AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_synecho_ctra_300.orf -o047_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 RCY28537 38 Synechocystis #2 RCY25783 171 Synechocystis #3 RCY43089 119 Synechocystis #4 RCY42092 106 Synechocystis #5 RCY13382 161 Synechocystis #6 RCY40018 39 Synechocystis #7 RCY30329 44 Synechocystis #8 RCY35247 34 Synechocystis #9 RCY43999 50 Synechocystis #10 RCY08473 151 Synechocystis #11 RCY16635 290 Synechocystis #12 RCY06400 56 Synechocystis #13 RCY28245 63 Synechocystis #14 RCY37471 66 Synechocystis #15 RCY24448 85 Synechocystis #16 RCY05831 277 Synechocystis #17 RCY50309 68 Synechocystis #18 RCY54010 66 Synechocystis #19 RCY22900 17 Synechocystis #20 RCY19565 32 Synechocystis #21 RCT00174 300 Chlamydia_trachomatis #22 RCT00382 165 Chlamydia_trachomatis #23 RCT00385 300 Chlamydia_trachomatis Motif number 1 GTTGAACAATGGCGATCGCCAAAGTAAGCT 2 110 1 GGCGATCGCC 0.499992 -62 AGGCGATCGCCTAGGAATTTG 3 2 1 GGCGATCGCC 0.499992 -118 TCCTCTAGAGGGCGATCGCCAAATGAAAAC 4 11 1 GGCGATCGCC 0.499992 -96 TTTAAAGTTTGGTGATCGAGGGATTAGTGT 10 40 0 GGTGATCGAG 0.766473 -112 ACTTTAAAGTGGAGAACTCCACCGCTGAGG 10 62 1 GGAGAACTCC 0.624267 -90 GGCATTGTATGGCGATCAACGGCTTGGTGT 11 41 0 GGCGATCAAC 0.741373 -250 GTAGTGGGGAGGCGAACGATCATTCTAGTA 11 108 0 GGCGAACGAT 0.778238 -183 TAATGGGTACAGCGGTCTCCGAAACTCGAT 16 152 1 AGCGGTCTCC 0.884304 -126 GAGCATGGATGACGGTCGAGGAGGGGTGTC 16 224 0 GACGGTCGAG 0.833112 -54 GAAACGCAACGGCGGACTACCCATATTCTA 17 42 0 GGCGGACTAC 0.944781 -27 CTTGATTGTTAACGATCTCCTTGTTAGGAT 21 175 1 AACGATCTCC 0.683259 -126 TTTCTCTACGGGCGGTCTCGGAGTATAATT 23 154 1 GGCGGTCTCG 0.965053 -147 ********** Masking position 7 Map Score: 14.1429 Number of sites scoring better than the average of aligned sites = 7703 Number in coding regions = 7011 Number in noncoding regions = 692 Number of orfs with sites within 600 bp upstream = 409 Fraction of orfs with sites within 600 bp upstream = 0.0656923 Motif number 2 AACAAACAAATGGTTTTATGAGCTATTGAAGGATTTTA 2 18 1 TGTTTTGTAG 0.785655 -154 CAAGATAATCCTATTTTAATGGGTAGCTTACTTTGGCG 2 126 0 CATTTTGTAT 0.788454 -46 AATTGAACAATTATTTTTTTGGCTTTGTCTGGTAAGCT 5 97 1 TATTTTGTTT 0.950983 -65 CCCATAGTAGTCATTTTTGCTGGGTTTTTGTT 6 5 0 TATTTTGGTT 0.73891 -35 AGCAGTTTATTTTCCCCGTTAAGTAAATTAAGAA 10 128 0 TATTTTGTAT 0.962336 -24 TCGTTTTTATTGCTAAATCCCGCATTTA 11 1 1 TGTTTTGTAT 0.958744 -290 CGAAACTCGATAATTTTGATTGATAATTTCTGATCGTC 16 171 1 TATTTTGTAT 0.962336 -107 TAGAAGTGTATGATTTATGATGTTATTTACTATTTTTC 21 11 0 TATTTAGTAT 0.747436 -290 TTTTGAAACTTGATTTTTAATGTTTTATATGCGATCCT 22 17 1 TATTTTGTTT 0.950983 -149 CGGGATACCCTCGTTTGGAAGGCTACTTGGGTAAAGAG 22 56 1 TGTTTGGTAT 0.880124 -110 