AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_synecho_ctra_300.orf -o255_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 RCY18467 300 Synechocystis #2 RCY52233 205 Synechocystis #3 RCY20619 187 Synechocystis #4 RCY32067 88 Synechocystis #5 RCY21220 22 Synechocystis #6 RCY46107 44 Synechocystis #7 RCY43084 300 Synechocystis #8 RCY00997 233 Synechocystis #9 RCY02791 295 Synechocystis #10 RCY10850 106 Synechocystis #11 RCY43048 300 Synechocystis #12 RCT00326 28 Chlamydia_trachomatis #13 RCT00843 196 Chlamydia_trachomatis #14 RCT00327 300 Chlamydia_trachomatis #15 RCT00373 300 Chlamydia_trachomatis #16 RCT00374 86 Chlamydia_trachomatis #17 RCT00376 25 Chlamydia_trachomatis Motif number 1 CTAATAATTCCAAAAAAAACCAAAAACCTGC 3 33 0 CAAAAAAACC 0.790819 -155 ATTATTAGTCACAAAAAAGCTGTCGTATAGT 3 56 1 AAAAAAAGCT 0.7197 -132 CGGAAAAAGCCTTGGCAGGAC 3 177 0 CGAAAAAGCC 0.98388 -11 AGATGAAATGCGGAAAAAGCCGCCCGAATTT 7 13 1 CGAAAAAGCC 0.98388 -288 TCAAAAATAGCGAGGAAAGCCCTAGGCGTTA 7 178 0 CAGGAAAGCC 0.849966 -123 AATTATGGGCAGGGAAAAGCCTATTCGACCT 7 263 0 AGGAAAAGCC 0.894054 -38 TTTTGCAAGACTGAAAACGCCGAAAATAGAA 8 48 0 CGAAAACGCC 0.912875 -186 CCTCCTCTTCCAAGAAAAGCCGTGCCGTTGC 9 48 0 CAGAAAAGCC 0.970589 -248 ACAGTAAACACTACAGAAGCCTTGTCAATTA 10 61 1 CACAGAAGCC 0.873131 -46 ACCGACTTTACTAAAAAAGCTCATTTATAAT 14 191 0 CAAAAAAGCT 0.920831 -110 AAAAATGCAAATAAAGAAGCCTCCGTTCTTT 15 188 1 AAAAGAAGCC 0.866709 -113 ACCCTGCTTTCTGAAGAAGCTCGTAGGAAAG 15 215 0 CGAAGAAGCT 0.882799 -86 * ********* Masking position 7 Map Score: 11.0678 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 389 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 CTTAGTTCTCGGAAGTGCAGGTTTCCGTACC 2 65 0 GGAAGTCAGG 0.942702 -141 GATTTAGGCTGGCAAAGCAGGTTTTTGGTTT 3 17 1 GGCAAACAGG 0.902833 -171 AAAAAGCCTTGGCAGGACAGGTTCAGTTTAA 3 164 0 GGCAGGCAGG 0.992749 -24 GTGCAACTACGGAAGATCAGGGAAAAGTAGA 4 52 0 GGAAGACAGG 0.985227 -37 ACTGTGACAAGACTGGGCAAGCCTAGTCAAA 7 204 0 GACTGGCAAG 0.772552 -97 TGGGCTCTAAGGATGGCCAAGTGGGGCTTAA 8 132 1 GGATGGCAAG 0.960597 -102 GGCTTTTCTTGGAAGAGGAGGAAGATGTCAT 9 58 1 GGAAGAGAGG 0.906454 -238 CCCAGACAAAGGCAGAACAAGACAATCAGGG 11 107 0 GGCAGACAAG 0.985227 -194 CCAGGCGTTGGGCTGGGTAAGATTGTGTTTA 11 226 0 GGCTGGTAAG 0.792158 -75 CAAAATCCTTGGAAGAGCAAGGGTTGTGTGC 14 24 1 GGAAGACAAG 0.976646 -277 ****** **** Masking position 9 Map Score: 9.74536 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 448 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 ACTCAACGTGGGTTCGAATCCCACCCTCTCC 1 83 1 GGTTCAATCC 0.975468 -218 TTAATTGATGGGATATAATCCAGGGCACACC 1 133 1 GGATAAATCC 0.850126 -168 GAAAAGCCATGGTTCCAATCCATTGCCTGGG 2 132 0 GGTTCAATCC 0.975468 -74 TAATAACCCGGCTCATTATCCCGAATTTGCC 7 75 0 GCTCATATCC 0.816459 -226 CCTGAAAAAAACTCCGAATCCGATCGGGAGT 9 227 0 ACTCCAATCC 0.815933 -69 CAGTAATATCGCTCAAAATCCCAACAGAGTA 11 156 0 GCTCAAATCC 0.969341 -145 ATAAAAGTGGTGTTACAATCCCCGGTCTCTT 