AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_Glycolysis___PPS_synecho_reg_300.orf -o013_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 RCY22255 300 Synechocystis #2 RCY49058 126 Synechocystis #3 RCY53506 106 Synechocystis #4 RCY17695 300 Synechocystis #5 RCY44898 206 Synechocystis #6 RCY48136 300 Synechocystis #7 RCY07219 86 Synechocystis #8 RCY02847 174 Synechocystis #9 RCY27715 133 Synechocystis Motif number 1 GGGCTAGCTCAGGGAGCCAGGACCACAATCAGTGTTGG 1 85 0 AGGAGCCCCA 0.987063 -216 ATAATGACTACGGGAACCAAGTCCTATACTCAGTAACA 1 221 0 CGGAACCCCA 0.996308 -80 GAAATTTTTCCTGAAAACTTTGCCAGAAAAAGAAAACT 3 22 1 CTGAAACCCA 0.943049 -85 TCCCGGTAGCCATAACTGGGATGGGATGTGG 4 4 1 CGGAGCCCTA 0.985717 -297 AAAAATGGGTCTGAAACCCCGCCCTTGAGGACGGCCTT 4 270 0 CTGAACCCCA 0.985261 -31 TAGCAACTTTAGGAGAGCAGTTCCTCCACCTGGGCCAG 5 69 0 AGGGAGCCCA 0.888765 -138 ACCCTTTCCTCGGTGACCTAAACTGCTAAAAGACAGGA 5 148 1 CGGGACCCTA 0.980004 -59 ATCCCGACACAGGAAGCGATTCCCAGCAAACCAGACAA 6 194 0 AGGAGCGCCA 0.891717 -107 GCCAATCCTAGGGTAACCAATCCCGACACAGGAAGCGA 6 213 0 GGGAACCCCA 0.975132 -88 TTTACCTAAACGGGAAACGACTCCAAGATGGAGGGGAA 7 28 1 CGGAAACCCA 0.985261 -59 ATTGCTTCATCTGTGGACTGCCCTAAAAATTGCCATAA 8 130 0 CTGGGACCTA 0.776952 -45 AAGATTTTCACAGAGGCCTTGTCCGGAAAGGCTAATTT 9 57 1 CAGGGCCCCA 0.961712 -77 *** **** ** * Masking position 18 Map Score: 14.0662 Number of sites scoring better than the average of aligned sites = 1037 Number in coding regions = 992 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 2 GAAGCTGTAGGCGGTTTTTCTTTACCAACACTG 1 61 1 GGTTTTTCTT 0.989776 -240 GGGAGAAGTTGACAATTTTCTTTAGATTCATGG 1 161 0 GAATTTTCTT 0.889587 -140 CGCCTCTGGTGGGGTTTTTCGTTGTAAGATGCA 2 72 1 GGTTTTTCTT 0.989776 -55 TAAGATGCAGGCAGATTTCCCTTCTTGGTGGGC 2 96 1 GGATTTCCTT 0.953721 -31 AACTGAGAAAGAAATTTTTCCTGAAAACTTTGC 3 12 1 GATTTTTCTG 0.798313 -95 CACAATTCCCGAAAGTTTTCTTTTTCTGGCAAA 3 40 0 GAGTTTTCTT 0.825358 -67 TTTTTGGCCGGATGTTTTTTCCTGTTTAATAAA 4 207 1 GGTTTTTTCT 0.811862 -94 TACGATCAAAGCTGTTTTCCCTTTAGGTTTCGT 5 13 0 GGTTTTCCTT 0.98466 -194 CCATTTAACGGTTAATTTCCTCTGGCCCAGGTG 5 48 1 GAATTTCCCT 0.672171 -159 AGGATTTTGTGTAGTTTTTCAATGGCTTTGGGG 5 182 1 GGTTTTTCAT 0.971765 -25 CCATCTTGGAGTCGTTTCCCGTTTAGGTAAAGG 7 26 0 GGTTTCCCTT 0.903508 -61 TTCGACTCCAGATGTTTTTCTAATTTCCTCACA 8 70 0 GGTTTTTCAA 0.785529 -105 AAACACCTGGGGCGTCTTTCCTTGTTTCGACTC 8 95 0 GGTCTTTCTT 0.933869 -80 AGACGCCCCAGGTGTTTTTTTATGGCAATTTTT 8 111 1 GGTTTTTTAT 0.799897 -64 * ******* ** Masking position 7 Map Score: 12.029 Number of sites