AGGGTTGTCATAGTTTTTGCAGGTTGTTCGTTTAGGAA 22 119 1 TGTTTTGTTT 0.94637 -47 TTCTTGATTGTGATTTGTGGTGATTTTTTTTCAAAAGT 23 19 1 TATTTGGTTT 0.859734 -282 ACCACGGTTTTTATTTTAATGGATAAAATCCTGTGTCT 23 85 1 TATTTTGTAA 0.73111 -216 TTCGTGTATCTAGTTTTTCAAGATTGCTAAAAAGTATT 23 239 1 TGTTTTGTTT 0.94637 -62 * ***** * ** * Masking position 6 Map Score: 12.5803 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 101 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 AATGTCGCCATTGCCATACACCTTTAAAG 7 1 1 ATGCTTCAAC 0.980188 -44 AGGAGTTGCTTATTTTCTTTACCTGCTCAACA 8 13 0 ATTTTTCTAC 0.517964 -22 TTTATGTCTAAATTCCGCGTTTACTACACTAATCCCTCG 10 15 1 ATGCTTCAAC 0.980188 -137 TTACTACACTAATCCCTCGATCACCAAACTTTAAAGTGG 10 35 1 ATTCTCCAAC 0.899482 -117 TTTATTGCTAAATCCCGCATTTACTACACCAAGCCGTTG 11 16 1 ATGCTTCAAC 0.980188 -275 TTACTACACCAAGCCGTTGATCGCCATACAATGCCCATT 11 36 1 AGTTTCCAAC 0.742424 -255 CTAGTACATGCAGATTGTGATTCCTAAAAAACGACTAAT 11 75 0 CGGTTTCAAA 0.551017 -216 ATTCACTACACCTGTTTCGATTTCGACAATGATTTCATA 11 156 0 CTTCTTCAAA 0.703635 -135 AGGTGTAGTGAATGGGTCATTTCCAAAACGAGCATTACG 11 182 1 ATTCTTCAAC 0.968582 -109 GGTTGATGTAAATCATGCCATTCTAAAACATGACGTAAT 11 215 0 ATGCTTTAAC 0.750721 -76 CTGATCGTCCCTGATGTCCGTTGCGACACCCCTCCTCGA 16 200 1 CGTCTTCAAC 0.948961 -78 ACTTCTTATACAGTAGGCCCTTACCAAACATATTCATAT 21 235 0 CGGCTTCAAC 0.967572 -66 GGGCGCCCTACTCAAGTTCTTCCTAAACGAACAACCTG 22 138 0 ATGTTTCAAC 0.946006 -28 CCTTTCTAAGAAGAGGTTCTTTTCAACACAAGACACAGG 23 114 0 AGTTTTCAAC 0.908509 -187 * * ** ** * * ** Masking position 18 Map Score: 10.9296 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 229 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 AGTTGAACAATGGCGATCGCCAAAGTAAGCTA 2 109 1 TGGCATCGCA 0.495086 -63 TCACATTGAGGGTCAGGGCAAGATAATCCTA 2 151 0 GGGTAGGGCA 0.9854 -21 GATGATTTCATTGTAATGGGCAAATTCCTAGG 3 20 0 TTGTATGGGA 0.682309 -100 TCCTCTAGAGGGCGATCGCCAAATGAAAACC 4 10 1 GGGCATCGCA 0.772336 -97 TTTTTTTTGTGGTCTATGGCTAATTCCTAAAA 5 11 1 GGTCATGGCA 0.829194 -151 TTACGCTATCTGGTTAGGGCGTTTTAAAAACT 5 134 1 TGGTAGGGCT 0.904522 -28 TAAAGGTGTATGGCAATGGCGACATT 7 5 0 TGGCATGGCA 0.964164 -40 GTATCTTGCATGGTAGTGGGGAGGCGAACGAT 11 118 0 TGGTGTGGGA 0.837183 -173 TACCCAAAGCGGGTGAGGGGAATCGAACCCCT 16 122 0 GGGTAGGGGA 0.975271 -156 CACCCGCTTTGGGTAATGGGTACAGCGGTCTC 16 139 1 GGGTATGGGA 0.979567 -139 TTTCCCTGGGTAATGGAAAGGGTAGGCTT 20 8 1 GGGTATGGAA 0.901828 -25 TGAATATGTTTGGTAAGGGCCTACTGTATAAG 21 238 1 TGGTAGGGCT 0.904507 -63 **** ***** * Masking position 9 Map Score: 11.3704 Number of sites scoring better than the average of aligned sites = 1975 Number in coding regions = 1830 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 5 GTTACTAAATCCAGAGTTTTTTCCTGATTAAGAA 5 65 1 CCAGATTTTC 