13 118 1 TGTTAAATCC 0.863432 -79 TGGGCAACTAGTTCAAAATCCTTGGAAGAGC 14 11 1 GTTCAAATCC 0.888365 -290 CGGTTTTAACGGTTATAATCCTTTGTCTAAA 14 260 1 GGTTAAATCC 0.981247 -41 AATCTGAACTAGTTAAAATCCAATAAGAACA 15 41 1 AGTTAAATCC 0.917676 -260 ***** ***** Masking position 8 Map Score: 8.61513 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 203 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 AGGGGCTTAGTTCTCGGAAGTGCAGGTTTC 2 71 0 TTCTCGGAAG 0.894279 -135 CACTGACGGTTTCTGGGGAGTCGGAAGACA 3 106 0 TTCTGGGGAG 0.892373 -82 CGGAAAAAGCCTTGGCAGGACAGGTTCA 3 170 0 GCCTTGGCAG 0.927721 -18 CCTATCCCCGTCCCTGGCAGTGTCAACGCT 7 123 1 TCCCTGGCAG 0.927721 -178 GTTAGTACAATTATGGGCAGGGAAAAGCCT 7 272 0 TTATGGGCAG 0.876857 -29 GGCACGGCTTTTCTTGGAAGAGGAGGAAGA 9 53 1 TTCTTGGAAG 0.969557 -243 AGGTGGGGATTTCTGGGCAACCATCTGGGG 10 18 1 TTCTGGGCAA 0.740209 -89 GTCCCATTGGTCATTGGCAGTAATATCGCT 11 174 0 TCATTGGCAG 0.930657 -127 TAGTTCAAAATCCTTGGAAGAGCAAGGGTT 14 19 1 TCCTTGGAAG 0.977137 -282 TTTATTTGCATTTTTGGAAGTTCTGTAAAA 15 173 0 TTTTTGGAAG 0.780531 -128 TTAGGATAACTCGTTGGAAGAGAGGTGTGT 15 279 0 TCGTTGGAAG 0.876141 -22 ********** Masking position 9 Map Score: 7.4554 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 409 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 ACTCCCCTTTTGACCAATGGCATACGGCTA 2 23 1 TGACCAATGG 0.98777 -183 TACCTAGAAGTCACCAATTGTTTTTCGGGG 8 205 1 TCACCAATTG 0.925899 -29 TCACCGATGGTCACCATTGGCTAGGGAATA 9 122 0 TCACCATTGG 0.960842 -174 TTGTGAATAATCACCGATGGTCACCATTGG 9 132 0 TCACCGATGG 0.966654 -164 TTACTGCCAATGACCAATGGGACTTAGGCA 11 181 1 TGACCAATGG 0.98777 -120 CTAAAATTCTTGACCAGTGGAGACGGTTTT 16 30 1 TGACCAGTGG 0.97323 -57 ********** Masking position 3 Map Score: 6.70035 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 99 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ACCAGCAACGGCCCAAGCAAATCCTGGGTAA 1 161 1 GCCCAACAAA 0.972277 -140 AACGTGTCGGCCCCAGGCAATGGATTGGAAC 2 121 1 CCCCAGCAAT 0.885237 -85 TCAAAAATTAACCTAAACAAA 4 1 0 ACCTAACAAA 0.826028 -88 GACTGGGCAAGCCTAGTCAAAAATAGCGAGG 7 194 0 GCCTAGCAAA 0.985466 -107 GTAAACTATTCCCTAGCCAATGGTGACCATC 9 116 1 CCCTAGCAAT 0.903397 -180 CACTACAGAAGCCTTGTCAATTATTGTTAAG 10 69 1 GCCTTGCAAT 0.812034 -38 CCAAATGGTAGCCCAGACAAAGGCAGAACAA 11 118 0 GCCCAGCAAA 0.982434 -183 TGGCTCCAATGCCTAAACACAATCTTACCCA 11 213 1 GCCTAACACA 0.898654 -88 ATCTCTTGAAGCCTAAATAAAAGTGGTGTTA 13 102 1 GCCTAATAAA 0.787899 -95 ATTCGCTGTCGCCAAATCAAAACCGACTTTA 14 212 0 GCCAAACAAA 0.898242 -89 ****** **** Masking position 9 Map Score: 6.44766 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 387 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 TGCGTGGCGTTAACTCCCCTTTTGACCAATG 2 11 1 TAACTCCCTT 0.983203 -195 AATTTTAATTAACTCCCGTTAACAAGTAAG 2 186 0 TAACTCCCTT 0.983203 -20 AACATCGTCATAACTCCCGATCGGATTCGGA 9 215 1 TAACTCCCAT 0.912965 -81 GCCAAATGCCTAAGTCCCATTGGTCATTGGC 11 186 0 TAAGTCCCTT 