AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_synecho_ctra_300.orf -o017_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 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 #10 RCT00174 300 Chlamydia_trachomatis #11 RCT00177 116 Chlamydia_trachomatis #12 RCT00178 24 Chlamydia_trachomatis #13 RCT00359 112 Chlamydia_trachomatis #14 RCT00361 28 Chlamydia_trachomatis #15 RCT00362 68 Chlamydia_trachomatis #16 RCT00363 300 Chlamydia_trachomatis Motif number 1 CTGCCTGCATCTTACAACGAAAAACCCCACCAG 2 77 0 CACACGAAAA 0.763025 -50 AGGTAAGGGCCCACCAAGAAGGGAAATCTGCC 2 105 0 CACCAGAAGG 0.777613 -22 AAAACTTTGCCAGAAAAAGAAAACTTTCGGGAA 3 35 1 CAAAAGAAAA 0.903613 -72 CCCGCAACACCAACCCCAGAAAATTCCCTCGGA 4 140 0 CCCCAGAAAA 0.902855 -161 GGACGAAACCTAAAGGGAAAACAGCTTTGAT 5 9 1 CAAAGGAAAA 0.893292 -198 TCCTCCACCTGGGCCAGAGGAAATTAACCGTTA 5 53 0 GCCAAGGAAA 0.709208 -154 CTAAAACTTGCTGAAACGGGAGAATTTTAGCTT 5 104 1 CAAAGGGAGA 0.899007 -103 AGCAGTTTAGGTCACCGAGGAAAGGGTCACCAA 5 142 0 GACCAGGAAA 0.841149 -65 AAAAATCTGACCAACCCAGAAAAAAATATTTTG 6 163 0 CACCAGAAAA 0.951111 -138 GTAACCAATCCCGACACAGGAAGCGATTCCCAG 6 206 0 CACAAGGAAG 0.841914 -95 AATTCCTTTACCTAAACGGGAAACGACTCCAAG 7 22 1 CAAAGGGAAA 0.915612 -65 GTCAAGGCTTCAGACCTGGAAAAAAAC 8 5 0 CACCGGAAAA 0.94557 -170 CATCTGGAGTCGAAACAAGGAAAGACGCCCCAG 8 89 1 CAACAGGAAA 0.926486 -86 ACCCGACCATCCTAACAAGGAGATCGTTAACAA 10 180 0 CAACAGGAGA 0.911815 -121 TATCACATTTCCTCAAAAGGAGAATC 13 97 1 CCAAAGGAGA 0.826459 -16 GTTCTCTTCTCTTCAAGAGAAGAGGGCGTTTTT 16 186 1 CCAAAGAAGA 0.786068 -115 GCAAATCATACACACAGGGAAGAGAAAAGAAAT 16 238 0 CACAGGAAGA 0.932162 -63 GTTAAGAGAAGAAACAAGGAAAACAAATCTA 16 280 1 GACAGGAAAA 0.77863 -21 * *** ****** Masking position 11 Map Score: 16.2818 Number of sites scoring better than the average of aligned sites = 1149 Number in coding regions = 992 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 AGTTGACAATTTTCTTTAGATTCATGGTAG 1 158 0 TTTCTTTAGA 0.857749 -143 ATTGTACACGTTTTTTTCGAAAGAGTGGGA 1 190 0 TTTTTTTCGA 0.821132 -111 TTCAAACAAGTGTCTTAAGAAGACGGACTC 2 15 0 TGTCTTAAGA 0.939189 -112 TCTTTCTAATTGTCTTAAGATGTGAACGCA 4 241 1 TGTCTTAAGA 0.939189 -60 ATCTTAATACTTTTTTAAGATTTTCACAGA 9 41 1 TTTTTTAAGA 0.952415 -93 TATTTGATTATTTTTCACGAATGAAACGCG 10 102 0 TTTTTCACGA 0.774982 -199 GGCAAAGCCATGTTTTATGAGAGAGAAATC 11 21 1 TGTTTTATGA 0.747445 -96 AGAGTGTTAATTTTTTAAGAGAGAGCCCAC 