AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i182_synecho_ctra_300.orf -o182_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 RCY15119 104 Synechocystis #2 RCY05413 300 Synechocystis #3 RCY49636 271 Synechocystis #4 RCY36009 224 Synechocystis #5 RCY14921 295 Synechocystis #6 RCY19765 134 Synechocystis #7 RCY00557 221 Synechocystis #8 RCY19918 108 Synechocystis #9 RCT00385 300 Chlamydia_trachomatis #10 RCT00699 41 Chlamydia_trachomatis #11 RCT00700 109 Chlamydia_trachomatis Motif number 1 GACTCACCCCGAAGGAGACGAGTTGACCTAAG 2 65 0 GAGGAGAGAG 0.936802 -236 GGATGGGGGCCAGCGGAACCAGG 3 2 1 GTGGGGGCAG 0.983976 -270 TTTCTTCGTCGTAGGGGATGAATTTCTCTAAA 3 82 0 GAGGGGAGAA 0.973409 -190 AACTTAAGAAGCTGGAGGAAAATTGACAACGG 3 188 0 GTGGAGGAAA 0.966701 -84 AAACGTTCAAGGTGCAGAAAAGGAAAAAGTTA 3 221 0 GTGCAGAAAG 0.821485 -51 CAATGCCATGGCTGGAGGGAGAGTTGCAGCTC 4 155 0 GTGGAGGAGA 0.820752 -70 AATTGTGCCAGTTGGGGGCCAATGCCATGGCT 4 174 0 GTGGGGGCAA 0.983676 -51 GCTTTTCTTGGAAGAGGAGGAAGATGTCATAG 5 226 0 GAGAGGAGAA 0.742559 -70 ATTTATTGCCGAAGGGGGAAAAATAATTTCGT 5 272 0 GAGGGGGAAA 0.979028 -24 ATAGCGATGGGGGTGAGGGGGGAATTA 6 6 1 GTGGGGGGAG 0.987753 -129 GGGCCGAGTTGTTGCGGAAAAGGCGCTAGTGT 6 101 0 GTGCGGAAAG 0.920511 -34 TAGGGTCAGAGTAGGGGAGCAAACTGGAGACA 7 84 0 GAGGGGACAA 0.965362 -138 GTAAGCAGTAGTTGGAGAGAAAGAAGAGAAAT 7 176 0 GTGGAGAAAA 0.954572 -46 * ****** *** Masking position 7 Map Score: 16.7256 Number of sites scoring better than the average of aligned sites = 1565 Number in coding regions = 1412 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 GGGCTGTGGGGGATAGCCCCGAAAAACTCTG 1 51 1 GGATGCCCCG 0.943856 -54 GGTAATTAAGGACTCACCCCGAAGGAGACGA 2 76 0 GACTACCCCG 0.986724 -225 GCACATAGCCGGATTACCCAGAGGCGATCGC 2 151 0 GGATACCCAG 0.974247 -150 AATTGAGCAAGACTGTCCCCGGCTGAAATCC 2 261 0 GACTTCCCCG 0.953834 -40 AAGAAACCAAAGCCTTCCCAGAAAAGCTTTA 3 108 1 AGCCTCCCAG 0.871684 -164 CTTTGCCTTCGGTCAACCCCGGAAAACGGTC 4 56 0 GGTCACCCCG 0.98655 -169 TCCCTAACCTTGACCACCCCGAGCTGCAACT 4 135 1 TGACACCCCG 0.930634 -90 GTCATAGCAAGACCTACCCAGATTCGTATGA 5 202 0 GACCACCCAG 0.986724 -94 GGGATCTCCTGACCCACCCAAGGACGAAATA 7 114 0 GACCACCCAA 0.854151 -108 TTTTAGCAACGGATTACCCAGCAATTCCCGA 8 27 0 GGATACCCAG 0.974247 -82 TCTCAATCTACCCCGTTTTTGAGGA 11 95 0 AATCACCCCG 0.869564 -15 **** ****** Masking position 7 Map Score: 12.6378 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 655 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 TCCCGGTAATTTCCCCATGGCCTGGGCTGTGG 1 28 1 