AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i248_synecho_ctra_300.orf -o248_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY22631 194 Synechocystis #2 RCY51824 142 Synechocystis #3 RCY05216 230 Synechocystis #4 RCY35933 256 Synechocystis #5 RCY04292 53 Synechocystis #6 RCY31157 272 Synechocystis #7 RCY24367 125 Synechocystis #8 RCY12587 220 Synechocystis #9 RCY33712 164 Synechocystis #10 RCY53924 189 Synechocystis #11 RCY50562 300 Synechocystis #12 RCT00440 300 Chlamydia_trachomatis #13 RCT00784 69 Chlamydia_trachomatis Motif number 1 CAAAGTACCCTTGCCAACGCCCTCTACCTGC 1 48 1 TTGCCAAGCC 0.943623 -147 CGCTTGGCGATCGCCATTGGCCGGAAACTGC 1 91 0 TCGCCATGGC 0.963088 -104 CCGCTGGGCCTTGCCACTGTCAGGATTGGGA 1 145 1 TTGCCACGTC 0.918526 -50 GATTTTTCCCTGGGCAACTATGCGG 2 5 1 TTTCCCTGGC 0.986921 -138 GCGTTGAACCATTCCACTGCCAAATTCAGCT 3 15 0 ATTCCACGCC 0.740919 -216 GCTGATTAGGTTTCCCTAGCTTGTGATTAAG 3 191 0 TTTCCCTGCT 0.924881 -40 CGGCGATGTATTTCCCCAGGTTTTAACCTTC 4 35 0 TTTCCCCGGT 0.909921 -222 TACATCGCCGTTTCCCTTGTCCCCTGAAGTT 4 56 1 TTTCCCTGTC 0.943368 -201 TTTGCCCAAATTGCCAATGGCAGGCCAAAAA 6 64 1 TTGCCAAGGC 0.943623 -209 ACTTTTTCTCTCGCCATCACCCATGGATACA 7 78 1 TCGCCATACC 0.754854 -48 GGTTGCTTTGTTGCCCTTGGTTGTTGCTGTA 7 105 0 TTGCCCTGGT 0.963374 -21 AACCCGCTTGTTGCCCTGCCCAAA 8 4 0 TTGCCCTCCC 0.917761 -217 CTGAATTTTATTTCCACCAGCCATAAATTGT 8 89 0 TTTCCACAGC 0.738309 -132 CTTCTTTAATACGCCATGGCCA 9 2 0 ACGCCATGCC 0.757353 -163 ACCCCAAACTTTTCCCTTGGCTAGGCTTTTT 9 76 0 TTTCCCTGGC 0.986921 -89 AAAGGAAAAATTGCCCTGGTTTTTAGCCCCT 10 50 1 TTGCCCTGTT 0.853079 -140 CCCTGGTTTTTAGCCCCTGCCTCCCCGGTGT 10 63 1 TAGCCCCGCC 0.913962 -127 TTTATCGGTTTTTCCCACACCGGGGAGGCAG 10 79 0 TTTCCCAACC 0.705413 -111 TTCTAGGCGATCGCCCTGGGATGGAAATCCC 10 138 0 TCGCCCTGGA 0.770163 -52 AGTCCTGGGTTTGCCCCAGGCGAGAGGAGAT 11 241 0 TTGCCCCGGC 0.992496 -60 CAAAGAGCTATTTTCCTTGCCAGTTATTTCC 12 129 0 TTTTCCTGCC 0.750053 -172 ******* *** Masking position 5 Map Score: 26.1735 Number of sites scoring better than the average of aligned sites = 4766 Number in coding regions = 4351 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 416 Fraction of orfs with sites within 600 bp upstream = 0.0668166 Motif number 2 GCCGGAAACTGCCCAGGGACTAATGCAGGTAGA 1 70 0 GCCAGGGCTA 0.988176 -125 AATGGCGATCGCCAAGCGTCGTATATTAGGCAT 1 104 1 GCAAGCGCGA 0.945652 -91 CAGTGGCAAGGCCCAGCGGCTCAATATATGCCT 1 131 0 GCCAGCGCTA 0.993916 -64 AGAAAGGGAGGAGAAGGGGCTCCGTATTCTAAG 2 74 0 GAAAGGGCTC 0.88713 -69 TGCCCGCCGTGGTCAGCGCCCAAGCCTAATTAC 