AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_synecho_ctra_100.orf -o320_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 RCY50998 180 Synechocystis #2 RCY24801 300 Synechocystis #3 RCY46934 166 Synechocystis #4 RCT00475 159 Chlamydia_trachomatis #5 RCT00517 300 Chlamydia_trachomatis Motif number 1 TGAACAGCAGGAGTTAGGGGTGAGAAGTAAGCGTTAAATGGGA 1 70 0 GGAGGAGGGG 0.999094 -111 CTTGCATGGCATGCAAGGGGTCAGCGGTTCGAGCCCGCTTAGC 2 18 0 AGAGGAGGGG 0.998834 -283 CTGTGACTCGGGGCTATAGCTCAGTTGGTAGAGCACTTGCATG 2 53 0 GGAAGAGGGG 0.99724 -248 CATCTGCACCAAGAAAAGGCTTAGGCTATATTGACTAGGAAAA 3 55 0 AGAGGAGTTG 0.964934 -112 TTTCGTTTCTATGGAAGAGATGACTCGCTTGTGCGTGCTATGG 4 95 1 AGAAGACGGG 0.976068 -65 TCGCTTGTGCGTGCTATGGCACAGGAGAAAGAGAGGCAAAAAG 4 119 1 GGAGGAGGGG 0.999094 -41 TTGCTGTGTAAAGAGAGGGAGTAGGGGTGAGGATGCGGCGTAT 5 79 1 AGAGGAGGGA 0.98823 -222 CGTATTGTGGATGGATAAGCGGAGAGTAAGGTGTGTCAAATAA 5 117 1 AGTAGAGTGG 0.935494 -184 AAATAATAGAGAGAAAAGGAGCAGGTTTTCGAGTAGTCCTGAA 5 163 1 GGAGGAGTGG 0.99724 -138 * * * ** ** * * * Masking position 13 Map Score: 15.5589 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 168 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 TCACCCCTAACTCCTGCTGTTCAACGAAATTTTGCTT 1 90 1 CCCTGTAAGA 0.98842 -91 ACCACCCTGGCGATCGCTGTTCCAGAACCCTAGGGGA 2 163 0 CTCTGTCAAA 0.9709 -138 CCTCCTTTTGCTTTTTCTGTTAAAAAAACTTAACAAT 2 269 0 CTCTGTAAAA 0.983311 -32 CCCTGGCGATCGGCATCTGCACCAAGAAAAGGCTTAG 3 74 0 CCCTGCCAGA 0.979328 -93 AGTTCGGCTCAGTTCCTGTCAAACAAATACGTTCCT 3 141 0 CTCTGTAAAA 0.983311 -26 GCATTTTCAGAAATACCTGCGAAAGGATCCCTGATTT 4 11 0 ATCTGCAAGA 0.942852 -149 GAAGACAATACGTTTGCTGTGTAAAGAGAGGGAGTAG 5 66 1 CTCTGTAAGA 0.993409 -235 TTTTAAAGTTCTTTTTTTGCGCAAAGAACGAGACCAC 5 226 0 CTTTGCAAGA 0.942849 -75 * * **** ** ** Masking position 14 Map Score: 6.69372 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 105 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 CACTTGCATGGCATGCAAGGGGTCAGCGGTT 2 32 0 GCATGCAGGG 0.963295 -269 CGCTGTTCCAGAACCCTAGGGGAAAAGAAGA 2 155 0 GAACCCAGGG 0.991074 -146 CTGGAACAGCGATCGCCAGGGTGGTTTTCCC 2 175 1 GATCGCAGGG 0.997483 -126 AACCAGCCCCCATCGATAGGGGAAAACCACC 2 194 0 CATCGAAGGG 0.933592 -107 TGCAGATGCCGATCGCCAGGGAGCAATGGGT 3 90 1 GATCGCAGGG 0.997483 -77 AACCTTAGCGGATTCCGAGGACCCATTGCTC 3 110 0 GATTCCAGGA 0.91546 -57 ****** **** Masking position 8 Map Score: 5.18573 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 641 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 TCACCCCTAACTCCTGCTGTTCAACGAAAT 1 90 1 CTCCTGCTGT 0.928572 -91 TATCCTTGATCTTCTTTTCCCCTAGGGTTC 2 146 1 CTTCTTTTCC 0.947688 -155 GGCAACCTCCTTTTGCTTTTTCTGTT 2 285 0 CTCCTTTTGC 0.987532 -16 CTTTTTGCCTCTCTTTCTCCTGTGCCATAG 4 132 0 CTCTTTCTCC 0.968098 -28 CTCACCCCTACTCCCTCTCTTTACACAGCA 5 80 0 CTCCCTCTCT 0.928572 -221 CGAAAACCTGCTCCTTTTCTCTCTATTATT 5 164 0 CTCCTTTTCT 0.980367 -137 GTCCTGAAAACTCTTTTGGTGTAACATGGT 5 198 1 CTCTTTTGGT 0.838302 -103 TTTTAAAGTTCTTTTTTTGCGCAAAGAACG 5 233 0 CTTTTTTTGC 0.876258 -68 ********** Masking position 2 Map Score: 5.01562 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 533 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 GCTAATTGCTGAACCCGCTCCGACTCCCATTT 1 46 1 GAACCGCTCG 0.990464 -135 CCGCAATAATGAGTACGCATAGAGGTGTTAAT 1 128 0 GAGACGCAAG 0.974412 -53 TCAGCGGTTCGAGCCCGCTTAGCTCCATTT 2 9 0 GAGCCGCTAG 0.994664 -292 TCTGCACCAAGAAAAGGCTTAGGCTATATTGA 3 64 0 GAAAGGCTAG 0.973192 -103 TGGGTCCTCGGAATCCGCTAAGGTTAGGAACG 