0.829 -97 ATGTCTAAATTCCGCGTTTACTACACTAATCCCT 10 18 1 TCCGCTTTTC 0.973942 -134 ATTGCTAAATCCCGCATTTACTACACCAAGCCGT 11 19 1 CCCGCTTTTC 0.996542 -272 CTAAACTACACCCGCGTGTTGTCCTAGCGTTTTT 16 57 0 CCCGCTGTTC 0.988847 -221 ATTCCCCTCACCCGCTTTGGGTAATGGGTACAGC 16 131 1 CCCGCTTGTA 0.920002 -147 TCTATTTTGCCCCGCCATTGTTGCGAGATTATTA 17 12 0 CCCGCATTTC 0.983556 -57 TTCGACACCTCCCGCGTTTCATTCGTGAAAAATA 21 90 1 CCCGCTTTTC 0.996542 -211 ***** *** * * Masking position 12 Map Score: 5.29377 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 79 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 AACAAAAACCCAGCAAAAATGACTACTATGGGA 6 5 1 AAACCAGGAC 0.846165 -35 TCTGAAATAAATAACCCTGATATGTGGAGTTCAAATTAA 12 18 1 AAACCTGGAG 0.991721 -39 GTTTAGTGGTAAAACCTTAGCCTTCCAAGCTAATGATAG 16 85 1 AAACCTAAAG 0.936996 -193 CGCTGTACCCATTACCCAAAGCGGGTGAGGGGAATCGAA 16 127 0 ATACCAAGAG 0.810493 -151 CAGATAACCGTGCAGAACCGAGGAATTATCGA 16 256 0 AAACCTGGAG 0.991722 -22 AGAAAAATTGAGCACCATAGCAAGAAAAGTT 18 46 1 ACACCTAAAG 0.797984 -21 AAAAACTATGACAACCCTAAAGGGCTGAGACAGACTCTT 22 98 0 AAACCTAGAG 0.986933 -68 CATTAAAATAAAAACCGTGGTATCTTGAGCGTCCTGCAG 23 67 0 AAACCTGGAG 0.991722 -234 GCCCGTAGAGAAAACCTTTCTAAGAAGAGGTTCTTTTCA 23 128 0 AAACCTTGAG 0.958256 -173 * **** ** *** Masking position 4 Map Score: 4.90617 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 63 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 TTATGTCTAAATTCCGCGTTTACTACACTA 10 16 1 ATTCCGCGTT 0.895803 -136 TACTACACTAATCCCTCGATCACCAAACTT 10 36 1 ATCCCTCGAT 0.820277 -116 AGCAGTTTATTTTCCCCGTTAAGTAAATTA 10 132 0 TTTCCCCGTT 0.621255 -20 TTATTGCTAAATCCCGCATTTACTACACCA 11 17 1 ATCCCGCATT 0.906082 -274 GATTTACATCAACCCGAGTTAATAGCCAAT 11 240 1 AACCCGAGTT 0.776868 -51 CACTAAACTACACCCGCGTGTTGTCCTAGC 16 63 0 CACCCGCGTG 0.940719 -215 CGATTCCCCTCACCCGCTTTGGGTAATGGG 16 129 1 CACCCGCTTT 0.900948 -149 GTCATCCATGCTCCCTCGATAATTCCTCGG 16 241 1 CTCCCTCGAT 0.899696 -37 TATTCGACACCTCCCGCGTTTCATTCGTGA 21 88 1 CTCCCGCGTT 0.990325 -213 CGCACCCCCATTAATGACGTCC 21 289 0 CACCCCCATT 0.850245 -12 TCCTTCGGGATACCCTCGTTTGGAAGGCTA 22 51 1 TACCCTCGTT 0.892466 -115 ********** Masking position 5 Map Score: 6.091 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 276 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 GGCCTTTGGGCGTAGCAAAAATTGACCTCA 1 16 1 CGTAGCAAAA 0.945337 -23 CCATGGCAACAAACAAATGGT 2 2 1 CATGGCAACA 0.901522 -170 TGGGTTTGACCGTGGCACAAGTTGCTCAGG 2 73 1 CGTGGCACAA 0.849561 -99 CATTGAGGGTCAGGGCAAGATAATCCTATT 2 149 0 CAGGGCAAGA 0.797437 -23 AACAAAAACCCAGCAAAAATGACTACTA 6 9 1 CCCAGCAAAA 0.765396 -31 CTGATAGAAACCTTACAACAA 13 53 1 CCTTACAACA 0.441651 -11 CTGAATTTTGCGGAACAAAATATGCAGTAG 15 43 1 CGGAACAAAA 