AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i214_synecho_ctra_300.orf -o214_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 RCY42399 64 Synechocystis #2 RCY23794 104 Synechocystis #3 RCY53156 108 Synechocystis #4 RCY31741 108 Synechocystis #5 RCY09512 82 Synechocystis #6 RCY38222 137 Synechocystis #7 RCY33689 119 Synechocystis #8 RCY05922 107 Synechocystis #9 RCY14231 101 Synechocystis #10 RCY17023 68 Synechocystis #11 RCY34894 39 Synechocystis #12 RCY03648 59 Synechocystis #13 RCY03870 91 Synechocystis #14 RCY00359 106 Synechocystis #15 RCY25341 23 Synechocystis #16 RCY37057 40 Synechocystis #17 RCY34487 29 Synechocystis #18 RCY46798 32 Synechocystis #19 RCY53151 73 Synechocystis #20 RCY50421 39 Synechocystis #21 RCY31267 300 Synechocystis #22 RCT00118 300 Chlamydia_trachomatis #23 RCT00123 222 Chlamydia_trachomatis #24 RCT00124 25 Chlamydia_trachomatis Motif number 1 GGGACATAATTATTTGCCTTGCTAATTTGG 1 16 0 TATTTGCCTT 0.963262 -49 ACAGTTAAATTTTTTGCTAACAGCTTTTTT 3 12 1 TTTTTGCTAA 0.482693 -97 GGGACATTCTTTTTTGCCTTTTTGGGCCCA 4 82 0 TTTTTGCCTT 0.97871 -27 AAGCATTAATTTTTTACCTTTGCCACCGTC 6 21 0 TTTTTACCTT 0.818405 -117 GTTAATTTAATATTTGCCATGACACGGCCA 6 67 1 TATTTGCCAT 0.916395 -71 AGTAATTTCCTTGGATGTTAAT 11 28 0 TAATTTCCTT 0.661611 -12 AATTTTGTTCCTTCAGCAGTGAC 20 27 0 TTTGTTCCTT 0.893692 -13 TCATCCCCCTTTTGTGCCTATGTAGGACTA 21 55 1 TTTGTGCCTA 0.898412 -246 GCCCAGCTTTGTTCCTAAAATACCGAT 21 284 0 TTTGTTCCTA 0.778482 -17 TCCCCAAAAATAATTGCCATTGTACACTCT 22 193 1 TAATTGCCAT 0.672866 -108 ATCTCTTTTCTTTTTGCCTTCAAAAATAGC 23 88 0 TTTTTGCCTT 0.97871 -135 CTTTTTGAAATTTTTTCTTTTCTAAATTCT 23 118 1 TTTTTTCTTT 0.679664 -105 AAAGCAGCTGTATTTGCCTTCTAAAGAATT 23 142 0 TATTTGCCTT 0.963262 -81 TTGATGATTATTTTTTCCAAACAAAAAGCA 23 166 0 TTTTTTCCAA 0.761476 -57 ********** Masking position 5 Map Score: 14.5556 Number of sites scoring better than the average of aligned sites = 853 Number in coding regions = 717 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 2 TCAATAAACAGGACAGGGATGGGGGGAAGA 4 11 0 GGACAGGGAT 0.818079 -98 TCCCCACTGAGGGGAAGCATTAATTTTTTA 6 35 0 GGGGAAGCAT 0.759972 -103 TCCCCTCAGTGGGGAGAGTTAATTTAATAT 6 50 1 GGGGAGAGTT 0.981613 -88 CTATTTTTACGGGCAGAGTTGCATCAATCA 8 17 1 GGGCAGAGTT 0.912651 -91 CCCAGGCTATGGGGAAGGATTTTGGTTACC 9 15 0 GGGGAAGGAT 0.910023 -87 ATAGCCTGGGAGAGAGCGATAATAGGTTAA 9 35 1 AGAGAGCGAT 0.824729 -67 AGGTGGATTGATGGAGACTTATTGCTGACC 13 34 0 ATGGAGACTT 0.725205 -58 CCCTAGCGGTAGGGAGAGTTAGTCCTACAT 21 74 0 AGGGAGAGTT 0.954984 -227 AGTTACGTCGATGGAGCGTTTCAATCAAGC 21 127 0 ATGGAGCGTT 0.910556 -174 CTTTATGTCCGGGGAGCCTTTCTGCTTGTT 21 216 1 GGGGAGCCTT 0.952791 -85 TTTTATTTAGGTAGAGGGTTACCGTGTCTA 21 255 1 GTAGAGGGTT 0.934594 -46 ACTGATTGCTATGGAGGGATTCAAGAAAAT 22 74 1 ATGGAGGGAT 0.92659 -227 CCTTCTTATCGTAGAGGGTTAAAATTTTTG 22 223 1 GTAGAGGGTT 0.934594 -78 ********** Masking position 5 Map Score: 