AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i298_synecho_ctra_100.orf -o298_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 RCY20391 256 Synechocystis #2 RCY49700 117 Synechocystis #3 RCT00023 187 Chlamydia_trachomatis #4 RCT00025 59 Chlamydia_trachomatis #5 RCT00028 25 Chlamydia_trachomatis #6 RCT00029 63 Chlamydia_trachomatis #7 RCT00748 194 Chlamydia_trachomatis Motif number 1 GCCCATTTAGTCTCCCCTTACCC 1 3 0 TCTCCCTTAC 0.819218 -254 TTCAGTTTGGCTCGACTTTTTAGTAAGCACA 1 133 0 CTCGCTTTTT 0.768781 -124 TGCTATCTAGCCCCTGTTTTTGCTTGTTAAT 1 191 1 CCCCGTTTTT 0.849094 -66 TGCCCCCGTAGTTGACTTTTTCTGTACCT 2 99 1 GTTGCTTTTT 0.656435 -19 GGGGTGTTCGCCCCGCTTTTCTCTAGATAAC 3 28 0 CCCCCTTTTC 0.987598 -160 GGGGCGAACACCCCGCTTTTTTTGTTTTAAT 3 45 1 CCCCCTTTTT 0.982946 -143 TTTTAATAAGTCTCTCTTTTTGAATCTGACT 3 69 1 TCTCCTTTTT 0.983191 -119 TCTTTTTGAATCTGACTTTTCAGAGTAAAGT 3 83 1 TCTGCTTTTC 0.973576 -105 AACGACTTCTTCTGCCTTTACTCTAGTATCT 3 166 0 TCTGCTTTAC 0.929074 -22 AATATTTTCTCCTCACTTTTTACCGCAAAGA 4 37 1 CCTCCTTTTT 0.98742 -23 GCTTAATGCCGCTCTCTTTTCTTTA 6 5 0 GCTCCTTTTC 0.978614 -59 CTCATAATTTTCTCTCTTTGTTTAATTGTAA 7 45 1 TCTCCTTTGT 0.924232 -150 CGGAACAATGTCTCTCTTTACAACCTGTGCA 7 160 1 TCTCCTTTAC 0.966365 -35 **** ****** Masking position 8 Map Score: 19.6376 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 492 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 GGGTAAGGGGAGACTAAATGGGC 1 4 1 TAAGGGGAGA 0.803634 -253 AACGAAGCGCTCCGGGGAAAAGATCCGTTA 1 75 0 TCCGGGGAAA 0.970231 -182 ATAGCAATATAGCTGGGCAATACTGGGTGG 1 167 0 AGCTGGGCAA 0.909393 -90 ACAAGCAAAAACAGGGGCTAGATAGCAATA 1 188 0 ACAGGGGCTA 0.930608 -69 GTTAATTCCTTCGGGGGTTACTCATAATTA 1 216 1 TCGGGGGTTA 0.858794 -41 CACAAGTTTCTGGTGGGGAAGGATTTAAAC 2 43 0 TGGTGGGGAA 0.781828 -75 GGCAATGGGGTGAGGGGCGACAGCGGTGGC 2 73 0 TGAGGGGCGA 0.987763 -45 AAAGTCAACTACGGGGGCAATGGGGTGAGG 2 88 0 ACGGGGGCAA 0.973841 -30 TCTAGAGAAAAGCGGGGCGAACACCCCGCT 3 32 1 AGCGGGGCGA 0.991394 -156 AAACAAAAAAAGCGGGGTGTTCGCCCCGCT 3 42 0 AGCGGGGTGT 0.784477 -146 CGGTAAAAAGTGAGGAGAAAATATTAGATA 4 32 0 TGAGGAGAAA 0.733259 -28 GAGACATTGTTCCGGAGGGATAAGGTTATC 7 144 0 TCCGGAGGGA 0.886302 -51 ********** Masking position 5 Map Score: 9.39673 Number of sites scoring better than the average of aligned sites = 4299 Number in coding regions = 3868 Number in noncoding regions = 431 Number of orfs with sites within 600 bp upstream = 415 Fraction of orfs with sites within 600 bp upstream = 0.066656 Motif number 3 TAAATGGGCTAATCTTTAAGAAAAGTTTAC 1 25 1 AATCTTTAAG 0.854972 -232 AGTATTTGAGGATTTTAAGGTTGTGCTTAC 1 112 1 GATTTTAAGG 0.883454 -145 TTTTTTCATTAATCTTTGGGCTGGTTATGG 