AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_synecho_ctra_300.orf -o216_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 RCY44131 300 Synechocystis #2 RCY51226 208 Synechocystis #3 RCY49691 112 Synechocystis #4 RCY12795 137 Synechocystis #5 RCY04561 102 Synechocystis #6 RCY30742 53 Synechocystis #7 RCY03877 300 Synechocystis #8 RCY26596 300 Synechocystis #9 RCT00022 75 Chlamydia_trachomatis #10 RCT00023 187 Chlamydia_trachomatis #11 RCT00025 59 Chlamydia_trachomatis #12 RCT00028 25 Chlamydia_trachomatis #13 RCT00029 63 Chlamydia_trachomatis #14 RCT00628 300 Chlamydia_trachomatis #15 RCT00629 98 Chlamydia_trachomatis Motif number 1 CTGTCCCCTGGGAGTTTCCCT 1 1 1 CTGCCCCTGG 0.931122 -300 AAGCCGTAGATATTCCCAGGGAAACTCCCAG 1 18 0 TATCCCAGGG 0.654634 -283 AACCTACCCTCTGGCCCAGTGAACTATTCCC 1 156 0 CTGCCCAGTG 0.935516 -145 GTAGGCCACCTTGCCCCTGTCCACACCACTG 1 244 1 TTGCCCTGTC 0.715328 -57 CATCCCAAAGCGGTCCCAGTGGTGTGGACAG 1 260 0 CGGCCCAGTG 0.948134 -41 TTCTCTCCCTTTTCCCCCGGGGGAGTGATAC 2 118 1 TTTCCCCGGG 0.955872 -91 TGCCTTGCTGTTGCGCCCGGACTGTTGGCCG 4 49 0 TTGGCCCGGA 0.885338 -89 TATCGGCTAACGATCCCCGGATCACGGTAAC 5 23 0 CGACCCCGGA 0.88181 -80 CGACGGTTTATTAGCCCAGTCTTTCCTATTA 5 52 0 TTACCCAGTC 0.84951 -51 TAACCATGGGCGGACCCAGGCCTCTCCTCCC 7 183 0 CGGCCCAGGC 0.975596 -118 CCCACTAAATTTATCCCCGGCCTACCGGATT 8 40 0 TTACCCCGGC 0.963322 -261 CTGAGTCAGTTTGTGCCCGGGGGAGAGTTCG 8 127 1 TTGGCCCGGG 0.968916 -174 TCGGAATCCTTGACCCCATTGGGAAAGCCCT 8 155 1 TGACCCATTG 0.653356 -146 GGGAAAGCCCTGGTGCCATGGCTATCTGCGG 8 175 1 TGGGCCATGG 0.830274 -126 GCGATTGAGCTGGGCCCCTGAAAATTTACGA 8 205 1 TGGCCCCTGA 0.859823 -96 AACGCGAAATTTTTCCCAGTCTATTTTTATT 8 276 1 TTTCCCAGTC 0.778703 -25 TGCTAGCCTGTGAAGCCCGGCAGGTGGTTCT 14 160 1 TGAGCCCGGC 0.91314 -141 *** ******* Masking position 6 Map Score: 14.8455 Number of sites scoring better than the average of aligned sites = 4330 Number in coding regions = 3971 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 362 Fraction of orfs with sites within 600 bp upstream = 0.0581433 Motif number 2 GAAAACATTCAATTTTTAGGGATAGAAATC 8 14 1 AATTTTTAGG 0.977902 -287 TAGGGTCGTAAATTTTCAGGGGCCCAGCTC 8 211 0 AATTTTCAGG 0.961625 -90 TTGGGGCCAGAATTTTTAGGGTCGTAAATT 8 227 0 AATTTTTAGG 0.977902 -74 ATTCTAACCTATTTTTTGGGGCCAGAATTT 8 242 0 ATTTTTTGGG 0.926356 -59 AAAATGTTCGGGTATGCTCTCC 9 3 1 AATGTTCGGG 0.913473 -73 ATTGGCAATCAATTTTTGGGGAACACTAGA 10 113 0 AATTTTTGGG 0.985953 -75 AATATTAGATAATTTTTGCGATAAAGAACT 11 13 0 