AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_synecho_ctra_100.orf -o054_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 RCY49951 123 Synechocystis #2 RCY44999 300 Synechocystis #3 RCY06294 263 Synechocystis #4 RCY42481 107 Synechocystis #5 RCY13624 170 Synechocystis #6 RCY49190 245 Synechocystis #7 RCY34497 112 Synechocystis #8 RCY01339 233 Synechocystis #9 RCT00741 247 Chlamydia_trachomatis Motif number 1 AATTTGGATATGGTCTGCAGGGGTAGGGTCACC 1 72 0 TGGCTGGGGG 0.990712 -52 CGCGTTAGACTGGCCAAATTTGGATATGGTCTG 1 88 0 TGGCAATTGG 0.945828 -36 CCTTGGCTGACGGACAGTATGGTTTTTGCTCAG 2 66 1 CGGCAGTGGT 0.888472 -235 TTATCCAGTCTGGGCAAATTTGGGCTTTGATTA 2 160 1 TGGCAATTGG 0.945828 -141 GTGCTTGGTTGGGGCATACGGGGTTTCACTGGT 2 201 1 GGGCATGGGG 0.882053 -100 TGGGATGGGGGGATTTCGTTGTG 2 288 0 TGGATGGGGA 0.679368 -13 AGACAACGGCTGGGCTATGTGGAAGACTTGACT 3 25 0 TGGCTATGGA 0.868666 -239 CCCATCTCTACGGGCGGAAGGGTTAGATAAAGT 3 64 0 CGGCGGGGGT 0.851283 -200 GCTAGGTGAATGGTCGAGATGGGTTTTAGCTCC 3 234 0 TGGCGATGGG 0.964965 -30 TTGCGTACAATGGCTAGACGGGGGTTAGGTCCG 6 55 0 TGGTAGGGGG 0.94061 -191 GCAATATCTCTGGGCAGAAGGATCCCGGAAAAA 6 114 1 TGGCAGGGAT 0.871188 -132 AGTTCGCCATTGGGCAATTTTGATATTAGAATT 6 169 1 TGGCAATTGA 0.776588 -77 ACTCGGTTAATGGTCTTGGGGGGATGGCAGTGA 7 20 0 TGGCTTGGGG 0.954554 -93 TAACCGAGTATGGCAAAATGGGGCTTAATTCGA 7 44 1 TGGAAAGGGG 0.951885 -69 ACCACCACATTGGACAATCGGGGATAACGGCT 7 91 1 TGGCAAGGGG 0.994982 -22 GTCCGTGGAATGGTCAAACGGAGTCGATCTCAG 8 32 1 TGGCAAGGAG 0.948668 -202 AGTAATGTCTTGGTCAGAATTGTTTGTTTTAAC 8 169 0 TGGCAGTTGT 0.864674 -65 *** *** **** Masking position 3 Map Score: 22.4103 Number of sites scoring better than the average of aligned sites = 2425 Number in coding regions = 2229 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 2 AAGATCAGGAGACAATTATTTCAGAGGGGTGACC 1 45 1 GCAATATCAG 0.987023 -79 CCAGACTGGATAAAATTATTCCAGGCATTTTGGA 2 139 0 TAAATATCAG 0.696061 -162 GTGATAGTTAGCAAATGATGGCGGAGTAGTTAGT 2 257 0 GAAATATCGG 0.861677 -44 GGCGGTCACAGTCAAGTCTTCCACATAGCCCAGC 3 16 1 GCAAGCTCAC 0.890401 -248 CCTTGATTGTGGCAAGATTCTCAGTAATGCCCCT 3 132 0 GCAAGTTCAG 0.97559 -132 GTCAAAACTGTTCAGGGCTAACAGTTGCCTTGAT 3 159 0 TCAGGCTCAG 0.827971 -105 TTCAACCCCGGTCAGGAATTGCTGATTTTCGCCT 4 30 0 GCAGGATCTG 0.895677 -78 AAACTCAGAGGCCAATCATAGCAGTTCTGCTCGG 4 80 0 GCAATATCAG 0.987023 -28 GAAAAAAGACGCAAAGTAGGACAGAGTTAGACCA 6 13 1 GAAAGAGCAG 0.858979 -233 TTGGGGGGATGGCAGTGATGTCAGAAA 7 4 0 GCAGTATCAG 0.972224 -109 CCCATCGAATGTCAAGCTTTCCAGATAGAGCGTA 8 71 0 GCAAGTTCAG 0.97559 -163 GATAGCCGAGGCAAAGGATTTCGGCAGTGTTAAA 8 141 1 GAAAGATCGG 0.929538 -93 AGTTACTTGTGGCAATCCTTTCAGACAGGTTTTT 9 66 0 GCAATCTCAG 0.977023 -182 TTTTCACAATGACAAGAATAAAAGCAAAAAGAAA 9 109 1 GCAAGATAAG 0.90745 -139 * **** ** *** Masking position 4 Map Score: 15.382 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 446 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 3 GGTTGGGGCATACGGGGTTTCACTGGTGGT 