AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_synecho_ctra_100.orf -o047_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 RCY16635 290 Synechocystis #2 RCY06400 56 Synechocystis #3 RCY28245 63 Synechocystis #4 RCY37471 66 Synechocystis #5 RCY24448 85 Synechocystis #6 RCY05831 277 Synechocystis #7 RCY50309 68 Synechocystis #8 RCY54010 66 Synechocystis #9 RCY22900 17 Synechocystis #10 RCY19565 32 Synechocystis #11 RCT00174 300 Chlamydia_trachomatis #12 RCT00382 165 Chlamydia_trachomatis Motif number 1 ATCAACGGCTTGGTGTAGTAAATGCGGGATTT 1 25 0 TGGTGTGAAA 0.941377 -266 TGCATGGTAGTGGGGAGGCGAACGATCATTCT 1 112 0 TGGGGAGGAA 0.903909 -179 AAATCGAAACAGGTGTAGTGAATGGGTCATTT 1 172 1 AGGTGTGGAA 0.947193 -119 TATTAACTCGGGTTGATGTAAATCATGCCATT 1 232 0 GGTTGAGAAA 0.831837 -59 GACAACACGCGGGTGTAGTTTAGTGGTAAAAC 6 68 1 GGGTGTGTTA 0.827138 -210 TACCCAAAGCGGGTGAGGGGAATCGAACCCCT 6 122 0 GGGTGAGGAA 0.991749 -156 CACCCGCTTTGGGTAATGGGTACAGCGGTCTC 6 139 1 GGGTAAGGTA 0.924723 -139 GGTCGAGGAGGGGTGTCGCAACGGACATCAGG 6 209 0 GGGTGTGAAC 0.910912 -69 GGATAATTTTTGGGGATGCAAACTGATTGACT 8 12 1 TGGGGAGAAA 0.854593 -55 TTTCCCTGGGTAATGGAAAGGGTAGGCTT 10 8 1 GGGTAAGAAA 0.955728 -25 GAAACGCGGGAGGTGTCGAATATAGGAACGAA 11 78 0 AGGTGTGATA 0.799372 -223 TTCCAAACGAGGGTATCCCGAAGGATCGCATA 12 44 0 GGGTATCGAA 0.744347 -122 AAGGCTACTTGGGTAAAGAGGACGAAGAGTCT 12 74 1 GGGTAAGGGA 0.878133 -92 ****** * *** Masking position 2 Map Score: 10.0025 Number of sites scoring better than the average of aligned sites = 1274 Number in coding regions = 1127 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 2 TTAAAGGGCTTTTTTTCTCT 3 1 1 TTAAAGGGCT 0.798451 -63 TTGTTGTAAGGTTTCTATCAGAA 3 51 0 TTGTAAGGTT 0.891538 -13 GTGTACAAAATGAACAGGTTTAA 4 54 1 TGAACAGGTT 0.730774 -13 TATCATTAGCTTGGAAGGCTAAGGTTTTAC 6 93 0 TTGGAAGGCT 0.953491 -185 TCCAAGCTAATGATAGGGGTTCGATTCCCC 6 108 1 TGATAGGGGT 0.901987 -170 CCCTGGGTAATGGAAAGGGTAGGCTTAGA 10 14 1 TGGAAAGGGT 0.95878 -19 AGAGAGCCTATGAGAAGGCTTGTAAATATC 11 49 0 TGAGAAGGCT 0.953491 -252 CTTGTTAGGATGGTCGGGTTCTGTGTACTA 11 194 1 TGGTCGGGTT 0.855006 -107 TGAATATGTTTGGTAAGGGCCTACTGTATA 11 238 1 TGGTAAGGGC 0.863319 -63 ATACCCTCGTTTGGAAGGCTACTTGGGTAA 12 60 1 TTGGAAGGCT 0.953491 -106 ********** Masking position 1 Map Score: 4.91027 Number of sites scoring better than the average of aligned sites = 687 Number in coding regions = 584 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 GTGGGGAGGCGAACGATCATTCTAGTACAT 1 105 0 GAACGATCAT 0.880341 -186 TCATTTCAATTAACGATGAGAGAATTTAAT 4 11 1 TAACGATGAG 0.933669 -56 CGGACATCAGGGACGATCAGAAATTATCAA 6 190 0 GGACGATCAG 0.986804 -88 