TTCCCCATGC 0.945997 -77 TTCGGGGCTATCCCCCACAGCCCAGGCCATGG 1 42 0 TCCCCCACGC 0.98915 -63 GGTGGGAAATTTTTCCCCGGTCAATGAAACCA 2 108 0 TTTTCCCCGC 0.873474 -193 CGGGGAAAAATTTCCCACCCACAGAGCTAGGC 2 121 1 TTTCCCACCC 0.947738 -180 GGCTATGTGCTTCCCTCAGGGCACATATTTTG 2 172 1 TTCCCTCAGC 0.786926 -129 CCGGCTGAAATCCTCGACAGTCGCTGATATGG 2 242 0 TCCTCGACGC 0.9052 -59 ATCATCTCTTCGACGGACAAGAACAGTA 4 7 1 TCTTCGACGC 0.692696 -218 AGCTGCAACTCTCCCTCCAGCCATGGCATTGG 4 156 1 CTCCCTCCGC 0.883827 -69 GAAATTATTTTTCCCCCTTCGGCAATAAATTG 5 274 1 TTCCCCCTCG 0.732899 -22 ACAGAGCTAATTCCCCCCTCACCCCCATCGCT 6 13 0 TTCCCCCCCC 0.984398 -122 TCCAGTTTGCTCCCCTACTCTGACCCTATTTC 7 88 1 TCCCCTACCG 0.887259 -134 TACCCAGCAATTCCCGACTGTGAGTAATGAAT 8 12 0 TTCCCGACGG 0.961622 -97 TAGATTCCATTTCCCTACCCTGCCATGATCTC 8 74 1 TTCCCTACCG 0.928673 -35 TAGAAAGGTTTTCTCTACGGGCGGTCTCGGAG 9 145 1 TTCTCTACGC 0.941574 -156 ACAAAGAACGTTTCCCACTGGCTAAGTTTTCC 11 66 1 TTTCCCACGC 0.972681 -44 ******** * * Masking position 5 Map Score: 15.1427 Number of sites scoring better than the average of aligned sites = 2695 Number in coding regions = 2438 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 4 GTAGATCAGAGTTTTTCGGGGCTATCCCCC 1 58 0 GTTTTTCGGG 0.990689 -47 CTATTTTAAAGCTTTTCTGGGAAGGCTTTG 3 115 0 GCTTTTCTGG 0.87674 -157 GGTATTGACCGTTTTCCGGGGTTGACCGAA 4 50 1 GTTTTCCGGG 0.965824 -175 GATTCGGAGTTTTTTTCAGGTCGGGTTACG 5 49 0 TTTTTTCAGG 0.93165 -247 TTATGGTGGCATTTTTCGGGATCTCCTGAC 7 132 0 ATTTTTCGGG 0.966695 -90 CGTGTATCTAGTTTTTCAAGATTGCTAAAA 9 241 1 GTTTTTCAAG 0.90774 -60 TCGCTATCTGATTTTTCAGGTTGAGTAT 10 24 1 ATTTTTCAGG 0.960057 -18 AATCTACCCCGTTTTTGAGGAAAACTTAGC 11 86 0 GTTTTTGAGG 0.935826 -24 ********** Masking position 5 Map Score: 7.76614 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 228 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 GTAATTTCCCCATGGCCTGGGCTGTGGGGGA 1 33 1 CATGGCCTGG 0.830545 -72 TGTCGAGGATTTCAGCCGGGGACAGTCTTGC 2 255 1 TTCAGCCGGG 0.804805 -46 CAGGGCGCTTTCCATCATAGGACTATAGCCA 3 30 1 TCCATCATGG 0.739354 -242 ATCATAGGACTATAGCCATGGCAGAATAAGT 3 43 1 TATAGCCAGG 0.927956 -229 CAACTCTCCCTCCAGCCATGGCATTGGCCCC 4 161 1 TCCAGCCAGG 0.979598 -64 TAAACTATTCCCTAGCCAATGGTGACCATCG 5 169 0 CCTAGCCATG 0.891096 -127 GGGAATTAGCTCTGTCCATGGACCATTGATA 6 30 1 TCTGTCCAGG 0.932462 -105 AGACAGTGCACCTATCAATGGTCCATGGACA 6 42 0 CCTATCAAGG 0.883849 -93 GGCGCTAGTGTCTGGCATTGGTCAATGGTAA 6 81 0 TCTGGCATGG 0.908248 -54 CTGACCCTATTTCGTCCTTGGGTGGGTCAGG 7 107 1 TTCGTCCTGG 0.65892 -115 CTACTGGATTTTTAGCAACGGATTACCCAGC 