11 82 0 TTTTTTAAGA 0.952415 -35 ATTCTTATTTTTTTTAAGAATCATGTTGG 15 10 1 TTTTTTAAGA 0.952415 -59 ATTTCAAGCTTTTCTTACGACGCTGATAGA 16 102 1 TTTCTTACGA 0.947068 -199 ********** Masking position 5 Map Score: 9.53651 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 29 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 GGTCCTGGCTCCCTGAGCTAGCCCGCAAAACAGA 1 99 1 CCTGCAGCCC 0.970158 -202 GTAGATGCTAGGCTAAGCAAGGCCATTGGTCTGT 1 128 0 GGTGCAGGCC 0.806663 -173 CTATGCCCCTCCACATCCCATCCCAGTTATGGCT 4 18 0 CCCCCATCCC 0.98866 -283 CAACAAATAGTCACCTCCTATGCCCCTCCACATC 4 35 0 TCCCCATGCC 0.82301 -266 TGGTGGTTAACCACACACTGTCGCCAAACTTGCC 4 97 1 CCCACGTCGC 0.817214 -204 TGCGGGAAAAGCCTTGGCGATCGCCTTTTTTTGT 4 167 1 GCTGCATCGC 0.932942 -134 GAGAGCAGTTCCTCCACCTGGGCCAGAGGAAATT 5 61 0 CCCCCGGGCC 0.916232 -146 TTCAAATCCAGCTCGGCCCATCCCTTTTGCCCTT 6 23 0 GCCCCATCCC 0.990221 -278 GACTGTAAATCCGCTGGCTATGCCTACGCTGGTT 6 55 0 CCCGCATGCC 0.975179 -246 GCCAATCCTAGGGTAACCAATCCCGACACAGGAA 6 217 0 GGTCCATCCC 0.931651 -84 TTTAATAGTGGCACCCACTGTCCCTCTCTCTCTA 6 263 1 GCCACGTCCC 0.947944 -38 CAGGTCTGAAGCCTTGACAATCCCCGTTGGTGAT 8 20 1 GCTACATCCC 0.949181 -155 TACCATCCGCCAGCGCCATTGCTTCA 8 159 0 CCTGCAGCGC 0.902633 -16 TGTTCAAACTGGTCTGGAAATCCCGGTCGGTCGG 9 100 1 GGCGAATCCC 0.676794 -34 ** * ** ***** Masking position 14 Map Score: 10.0682 Number of sites scoring better than the average of aligned sites = 2194 Number in coding regions = 2044 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 4 TCATTATTAGGTGTGAGGAAAAGCTAAAAAT 1 252 1 GTGTGGGAAA 0.953943 -49 TCTGGCAAAGTTTTCAGGAAAAATTTCTTTC 3 18 0 TTTTCGGAAA 0.941376 -89 AAAGTTTTCTTTTTCTGGCAAAGTTTTCAGG 3 31 0 TTTTCGGCAA 0.915127 -76 AATGCTCGTATTGTGTGGCCACTTACGCTTT 3 82 0 TTGTGGGCCA 0.878465 -25 CTGGGGTTGGTGTTGCGGGAAAAGCCTTGGC 4 154 1 TGTTGGGGAA 0.825186 -147 GACTCCAAGATGGAGGGGAAAAACAAGATTA 7 46 1 TGGAGGGAAA 0.811124 -41 CTTAGGACAGGTGTGAGGAAATTAGAAAAAC 8 59 1 GTGTGGGAAA 0.953943 -116 CCAGGTGTTTTTTTATGGCAATTTTTAGGGC 8 118 1 TTTTAGGCAA 0.723573 -57 CACAGAGGCCTTGTCCGGAAAGGCTAATTTA 9 65 1 TTGTCGGAAA 0.966655 -69 CTGTTCAAACTGGTCTGGAAATCCCGGTCGG 9 99 1 TGGTCGGAAA 0.956869 -35 GATTCTCCTTTTGAGGAAATGTGATACGA 13 94 0 TTTTGGGAAA 0.965797 -19 ***** ***** Masking position 11 Map Score: 6.73666 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 357 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 