CATGGATGACGGTCGAGGAGGGGTGTCGCA 6 221 0 GGTCGAGGAG 0.953925 -57 TCGAATATAGGAACGAAGAGAGCCTATGAG 11 65 0 GAACGAAGAG 0.984496 -236 TGGGTAAAGAGGACGAAGAGTCTGTCTCAG 12 83 1 GGACGAAGAG 0.990084 -83 ********** Masking position 6 Map Score: 3.68981 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 52 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 TTTAATGTAAAATTATGGAGTGTACAAAAT 4 35 1 AATTATGGAG 0.923447 -32 TTGCGGAACAAAATATGCAGTAGCAGTTAG 5 50 1 AAATATGCAG 0.734457 -36 TATCAATCAAAATTATCGAGTTTCGGAGAC 6 166 0 AATTATCGAG 0.959029 -112 AGAACCGAGGAATTATCGAGGGAGCATGGA 6 245 0 AATTATCGAG 0.959029 -33 CTAATAATCTCGCAACAATGGC 7 3 1 AATAATCTCG 0.733021 -66 ATAATCTCGCAACAATGGCGGGGCAAAATA 7 14 1 AACAATGGCG 0.811324 -55 TTGACTAAAGAAAAATTGAGCACCATAGCA 8 38 1 AAAAATTGAG 0.752239 -29 GAAGGCTTGTAAATATCTAGAAGTGTATGA 11 36 0 AAATATCTAG 0.864598 -265 GGAGATCGTTAACAATCAAGATTATTCACA 11 165 0 AACAATCAAG 0.841112 -136 ATAAAACATTAAAAATCAAGTTTCAAAACT 12 15 0 AAAAATCAAG 0.864598 -151 ********** Masking position 5 Map Score: 3.99233 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 322 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 ATTTACTACACCAAGCCGTTGATCGCCATA 1 34 1 CCAAGCCGTT 0.837255 -257 TCTCTTTATAACTATCGTTCAACACTTCTG 3 26 1 ACTATCGTTC 0.733539 -38 ACATATTTTGCCTAGACTTTTGTCAGGAGA 6 20 0 CCTAGACTTT 0.872301 -258 CGCGTGTTGTCCTAGCGTTTTTAAGACTAA 6 49 0 CCTAGCGTTT 0.961017 -229 GTGGTAAAACCTTAGCCTTCCAAGCTAATG 6 90 1 CTTAGCCTTC 0.938603 -188 TCTAAGCCTACCCTTTCCATTACCCA 10 17 0 CCTACCCTTT 0.920207 -16 CTAGATATTTACAAGCCTTCTCATAGGCTC 11 46 1 ACAAGCCTTC 0.956555 -255 TCACAGAGCTACTAGCTTTCTTAACTTATT 11 140 0 ACTAGCTTTC 0.900376 -161 TCTTTACCCAAGTAGCCTTCCAAACGAGGG 12 63 0 AGTAGCCTTC 0.920207 -103 ********** Masking position 4 Map Score: 3.21024 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 452 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 6 AAATCCCGCATTTACTACACCAAGCCGTTG 1 25 1 TTTACTACAC 0.968908 -266 GAACGATCATTCTAGTACATGCAGATTGTG 1 95 0 TCTAGTACAT 0.90375 -196 AAATGACCCATTCACTACACCTGTTTCGAT 1 174 0 TTCACTACAC 0.933502 -117 AACCTGTTCATTTTGTACACTCCATAATTT 4 44 0 TTTTGTACAC 0.932416 -23 TGACTAGGGATCTAGTACACAGAACCCGAC 11 206 0 TCTAGTACAC 0.98 -95 ********** Masking position 6 Map Score: 0.783429 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 13 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 ********** No masking Map Score: 3.07908e-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 8 ********** No masking Map Score: 3.07908e-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: 3.07908e-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