AATTTTTGCG 0.920743 -47 AAAAAGAATTTTTAGGTGAAATACA 12 7 1 AATTTTTAGG 0.977902 -19 ********** Masking position 1 Map Score: 11.8823 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 82 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 AAACCGCCCTTTCTCTCCCTTTTCCCCCGGGGG 2 108 1 TTCTCCTTTT 0.97283 -101 TCCTCAATCCTTAACCTACTTTTAACTG 3 6 0 TTCCTCTTTT 0.945834 -107 TTTTTCCCACTTGCCTTGCTGTTGCGCCCGGAC 4 58 0 TTCTTCTGTT 0.73257 -80 TCATAACTGATTTACCCTCTTTTGCAAAAGTTG 4 93 0 TTCCCCTTTT 0.987516 -45 AAGGGTGTAATTTACCCTTTTTTCAACCAGAGT 7 48 1 TTCCCTTTTT 0.861738 -253 TCGGGTATGCTCTCCCTTCTGTTATGTGAGATT 9 18 1 TCCCTCTGTT 0.890367 -58 AGCGGGGTGTTCGCCCCGCTTTTCTCTAGATAA 10 29 0 TCCCCCTTTT 0.990667 -159 AGCGGGGCGAACACCCCGCTTTTTTTGTTTTAA 10 42 1 ACCCCCTTTT 0.976896 -146 TTGTTTTAATAAGTCTCTCTTTTTGAATCTGAC 10 66 1 AACTCCTTTT 0.747526 -122 TCTAATATTTTCTCCTCACTTTTTACCGCAAAG 11 34 1 TCCTCCTTTT 0.979612 -26 AGGGCTTAATGCCGCTCTCTTTTCTTTA 13 6 0 GCCTCCTTTT 0.91821 -58 CTTACAGATCATGCCCCAATTTTGCTAGCCTGT 14 138 1 ATCCCATTTT 0.712855 -163 ** *** ***** Masking position 10 Map Score: 9.52422 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 353 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 ATTGCGCTGCTTTATCGGGGAAATATGGCC 2 40 0 TTTATCGGGG 0.883931 -169 AAGCTGAAAAATTAGTGGGGCAAATTGATT 6 26 1 ATTAGTGGGG 0.936688 -28 AAAACATTCAATTTTTAGGGATAGAAATCC 8 15 1 ATTTTTAGGG 0.970085 -286 CGGGGATAAATTTAGTGGGGAGTGGCTGAC 8 52 1 TTTAGTGGGG 0.870115 -249 AGGGTCGTAAATTTTCAGGGGCCCAGCTCA 8 210 0 ATTTTCAGGG 0.940657 -91 TGGGGCCAGAATTTTTAGGGTCGTAAATTT 8 226 0 ATTTTTAGGG 0.970085 -75 TTCTAACCTATTTTTTGGGGCCAGAATTTT 8 241 0 TTTTTTGGGG 0.971758 -60 TAAGATAGTGATTTTGGGGTTGTCAA 9 60 1 ATTTTGGGGT 0.777234 -16 TTGGCAATCAATTTTTGGGGAACACTAGAC 10 112 0 ATTTTTGGGG 0.987011 -76 AAAAAGAATTTTTAGGTGAAATACA 12 8 1 ATTTTTAGGT 0.84862 -18 ********** Masking position 3 Map Score: 11.1029 Number of sites scoring better than the average of aligned sites = 575 Number in coding regions = 468 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 GGGAAACTCCCAGGGGACAG 1 1 0 CAGGGGACAG 0.965279 -300 CAGGGACCTTTGGGGGACAGGGGTTACAGT 1 63 0 TGGGGGACAG 0.931654 -238 GGTCCCAGTGGTGTGGACAGGGGCAAGGTG 1 250 0 GTGTGGACAG 0.793639 -51 CCCCGGGGGAAAAGGGAGAGAAAGGGCGGT 2 110 0 AAAGGGAGAG 0.772137 -99 CCTTTTCCCCCGGGGGAGTGATACGTTGTA 2 125 1 CGGGGGAGTG 0.978409 -84 GCTGATCACTCGAAGGAGAGAAACCAATAA 7 92 0 CGAAGGAGAG 0.92735 -209 ATCGCCATTGGGGAGGAGAGGCCTGGGTCC 7 173 1 GGGAGGAGAG 0.984575 -128 GATAAATTTAGTGGGGAGTGGCTGACGACA 8 56 1 GTGGGGAGTG 0.956409 -245 AGTTTGTGCCCGGGGGAGAGTTCGGAATCC 8 134 1 CGGGGGAGAG 0.994554 -167 TCACATAACAGAAGGGAGAGCATACCCGAA 9 17 0 GAAGGGAGAG 0.95634 -59 GCGGTAAAAAGTGAGGAGAAAATATTAGAT 11 33 0 GTGAGGAGAA 0.662838 -27 ********** Masking position 7 Map Score: 10.973 Number of sites scoring better than the average of aligned sites = 868 Number in coding regions = 758 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 6 TTCTCACAAAGAAGTTTTGCTGATTCGATTT 3 51 1 GAGTTTTGCT 0.961306 -62 CCTTGCCGATATAGTTCTGTTTTATTTGTAG 3 86 0 AAGTTCTGTT 0.973629 -27 CCGCTAGAATGCAGTTTTGCTGGATCATAAT 4 21 0 GAGTTTTGCT 0.961306 -117 TTTTTCAACCAGAGTTTTGTTGTCCATTATT 7 66 1 AAGTTTTGTT 0.968328 -235 TAGATAACAGAAAGTTCTGTTCAAA 10 5 0 AAGTTCTGTT 0.973629 -183 GAAAGTTTAGATAGTTTTGTTAACATTTCTT 14 195 1 AAGTTTTGTT 0.968328 -106 TTCAAAAGACGAAGTCCTGTTTTAAGGAGGC 14 277 1 GAGTCCTGTT 0.932059 -24 * ********* Masking position 3 Map Score: 6.81485 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 40 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 CCACTGGGACCGCTTTGGGATGGCCTTTTG 1 269 1 CGCTTTGGGA 0.934187 -32 CCCAGATCGCCAGTTAGGAACTGCTAGGAA 2 12 0 CAGTTAGGAA 0.921361 -197 GCCCGGGGGAGAGTTCGGAATCCTTGACCC 8 141 1 GAGTTCGGAA 0.914335 -160 ATGGCTCTGGAGGTTTGGGAGTTGCATGTG 14 69 1 AGGTTTGGGA 0.919501 -232 ATTGAAACAGCAGTTCGGGATTCTTACAGA 14 116 1 CAGTTCGGGA 0.982522 -185 CATTTCTTAACGGTTTGGAAGGTTGAATAA 14 218 1 CGGTTTGGAA 0.983908 -83 TTCCATGATACGGTTCGGAAAAGATTTATT 14 243 0 CGGTTCGGAA 0.989706 -58 ********** Masking position 10 Map Score: 4.96045 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 144 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GGAAAAGGGAGAGAAAGGGCGGTTTTTGCA 2 103 0 GAGAAAGGGC 0.976999 -106 TTCAGCTTTTCAGTAAAGTCAAG 6 4 0 CAGTAAAGTC 0.957208 -50 TTCGAGTGATCAGCAAGGTCATTACTGGAT 7 108 1 CAGCAAGGTC 0.964412 -193 CTCTAGATAACAGAAAGTTCTGTTCAAA 10 9 0 CAGAAAGTTC 0.856992 -179 TGACTTTTCAGAGTAAAGTCTAGTGTTCCC 10 95 1 GAGTAAAGTC 0.944515 -93 AGAGATACTAGAGTAAAGGCAGAAGAAGTC 10 164 1 GAGTAAAGGC 0.95363 -24 TTGAGAACAGCAGAAAGGGCTTAATGCCGC 13 24 0 CAGAAAGGGC 0.982392 -40 ********** Masking position 5 Map Score: 5.31666 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 104 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 CCCCAAAGGTCCCTGTTCACCCCCAATCGGGCA 1 78 1 CCTGTTCCCC 0.950166 -223 TAGTTGTGACCGTTTTTTGCCACCCCAGCTGCC 1 107 0 CGTTTTTCCC 0.971845 -194 TGGGTAAACTGAATATTTTCCTCTCTAGGGTCA 