GTTGGTAAAGAAAAACCGCCTACAGCTTCT 1 60 0 AAAAACCGCC 0.941673 -241 GCTAGCCCGCAAAACAGACCAATGGCCTTG 1 115 1 AAAACAGACC 0.795378 -186 AATAACTCTTTAACCCCGCCTCTGGTGGGG 2 56 1 TAACCCCGCC 0.945487 -71 TTACAACGAAAAACCCCACCAGAGGCGGGG 2 69 0 AAACCCCACC 0.980104 -58 AATGGGTCTGAAACCCCGCCCTTGAGGACG 4 275 0 AAACCCCGCC 0.989773 -26 TGCCACTATTAAACCACGGCACCGAGCCAA 6 246 0 AAACCACGGC 0.877414 -55 AATTGCCATAAAAAAACACCTGGGGCGTCT 8 111 0 AAAAAACACC 0.807042 -64 CTAGTACACAGAACCCGACCATCCTAACAA 10 195 0 GAACCCGACC 0.799408 -106 TTTTCAATGAAAAAAACGCCCTCTTCTCTT 16 200 0 AAAAAACGCC 0.891509 -101 ********** Masking position 3 Map Score: 5.64301 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 576 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 ACAGCTTCTGCTCACGGAACGATGATGTTGAT 1 37 0 CTCCGGACGA 0.965714 -264 TGCGGGCTAGCTCAGGGAGCCAGGACCACAAT 1 94 0 CTCGGGACCA 0.991834 -207 CTAATAATGACTACGGGAACCAAGTCCTATAC 1 230 0 CTAGGGACCA 0.984082 -71 TCCAAAATTCCTAAGTGAACCAACAAATAGTC 4 57 0 CTAGTGACCA 0.92409 -244 CCAGAAAATTCCCTCGGAGCAAAATGGGGCAA 4 126 0 CCCCGGACAA 0.77605 -175 TGACCCTTTCCTCGGTGACCTAAACTGCTAAA 5 146 1 CTCGTGACTA 0.820889 -61 CCATTAACCACTCGGGCATCGACCCATTGCTT 6 94 1 CTCGGCACGA 0.970341 -207 CGAGCCAATCCTAGGGTAACCAATCCCGACAC 6 222 0 CTAGGTACCA 0.889121 -79 CACTATTAAACCACGGCACCGAGCCAATCCTA 6 241 0 CCAGGCACGA 0.890587 -60 *** **** *** Masking position 8 Map Score: 3.71715 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 281 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 TTTCAGGAAAAATTTCTTTCTCAGTTC 3 7 0 AATTCTTTCT 0.89773 -100 CCTGTTTAATAAAATCTTTCTAATTGTCTTA 4 227 1 AAATCTTTCT 0.959963 -74 CTAGATATTTACAAGCCTTCTCATAGGCTCT 10 46 1 ACAGCCTTCT 0.90802 -255 TCACAGAGCTACTAGCTTTCTTAACTTATTG 10 139 0 ACAGCTTTCT 0.973875 -162 TATGTGCCTAAAAAGATTTCTCTCTCATAAA 11 34 0 AAAGATTTCT 0.724092 -83 TTTTACTTGTACTATCTTTCGTGATCTTTCG 13 49 0 ACATCTTTCG 0.909925 -64 GATACGAGAGACCTTCTTTCTTTTTACTTGT 13 70 0 ACTTCTTTCT 0.932991 -43 TTTTCATTGAAAAATCTTTCTATTTCTTTTC 16 217 1 AAATCTTTCT 0.959963 -84 ** ******** Masking position 1 Map Score: 3.41041 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 36 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 GTAGATGCTAGGCTAAGCAAGGCCATTGGTCT 1 130 0 GTAAGCAAGG 0.952711 -171 AAAAATTGAGGACAAAAAAAGGCGATCGCCAA 4 180 0 GAAAAAAAGG 0.802949 -121 GTCTTAAGATGTGAACGCAAGGCCGTCCTCAA 4 