scoring better than the average of aligned sites = 569 Number in coding regions = 483 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 TCTGTTTTGCGGGCTAGCTCAGGGAGCCAGGACCAC 1 97 0 GGGAGAGGAG 0.73538 -204 AGGTAAGGGCCCACCAAGAAGGGAAATC 2 109 0 GTAGGACCAG 0.928825 -18 GATGGGATGTGGAGGGGCATAGGAGGTGACTATTTG 4 30 1 GGAGGAGGGG 0.989998 -271 GAATTTTCTGGGGTTGGTGTTGCGGGAAAAGCCTTG 4 147 1 GGGGGTGCGG 0.987785 -154 AGGTCACCGAGGAAAGGGTCACCAAGCAAAAAGCTA 5 131 0 GGAGGACCAG 0.99335 -76 AGGGCAAAAGGGATGGGCCGAGCTGGATTTGAACCA 6 24 1 GGAGGAGCGG 0.996505 -277 ATTTGAACCAGCGTAGGCATAGCCAGCGGATTTACA 6 50 1 GCGGGAGCAG 0.963754 -251 TCCTGTGTCGGGATTGGTTACCCTAGGATTGGCTCG 6 218 1 GGAGGCCCAG 0.986489 -83 ACTCCAAGATGGAGGGGAAAAACAAGATTATCCATT 7 47 1 GGAGGAACAG 0.958519 -40 GTCGAAACAAGGAAAGACGCCCCAGGTGTTTTTTTA 8 97 1 GGAGACCCGG 0.893446 -78 CACAGATGAAGCAATGGCGCTGGCGGATGGTA 8 153 1 GCAGGTGGGG 0.914382 -22 TGTTCAAACTGGTCTGGAAATCCCGGTCGGTCGGGC 9 100 1 GGTGGTCCGG 0.944645 -34 *** ** *** ** Masking position 1 Map Score: 11.9699 Number of sites scoring better than the average of aligned sites = 954 Number in coding regions = 887 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 CTAGGCTAAGCAAGGCCATTGGTCTGTTTTG 1 124 0 CAAGGCCATG 0.731207 -177 AAAACCCCACCAGAGGCGGGGTTAAAGAGTT 2 59 0 CAGAGGCGGG 0.968817 -68 ATGGGATGTGGAGGGGCATAGGAGGTGACTA 4 31 1 GAGGGGCATG 0.957283 -270 GATGTGAACGCAAGGCCGTCCTCAAGGGCGG 4 259 1 CAAGGCCGTC 0.836537 -42 AGGCCGTCCTCAAGGGCGGGGTTTCAGACCC 4 271 1 CAAGGGCGGG 0.968519 -30 GTTCCTCCACCTGGGCCAGAGGAAATTAACC 5 57 0 CTGGGCCAGG 0.952106 -150 GGCCCCAAAGCCATTGAAAAACTACA 5 191 0 CAAAGCCATG 0.906004 -16 GGGCAAAAGGGATGGGCCGAGCTGGATTTGA 6 25 1 GATGGGCCGG 0.906136 -276 CCAGCGTAGGCATAGCCAGCGGATTTACAGT 6 57 1 CATAGCCAGG 0.951983 -244 ACTAGAGAGAGAGGGACAGTGGGTGCCACTA 6 268 0 GAGGGACAGG 0.867658 -33 TACCATCCGCCAGCGCCATTGCTTCATCTGT 8 154 0 CAGCGCCATG 0.9137 -21 AAGATTTTCACAGAGGCCTTGTCCGGAAAGG 9 57 1 CAGAGGCCTG 0.87214 -77 TTACCATGGCCCGACCGACCGGGAT 9 119 0 CATGGCCCGC 0.893141 -15 ********* * Masking position 7 Map Score: 11.276 Number of sites scoring better than the average of aligned sites = 2394 Number in coding regions = 2226 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 5 GACCAATGGCCTTGCTTAGCCTAGCATCTACCAT 1 131 1 CTTGCTCCTG 0.959704 -170 GAGTATAGGACTTGGTTCCCGTAGTCATTATTAG 1 228 1 CTTGGTCGTG 0.97624 -73 CTTAAACTATCTTGGAAGTCCCTGTTA 1 284 1 CTTGGACCCG 0.98018 -17 GATTTCCCTTCTTGGTGGGCCCTTACCT 2 109 1 CTTGGTCCCT 0.992143 -18 CGGGAAAAGCCTTGGCGATCGCCTTTTTTTGTCC 