGTGGCTAAAACTTTGCATAAAAAACGG 3 30 1 AAACTTTGCA 0.819308 -96 GGCTAGTAGTAAATTTTCCTTGCC 3 112 1 AAATTTTCCT 0.916408 -14 GCACAATATTCCCAGGGGTTCTAG 4 5 1 AATATTCCCA 0.934168 -81 ********** Masking position 2 Map Score: 3.22636 Number of sites scoring better than the average of aligned sites = 1348 Number in coding regions = 1152 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 5 CAGAGAGTAAGGCTCATTCATGTTAGCGAA 1 37 1 GGCTCATTCA 0.726697 -248 GAATTTGGTTGGCTTTGGGTAGAAGGAACC 1 64 1 GGCTTTGGGT 0.957234 -221 TTCCCGTTGTGGTTCCTTCTACCCAAAGCC 1 74 0 GGTTCCTTCT 0.933557 -211 ATCCTAACACGGCTCCTGGTGCCCCGATGA 2 17 0 GGCTCCTGGT 0.983663 -74 GCGATCGGTGGGTTTCGGCCCGCCGTTTGT 3 59 1 GGTTTCGGCC 0.9291 -67 TGTTGTCTGGGGTTTTTGGAGACTGGGGCT 3 86 1 GGTTTTTGGA 0.891642 -40 TATTCCCAGGGGTTCTAGCTACACTAGAAA 4 17 1 GGTTCTAGCT 0.922274 -69 ACGATGGACAGGTTAAGGGTTACTTTTCTA 4 41 0 GGTTAAGGGT 0.863181 -45 ********** Masking position 4 Map Score: 1.21034 Number of sites scoring better than the average of aligned sites = 1704 Number in coding regions = 1522 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 6 TTGAGGTCAGCAAAGTGAGGAAAACCGCAT 1 105 0 CAAAGTGAGG 0.989809 -180 CCGTATGGGGCAAGTTGAGGTCAGCAAAGT 1 119 0 CAAGTTGAGG 0.916758 -166 CTAAGGGAAGTTTGCACAGG 2 81 0 CTAAGGGAAG 0.966923 -10 TTTAGCGCTCCTAAGGGTGGCTAAAACTTT 3 17 1 CTAAGGGTGG 0.983636 -109 CCCCAGACAACAAACGGCGGGCCGAAACCC 3 68 0 CAAACGGCGG 0.979525 -58 ********** Masking position 3 Map Score: 1.59969 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 334 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 TTGGTTGGCTTTGGGTAGAAGGAACCACAAC 1 68 1 TTGGGTAAAG 0.787892 -217 GTATGAAGAATTGTGAAAATGATCACAGGTT 1 173 1 TTGTGAAATG 0.924997 -112 GAGGAAACTGTTGTGAACCTGTGATCATTTT 1 188 0 TTGTGAACTG 0.978358 -97 TTAATTAAACTTGGGAATCGGTGTAGTTGAC 1 233 0 TTGGGAACGG 0.996177 -52 AGGATGAAGTTTGGGATGCGCCTCCACGGCC 2 42 1 TTGGGATCGC 0.964094 -49 GTCTGGGGTTTTTGGAGACTGGGGCTAGTAG 3 90 1 TTTGGAGCTG 0.920315 -36 ATTAGGATTCGGTCAACTCCAA 4 74 0 TTAGGATCGG 0.955765 -12 ******* *** Masking position 2 Map Score: 2.46253 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 863 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 8 ********** No masking Map Score: 1.55852e-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 9 ********** No masking Map Score: 1.55852e-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: 1.55852e-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