11.5543 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 963 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 TAAGCGGGGGTATTTTTGAAAACT 1 51 1 TATTTTTGAA 0.891056 -14 CTGTTGTTAATTTTTTAGGAGTTCAGTTAC 2 57 1 TTTTTTAGGA 0.9201 -48 TTTATTGAACTTATTTAGAGGAAAATCAAC 5 63 1 TTATTTAGAG 0.663799 -20 ACGATGGCGCTTTTTTCGATACTTTATTCC 7 72 1 TTTTTTCGAT 0.75982 -48 CTTGACCGTCTTTTTTTGATTAATTT 8 92 1 TTTTTTTGAT 0.848177 -16 TCCGATTTTTTTAGGAAAACGCC 15 7 1 TTTTTTAGGA 0.9201 -17 ATTTACACTTTTATTTAGGTAGAGGGTTAC 21 247 1 TTATTTAGGT 0.665224 -54 TGTCTATCGGTATTTTAGGAACAAAGCTGG 21 279 1 TATTTTAGGA 0.908595 -22 CAATGGCAATTATTTTTGGGGAACTAAGAG 22 185 0 TATTTTTGGG 0.8762 -116 TTCGAAAAAATATTTTAGGGAAGTTCTTGA 23 39 0 TATTTTAGGG 0.8762 -184 CCCTAAAATATTTTTTCGAAAGAAGTGTAG 23 49 1 TTTTTTCGAA 0.842904 -174 AGTGTAAGGCTATTTTTGAAGGCAAAAAGA 23 80 1 TATTTTTGAA 0.891056 -143 AGAAAAGAGATCTTTTTGAAATTTTTTCTT 23 107 1 TCTTTTTGAA 0.715641 -116 GGAATGATTATAATTTTGATGATTATTTTT 23 181 0 TAATTTTGAT 0.585291 -42 ********** Masking position 5 Map Score: 7.82417 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 452 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 4 GAAGCTTTCAAGCAATCATTATGGCGCGTC 4 39 1 AGCAATCATT 0.959584 -70 ACTGAGGGGAAGCATTAATTTTTTACCTTT 6 30 0 AGCATTAATT 0.832615 -108 GCAGAGTTGCATCAATCAGTCTTATTAAAC 8 29 1 ATCAATCAGT 0.918629 -79 GTGATTGGTCAGCAATAAGTCTCCATCAAT 13 28 1 AGCAATAAGT 0.959584 -64 CAGTTAATTCAGTATTCAGTGGTGGTCTAA 19 18 0 AGTATTCAGT 0.896588 -56 TAAAAGCCTAAGCATTCAGTATCC 21 5 0 AGCATTCAGT 0.98526 -296 ATCCCTCCATAGCAATCAGTGCTTTCGTAT 22 64 0 AGCAATCAGT 0.98864 -237 ********** Masking position 4 Map Score: 7.14537 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 28 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 5 TAATTTGACGGTGGCAAAGGTAAAAAATTA 6 15 1 GTGGCAAAGG 0.93387 -123 GCTTGCAGTGTTGCCAAAGAAAATCAGGC 6 119 1 TTGCCAAAGA 0.842271 -19 GAGCATAGGTTGGCCAATGGAGCAACCTAT 7 28 1 TGGCCAATGG 0.957092 -92 TTTGTTGTGATTGACGATGGCGCTTTTTTC 7 59 1 TTGACGATGG 0.855564 -61 CATTGCTTGCGGGGCAAAGGTGATAGCCA 14 10 0 GGGGCAAAGG 0.957483 -97 AGAGAGTAGATGGACGAAGGGAACTCGAGC 14 59 0 TGGACGAAGG 0.954258 -48 CCTACCGCTAGGGCCGAAGGTGGTCTCTCA 21 91 1 GGGCCGAAGG 0.982999 -210 ATGAAGCTGTTGACCAAAGGTTATTGCCGC 21 177 1 TGACCAAAGG 0.811455 -124 CCAAAGGTTATTGCCGCTGGTCGTCGCTTT 21 190 1 TTGCCGCTGG 0.759633 -111 GGGGTAATTTGTGACAAAGAAT 24 14 1 GTGACAAAGA 0.693387 -12 ********** Masking position 5 Map Score: 6.4305 Number of sites scoring better than the average of aligned sites = 1797 Number in coding regions = 1612 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 6 CAAGCTCAATGGGTTTGATTACTGCTGC 2 6 1 TCTGGGTTGA 0.938634 -99 GCTATCTCAGTCAGAGGAAATTACGATTTGCTC 3 42 0 TCAGGAATTA 0.892429 -67 TATCGCTCTCTCCCAGGCTATGGGGAAGGATTT 9 23 0 TCAGGCATGG 0.957798 -79 AAAATTAAGTTCACAGGAGATGGAATTTTCACT 10 35 0 TCAGGAATGG 0.971215 -34 