2 207 1 TACGGGGTTT 0.831857 -94 TGGGATGGGGGGATTTCGTTGTG 2 288 0 GATGGGGGGA 0.913349 -13 CGGACCCATTGCCAGGGGCATTACTGAGAA 3 119 1 GCCAGGGGCA 0.819786 -145 GAATGGTCGAGATGGGTTTTAGCTCCGGGG 3 230 0 GATGGGTTTT 0.812605 -34 AGCAATTCCTGACCGGGGTTGAAGGACCAA 4 41 1 GACCGGGGTT 0.989419 -67 TAGCAGTTCTGCTCGGGGTTAATTATTGGT 4 66 0 GCTCGGGGTT 0.94208 -42 GGACAGGGGCAGAAAAATTGA 5 2 1 GACAGGGGCA 0.922194 -169 AGTAAAATGCGATCGGGTTTTGAGCCCGTT 5 114 1 GATCGGGTTT 0.950453 -57 ACAATGGCTAGACGGGGGTTAGGTCCGATC 6 52 0 GACGGGGGTT 0.993478 -194 CTTGACATTCGATGGGGTGTGAGATTCAAC 8 89 1 GATGGGGTGT 0.930651 -145 TCGGCTATCTGTCAGGGGTTTTGCCTAGCC 8 120 0 GTCAGGGGTT 0.916033 -114 AATCCTTTCAGACAGGTTTTTTGTACGAAA 9 57 0 GACAGGTTTT 0.829817 -191 ********** Masking position 5 Map Score: 10.9287 Number of sites scoring better than the average of aligned sites = 1369 Number in coding regions = 1221 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 4 CTGTCCGTCAGCCAAGGAAAAGAAATTATTT 2 52 0 GCCAAGGAAA 0.993337 -249 TCCCATCGCCAAGGGACAAAGGCGAAAA 4 8 1 GCCAAGGACA 0.991974 -100 CTGTGAAAGGGCCAAGGGAAATTCCCCTCAG 5 54 1 GCCAAGGAAA 0.993337 -117 CCTCAGCTAAGGCTAGGTACAAGGGGAGCCC 5 79 1 GGCTAGGACA 0.9783 -92 AGATTCAACGGGCTAGGCAAAACCCCTGACA 8 110 1 GGCTAGGAAA 0.981943 -124 CTGACAGATAGCCGAGGCAAAGGATTTCGGC 8 135 1 GCCGAGGAAA 0.988694 -99 ******* *** Masking position 5 Map Score: 9.56485 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 92 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 ATATCCAAATTTGGCCAGTCTAACGCGTTA 1 94 1 TTGGCCAGTC 0.712108 -30 ATTTGAGACATTTGCCAGTGGATATAACTG 2 26 0 TTTGCCAGTG 0.892523 -275 CTGGGCAAATTTGGGCTTTGATTATTGGTT 2 169 1 TTGGGCTTTG 0.967149 -132 GGCTTTGATTATTGGTTTTGTGCTTGGTTG 2 182 1 ATTGGTTTTG 0.496488 -119 CTTGACTGTGACCGCCTTTGT 3 2 0 ACCGCCTTTG 0.771974 -262 ATTGCTGATTTTCGCCTTTGTCCCTTGGCG 4 17 0 TTCGCCTTTG 0.958587 -91 ACTGCTATGATTGGCCTCTGAGTTTGAGA 4 89 1 TTGGCCTCTG 0.91321 -19 CGTCCTAATTATGGCCTGTGAAAGGGCCAA 5 39 1 ATGGCCTGTG 0.962032 -132 TAAAATGCGATCGGGTTTTGAGCCCGTTTG 5 116 1 TCGGGTTTTG 0.672475 -55 TTTGAGCCCGTTTGGTTGTGACTCTTTTGT 5 132 1 TTTGGTTGTG 0.773197 -39 GGGGATCAAGTTCGCCATTGGGCAATTTTG 6 161 1 TTCGCCATTG 0.914646 -85 TTGACATTCGATGGGGTGTGAGATTCAACG 8 90 1 ATGGGGTGTG 0.738539 -144 GGCAAAGGATTTCGGCAGTGTTAAAACAAA 8 150 1 TTCGGCAGTG 0.936572 -84 ********** Masking position 9 Map Score: 8.04408 Number of sites scoring better than the average of aligned sites = 2014 Number in coding regions = 1859 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 6 ATCCAGTCTGGGCAAATTTGGGCTTTGATT 2 162 1 GGCAAATTTG 0.816209 -139 TAAAGGCAACGTCAAAACTGTTCAGGGCTA 3 173 0 GTCAAAACTG 0.955514 -91 AGCTCCGGGGAGCAAAACTGCCTGTCAGTT 3 210 0 AGCAAAACTG 0.975058 -54 ATTAACCCCGAGCAGAACTGCTATGATTGG 4 73 1 AGCAGAACTG 0.96532 -35 GGACAGGGGCAGAAAAATTGACAATAACCG 5 11 1 AGAAAAATTG 0.809082 -160 GAATTCTAATATCAAAATTGCCCAATGGCG 6 173 0 ATCAAAATTG 0.912753 -73 AACCGAGTATGGCAAAATGGGGCTTAATTC 7 45 1 GGCAAAATGG 0.868109 -68 GATAGAGCGTATCAAAACTGAGATCGACTC 8 52 0 ATCAAAACTG 0.94345 -182 TAATGTCTTGGTCAGAATTGTTTGTTTTAA 8 170 0 GTCAGAATTG 0.90557 -64 TGCTTTTACCTGAAGAACTGGTTCAATGTG 8 212 0 TGAAGAACTG 0.542773 -22 ********** Masking position 6 Map Score: 8.58555 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 573 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 GGTCACCCCTCTGAAATAATTGTCTCCTGA 1 49 0 CTGAAATAAT 0.960292 -75 TGGCAAATGTCTCAAATAATTTCTTTTCCT 2 39 1 CTCAAATAAT 0.895352 -262 TCCAAAATGCCTGGAATAATTTTATCCAGT 2 139 1 CTGGAATAAT 0.952493 -162 CCGAGCAGAACTGCTATGATTGGCCTCTGA 4 80 1 CTGCTATGAT 0.80596 -28 GTTCTCAAATCTCAAATAATGCCAACAGAT 6 225 0 CTCAAATAAT 0.895352 -21 CAAGACATTACTGCTAGAATGGCACATTGA 8 190 1 CTGCTAGAAT 0.877957 -44 AAAAACCTGTCTGAAAGGATTGCCACAAGT 9 66 1 CTGAAAGGAT 0.930664 -182 CTAAAACTATCTGGACGAATAAGCCGGATG 9 184 1 CTGGACGAAT 0.839222 -64 ********** Masking position 9 Map Score: 2.41948 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 89 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 ATTATTTCAGAGGGGTGACCCTACCCCTGC 1 59 1 AGGGGTGACC 0.872629 -65 TTGGGGCATACGGGGTTTCACTGGTGGTTA 2 209 1 CGGGGTTTCA 0.86865 -92 TTAGTTTGAGAGGGGAAAAATATTAACCAC 2 232 0 AGGGGAAAAA 0.724343 -69 GTTTTAGCTCCGGGGAGCAAAACTGCCTGT 3 215 0 CGGGGAGCAA 0.974663 -49 AATTCCTGACCGGGGTTGAAGGACCAATAA 4 44 1 CGGGGTTGAA 0.922379 -64 CAGTTCTGCTCGGGGTTAATTATTGGTCCT 4 63 0 CGGGGTTAAT 0.866804 -45 GCTAGGTACAAGGGGAGCCCAACGAGTAAA 5 90 1 AGGGGAGCCC 0.910657 -81 TTTGCTAAACCGGGGATCAAGTTCGCCATT 6 150 1 CGGGGATCAA 0.975153 -96 ATTGGACAATCGGGGATAACGGCT 7 99 1 CGGGGATAAC 0.969563 -14 ********** Masking position 5 Map Score: 4.41128 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 778 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 9 ********** No masking Map Score: 6.70342e-13 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 10 TAATATTTTTCCCCTCTCAAACTAACTACT 2 237 1 CCCCTCTCAA 0.904096 -64 CTTATTTCTGCCCATCTCTACGGGCGGAAG 3 77 0 CCCATCTCTA 0.967058 -187 TTGCAGCGGACCCATTGCCAGGGGCATTAC 3 113 1 CCCATTGCCA 0.938481 -151 GGAGCTAAAACCCATCTCGACCATTCACCT 3 234 1 CCCATCTCGA 0.96105 -30 GGCGATCGCTAGGTGAATGGT 3 253 0 GCGATCGCTA 0.852462 -11 TCCCATCGCCAAGGGACAAAG 4 2 1 CCCATCGCCA 0.992733 -106 GCAAAGTTGACCGCTCCCCAGGACGGACTA 6 84 1 CCGCTCCCCA 0.949467 -162 TGACATCACTGCCATCCCCCCAAGACCATT 7 15 1 GCCATCCCCC 0.898094 -98 ********** Masking position 5 Map Score: 3.58569 Number of sites scoring better than the average of aligned sites = 1155 Number in coding regions = 1033 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 11 ********** No masking Map Score: 6.70342e-13 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 12 ********** No masking Map Score: 6.70342e-13 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: 6.70342e-13 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