3 100 1 GGCAGCGCCA 0.973118 -131 CTTGTTACGTGATCAGCGCCTACCCGATACCAA 4 164 0 GACAGCGCTC 0.984132 -93 AGGATATGGGCCAAAGCGTCCACATGCTCTACC 6 132 1 CCAAGCGCCC 0.887015 -141 CAATAATGACGAACAGCGTCGCCGAAAACGTTA 6 199 0 GACAGCGCGC 0.963853 -74 CCCTTTTAAGCCCCAGCGGCTTAGGCCACTAAC 7 47 1 CCCAGCGCTA 0.984527 -79 CAGACAGTAGCGATAGCGACTTCTATCAAGCTT 8 117 1 CGTAGCGCTC 0.788312 -104 GGTGCTCAGGGTCTAATGTTGCTAGT 9 149 0 GCCAGGGCTA 0.988176 -16 CACACCGGGGAGGCAGGGGCTAAAAACCAGGGC 10 62 0 AGCAGGGCTA 0.80852 -128 ** ***** ** * Masking position 5 Map Score: 12.1033 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 285 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 GAGGATACATGGGGGACAAGTTTCCCCTT 1 10 0 GGGGGACAAG 0.65878 -185 TATCCTCGTCCAGTGCAAAGTACCCTTGCC 1 33 1 CAGTGCAAAG 0.659414 -162 GGAGTGGTGAGGATGCAAAGCCGTCTCCTT 2 113 0 GGATGCAAAG 0.861407 -30 GGGGTCAAGGGGAGTGGTGA 2 133 0 GGGGTCAAGG 0.958765 -10 CTGAACTTCAGGGGACAAGGGAAACGGCGA 4 60 0 GGGGACAAGG 0.712175 -197 CAAATTTTTAGGATGCAACGATCGCCTCCA 6 29 0 GGATGCAACG 0.625264 -244 AAGCCGCTGGGGCTTAAAAGGGGTGACTGG 7 39 0 GGCTTAAAAG 0.682859 -87 GGAAAAGTTTGGGGTTAACGGGCTGAAATT 9 92 1 GGGGTTAACG 0.778944 -73 CAATTTGGAAGTCAAAGGAATAATTTC 11 8 1 GAAGTCAAAG 0.900353 -293 TACTTGGATTGGCGTCAAAGACTGTTTTTG 11 165 1 GGCGTCAAAG 0.927425 -136 TTAATCCTGGCAGGTCAAAGATAGTCCTGG 11 264 0 CAGGTCAAAG 0.875462 -37 TGACCTGCCAGGATTAAAAGCCAAAGTTCA 11 277 1 GGATTAAAAG 0.79177 -24 GAGGTAAAAGCGAATTAGAA 12 1 1 GAGGTAAAAG 0.909245 -300 TGAAAAAGAAGAGTTTAAAGTTGGATATTT 12 158 1 GAGTTTAAAG 0.677856 -143 AAGAGACCTCCGAGTTAAAGCCAAACCTTC 12 247 0 CGAGTTAAAG 0.595303 -54 CTTTTCCTTCCGGGTCAAAGAGACCTCCGA 12 264 0 CGGGTCAAAG 0.946112 -37 CTTTGACCCGGAAGGAAAAGAAAATGAGTT 12 274 1 GAAGGAAAAG 0.723422 -27 AAAAGAAAATGAGTTAAAGGAA 12 289 1 GAGTTAAAGG 0.610681 -12 ********** Masking position 8 Map Score: 11.9345 Number of sites scoring better than the average of aligned sites = 2750 Number in coding regions = 2460 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 4 AGGCCCTCCCAATCCTGACAGTGGCAAGGCC 1 151 0 AATCCGACAG 0.962282 -44 TCCACTGCCAAATTCAGCTAATT 3 3 0 AATTCGCTAA 0.850501 -228 GCAGGCAGATAATCCGCCCAACTCTTAATCT 3 55 1 AATCCCCCAA 0.962237 -176 GAATTGAATCCTCCCAACTGCTGATTA 3 214 0 AATCCCCCAA 0.962237 -17 ACCAAAACATAAGTCCCCCAAAGTCTGAACT 4 83 0 AAGTCCCCAA 0.805922 -174 TGCCATTGGCAATTTGGGCAAAGGGTGCAAA 6 55 0 AATTTGGCAA 0.703014 -218 TGACTATGCTAATCCACCTAGTCTTATTCCT 6 236 0 AATCCCCTAG 0.857306 -37 GTGGAAATAAAATTCAGACAGTAGCGATAGC 8 103 1 AATTCGACAG 0.900348 -118 CTTTTAATACAAGCTTGATAGAAGTCGCTAT 8 129 0 AAGCTGATAG 0.518732 -92 GAAAAATACGAAGCCGGCCAAAATTCTAGGC 10 161 0 AAGCCGCCAA 0.966121 -29 AAAATTAACAAATCTTGACAAACACGATAAG 11 87 1 AATCTGACAA 0.908537 -214 TTTGGCTTTTAATCCTGGCAGGTCAAAGATA 11 271 0 AATCCGGCAG 0.944957 -30 TCTCATGCATAATCTTGCTAACCTTTCGCAA 12 187 0 AATCTGCTAA 0.850501 -114 TATGCATGAGAATTTTGACAAACGATTGGAA 12 207 1 AATTTGACAA 0.778653 -94 ***** ***** Masking position 2 Map Score: 9.5924 Number of sites scoring better than the average of aligned sites = 1353 Number in coding regions = 1192 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 5 CGGCTTTGCATCCTCACCACTCCCCTTGACCC 2 120 1 TCCTCCACTC 0.979222 -23 AGGCAGATAATCCGCCCAACTCTTAATCTTAG 3 57 1 TCCGCCACTC 0.96509 -174 TGTACGCTGATCCCCCCCTCTGATAGACTTTT 3 148 1 TCCCCCTCTG 0.976704 -83 GAATTGAATCCTCCCAACTGCTGATTAGGT 3 211 0 TCCTCCACTG 0.989183 -20 AAAACATAAGTCCCCCAAAGTCTGAACTTCAG 4 79 0 TCCCCAAGTC 0.803957 -178 GGGGTTTGATTACCCGCTACTGATTATCCATA 4 129 1 TACCCCACTG 0.958221 -128 TGTTGATGAATCCCCCTCAGTGCGGGGCTAGC 11 121 1 TCCCCTAGTG 0.888363 -180 AGAACTAATCTCCTCTCGCCTGGGGCAAACCC 11 234 1 TCCTCCCCTG 0.960458 -67 GTTTTAGCTGTCACCGCCACTGTAATAGTGGA 12 100 1 TCACCCACTG 0.958221 -201 ***** * **** Masking position 11 Map Score: 6.48219 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 328 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 TGGGCAGTTTCCGGCCAATGGCGATCGCCA 1 88 1 CCGGCCAATG 0.761966 -107 CATAGTTGCCCAGGGAAAAATC 2 3 0 CAGGGAAAAA 0.79164 -140 TGGTTCAACGCAGTCAAAAAGCAGGCAGAT 3 35 1 CAGTCAAAAA 0.849038 -196 TTACTATGACCCAACCAAAACATAAGTCCC 4 97 0 CCAACCAAAA 0.751244 -160 TTGCCAATGGCAGGCCAAAAACTCCCGACT 6 74 1 CAGGCCAAAA 0.977609 -199 TTTATTTCCACCAGCCATAAATTGTGATAC 8 84 0 CCAGCCATAA 0.796508 -137 ATAGCTAATTCAATCAAAAATAGGGCAACA 8 175 0 CAATCAAAAA 0.747286 -46 CCGTAATATTCCGGCAAAAAGCCTAGCCAA 9 61 1 CCGGCAAAAA 0.977609 -104 AAATACGAAGCCGGCCAAAATTCTAGGCGA 10 159 0 CCGGCCAAAA 0.983219 -31 TTTGACTAGCCAAGCAAAATTAACAAATCT 11 72 1 CAAGCAAAAT 0.729477 -229 GCCAAACCTTCAAGCAAAAGTTCCAATCGT 12 228 0 CAAGCAAAAG 0.880312 -73 ********** Masking position 7 Map Score: 6.31078 Number of sites scoring better than the average of aligned sites = 1272 Number in coding regions = 1147 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 7 GTCAAGGGGAGTGGTGAGGATGCAAAGCCG 2 120 0 GTGGTGAGGA 0.79862 -23 GGGGTCAAGGGGAGTGGTGAGGA 2 130 0 GTCAAGGGGA 0.792699 -13 AAGATTAAGAGTTGGGCGGATTATCTGCCT 3 57 0 GTTGGGCGGA 0.969309 -174 GTACAGCATTGTTGAGGGGGGTAATTAGGC 