3 116 1 GAACCGCTAG 0.993563 -51 AGGTATTTCTGAAAATGCTGAGCTAAGTTATA 4 30 1 GAAATGCTAG 0.977371 -130 GAGTAGGGGTGAGGATGCGGCGTATTGTGGAT 5 97 1 GAGATGCGCG 0.92771 -204 *** ***** ** Masking position 2 Map Score: 7.07201 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 18 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 AGAGGTGTTAATCAAGCAAAATTTCGTTGAAC 1 108 0 ATCAGAAAAT 0.977908 -73 GGAAAAGAAGATCAAGGATAATTTTGGTAAAA 2 134 0 ATCAGATAAT 0.966975 -167 GGGGCTGGTTACCATTCATAATCCCGATGCCC 2 215 1 ACCATATAAT 0.760302 -86 CGATGCCCAAACCATGTAAAATACAGGGTGAT 2 239 1 ACCAGAAAAT 0.979758 -62 GGCTATATTGACTAGGAAAAATCCCCAGATAG 3 43 0 ACTAGAAAAT 0.917162 -124 AAATCAGGGATCCTTTCGCAGGTA 4 3 1 ATCAGATCCT 0.822474 -157 TCTAAAAGCTATTAAGCTAAATGAAAGGAGTA 5 36 0 ATTAGTAAAT 0.641261 -265 AAAAGGTGAGATCACGAAACATTTTTCGTGAG 5 260 1 ATCAGAACAT 0.965489 -41 **** * ***** Masking position 4 Map Score: 2.54062 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 225 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 AGCGGGTTCAGCAATTAGCCACTCAACACT 1 35 0 GCAATTAGCC 0.94539 -146 GCTTTTTACCAAAATTATCCTTGATCTTCT 2 131 1 AAAATTATCC 0.829605 -170 TCGATAGGGGAAAACCACCCTGGCGATCGC 2 183 0 AAAACCACCC 0.970222 -118 ATTATGAATGGTAACCAGCCCCCATCGATA 2 207 0 GTAACCAGCC 0.939657 -94 AAAAAACTTAACAATCACCCTGTATTTTAC 2 254 0 ACAATCACCC 0.976972 -47 AATTGTGTTGAAAATCAGCCTCATTTCGTT 4 72 1 AAAATCAGCC 0.982832 -88 ********** Masking position 4 Map Score: 1.41479 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 240 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 TGTTTAGCAATTTAGTGTTGAGTGGCTAATTGCTG 1 22 1 TTGTGTGTGG 0.988474 -159 GGGGTGAGAAGTAAGCGTTAAATGGGAGTCGGAGC 1 62 0 GTGCGTATGG 0.983339 -119 CAGTATTCTATTGTGCTGAAAGTGGTGCCCATTGT 2 93 1 TTGCTGGTGG 0.934883 -208 GATGACTCGCTTGTGCGTGCTATGGCACAGGAGAA 4 113 1 TTGCGTATGG 0.993843 -47 GGGGTGAGGATGCGGCGTATTGTGGATGGATAAGC 5 102 1 TGGCGTGTGG 0.98934 -199 TGAAAACTCTTTTGGTGTAACATGGTGGTCTCGTT 5 202 1 TTGTGTATGG 0.981995 -99 ** **** **** Masking position 13 Map Score: 1.88766 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 85 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AAATTGCTAAACACCAAACCTTAG 1 5 0 ACACCAAACC 0.960804 -176 GGGTTCTGGAACAGCGATCGCCAGGGTGGT 2 170 1 ACAGCGATCG 0.945096 -131 AGTTTTTTTAACAGAAAAAGCAAAAGGAGG 2 276 1 ACAGAAAAAG 0.914473 -25 CTCTCTTTACACAGCAAACGTATTGTCTTC 5 66 0 ACAGCAAACG 0.992109 -235 CCACCATGTTACACCAAAAGAGTTTTCAGG 5 200 0 ACACCAAAAG 0.974559 -101 ********** Masking position 7 Map Score: 1.18741 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 82 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 TTTAGCAATTTAGTGTTGAGTGGCTAATTG 1 24 1 TAGTGTTGAG 0.975352 -157 CAGCAGGAGTTAGGGGTGAGAAGTAAGCGT 1 79 0 TAGGGGTGAG 0.980674 -102 CAGTATTCTATTGTGCTGAAAGTGGTGCCC 2 93 1 TTGTGCTGAA 0.954194 -208 TTTCTTACAATTGTGTTGAAAATCAGCCTC 4 64 1 TTGTGTTGAA 0.930973 -96 AGAGAGGGAGTAGGGGTGAGGATGCGGCGT 5 90 1 TAGGGGTGAG 0.980674 -211 GGTTTTCGAGTAGTCCTGAAAACTCTTTTG 5 186 1 TAGTCCTGAA 0.899244 -115 ********** Masking position 7 Map Score: 4.11475 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 101 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 ********** No masking Map Score: 2.37564e-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: 2.37564e-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 13 ********** No masking Map Score: 2.37564e-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