AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_synecho_ctra_100.orf -o013_synecho_ctra_100.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 RCY53506 106 Synechocystis #2 RCY17695 300 Synechocystis #3 RCY44898 206 Synechocystis #4 RCY48136 300 Synechocystis #5 RCY07219 86 Synechocystis #6 RCY02847 174 Synechocystis #7 RCT00177 116 Chlamydia_trachomatis #8 RCT00178 24 Chlamydia_trachomatis #9 RCT00359 112 Chlamydia_trachomatis Motif number 1 TTCCCGAAAGTTTTCTTTTTCTGGCAAAGTTTT 1 35 0 TTTTCTTTTG 0.876615 -72 GTCGCCAAACTTGCCCCATTTTGCTCCGAGGGA 2 116 1 TTGCCCATTG 0.647959 -185 TCCGAGGGAATTTTCTGGGGTTGGTGTTGCGGG 2 140 1 TTTTCTGGGG 0.856255 -161 GCCGGATGTTTTTTCCTGTTTAATAAAATCTTT 2 213 1 TTTTCCGTTA 0.547536 -88 TTAATAAAATCTTTCTAATTGTCTTAAGATGTG 2 232 1 CTTTCTATTC 0.421173 -69 ATCAAAGCTGTTTTCCCTTTAGGTTTCGTCC 3 9 0 TTTTCCTTTG 0.853563 -198 TAACGGTTAATTTCCTCTGGCCCAGGTGGAGGA 3 53 1 TTTCCTTGGC 0.737874 -154 ATTTTAGCTTTTTGCTTGGTGACCCTTTCCTCG 3 127 1 TTTGCTGGTC 0.902913 -80 TTGGTGACCCTTTCCTCGGTGACCTAAACTGCT 3 142 1 TTTCCTGGTC 0.968286 -65 CCCATCCCTTTTGCCCTTGTAGCTCAGTGG 4 8 0 TTGCCCTGTC 0.834331 -293 CAAAATATTTTTTTCTGGGTTGGTCAGATTTTT 4 163 1 TTTTCTGGTG 0.964527 -138 GGTCAGATTTTTGTCTGGTTTGCTGGGAATCGC 4 184 1 TTGTCTGTTC 0.877866 -117 CTGGGAATCGCTTCCTGTGTCGGGATTGGTTAC 4 206 1 CTTCCTTGTG 0.759537 -95 TACCCTAGGATTGGCTCGGTGCCGTGGTTTAAT 4 236 1 TTGGCTGGTC 0.816275 -65 CTTGGAGTCGTTTCCCGTTTAGGTAAAGGAATT 5 22 0 TTTCCCTTTG 0.880163 -65 GTTTTTTTCCAGGTCTGAAGCCTTGAC 6 5 1 TTTTCCGGTG 0.957094 -170 CTCCAGATGTTTTTCTAATTTCCTCACACCTGT 6 65 0 TTTTCTATTC 0.76859 -110 CTGGGGCGTCTTTCCTTGTTTCGACTCCAGATG 6 89 0 TTTCCTGTTG 0.955102 -86 ****** *** * Masking position 2 Map Score: 15.2801 Number of sites scoring better than the average of aligned sites = 1754 Number in coding regions = 1507 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 2 CTATGCCCCTCCACATCCCATCCCAGTTATGGCT 2 18 0 CCCCCATCCC 0.996267 -283 CAACAAATAGTCACCTCCTATGCCCCTCCACATC 2 35 0 TCCCCATGCC 0.941462 -266 TGGTGGTTAACCACACACTGTCGCCAAACTTGCC 2 97 1 CCCACGTCGC 0.962196 -204 TGCGGGAAAAGCCTTGGCGATCGCCTTTTTTTGT 2 167 1 GCTGCATCGC 0.939039 -134 GAGAGCAGTTCCTCCACCTGGGCCAGAGGAAATT 3 61 0 CCCCCGGGCC 0.961513 -146 TTCAAATCCAGCTCGGCCCATCCCTTTTGCCCTT 4 23 0 GCCCCATCCC 0.996266 -278 GACTGTAAATCCGCTGGCTATGCCTACGCTGGTT 4 55 0 CCCGCATGCC 0.98333 -246 GCCAATCCTAGGGTAACCAATCCCGACACAGGAA 4 217 0 GGTCCATCCC 0.919682 -84 TTTAATAGTGGCACCCACTGTCCCTCTCTCTCTA 4 263 1 GCCACGTCCC 