2 11 1 AATCTTTGGG 0.978731 -107 ATTGGCAATCAATTTTTGGGGAACACTAGA 3 113 0 AATTTTTGGG 0.985588 -75 AATATTAGATAATTTTTGCGATAAAGAACT 4 13 0 AATTTTTGCG 0.940048 -47 AAAAAGAATTTTTAGGTGAAATACA 5 7 1 AATTTTTAGG 0.982648 -19 CTCTTTGTTTAATTGTAAGGAATTGCTTTA 7 58 1 AATTGTAAGG 0.883454 -137 ********** Masking position 2 Map Score: 5.7041 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 367 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 CGGATGTAAATTCCTAGGGTAACGGATCTTT 1 56 1 TTCTAGGGTA 0.972287 -201 GAGCGCTTCGTTCCTAGGGAGTATTTGAGGA 1 93 1 TTCTAGGGAG 0.983363 -164 AACTTTCTGTTATCTAGAGAAAAGCGGGGCG 3 20 1 TACTAGAGAA 0.876574 -168 TGAATCTGACTTTTCAGAGTAAAGTCTAGTG 3 89 1 TTTCAGAGTA 0.804572 -99 TGGCAATCAATTTTTGGGGAACACTAGACTT 3 110 0 TTTTGGGGAA 0.913117 -78 ACTCTGGTCTTTGTTAGAGAGATACTAGAGT 3 147 1 TTTTAGAGAG 0.960808 -41 TGTTAGAGAGATACTAGAGTAAAGGCAGAAG 3 158 1 ATCTAGAGTA 0.815919 -30 GAGAAACTGGTTATTAGGGAGCTTGCTCATC 7 17 0 TTTTAGGGAG 0.974922 -178 ** ******** Masking position 7 Map Score: 4.27379 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 307 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 CAGCGGTGGCCACAAGTTTCTGGTGGGGAAG 2 52 0 CACAATTTCT 0.923266 -66 TTTGAACAGAACTTTCTGTTATCTAGA 3 7 1 CAGAATTTCT 0.958171 -181 TTTTTGTTTTAATAAGTCTCTCTTTTTGAAT 3 63 1 AATAATCTCT 0.868495 -125 GTACATTGGCAATCAATTTTTGGGGAACACT 3 116 0 AATCATTTTT 0.722381 -72 GAGCGGCATTAAGCCCTTTCTGCTGTTCTCA 6 22 1 AAGCCTTTCT 0.927618 -42 ATAAAGGCAATCTCTTGACGTTGAG 6 49 0 AGGCATCTCT 0.862174 -15 GCTCCCTAATAACCAGTTTCTCATAATTTTC 7 26 1 AACCATTTCT 0.966255 -169 ACCAGTTTCTCATAATTTTCTCTCTTTGTTT 7 37 1 CATAATTTCT 0.91767 -158 AGGCTAGATAAAGCAATTCCTTACAATTAAA 7 65 0 AAGCATTCCT 0.921825 -130 ***** ***** Masking position 7 Map Score: 3.55779 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 425 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 GCTGTCGCCCCTCACCCCATTGCCCCCGTA 2 79 1 CTCACCCCAT 0.925758 -39 TTAGTTCTTTATCGCAAAAATTATCTA 4 8 1 TTTATCGCAA 0.959935 -52 CTCCTCACTTTTTACCGCAAAGAGG 4 45 1 TTTACCGCAA 0.962776 -15 AGGGAGCTTGCTCATCGCATGT 7 3 0 CTCATCGCAT 0.976003 -192 CCCAGACGAATTCATTGCAATCCACGCATC 7 112 0 TTCATTGCAA 0.911854 -83 ********** Masking position 4 Map Score: 0.083238 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 118 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 ********** No masking Map Score: -8.07587e-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 8 ********** No masking Map Score: -8.07587e-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 9 ********** No masking Map Score: -8.07587e-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