0.777485 -43 GGAAAGTTCTCCTGACAAAAGTCTAGGCAA 16 13 1 CCTGACAAAA 0.895465 -265 GCAACAATGGCGGGGCAAAATAGAATATGG 17 22 1 CGGGGCAAAA 0.953711 -47 AATTGAGCACCATAGCAAGAAAAGTT 18 51 1 CATAGCAAGA 0.767691 -16 TTTGCTAGGTCGTGACAACAATACTTTTTA 23 266 0 CGTGACAACA 0.883103 -35 GTTGTCACGACCTAGCAAAGGTATTTAATT 23 277 1 CCTAGCAAAG 0.7054 -24 ********** Masking position 7 Map Score: 3.29628 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 815 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 9 ATTTTAATGGGTAGCTTACTTTGGCGATCG 2 122 0 GTAGCTTACT 0.834967 -50 CCAGATAGCGTAAGCTTACCAGACAAAGCC 5 117 0 TAAGCTTACC 0.881431 -45 TGGTAAAACCTTAGCCTTCCAAGCTAATGA 16 91 1 TTAGCCTTCC 0.963007 -187 TCTAAGCCTACCCTTTCCATTA 20 21 0 TAAGCCTACC 0.938852 -12 TAGATATTTACAAGCCTTCTCATAGGCTCT 21 47 1 CAAGCCTTCT 0.912659 -254 CACAGAGCTACTAGCTTTCTTAACTTATTG 21 139 0 CTAGCTTTCT 0.868211 -162 CTTTACCCAAGTAGCCTTCCAAACGAGGGT 22 62 0 GTAGCCTTCC 0.965638 -104 ********** Masking position 3 Map Score: 1.39996 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 89 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 TTAATTCACTCTTCTAAGCTGCACCATTATG 4 53 1 CTTCAAGCTG 0.986727 -54 GGAATGTTTGCTTTAAAGGTGTATGGCAATG 7 19 0 CTTTAAGGTG 0.911345 -26 AGCATCTTTTCTTCATAGCTGGCCTCAGCGG 10 83 0 CTTCTAGCTG 0.98194 -69 AAACCTTAGCCTTCCAAGCTAATGATAGGGG 16 96 1 CTTCAAGCTA 0.937396 -182 AGAAGTTTTGCTTCTTAGGTGGGACGTCATT 21 268 1 CTTCTAGGTG 0.973084 -33 **** ****** Masking position 7 Map Score: 0.919381 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 33 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 ********** No masking Map Score: -6.07271e-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: -6.07271e-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 CAACTGTATTTAAAATCCTTCAATAGCTCA 2 36 0 TAAAATCCTT 0.810822 -136 CGCAGAAAACTGACAACTTTTAGGAATTAG 5 30 0 TGACAACTTT 0.809437 -132 TAGGGCGTTTTAAAAACTTTATTT 5 148 1 TAAAAACTTT 0.913308 -14 CCAACAATTATAAAAACTTTTTTGA 9 6 0 TAAAAACTTT 0.913308 -45 AGTGACCTTTTAGCATCTTTTCTTCATAGC 10 95 0 TAGCATCTTT 0.69372 -57 AATAGCCAATTGGCAACTTTGTCGCCAACA 11 260 1 TGGCAACTTT 0.777955 -31 ACACTTCTGATAGAAACCTTACAACAA 13 47 1 TAGAAACCTT 0.917949 -17 TCCATTAAAATAAAAACCGTGGTATCTTGA 23 78 0 TAAAAACCGT 0.760134 -223 AGACAATTAAATACCTTTGCTAGGTCG 23 284 0 TAAATACCTT 0.68134 -17 ********** Masking position 1 Map Score: 0.578001 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 147 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 14 ********** No masking Map Score: -6.07271e-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 15 ********** No masking Map Score: -6.07271e-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