8 36 0 TTTAGCAAGG 0.905213 -73 GTTGTCACGACCTAGCAAAGGTATTTAATTG 9 277 1 CCTAGCAAGG 0.959071 -24 TTGAGGAAAACTTAGCCAGTGGGAAACGTTC 11 71 0 CTTAGCCATG 0.755977 -39 ******** ** Masking position 6 Map Score: 7.15748 Number of sites scoring better than the average of aligned sites = 3126 Number in coding regions = 2834 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 305 Fraction of orfs with sites within 600 bp upstream = 0.0489881 Motif number 6 GGGAGGCGATCGCCCTATCCCGGT 1 4 1 AGGGATCGCC 0.939404 -101 AGTTGACCTAAGCAGAACCGGTTCATATCTA 2 46 0 AGCGAACCGG 0.975274 -255 CCACAGAGCTAGGCGATCGCCTCTGGGTAAT 2 139 1 AGGGATCGCC 0.939404 -162 GATGGGGGCCAGCGGAACCAGGGCGCTTTCC 3 12 1 AGCGAACCAG 0.908486 -260 ACTTTATCTAAGCGTAACCCGACCTGAAAAA 5 37 1 AGCTAACCCG 0.86278 -259 AAAACTCCGAATCCGATCGGGAGTTATGACG 5 66 1 ATCGATCGGG 0.952142 -230 TGGGTGGGTCAGGAGATCCCGAAAAATGCCA 7 125 1 AGGGATCCCG 0.984386 -97 GTTTGCCTTGATCAGATCCGGAGAGGGCTTT 9 208 1 ATCGATCCGG 0.961004 -93 AACCTGAAAAATCAGATAGCGAGAGAGATGC 10 15 0 ATCGATAGCG 0.760378 -27 *** ******* Masking position 6 Map Score: 3.78689 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 435 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 AGGAGACGAGTTGACCTAAGCAGAACCGGT 2 55 0 TTGACCTAAG 0.937504 -246 TCGTTGAATCTTTCCCTAAGTAAGCTACCA 2 202 0 TTTCCCTAAG 0.982287 -99 AGGGGATGAATTTCTCTAAAAAAGGGAAAC 3 72 0 TTTCTCTAAA 0.702051 -200 TTTTCCGGGGTTGACCGAAGGCAAAGGTAT 4 61 1 TTGACCGAAG 0.77802 -164 TCTAGACTCGTTTCCCTAACCTTGACCACC 4 123 1 TTTCCCTAAC 0.951523 -102 AGTTGTACACTTTATCTAAGCGTAACCCGA 5 29 1 TTTATCTAAG 0.856293 -267 AGCCGTGCCGTTGCCCTACGAAATTATTTT 5 255 1 TTGCCCTACG 0.974197 -41 CTAGATTCCATTTCCCTACCCTGCCATGAT 8 73 1 TTTCCCTACC 0.94184 -36 TTAGAAAGGTTTTCTCTACGGGCGGTCTCG 9 144 1 TTTCTCTACG 0.937505 -157 ********** Masking position 8 Map Score: 7.61744 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 319 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 8 TAGATCGGGTTAGCGGTAGATCAGAGTTTT 1 73 0 TAGCGGTAGA 0.873961 -32 TTAGGATGGGCAGCGAGAGACTCGAACTCT 2 12 0 CAGCGAGAGA 0.978548 -289 TCGAGGATTTCAGCCGGGGACAGTCTTGCT 2 257 1 CAGCCGGGGA 0.953164 -44 ATAGCGATGGGGGTGAGGGGG 6 2 1 TAGCGATGGG 0.951378 -133 AAAAATCAGATAGCGAGAGAGATGCAAGG 10 10 0 TAGCGAGAGA 0.974209 -32 ACTCTGCGCACAGCGAGGGGATTATAGACA 11 39 1 CAGCGAGGGG 0.988587 -71 GAGGAAAACTTAGCCAGTGGGAAACGTTCT 11 70 0 TAGCCAGTGG 0.88396 -40 ********** Masking position 2 Map Score: 3.72811 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 