0.984909 -38 CAGGTCTGAAGCCTTGACAATCCCCGTTGGTGAT 6 20 1 GCTACATCCC 0.974533 -155 TACCATCCGCCAGCGCCATTGCTTCA 6 159 0 CCTGCAGCGC 0.899631 -16 ** * ** ***** Masking position 8 Map Score: 12.0459 Number of sites scoring better than the average of aligned sites = 1619 Number in coding regions = 1508 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 TTAAAATAACTCACAATTCCCGAAAGTTTT 1 54 0 TCACAATTCC 0.980136 -53 AAAGTTCTGTCCAAAATTCCTAAGTGAACC 2 68 0 CCAAAATTCC 0.915437 -233 AAGGCTTTTCCCGCAACACCAACCCCAGAA 2 152 0 CCGCAACACC 0.969442 -149 CGATTAGCCATCATAACACCTTATTGTTGA 4 129 1 TCATAACACC 0.786731 -172 CACTATTAAACCACGGCACCGAGCCAATCC 4 243 0 CCACGGCACC 0.893914 -58 AGAAATTCCACAATTCCTTTACCTAAA 5 8 1 CCACAATTCC 0.98979 -79 AAGAGAGAGCCCACAATACCAAAAAAACGA 7 66 0 CCACAATACC 0.987451 -51 TCGTGATCTTTCGCGATTCCATTTTTGTAG 9 32 0 TCGCGATTCC 0.921809 -81 GTCTCTCGTATCACATTTCCTCAAAAGGAG 9 89 1 TCACATTTCC 0.898398 -24 ********** Masking position 2 Map Score: 9.3355 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 454 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 AGAAAGAAATTTTTCCTGAAAACTTTGCCAGA 1 17 1 TTTCCTAAAA 0.912155 -90 TCCTGAAAACTTTGCCAGAAAAAGAAAACTTT 1 30 1 TTTCCAAAAA 0.893218 -77 AATTCCTAAGTGAACCAACAAATAGTCACCTC 2 52 0 TGACCACAAA 0.904307 -249 CAGTGTGTGGTTAACCACCAAAGTTCTGTCCA 2 85 0 TTACCACAAA 0.929933 -216 GCTTTCACGATTAGCCATCATAACACCTTATT 4 122 1 TTACCACATA 0.627753 -179 ACAGGAAGCGATTCCCAGCAAACCAGACAAAA 4 192 0 ATTCCACAAA 0.95145 -109 TGCCCTAAAAATTGCCATAAAAAAACACCTGG 6 118 0 ATTCCAAAAA 0.954518 -57 AAAACGAATATGTGCCTAAAAAGATTTCTCTC 7 41 0 TGTCCTAAAA 0.909939 -76 GAGAGCCCACAATACCAAAAAAACGAATATGT 7 60 0 AATCCAAAAA 0.790125 -57 AAAGATCGATTGTTCTACAAAAATGGAATCGC 9 18 1 TGTCTAAAAA 0.665593 -95 CTCGTATCACATTTCCTCAAAAGGAGAATC 9 93 1 ATTCCTAAAA 0.893241 -20 *** *** **** Masking position 10 Map Score: 8.22328 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 488 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 5 TTGGACAGAACTTTGGTGGTTAACCACACA 2 84 1 CTTTGGTGGT 0.8428 -217 AATGGGGCAAGTTTGGCGACAGTGTGTGGT 2 106 0 GTTTGGCGAC 0.910916 -195 AATTTTCTGGGGTTGGTGTTGCGGGAAAAG 2 148 1 GGTTGGTGTT 0.79847 -153 GCGGGAAAAGCCTTGGCGATCGCCTTTTTT 2 168 1 CCTTGGCGAT 0.932619 -133 GAAACCCCGCCCTTGAGGACGGCCTTGCGT 2 266 0 CCTTGAGGAC 0.825856 -35 TTAGCTTTTTGCTTGGTGACCCTTTCCTCG 3 130 1 GCTTGGTGAC 0.974309 -77 GTGACCCTTTCCTCGGTGACCTAAACTGCT 3 145 1 CCTCGGTGAC 0.96796 -62 TTTTCAATGGCTTTGGGGCC 3 197 1 CTTTGGGGCC 