3 123 0 GTTGAGGGGG 0.908581 -108 AAGTCTATCAGAGGGGGGGATCAGCGTACA 3 148 0 GAGGGGGGGA 0.903665 -83 CTAATCAGCAGTTGGGAGGATTCAATTC 3 213 1 GTTGGGAGGA 0.953309 -18 AGGTTTTAACCTTCTGGGGATAGTTGCCGA 4 19 0 CTTCTGGGGA 0.910165 -238 AAAGTCTGAACTTCAGGGGACAAGGGAAAC 4 65 0 CTTCAGGGGA 0.949757 -192 GAAGTTCAGACTTTGGGGGACTTATGTTTT 4 81 1 CTTTGGGGGA 0.903361 -176 TTAGATACATGTTCAGCGGAATTTAAATAG 8 39 0 GTTCAGCGGA 0.908091 -182 TAGCCCCGCACTGAGGGGGATTCATCAACA 11 121 0 CTGAGGGGGA 0.921485 -180 ********** Masking position 6 Map Score: 4.89346 Number of sites scoring better than the average of aligned sites = 1162 Number in coding regions = 994 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 8 ACGACGCTTGGCGATCGCCATTGGCCGGAA 1 96 0 GCGATCGCCA 0.994353 -99 GGGCAACTATGCGGTCATCAGATATTTAAA 2 22 1 GCGGTCATCA 0.939945 -121 GCTGACCACGGCGGGCACCAAAGATCCTCT 3 87 0 GCGGGCACCA 0.974752 -144 TTAGGATGCAACGATCGCCTCCATAAAATA 6 22 0 ACGATCGCCT 0.908564 -251 CAACAGTCAGGAGAGCATCAAATAAAGTCG 6 99 0 GAGAGCATCA 0.66998 -174 GAATATTACGGCGATCGCCATACAGTCACA 9 42 0 GCGATCGCCA 0.994353 -123 CCATCCCAGGGCGATCGCCTAGAATTTTGG 10 145 1 GCGATCGCCT 0.987114 -45 ********** Masking position 6 Map Score: 5.95558 Number of sites scoring better than the average of aligned sites = 6131 Number in coding regions = 5576 Number in noncoding regions = 555 Number of orfs with sites within 600 bp upstream = 353 Fraction of orfs with sites within 600 bp upstream = 0.0566977 Motif number 9 CCCATATCCTGCTCAACAGTCAGGAGAGCAT 6 111 0 GCCAACAGTC 0.973587 -162 GATAAACTAGGCACAATGGTCATTTGAAAAC 10 104 1 GCCAATGGTC 0.993578 -86 TGCGGGGCTAGCCCAATGGTCATATACTTGG 11 141 1 GCCAATGGTC 0.972706 -160 GACTGTTTTTGCTCAATGATCACCGAATTAA 11 184 1 GCCAATGATC 0.968266 -117 TCAATTTCTTGCGTAATAGTCCGAGGAATAA 12 37 0 GCTAATAGTC 0.940067 -264 ** ******** Masking position 6 Map Score: 3.37019 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 22 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ATAGTTGCCCAGGGAAAAATC 2 2 0 AGGGAAAAAT 0.926268 -141 TAATCCTTGTAGGAGAAAATTGATGTCAAC 5 33 1 AGGAGAAAAT 0.854913 -21 TTATTGGGGCAGGAATAAGACTAGGTGGAT 6 226 1 AGGAATAAGA 0.727912 -47 AGCCTAGCCAAGGGAAAAGTTTGGGGTTAA 9 80 1 AGGGAAAAGT 0.931325 -85 AGGTGGCAAAAGGAAAAATTGCCCTGGTTT 10 42 1 AGGAAAAATT 0.956868 -148 TGGAAGTCAAAGGAATAATTTCTGTATCCA 11 16 1 AGGAATAATT 0.932564 -285 TAATAGTCCGAGGAATAAATCGTTTTCTAA 12 25 0 AGGAATAAAT 0.932564 -276 AAAGATAAGGAGGAAAAATTAAAGGGTTAT 13 13 0 AGGAAAAATT 0.956868 -57 ********** Masking position 7 Map Score: 