252 1 GAACGCAAGG 0.950199 -49 ATGGCTAATCGTGAAAGCAATGGGTCGATGCC 6 108 0 GAAAGCAATG 0.963983 -193 AAGATGGAGGGGAAAAACAAGATTATCCATTC 7 52 1 GAAAACAAGA 0.802949 -35 AACATCTGGAGTCGAAACAAGGAAAGACGCCC 8 87 1 GGAAACAAGG 0.976043 -88 GCAGTCCACAGATGAAGCAATGGCGCTGGCGG 8 147 1 GGAAGCAATG 0.963281 -28 GATCCCTCATGGCAAAGCCATGTTTTATGAGA 11 11 1 GAAAGCCATG 0.862132 -106 TGAGTTAAGAGAAGAAACAAGGAAAACAAATC 16 277 1 GGAAACAAGG 0.976043 -24 * ********* Masking position 5 Map Score: 5.08133 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 252 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 AACGATGATGTTGATGGTTAATAACAGATTA 1 21 0 TTGAGGTTAA 0.981912 -280 AGACACTTGTTTGAAAGTTAAACTCTAATAA 2 30 1 TTGAAGTTAA 0.905652 -97 GGACAGAACTTTGGTGGTTAACCACACACTG 4 86 1 TTGGGGTTAA 0.952664 -215 CGTAACCCATTTAACGGTTAATTTCCTCTGG 5 42 1 TTAAGGTTAA 0.704823 -165 CACCTTATTGTTGATGGTCAAAATATTTTTT 6 145 1 TTGAGGTCAA 0.930836 -156 GTGAATAATCTTGATTGTTAACGATCTCCTT 10 166 1 TTGATGTTAA 0.944479 -135 CAACCTAGTATAGAGTGTTAATTTTTTAAGA 11 92 0 TAGATGTTAA 0.821006 -25 **** ****** Masking position 10 Map Score: 2.92391 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 71 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 AGTCATTATTAGGTGTGAGGAAAAGCTAAA 1 250 1 AGGTGTGAGG 0.99014 -51 ATCAACAATAAGGTGTTATGATGGCTAATC 6 130 0 AGGTGTTATG 0.937733 -171 TACTTAGGACAGGTGTGAGGAAATTAGAAA 8 57 1 AGGTGTGAGG 0.99014 -118 CACGAATGAAACGCGGGAGGTGTCGAATAT 10 87 0 ACGCGGGAGG 0.940565 -214 TTTGCTTCTTAGGTGGGACGTCATTAATGG 10 274 1 AGGTGGGACG 0.968805 -27 TTATACAAGGCGTTATGTGTTTAACTT 16 8 1 AGGCGTTATG 0.925844 -293 ********** Masking position 8 Map Score: 2.88042 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 39 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 AAAACTTTCGGGAATTGTGAGTTATTTTAA 3 54 1 GGAATTGTGA 0.978866 -53 GGTTCACTTAGGAATTTTGGACAGAACTTT 4 68 1 GGAATTTTGG 0.925419 -233 TTCTGGGGTTGGTGTTGCGGGAAAAGCCTT 4 152 1 GGTGTTGCGG 0.896014 -149 TTTAGGTAAAGGAATTGTGGAATTTCT 7 8 0 GGAATTGTGG 0.989655 -79 TCGTTTTTTTGGTATTGTGGGCTCTCTCTT 11 66 1 GGTATTGTGG 0.976535 -51 CTACAAAAATGGAATCGCGAAAGATCACGA 13 32 1 GGAATCGCGA 0.905574 -81 CTCCTTTTGAGGAAATGTGATACGAGAGAC 13 89 0 GGAAATGTGA 0.905801 -24 ********** Masking position 2 Map Score: 4.01409 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 302 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 