0.94326 -115 CCGGGGATTGTAACACCACTTTTATTTAGGC 13 112 0 TAACACCATT 0.908705 -85 CGTTATTAAATAAAACCAATTACGTATTAAG 13 169 1 TAAAACCATT 0.828157 -28 TTATAACCGTTAAAACCGTTTTAATTCAAAA 14 247 0 TAAAACCGTT 0.802005 -54 TGTGTATGAGTAAATCCCTTTAGATGTTTTG 15 253 0 TAAATCCCTT 0.965918 -48 ******** ** Masking position 3 Map Score: 4.93242 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 83 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 CACTCTGCCACCTCTCCAGGGGGTCAAAGA 1 17 0 CCTCTCCAGG 0.950502 -284 GAATTTGCCATCAAACCAGGCGGCAAAGTT 7 54 0 TCAAACCAGG 0.936535 -247 AAAACTCCGATCACTCCAGGGTCGAAGAAT 8 76 1 TCACTCCAGG 0.98948 -158 CGATGTTATTTCAATTCAGGTAAGTTAGTG 9 192 0 TCAATTCAGG 0.902474 -104 TCTAATTCAACCACTCCAGGCGTTGGGCTG 11 242 0 CCACTCCAGG 0.987334 -59 TTTGTCTAAATCAATCTAGGAGTTTAGGCC 14 281 1 TCAATCTAGG 0.902471 -20 ********** Masking position 8 Map Score: 3.76741 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 104 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 TTGAAATCGGGTTTGGGGAAACTCAACGTGG 1 63 1 GTTGGGGAAA 0.961465 -238 GTTTAAAAGCTTATGGGGAAATAGCACGGAA 3 139 0 TATGGGGAAA 0.939718 -49 AACTACGGAAGATCAGGGAAAAGTAGAGGGA 4 48 0 GTCAGGGAAA 0.770886 -41 ACACTGCCAGGGACGGGGATAGGGGGGACTA 7 115 0 GACGGGGATA 0.967877 -186 CAGGGTCGAAGAATGGGAAAAAAGGAATGGG 8 92 1 GATGGGAAAA 0.939719 -142 GGGAAAAAAGGAATGGGAATATAAAATGGGC 8 106 1 GATGGGAATA 0.850899 -128 ATTTATTGCCGAAGGGGGAAAAATAATTTCG 9 13 1 GAGGGGGAAA 0.968457 -283 CACAGTGGATTCACGGGGAAATTTTTTCACT 11 26 0 TACGGGGAAA 0.949559 -275 * ********* Masking position 9 Map Score: 4.04549 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 558 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 10 GGGCGCGATTTAGGCTGGCAAAGCAGGTT 3 5 1 GCGATTAGGC 0.806505 -183 GTTATTAGTGGTGATTTAGTCCCCCCTATCCCCGT 7 99 1 GTGATTAGCC 0.962563 -202 CTGCCCATAATTGTACTAACTTCACACCG 7 282 1 TTGTCTAACC 0.746334 -19 CCTGGAGTGGTTGAATTAGAATCGCCCCTTTAATT 11 252 1 TTGATTAGCC 0.978362 -49 TCTTGTGCGTTCGAGCTAGGCGCGCGTTATTAAAT 13 145 1 TCGACTAGCC 0.986025 -52 TCCAAGGATTTTGAACTAGTTGCCCA 14 2 0 TTGACTAGCC 0.986305 -299 CTATACTTTCTCGTGTTAGATGCACTAATTGTTGC 14 98 0 TCGTTTAGCC 0.942169 -203 ATCACAGAGATTGATCTAGAAACACTCCTATGCTA 15 77 1 TTGACTAGCC 0.986272 -224 **** **** * * Masking position 8 Map Score: 2.32051 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 36 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 TGTTTCCTAAATTGCGGGCTAAAG 1 287 0 TTTCTAATTG 0.845769 -14 TTGTGTCTTATATTCTTACTTGTTAACGGGAG 2 172 1 TATCTTATTG 0.757734 -34 AGTTGCACTGTTTCCTTAGTTGAG 4 75 1 TTTCTTATTG 0.956949 -14 CCTGTAACATTTTGCTTAATTGACGGTGGGCA 7 234 0 TTTCTTATTG 0.956949 -67 ATTTTCGGCGTTTTCAGTCTTGCAAAAACTCC 8 52 1 TTTCAGTTTG 0.749194 -182 CGGGGAAATTTTTTCACTTTTGAACAATCCAT 11 12 0 TTTCACTTTG 0.888982 -289 TTTGGTGCGCTTTACTCTGTTGGGATTTTGAG 11 144 1 TTTCTCTTTG 0.946479 -157 AAGAGTTTTGTTTACTTGTTTGGTAATTTTTA 13 41 1 TTTCTTGTTG 0.890442 -156 ATAGCAGGGTTTTTATCAATTGCAGCAAAGAG 14 129 1 TTTATCATTG 0.655589 -172 GGCTTCTTTATTTGCATTTTTGGAAGTTCTGT 15 177 0 TTTCATTTTG 0.890943 -124 *** **** *** Masking position 3 Map Score: 2.31491 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 139 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 GGGCGCGATTTAGGCTGGCA 3 1 1 GGGCGCGATT 0.964671 -187 GTTAATTTTTGAGCACCATTGAGCTTATTC 4 20 1 GAGCACCATT 0.716326 -69 CAGTCATTTTGGGGGACATTCCACTGTCCC 8 15 1 GGGGGACATT 0.9734 -219 AAAATAGAACGAGGGACAGTGGAATGTCCC 8 27 0 GAGGGACAGT 0.928897 -207 AACCATCTGGGGGCGAGAGTTTGCTACAGT 10 36 1 GGGCGAGAGT 0.940392 -71 TTGGGATTTTGAGCGATATTACTGCCAATG 11 163 1 GAGCGATATT 0.815528 -138 CGAAAATTAAAGGGGCGATTCTAATTCAAC 11 261 0 AGGGGCGATT 0.752971 -40 TGTAAAACAGGAGGGACATTCTCATAGGGA 15 150 0 GAGGGACATT 0.958453 -151 ********** Masking position 8 Map Score: 1.46821 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 310 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 GACCACTCTGCCACCTCTCCAGGGGGTCAA 1 20 0 CCACCTCTCC 0.979087 -281 CGGGCGCATTCGACCACTCTGCCACCTCTC 1 31 0 CGACCACTCT 0.887732 -270 GTTCGAATCCCACCCTCTCCGCTTGCTTAA 1 94 1 CACCCTCTCC 0.966869 -207 TGATTTAGTCCCCCCTATCCCCGTCCCTGG 7 110 1 CCCCCTATCC 0.803395 -191 GCAAAAACTCCGATCACTCCAGGGTCGAAG 8 73 1 CGATCACTCC 0.943278 -161 TACTTTTTCGTAATCACTCCACAGTGGATT 11 46 0 TAATCACTCC 0.666466 -255 GATTCTAATTCAACCACTCCAGGCGTTGGG 11 245 0 CAACCACTCC 0.9826 -56 ********** Masking position 8 Map Score: 1.19162 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 331 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 14 GTGGCAGAGTGGTCGAATGCGCCCGACTTG 1 36 1 GGTCGAATGC 0.941355 -265 GGGGGCATCTAGCCGTATGCCATTGGTCAA 2 32 0 AGCCGTATGC 0.90914 -174 TGAACGTGTCGGCCCCAGGCAATGGATTGG 2 119 1 GGCCCCAGGC 0.907969 -87 TAGCGAGGAAAGCCCTAGGCGTTAGCTTCA 7 172 0 AGCCCTAGGC 0.928903 -129 CAAGCTGGTGAGTACAATGCGCAAAAGTAC 11 73 0 AGTACAATGC 0.703422 -228 TAGGCATTTGGCTCCAATGCCTAAACACAA 11 205 1 GCTCCAATGC 0.941355 -96 AATCTTACCCAGCCCAACGCCTGGAGTGGT 11 233 1 AGCCCAACGC 0.954462 -68 CGCGCGCCTAGCTCGAACGCACAAGAGACC 13 141 0 GCTCGAACGC 0.847712 -56 ATCTAGAAACACTCCTATGCTAAGATGCTC 15 90 1 ACTCCTATGC 0.886 -211 ********** Masking position 7 Map Score: 0.747606 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 503 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 15 GATTATATCCCATCAATTAAAAGTGAAAGT 1 123 0 CATCAATTAA 0.902312 -178 CAATGGTGCTCAAAAATTAACCTAAACAAA 4 11 0 CAAAAATTAA 0.916387 -78 CAGTGCCCACCGTCAATTAAGCAAAATGTT 7 231 1 CGTCAATTAA 0.884495 -70 GCAGTGGCATCGAAAATTAAAGGGGCGATT 11 271 0 CGAAAATTAA 0.900855 -30 TACAAAATCGCAACAATTAGTGCATCTAAC 14 89 1 CAACAATTAG 0.86304 -212 CGTTTTAATTCAAAAATTAATTCGCTGTCG 14 232 0 CAAAAATTAA 0.916387 -69 ********** Masking position 5 Map Score: 0.350237 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 112 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912