0.943614 -10 GAAAGCAATGGGTCGATGCCCGAGTGGTTA 4 98 0 GGTCGATGCC 0.514575 -203 CCTAGGATTGGCTCGGTGCCGTGGTTTAAT 4 239 1 GCTCGGTGCC 0.931652 -62 CTCTCTAGTTCTTTGGGGTTT 4 290 1 CTTTGGGGTT 0.799804 -11 TGACAATCCCCGTTGGTGATTTATACTTAG 6 34 1 CGTTGGTGAT 0.951889 -141 CTTGTACTATCTTTCGTGATCTTTCGCGAT 9 45 0 CTTTCGTGAT 0.663357 -68 ********** Masking position 3 Map Score: 9.20881 Number of sites scoring better than the average of aligned sites = 2482 Number in coding regions = 2275 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 6 TTGCCCCATTTTGCTCCGAGGGAATTTTCTG 2 126 1 TTGCTCGAGG 0.979111 -175 TCCTCAATTTTTGGCCGGATGTTTTTTCCTG 2 200 1 TTGGCCGATG 0.979111 -101 TTCCTCCACCTGGGCCAGAGGAAATTAACCG 3 56 0 TGGGCCGAGG 0.991054 -151 AGATTATCCATTCCCCAGAGGTTTCC 5 71 1 TTCCCCGAGG 0.988512 -16 AAACATGGCTTTGCCATGAGGGATC 7 5 0 TTGCCAGAGG 0.990327 -112 TTTGTTTTGCAAGAGGTTGTATAC 8 6 1 TTTGCAGAGG 0.951499 -19 ****** **** Masking position 9 Map Score: 4.32959 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 379 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 CACCAAAGTTCTGTCCAAAATTCCTAAGTG 2 72 0 CTGTCCAAAA 0.927889 -229 TCGCCTTTTTTTGTCCTCAATTTTTGGCCG 2 187 1 TTGTCCTCAA 0.917299 -114 ATCTTTCTAATTGTCTTAAGATGTGAACGC 2 240 1 TTGTCTTAAG 0.71735 -61 GAACGCAAGGCCGTCCTCAAGGGCGGGGTT 2 264 1 CCGTCCTCAA 0.89132 -37 GGAGGAACTGCTCTCCTAAAGTTGCTAAAA 3 80 1 CTCTCCTAAA 0.975949 -127 TTCCTCACACCTGTCCTAAGTATAAATCAC 6 49 0 CTGTCCTAAG 0.975201 -126 GCCCTAAAAATTGCCATAAAAAAACACCTG 6 119 0 TTGCCATAAA 0.717352 -56 CATCTGTGGACTGCCCTAAAAATTGCCATA 6 131 0 CTGCCCTAAA 0.975202 -44 AAAGATTTCTCTCTCATAAAACATGGCTTT 7 24 0 CTCTCATAAA 0.902735 -93 ATTGTGGGCTCTCTCTTAAAAAATTAACAC 7 79 1 CTCTCTTAAA 0.902735 -38 ********** Masking position 9 Map Score: 8.73774 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 155 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 CAGGAAAAATTTCTTTCTCAGTTC 1 5 0 TTCTTTCTCA 0.970476 -102 CCCGAAAGTTTTCTTTTTCTGGCAAAGTTT 1 36 0 TTCTTTTTCT 0.835668 -71 CCCACTGTCCCTCTCTCTCTAGTTCTTTGG 4 276 1 CTCTCTCTCT 0.977196 -25 CTAAAAAGATTTCTCTCTCATAAAACATGG 7 28 0 TTCTCTCTCA 0.98102 -89 GTATTGTGGGCTCTCTCTTAAAAAATTAAC 7 77 1 CTCTCTCTTA 0.935398 -40 ACGAGAGACCTTCTTTCTTTTTACTTGTAC 9 68 0 TTCTTTCTTT 0.917405 -45 ********** Masking position 6 Map Score: 3.54517 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 28 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 AGGCGATCGCCAAGGCTTTTCCCGCAACACCA 2 161 0 CAAGGCTTTC 0.874378 -140 