CCCATTAACATCCAAGGAAATTACT 11 25 1 TCAGGAATTA 0.892465 -15 TGGTAGATTCTCCTAAGGGATGATGATTCAGGT 13 60 0 TCAAGGATGA 0.914419 -32 ATTTACAGGGTCTCTGGGCTTGGTCAGAGAGTA 14 81 0 TCTGGGTTGG 0.910407 -26 TTGTTTTTATTCGTTGGAACTGAACT 18 17 1 TCTGGACTGA 0.913466 -16 AATTAGTTATTCACTGGCTATGAAGCTGTTGAC 21 158 1 TCTGGCATGA 0.947019 -143 CTCATTTCCTTCTGTAGAGATGACGCACATACA 22 268 0 TCTAGAATGA 0.874751 -33 AATCACCTTATCAGAGGGAATGATTATAATTTT 23 194 0 TCAGGGATGA 0.983333 -29 ** **** **** Masking position 11 Map Score: 9.20316 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 341 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 TTAGGAGTTCAGTTACCATGCGACACAGAT 2 71 1 AGTTACCATG 0.946585 -34 TTCTCCTAGTGATTACCATTCCGGTCTGTC 5 14 1 GATTACCATT 0.837654 -69 AATTATAACAAGTTATCGTGGCCGTGTCAT 6 85 0 AGTTATCGTG 0.842263 -53 GAAGGATTTTGGTTACCATTG 9 2 0 GGTTACCATT 0.97089 -100 TAATGGGTTTGGTTAACGTTG 11 2 0 GGTTAACGTT 0.9095 -38 TTAGGTAGAGGGTTACCGTGTCTATCGGTA 21 261 1 GGTTACCGTG 0.988019 -40 ********** Masking position 5 Map Score: 0.956471 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 178 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 AAAAATTAACAACAGGGGGTTACTCTAAGG 2 42 0 AACAGGGGGT 0.921785 -63 GGGATGATGATTCAGGTGGATTGATGGAGA 13 47 0 TTCAGGTGGA 0.826784 -45 ACATAGGCACAAAAGGGGGATGACCGCAAT 21 48 0 AAAAGGGGGA 0.964894 -253 ATGTAAAGAGAAAAGGAGGATAGAGGGAAA 22 155 1 AAAAGGAGGA 0.945887 -146 ACCCTCTACGATAAGAAGGAGAGTGTACAA 22 212 0 ATAAGAAGGA 0.86666 -89 GCGTCATCTCTACAGAAGGAAATGAGAGAA 22 275 1 TACAGAAGGA 0.883777 -26 AAATCACCTTATCAGAGGGAATGATTATAA 23 198 0 ATCAGAGGGA 0.954768 -25 ********** Masking position 4 Map Score: 0.622113 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 332 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 CAGGGGGTTACTCTAAGGCAAGCAGCAGTAA 2 29 0 CTCTAAGCAA 0.966258 -76 TTTATTGAAGCTTTCAAGCAATCATTATGGC 4 33 1 CTTTCAGCAA 0.730503 -76 TTATCGCTCTCTCCCAGGCTATGGGGAAGGA 9 26 0 CTCCCAGCTA 0.935991 -76 TCACCTTTGCCCCGCAAGCAATGCTAGACCC 14 17 1 CCCGCAGCAA 0.935919 -90 CAATGCTAGACCCTAACCCGATGTGCTCGAG 14 35 1 CCCTAACCGA 0.729977 -72 GACTAACTCTCCCTACCGCTAGGGCCGAAGG 21 80 1 CCCTACGCTA 0.759239 -221 CGAAGGTGGTCTCTCAAGCAAAGCTTGATTG 21 105 1 CTCTCAGCAA 0.968775 -196 GCTTTCGTATCGCCAATGCAACATGTTCTAC 22 43 0 CGCCAAGCAA 0.930943 -258 TCTTGAATCCCTCCATAGCAATCAGTGCTTT 22 69 0 CTCCATGCAA 0.8532 -232 GACAGGCACACCCCAAAGCGATTCTGCACTG 22 115 0 CCCCAAGCGA 0.96413 -186 ****** **** Masking position 11 Map Score: 2.9355 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 641 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 10 ********** No masking Map Score: 6.96575e-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 11 ********** No masking Map Score: 6.96575e-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 12 ********** No masking Map Score: 6.96575e-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