4 169 1 CTTGGCCGCT 0.95934 -132 TAGCTTTTTGCTTGGTGACCCTTTCCTCGGTGAC 5 131 1 CTTGGTCCTT 0.985791 -76 CTGTGTCGGGATTGGTTACCCTAGGATTGGCTCG 6 220 1 ATTGGTCCTG 0.923116 -81 AATGGATAATCTTGTTTTTCCCCTCCATCTTGGA 7 49 0 CTTGTTCCCT 0.946649 -38 GGTCTGAAGCCTTGACAATCCCCGTTGGTGATTT 8 22 1 CTTGACCCCG 0.951746 -153 ****** *** * Masking position 3 Map Score: 7.26223 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 308 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 ACGATGATGTTGATGGTTAATAACAGATTA 1 21 0 TGATGGTTAA 0.986611 -280 CCACAATCAGTGTTGGTAAAGAAAAACCGC 1 71 0 TGTTGGTAAA 0.939879 -230 GGTGACTATTTGTTGGTTCACTTAGGAATT 4 54 1 TGTTGGTTCA 0.949491 -247 GACAGAACTTTGGTGGTTAACCACACACTG 4 87 1 TGGTGGTTAA 0.977391 -214 TAAGGTGTTATGATGGCTAATCGTGAAAGC 6 122 0 TGATGGCTAA 0.964218 -179 ACCTTATTGTTGATGGTCAAAATATTTTTT 6 146 1 TGATGGTCAA 0.97076 -155 ********** Masking position 4 Map Score: 4.60688 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 85 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 TTTTTAGCTTTTCCTCACACCTAATAATGA 1 252 0 TTCCTCACAC 0.962657 -49 AAAGAAATTTTTCCTGAAAACTTTGCCAGA 3 19 1 TTCCTGAAAA 0.837656 -88 TAACTCACAATTCCCGAAAGTTTTCTTTTT 3 48 0 TTCCCGAAAG 0.905341 -59 TTGCCCCATTTTGCTCCGAGGGAATTTTCT 4 126 1 TTGCTCCGAG 0.765591 -175 GCCAAGGCTTTTCCCGCAACACCAACCCCA 4 155 0 TTCCCGCAAC 0.946621 -146 AGGAGAGCAGTTCCTCCACCTGGGCCAGAG 5 67 0 TTCCTCCACC 0.815285 -140 TCTCCTAAAGTTGCTAAAACTTGCTGAAAC 5 91 1 TTGCTAAAAC 0.584572 -116 TTGCTAAAACTTGCTGAAACGGGAGAATTT 5 101 1 TTGCTGAAAC 0.90095 -106 AGGGTAACCAATCCCGACACAGGAAGCGAT 6 212 0 ATCCCGACAC 0.673152 -89 AGATTATCCATTCCCCAGAGGTTTCC 7 71 1 TTCCCCAGAG 0.903928 -16 TTTTTCTAATTTCCTCACACCTGTCCTAAG 8 59 0 TTCCTCACAC 0.962657 -116 ATTTCCTCCGAAAATAAGCTAG 9 3 1 TTCCTCCGAA 0.806789 -131 ********** Masking position 2 Map Score: 4.69099 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 825 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 8 TGGGTCGATGCCCGAGTGGTTAATGGGGGCG 6 89 0 CCCGAGGGTT 0.99063 -212 ATTATCCATTCCCCAGAGGTTTCC 7 73 1 CCCCAGGGTT 0.996477 -14 CTTGTTTCGACTCCAGATGTTTTTCTAATTT 8 77 0 CTCCAGTGTT 0.97881 -98 AGGAAAGACGCCCCAGGTGTTTTTTTATGGC 8 106 1 CCCCAGTGTT 0.99458 -69 ****** **** Masking position 5 Map Score: 2.58246 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 34 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AGTCCGTCTTCTTAAGACACTTGTTTGAAA 2 16 1 CTTAAGACAC 0.837362 -111 CACTTAGGAATTTTGGACAGAACTTTGGTG 4 72 1 TTTTGGACAG 0.922118 -229 CGGCCAAAAATTGAGGACAAAAAAAGGCGA 