TTGGCGATCGCCTTTTTTTGTCCTCAATTTTT 2 180 1 CCTTTTTTTC 0.826052 -121 TTGAGGACGGCCTTGCGTTCACATCTTAAGAC 2 252 0 CCTTGCGTTC 0.966551 -49 GGCATCGACCCATTGCTTTCACGATTAGCCAT 4 108 1 CATTGCTTTC 0.98563 -193 GAATGGATAATCTTGTTTTTCCCCTCCATCTT 5 52 0 TCTTGTTTTC 0.826052 -35 GGGCGTCTTTCCTTGTTTCGACTCCAGATGTT 6 87 0 CCTTGTTTCC 0.960129 -88 CCGCCAGCGCCATTGCTTCATCTGTGGACTGC 6 147 0 CATTGCTTCC 0.974899 -28 TCTCATAAAACATGGCTTTGCCATGAGGGATC 7 11 0 CATGGCTTTC 0.9749 -106 ********* * Masking position 8 Map Score: 3.45474 Number of sites scoring better than the average of aligned sites = 526 Number in coding regions = 451 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 10 TTAGAAAGATTTTATTAAACAGGAAAAAACATC 2 217 0 TTATAAACGG 0.91925 -84 TTGCTAAAACTTGCTGAAACGGGAGAATTTTAG 3 101 1 TTCTAAACGG 0.976598 -106 TCCGCTGGCTATGCCTACGCTGGTTCAAATCCA 4 47 0 ATCCACGCGG 0.965888 -254 TCCGCCCCCATTAACCACTCGGGCATCGACCCA 4 87 1 TTACACTCGG 0.922958 -214 AGGGTAACCAATCCCGACACAGGAAGCGATTCC 4 209 0 ATCCACACGG 0.987251 -92 CACAATTCCTTTACCTAAACGGGAAACGACTCC 5 19 1 TTCCAAACGG 0.988531 -68 TTTTTCTAATTTCCTCACACCTGTCCTAAGTAT 6 56 0 TTCTACACTG 0.917895 -119 ** ** **** ** Masking position 7 Map Score: 1.62102 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 325 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 AAATAACTCACAATTCCCGAAAGTTTTCTT 1 51 0 CAATTCCCGA 0.95092 -56 ACCTCCTATGCCCCTCCACATCCCATCCCA 2 27 0 CCCCTCCACA 0.79523 -274 CCCGCAACACCAACCCCAGAAAATTCCCTC 2 143 0 CAACCCCAGA 0.79147 -158 AGCAATGGGTCGATGCCCGAGTGGTTAATG 4 95 0 CGATGCCCGA 0.955182 -206 ACACAGGAAGCGATTCCCAGCAAACCAGAC 4 196 0 CGATTCCCAG 0.838435 -105 CCTAGGGTAACCAATCCCGACACAGGAAGC 4 215 0 CCAATCCCGA 0.882573 -86 AGAAATTCCACAATTCCTTTAC 5 3 1 AAATTCCACA 0.558882 -84 AAACGGGAAACGACTCCAAGATGGAGGGGA 5 35 1 CGACTCCAAG 0.813122 -52 ACAAGATTATCCATTCCCCAGAGGTTTCC 5 68 1 CCATTCCCCA 0.96093 -19 TTCCTTGTTTCGACTCCAGATGTTTTTCTA 6 81 0 CGACTCCAGA 0.976503 -94 AAACAAGGAAAGACGCCCCAGGTGTTTTTT 6 101 1 AGACGCCCCA 0.808692 -74 ********** Masking position 6 Map Score: 3.56739 Number of sites scoring better than the average of aligned sites = 1226 Number in coding regions = 1109 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 12 ********** No masking Map Score: 2.98671e-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 13 ********** No masking Map Score: 2.98671e-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: 2.98671e-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