1 186 0 GATATTTCCC 0.868972 -115 AGAGAAAGGGCGGTTTTTGCAACTAAGCTTTAA 2 91 0 CGTTTTTCAC 0.827465 -118 GATTTTTAACCCCCACCCCTTAG 2 196 0 GATTTTACCC 0.853664 -13 GTTGCGCCCGGACTGTTGGCCGCTAGAATGCAG 4 38 0 GATGTTGCCC 0.909224 -100 TGCAAAAGTTGCTTTTTTCCCACTTGCCTTGCT 4 71 0 GCTTTTTCCC 0.968279 -67 TTTTTTCAATCAATTTGCCCCACTAATTTTTCA 6 30 0 CATTTGCCCC 0.758882 -24 GTGTAATTTACCCTTTTTTCAACCAGAGTTTTG 7 52 1 CCTTTTTCAC 0.785007 -249 CCTAAAAATTGAATGTTTTCCTC 8 1 0 GATGTTTCCC 0.977205 -300 CAGACAGTCGGGATGTTTTCTTCTATGATTGAT 8 89 0 GGTGTTTCTC 0.785387 -212 AAAAAAAGCGGGGTGTTCGCCCCGCTTTTCTCT 10 35 0 GGTGTTCCCC 0.966766 -153 ATTTTCTCCTCACTTTTTACCGCAAAGAGG 11 40 1 CATTTTTCCC 0.969568 -20 ** ***** ** * Masking position 6 Map Score: 9.74171 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 752 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 10 AGGGTCAACCTACCCTCTGGCCCAGTGAACT 1 162 0 TCCCTCTGGC 0.986691 -139 ATATTCAGTTTACCCAATGTCCAACATTACA 1 203 1 TCCCAATGTC 0.974684 -98 AGTTGCTTTTTTCCCACTTGCCTTGCTGTTG 4 67 0 TCCCACTTGC 0.956723 -71 AGGCCTCTCCTCCCCAATGGCGATCGCCGTG 7 166 0 TCCCAATGGC 0.992964 -135 GAAGAAAACATCCCGACTGTCTGTGCTCCTG 8 99 1 TCCGACTGTC 0.899359 -202 CACCAGGGCTTTCCCAATGGGGTCAAGGATT 8 159 0 TCCCAATGGG 0.964454 -142 TTTAAGCAGATTTCCTATGGCTCTGGAGGTT 14 53 1 TTCCTATGGC 0.888441 -248 * ********* Masking position 8 Map Score: 5.07959 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 534 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 11 TTAATTAAAGTTATGGAAAAATTTCGTTTT 2 154 0 TTATGGAAAA 0.875053 -55 TGCTGGATCATAATTGAAAAGCCG 4 5 0 TAATTGAAAA 0.866793 -133 CTTGACTTTACTGAAAAGCTGAAAAAT 6 8 1 TTACTGAAAA 0.875088 -46 TGGGGCAAATTGATTGAAAAAAT 6 41 1 TGATTGAAAA 0.946659 -13 CGGTTAATTATTATTGAAAACGTCC 7 6 0 TTATTGAAAA 0.963283 -295 AACAAAACTCTGGTTGAAAAAAGGGTAAAT 7 57 0 TGGTTGAAAA 0.824998 -244 AAAGAGAGACTTATTAAAACAAAAAAAGCG 10 58 0 TTATTAAAAC 0.625076 -130 TGTGATAAGTTTATTGAAACAGCAGTTCGG 14 104 1 TTATTGAAAC 0.937245 -197 ********** Masking position 7 Map Score: 2.93496 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 88 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 GAATATCTACGGCTTTCTCCAGCAAGCTGACTGTA 1 34 1 GGTTTCTGCA 0.988989 -267 GGTTTTCCTTGCCGATATAGTTCTG 3 98 0 GGTTTCCCCA 0.982667 -15 TTGTTGAGGTGGGTATCTAAACCAAATTACACGGC 7 137 1 GGTATCTCCA 0.967478 -164 CTGTAGCAAAGGGTTGCCCTGGCCAGAGAATCTGA 7 228 0 GGTTGCCGCA 0.958181 -73 CCGGCCTACCGGATTTCTATCCCTAAAAATTGAAT 8 20 0 GGTTTCTCCA 0.985587 -281 