219 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 GGGAAATTACCGGGATAGGGCGATCGCCTC 1 13 0 CGGGATAGGG 0.990703 -92 GTAAATCGGACGGGATACGGGGGACAGAAA 3 250 0 CGGGATACGG 0.969583 -22 CGGTCAACCCCGGAAAACGGTCAATACCTT 4 48 0 CGGAAAACGG 0.839789 -177 CAATTTATTGCCGAAGGGGGAAAAATAATT 5 276 0 CCGAAGGGGG 0.851455 -20 AGTGGCAAAATAGGGCCGAGTTGTT 6 120 0 CAAAATAGGG 0.887695 -15 GAAATAGGGTCAGAGTAGGGGAGCAAACTG 7 90 0 CAGAGTAGGG 0.951506 -132 CACCCAAGGACGAAATAGGGTCAGAGTAGG 7 101 0 CGAAATAGGG 0.94228 -121 GAGATCATGGCAGGGTAGGGAAATGGAATC 8 76 0 CAGGGTAGGG 0.961921 -33 TTGATCAGATCCGGAGAGGGCTTTTTCGTG 9 215 1 CCGGAGAGGG 0.969286 -86 ********** Masking position 1 Map Score: 8.18838 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 431 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 ATTATCGTTGAATCTTTCCCTAAGTAAGCTA 2 205 0 AATCTTTCCT 0.835447 -96 CTTAAGTTTTAACTTTTTCCTTTTCTGCACC 3 212 1 AACTTTTCCT 0.949879 -60 CAATTAAGCATACCTTTGCCTTCGGTCAACC 4 69 0 TACCTTTCCT 0.890424 -156 GTATGATGTAAACTATTCCCTAGCCAATGGT 5 177 0 AACTATTCCT 0.891826 -119 CTTTCTCTCCAACTACTGCTTACCATAAAGT 7 185 1 AACTACTCTT 0.827795 -37 TGTTGAAAAGAACCTCTTCTTAGAAAGGTTT 9 125 1 AACCTCTCTT 0.958133 -176 GTATAACACAAACCTCTACTTTCTGCGACC 11 10 0 AACCTCTCTT 0.958125 -100 ******* *** Masking position 2 Map Score: 0.216853 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 211 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 TACCGCTAACCCGATCTAGGGAACTACACC 1 85 1 CCGATCTAGG 0.911167 -20 AAATTTTTCCCCGGTCAATGAAACCAGGGT 2 104 0 CCGGTCAATG 0.942261 -197 GGGGACAGAAACGTTCAAGGTGCAGAAAAG 3 231 0 ACGTTCAAGG 0.918985 -41 CATCTCTTCGACGGACAAGAACAGTACCCA 4 13 1 ACGGACAAGA 0.840036 -212 ACCCCGGAAAACGGTCAATACCTTTACAAT 4 42 0 ACGGTCAATA 0.865802 -183 GCAGCTCGGGGTGGTCAAGGTTAGGGAAAC 4 132 0 GTGGTCAAGG 0.822532 -93 TGATAATCCTCCGGTCTAGTTAACTGGCCG 5 125 0 CCGGTCTAGT 0.802356 -171 ACCACAAATCACAATCAAGAATTGTGTTA 9 10 0 ACAATCAAGA 0.56035 -291 TATCTGCAGGACGCTCAAGATACCACGGTT 9 64 1 ACGCTCAAGA 0.895367 -237 CTCTCCGGATCTGATCAAGGCAAACAGCGG 9 203 0 CTGATCAAGG 0.86448 -98 ********** Masking position 8 Map Score: 0.571115 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 630 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 12 ********** No masking Map Score: -3.1808e-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: -3.1808e-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 14 ********** No masking Map Score: -3.1808e-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