5.01957 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 275 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 11 CCCTTTCTAAGCTAAAGGAGACGGCTTTGCA 2 99 1 GCAAAGGAGA 0.973105 -44 AACTTCAGGGGACAAGGGAAACGGCGATGTA 4 56 0 GAAAGGGAAA 0.826093 -201 GATGTAGGATGATAGAGAATATTGGGTAATG 4 235 1 GAAGAGAATA 0.598726 -22 ATGGGTGATGGCGAGAGAAAAAGTTAGTGGC 7 71 0 GCAGAGAAAA 0.935253 -55 AAAAAGCCTAGCCAAGGGAAAAGTTTGGGGT 9 76 1 GCAAGGGAAA 0.943932 -89 ACTGCCTAAGAAAACTGAAGCGCT 10 4 1 GCTAAGAAAA 0.745573 -186 TCCCTAGGTGGCAAAAGGAAAAATTGCCCTG 10 37 1 GCAAAGGAAA 0.977711 -153 TTTGCCCCAGGCGAGAGGAGATTAGTTCTAG 11 232 0 GCAGAGGAGA 0.957737 -69 ATAGCTCTTTGAAAAAGAAGAGTTTAAAGTT 12 149 1 GAAAAGAAGA 0.842954 -152 TGGATATTTTGCGAAAGGTTAGCAAGATTAT 12 179 1 GCAAAGGTTA 0.671096 -122 TGACCCGGAAGGAAAAGAAAATGAGTTAAAG 12 277 1 GGAAAGAAAA 0.792406 -24 ** ******** Masking position 11 Map Score: 5.60598 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 511 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 12 GTAGAGGGCGTTGGCAAGGGTACTTTGCAC 1 45 0 TTGGCAAGGG 0.951796 -150 AATCCTGACAGTGGCAAGGCCCAGCGGCTC 1 142 0 GTGGCAAGGC 0.912266 -53 ACTGTCAGGATTGGGAGGGCCTGGATTACC 1 160 1 TTGGGAGGGC 0.902735 -35 GGAGGTTGGGGACGGGGTAATCCAG 1 180 0 TTGGGGACGG 0.892498 -15 ATCATTGGTATCGGGTAGGCGCTGATCACG 4 160 1 TCGGGTAGGC 0.969407 -97 TTTAACGTTTTCGGCGACGCTGTTCGTCAT 6 197 1 TCGGCGACGC 0.930136 -76 TTTGGGCAGGGCAACAAGCGG 8 2 1 TTGGGCAGGG 0.920522 -219 AACTTTTCCCTTGGCTAGGCTTTTTGCCGG 9 71 0 TTGGCTAGGC 0.978024 -94 TTTTCCCACACCGGGGAGGCAGGGGCTAAA 10 71 0 CCGGGGAGGC 0.920889 -119 TTAATTTTGCTTGGCTAGTCAAATTATTAT 11 65 0 TTGGCTAGTC 0.795425 -236 ********** Masking position 4 Map Score: 5.99964 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 544 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 13 GTTGGGGACGGGGTAATCCAGGCCCTCCCA 1 171 0 GGGTAATCCA 0.975847 -24 TTGTTGAGGGGGGTAATTAGGCTTGGGCGC 3 115 0 GGGTAATTAG 0.92221 -116 AATCAGTAGCGGGTAATCAAACCCCAGTTA 4 124 0 GGGTAATCAA 0.979893 -133 CCAATGATATGGATAATCAGTAGCGGGTAA 4 138 0 GGATAATCAG 0.92221 -119 ACTGGGTTTAGTGTAATCCGTTTTTCTGAT 7 14 0 GTGTAATCCG 0.924092 -112 TGAGTAATCAAAGTTGATTGA 13 59 0 GAGTAATCAA 0.903276 -11 ********** Masking position 5 Map Score: 1.90513 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 106 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 ********** No masking Map Score: -6.88983e-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: -6.88983e-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