CTGGTGCCATGGCTATCTGCGGCGATTGAGCTGGG 8 184 1 GGTATCTGCA 0.975046 -117 ACCACCTGCCGGGCTTCACAGGCTAGCAAAATTGG 14 153 0 GGCTTCAGCA 0.89362 -148 ** ***** ** * Masking position 15 Map Score: 2.84135 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 84 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 AAACGGTCACAACTATAGCAACTGAGATGACG 1 125 1 AACTTGCAAC 0.800279 -176 CAATTTTAAGAATTCTCACAAAGAAGTTTTGC 3 39 1 AATTTACAAA 0.91187 -74 GGAAAAAAGCAACTTTTGCAAAAGAGGGTAAA 4 84 1 AACTTGCAAA 0.944903 -54 TAACCAATTCAACTGTAGCAAAGGGTTGCCCT 7 243 0 AACTTGCAAA 0.944903 -58 CTACAGTTGAATTGGTTACAAATAGTTAAAGT 7 257 1 ATTGTACAAA 0.804108 -44 ACTCTAGTATCTCTCTAACAAAGACCAGAGTG 10 146 0 CTCTTACAAA 0.840889 -42 TTAGTTCTTTATCGCAAAAATTATCTAA 11 7 1 CTTTTGCAAA 0.840893 -53 GATTCCGATTTGTTACAAACAAACTATTT 14 8 1 ATTTTACAAA 0.893597 -293 ACCGTTAAGAAATGTTAACAAAACTATCTAAA 14 200 0 AATGTACAAA 0.834737 -101 **** * ***** Masking position 6 Map Score: 0.444439 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 201 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 14 AGATATTCCCAGGGAAACTCCCAGGGGACA 1 12 0 AGGGAAACTC 0.918553 -289 TTTCCTCTCTAGGGTCAACCTACCCTCTGG 1 173 0 AGGGTCAACC 0.936825 -128 TGTTGGACATTGGGTAAACTGAATATTTTC 1 199 0 TGGGTAAACT 0.823766 -102 CTATATCGGCAAGGAAAACC 3 103 1 AAGGAAAACC 0.827231 -10 TTTGCAAAAGAGGGTAAATCAGTTATGATG 4 98 1 AGGGTAAATC 0.956185 -40 GGTTGAAAAAAGGGTAAATTACACCCTTAG 7 46 0 AGGGTAAATT 0.833084 -255 TTCTCTGGCCAGGGCAACCCTTTGCTACAG 7 233 1 AGGGCAACCC 0.944195 -68 TTGACCCCATTGGGAAAGCCCTGGTGCCAT 8 164 1 TGGGAAAGCC 0.85162 -137 ********** Masking position 7 Map Score: 0.629117 Number of sites scoring better than the average of aligned sites = 965 Number in coding regions = 853 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 15 GGGGTGAACAGGGACCTTTGGGGGACAGGGGT 1 69 0 GGGATTTGGG 0.970359 -232 CGCTTTGGGATGGCCTTTTGAGGAATATATTT 1 279 1 TGGCTTTGAG 0.964834 -22 AGTTCCTAACTGGCGATCTGGGCCATATTTCC 2 20 1 TGGCTCTGGG 0.969778 -189 AGGTCATTACTGGATTGTTGAGGTGGGTATCT 7 123 1 TGGAGTTGAG 0.964834 -178 TTGTGCCCGGGGGAGAGTTCGGAATCCTTGAC 8 137 1 GGGAGTTCGG 0.841504 -164 CCTGGTGCCATGGCTATCTGCGGCGATTGAGC 8 183 1 TGGCTCTGCG 0.901121 -118 CCTATGGCTCTGGAGGTTTGGGAGTTGCATGT 14 66 1 TGGATTTGGG 0.982996 -235 CTTAACGGTTTGGAAGGTTGAATAAATCTTTT 14 223 1 TGGAGTTGAA 0.753919 -78 **** ****** Masking position 9 Map Score: 1.00386 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 549 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639