AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i300_synecho_ctra_100.orf -o300_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 RCY43837 121 Synechocystis #2 RCY26609 38 Synechocystis #3 RCY32578 235 Synechocystis #4 RCT00316 275 Chlamydia_trachomatis #5 RCT00598 55 Chlamydia_trachomatis #6 RCT00599 52 Chlamydia_trachomatis #7 RCT00600 178 Chlamydia_trachomatis Motif number 1 AAGGCACTACTGAACCTTTGACAGTTCGCT 1 79 1 TGAACCTTTG 0.983555 -43 AAAACCTTTGCCAACATTGA 1 112 0 AAAACCTTTG 0.97909 -10 AAACATTCGGTGAACCAATGATGAATCCCC 3 103 0 TGAACCAATG 0.896937 -133 TCTCACACTTTAACCCATTGGGTGAAGGGA 3 168 0 TAACCCATTG 0.962227 -68 CTACTGCGACAGAACCATCGGGGTTTAATT 4 207 0 AGAACCATCG 0.933239 -69 GAAACAACCTTTGTCAAACAAAG 5 4 1 ACAACCTTTG 0.986614 -52 CTTTTTCTCATCAACCTTTGTTTGACAAAG 5 19 0 TCAACCTTTG 0.98356 -37 AGGTATTTAAACACCCTCTGGGGTT 6 6 0 ACACCCTCTG 0.941687 -47 ATAAATAAACCCATTGAACTATTAGA 7 163 0 AAACCCATTG 0.969121 -16 ********** Masking position 3 Map Score: 12.2794 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 296 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 CGTTAGTTAAACTTCTGCCAATTGTGCAAGT 1 35 0 ACTTCTGCAA 0.97836 -87 GCACTACTGAACCTTTGACAGTTCGCTCTTT 1 82 1 ACCTTTGCAG 0.983699 -40 AAAACCTTTGCCAACATTGAAAGA 1 108 0 ACCTTTGCAA 0.990704 -14 AAATTATGGAACTTTTTTCAGACTTCTCACA 3 191 0 ACTTTTTCAG 0.936995 -45 CGCAGTAGATACTTCAGGCAATCCCATTAAG 4 229 1 ACTTCAGCAA 0.943024 -47 GAAACAACCTTTGTCAAACAAAGGTTG 5 7 1 ACCTTTGCAA 0.990704 -49 CAACAAAAATAGTTTTTTCAAAGAGCCTCAG 7 122 0 AGTTTTTCAA 0.812968 -57 CTATTAGATTACCTAATACAACAAAAATAGT 7 140 0 ACCTAATCAA 0.790014 -39 ******* *** Masking position 10 Map Score: 7.55622 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 306 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 GCGAATTTGTTAAAGGCACTACTGAACCTT 1 67 1 TAAAGGCACT 0.8927 -55 CCCTACCTGTAAAATGGGCTCTAG 2 25 1 AAAATGGGCT 0.905462 -14 CTGTAAAACCAGAAGGCGCTGTATAACGGT 4 56 0 AGAAGGCGCT 0.996624 -220 CTGGTTTTACAGAAGGCGCTTGAGGACTGT 4 74 1 AGAAGGCGCT 0.996624 -202 GATGAGAAAAAGAAGGCAGTTGCTTAGAT 5 37 1 AGAAGGCAGT 0.95813 -19 GATAAAGCAGAGAATGAGCTGTTTATCACA 7 40 1 AGAATGAGCT 0.950307 -139 ********** Masking position 4 Map Score: 5.08811 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 66 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 TTCGCCCGTTAGTTAAACTTCTGCCAATTGTGCAAG 1 36 0 AGTAATTCCA 0.819654 -86 AACAAAGATTACTAAAGATTTACCCCCAGTTCTCTG 3 22 0 ACTAATTCCC 0.94503 -214 ATGACATCTTCGCTACCCTTTTCCCCAGCCTTCTCA 3 65 1 CGCACTTCCC 0.975245 -171 CATTCGGTGAACCAATGATGAATCCCCATTGAGAAG 3 94 0 ACCATTGCCC 0.917463 -142 TCATTGGTTCACCGAATGTTTTGTCCAGACTGTGAC 3 112 1 ACCAATTTCC 0.94503 -124 TTTTCAGACTTCTCACACTTTAACCCATTGGGTGAA 3 172 0 TCTACTTCCC 0.793259 -64 TCCATAATTTAGCCATCGTTAGTCCCAATCCACC 3 212 1 AGCATTTCCC 0.989185 -24 CCTCATAGATAGCCAAGATAGCTTCCACGGAATGAC 4 102 0 AGCAATATCC 0.805865 -174 CTGAGTTTTCAGCTACAATTAAACCCCGATGGTTCT 4 191 1 AGCACTTCCC 