12 CAATTTTTGGCCGGATGTTTTTTCCTGTTT 4 204 1 CCGGATGTTT 0.963604 -97 GTAGGCATAGCCAGCGGATTTACAGTCCGC 6 62 1 CCAGCGGATT 0.918773 -239 TATCCATTCCCCAGAGGTTTCC 7 75 1 CCAGAGGTTT 0.984482 -12 TGTTTCGACTCCAGATGTTTTTCTAATTTC 8 76 0 CCAGATGTTT 0.983269 -99 GAAAGACGCCCCAGGTGTTTTTTTATGGCA 8 108 1 CCAGGTGTTT 0.97181 -67 ********** Masking position 9 Map Score: 1.63395 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 84 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 TCCAAGATAGTTTAAGCATTTTTAGCTTTTCC 1 268 0 TTTAGCATTT 0.970135 -33 TTTCAGCAAGTTTTAGCAACTTTAGGAGAGCA 5 88 0 TTTAGCACTT 0.909053 -119 AACGGGAGAATTTTAGCTTTTTGCTTGGTGAC 5 118 1 TTTAGCTTTT 0.870867 -89 AAATCCTGTCTTTTAGCAGTTTAGGTCACCGA 5 157 0 TTTAGCATTT 0.970135 -50 AAGACAGGATTTTGTGTAGTTTTTCAATGGCT 5 177 1 TTTTGTATTT 0.765549 -30 GGATAATGTATTTGATTATTTTTCACGAATGA 10 108 0 TTTATTATTT 0.671064 -193 CAGCTCTTCCTTTGAGTAGTTTCCTACAATAA 16 51 0 TTTAGTATTT 0.940221 -250 *** **** *** Masking position 3 Map Score: 0.68702 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 83 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 AAAGGCGATCGCCAAGGCTTTTCCCGCAAC 4 165 0 GCCAAGGCTT 0.979531 -136 AACGGGGATTGTCAAGGCTTCAGACCTGGA 8 18 0 GTCAAGGCTT 0.969959 -157 AGCCTTTCCGGACAAGGCCTCTGTGAAAAT 9 60 0 GACAAGGCCT 0.979531 -74 GAGAGCCTATGAGAAGGCTTGTAAATATCT 10 48 0 GAGAAGGCTT 0.958627 -253 TTATACAAGGCGTTATGTGTTTA 16 4 1 TACAAGGCGT 0.901673 -297 ********** Masking position 5 Map Score: 0.620253 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 79 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 AAACTATCTTGGAAGTCCCTGTTA 1 287 1 GGAAGTCCCT 0.889488 -14 TTCCCTTCTTGGTGGGCCCTTACCT 2 112 1 GGTGGGCCCT 0.96001 -15 CCGCCCTTGAGGACGGCCTTGCGTTCACAT 4 260 0 GGACGGCCTT 0.937822 -41 TTCAAATCCAGCTCGGCCCATCCCTTTTGC 6 27 0 GCTCGGCCCA 0.936418 -274 AAACAAGGAAAGACGCCCCAGGTGTTTTTT 8 101 1 AGACGCCCCA 0.845833 -74 CTTCATCTGTGGACTGCCCTAAAAATTGCC 8 134 0 GGACTGCCCT 0.937822 -41 AATCCCGGTCGGTCGGGCCATGGTAA 9 118 1 GGTCGGGCCA 0.936417 -16 CTTCTTATACAGTAGGCCCTTACCAAACAT 10 243 0 AGTAGGCCCT 0.86725 -58 CCCCCATTAATGACGTCCCACCTAAGAAGC 10 277 0 TGACGTCCCA 0.787452 -24 ********** Masking position 8 Map Score: 1.24519 Number of sites scoring better than the average of aligned sites = 764 Number in coding regions = 717 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022