4 187 0 TTGAGGACAA 0.909091 -114 GCGTTCACATCTTAAGACAATTAGAAAGAT 4 240 0 CTTAAGACAA 0.768964 -61 AACCCCGCCCTTGAGGACGGCCTTGCGTTC 4 264 0 TTGAGGACGG 0.895606 -37 TTTTAGCAACTTTAGGAGAGCAGTTCCTCC 5 80 0 TTTAGGAGAG 0.916074 -127 CTTTTAGCAGTTTAGGTCACCGAGGAAAGG 5 150 0 TTTAGGTCAC 0.850314 -57 GTGATTTATACTTAGGACAGGTGTGAGGAA 8 49 1 CTTAGGACAG 0.984107 -126 TATGGCAATTTTTAGGGCAGTCCACAGATG 8 131 1 TTTAGGGCAG 0.952273 -44 ********** Masking position 2 Map Score: 3.50091 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 173 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 TTTAGCTTTTCCTCACACCTAATAATGACT 1 250 0 CCTCACACCT 0.994877 -51 GATTAGCCATCATAACACCTTATTGTTGAT 6 130 1 CATAACACCT 0.947148 -171 ATTGTCAAGGCTTCAGACCTGGAAAAAAAC 8 11 0 CTTCAGACCT 0.963717 -164 TTTCTAATTTCCTCACACCTGTCCTAAGTA 8 57 0 CCTCACACCT 0.994877 -118 ********** Masking position 5 Map Score: 2.03418 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 GCCATTGGTCTGTTTTGCGGGCTAGCTCAGG 1 110 0 TGTTTTGCGG 0.933798 -191 ATTGTACACGTTTTTTTCGAAAGAGTGGGAG 1 189 0 TTTTTTTCAA 0.842344 -112 CCGAAAGTTTTCTTTTTCTGGCAAAGTTTTC 3 34 0 TCTTTTTCGG 0.94688 -73 TTGTCCTCAATTTTTGGCCGGATGTTTTTTC 4 197 1 TTTTTGGCGG 0.925417 -104 GGTCAAAATATTTTTTTCTGGGTTGGTCAGA 6 160 1 TTTTTTTCGG 0.985318 -141 GTTGGTCAGATTTTTGTCTGGTTTGCTGGGA 6 181 1 TTTTTGTCGG 0.966507 -120 GTTTTTTTCCAGGTCTGAAGCC 8 2 1 TTTTTTTCAG 0.949839 -173 CGACTCCAGATGTTTTTCTAATTTCCTCACA 8 70 0 TGTTTTTCAA 0.723117 -105 GCCCCAGGTGTTTTTTTATGGCAATTTTTAG 8 115 1 TTTTTTTAGG 0.854298 -60 AAAAGCTAGCTTATTTTCGGAGGAAAT 9 7 0 TTATTTTCGA 0.727108 -127 ******** ** Masking position 5 Map Score: 7.8294 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 621 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 12 TGCGGGCTAGCTCAGGGAGCCAGGACCACAA 1 95 0 CTCGGGAGCC 0.980393 -206 CTAATAATGACTACGGGAACCAAGTCCTATA 1 231 0 CTAGGGAACC 0.993166 -70 TCCAAAATTCCTAAGTGAACCAACAAATAGT 4 58 0 CTAGTGAACC 0.984732 -243 TAGCTTTTTGCTTGGTGACCCTTTCCTCGGT 5 131 1 CTTGTGACCC 0.937395 -76 CGAGCCAATCCTAGGGTAACCAATCCCGACA 6 223 0 CTAGGTAACC 0.965334 -78 *** ******* Masking position 8 Map Score: 0.970815 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 58 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ********** No masking Map Score: 2.40407e-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 14 ********** No masking Map Score: 2.40407e-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: 2.40407e-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