0.99473 -85 AATCCCATTAAGCATCCTTTTATCCCTGGGGAATCT 4 248 1 AGCTCTTCCC 0.960004 -28 TTAAATACCTAGCTATGCTTGTATCAGGAGCTTAGT 6 26 1 AGCATTTTCA 0.777303 -27 *** ** ** *** Masking position 9 Map Score: 7.02118 Number of sites scoring better than the average of aligned sites = 1500 Number in coding regions = 1334 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 5 TGGCTCTACTTGCTTGCGGAACTTGCACAA 1 15 1 TGCTTGCGGA 0.832496 -107 CCCATTGAGAAGGCTGGGGAAAAGGGTAGC 3 76 0 AGGCTGGGGA 0.807494 -160 CCCAGCCTTCTCAATGGGGATTCATCATTG 3 88 1 TCAATGGGGA 0.918511 -148 GTCCAGACTGTGACTGGGGTTTTCCAACCT 3 134 1 TGACTGGGGT 0.924896 -102 CACACTTTAACCCATTGGGTGAAGGGAAGT 3 165 0 CCCATTGGGT 0.785247 -71 GGTGGATTGGGACTAACGATGG 3 224 0 TGGATTGGGA 0.872055 -12 CCAGATGACTTGCTTCGGGTACCGAGATTT 4 24 0 TGCTTCGGGT 0.853888 -252 TTACAGAAGGCGCTTGAGGACTGTCATTCC 4 80 1 CGCTTGAGGA 0.860489 -196 ATCTTGGCTATCTATGAGGAAATGTTTTCT 4 119 1 TCTATGAGGA 0.871527 -157 CATCCTTTTATCCCTGGGGAATCTGT 4 260 1 TCCCTGGGGA 0.955593 -16 ATTTAAACACCCTCTGGGGTT 6 2 0 CCTCTGGGGT 0.890591 -51 TAGCTATGCTTGTATCAGGAGCTTAGTT 6 35 1 TGTATCAGGA 0.741105 -18 CTATTTTTGTTGTATTAGGTAATCTAATAG 7 141 1 TGTATTAGGT 0.628866 -38 ********** Masking position 5 Map Score: 6.24379 Number of sites scoring better than the average of aligned sites = 3356 Number in coding regions = 2985 Number in noncoding regions = 371 Number of orfs with sites within 600 bp upstream = 383 Fraction of orfs with sites within 600 bp upstream = 0.0615162 Motif number 6 CCAACATTGAAAGAGCGAACTGTCAAAGGT 1 92 0 AAGAGCGAAC 0.863767 -30 GGCTACTACAGCAGAGAACTGGGGGTAAA 3 10 1 AGCAGAGAAC 0.987701 -226 AGTCACAGTCTGGACAAAACATTCGGTGAA 3 119 0 TGGACAAAAC 0.787689 -117 CTTCTTGAATAAGAGAAAACATTTCCTCAT 4 132 0 AAGAGAAAAC 0.954706 -144 TTATTCAAGAAGGAGAAACCAATTTGAACC 4 150 1 AGGAGAAACC 0.947515 -126 GTTTAATTGTAGCTGAAAACTCAGCTGTTC 4 185 0 AGCTGAAAAC 0.907695 -91 ACAAAGGTTGATGAGAAAAAGAAGGCAGTT 5 28 1 ATGAGAAAAA 0.701829 -28 AACTAGATAAAGCAGAGAATGAGCTGTTTA 7 35 1 AGCAGAGAAT 0.899681 -144 TGAGCTGTTTATCACAGAACAAGTGTAGTC 7 54 1 ATCACAGAAC 0.869673 -125 ********** Masking position 8 Map Score: 2.83333 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 502 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 7 GGCTACTACAGCAGAGAACTGGGGGT 3 7 1 TACAGCAGAG 0.992362 -229 AACCATGTCGAACAGCTGAGTTTTCAGCTA 4 176 1 AACAGCTGAG 0.979687 -100 AACCCCAGAGGGTGTTTAAA 6 1 1 AACCCCAGAG 0.966684 -52 AAAAACTAGATAAAGCAGAGAATGAGCTGT 7 32 1 TAAAGCAGAG 0.970904 -147 ********** Masking position 2 Map Score: 0.828084 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 26 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: -1.29786e-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 9 ********** No masking Map Score: -1.29786e-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 10 ********** No masking Map Score: -1.29786e-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