AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i038_synecho_ctra_300.orf -o038_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 RCY08845 202 Synechocystis #14 RCY39391 274 Synechocystis #15 RCY34559 88 Synechocystis #16 RCY18602 21 Synechocystis #17 RCY32056 160 Synechocystis #18 RCY16440 38 Synechocystis #19 RCY42175 94 Synechocystis Motif number 1 AACCCAATTCAGGCAACTGTATTTAAAATCCTTCAA 2 43 0 AGGCACGTTA 0.978636 -129 TAGCTTACTTTGGCGATCGCCATTGTTCAACTGTTC 2 105 0 TGGCATGCTT 0.974187 -67 AGGCGATCGCCTAGGAATTTGCCCAT 3 1 1 AGGCATGCAA 0.955902 -119 GGTTTTCATTTGGCGATCGCCCTCTAGAGGA 4 6 0 TGGCATGCTA 0.994098 -101 TGCACCATTATGGCTACCGTTTTAGACCTTCAGCCA 4 72 1 TGGCACGTTA 0.988804 -35 AATGTCGCCATTGCCATACACCTTTAAAGC 7 5 1 TCGCATGCTA 0.947127 -40 TCTTCATAGCTGGCCTCAGCGGTGGAGTTCTCCACT 10 69 0 TGGCTCGCTA 0.957629 -83 TTATGCTAGATGGCCATGGTAATGAATTGGAACTAC 14 188 1 TGGCATGTTA 0.987054 -87 CGCCCATCGGTGGCAACGGTGATCAACAGTTTATGC 15 35 0 TGGCACGTTA 0.988805 -54 TTAACCAAGTAGGCCATGGCAGTTCAGCGAATGATT 17 18 1 AGGCATGCTA 0.988683 -143 GCTCTAGGCGAGGCAACAGCTTGGGTTAATAGTCGA 19 46 1 AGGCACGCGT 0.825443 -49 GTTTGTTGCGTGGCCATTGTCGACTATTAACCCAAG 19 65 0 TGGCATGTAA 0.949794 -30 **** ** ** * * Masking position 4 Map Score: 18.2264 Number of sites scoring better than the average of aligned sites = 1178 Number in coding regions = 1049 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 2 CAGAAAACTGACAACTTTTAGGAATTAGCCATAG 5 24 0 ACCTTTAGAA 0.650462 -138 AGGAAAAAACTCTGGATTTAGTAACTCATCCGCA 5 56 0 TCGTTTAGAA 0.971435 -106 CAGAGTTTTTTCCTGATTAAGAATTGAACAATTA 5 76 1 TCGTTAAGAT 0.908699 -86 CAGTTTATTTTCCCCGTTAAGTAAATTAAGAACT 10 126 0 TCCTTAAGAA 0.921904 -26 TGTAGTAAATGCGGGATTTAGCAATAAAAACGA 11 10 0 GCGTTTAGAA 0.971953 -281 GCGATCAACGGCTTGGTGTAGTAAATGCGGGATT 11 26 0 GCGTGTAGAA 0.958296 -265 CCATTATTAGTCGTTTTTTAGGAATCACAATCTG 11 70 1 TCTTTTAGAA 0.839725 -221 ATGACGTAATGCTCGTTTTGGAAATGACCCATTC 11 191 0 GCGTTTGGAA 0.916306 -100 GAGCATTACGTCATGTTTTAGAATGGCATGATTT 11 211 1 TCGTTTAGAT 0.908699 -80 GGCTATTAACTCGGGTTGATGTAAATCATGCCAT 11 233 0 TCGTGATGAA 0.723136 -58 CTTTTAAATCTCAAGTTGAAGCAAATGTTACGGG 13 55 1 TCGTGAAGAA 0.957537 -148 TAAAGAAATGTCGATTTTAGGTAATGAACGATGT 14 61 1 TCTTTAGGAA 0.623385 -214 TGATTAGATTGCCTCTTGAAGAAACCCATTAAA 18 10 0 GCCTGAAGAA 0.888594 -29 CTAAGGTCAAGCAAGGTTAAGAATGGTATGCTCT 19 17 1 GCGTTAAGAT 0.910249 -78 ** * ***** ** Masking position 13 Map Score: 12.5704 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 229 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 GGCGTAGCAAAAATTGACCTCAAGT 1 24 1 AAATGACCTC 0.935538 -15 TTTGCCCATTACAATGAAATCATCTTCTCTC 3 28 1 ACATGAAATC 0.778096 -92 GGGCGATCGCCAAATGAAAACCAATTGTTAA 4 20 1 CAATGAAAAC 0.698966 -87 ACCAATTGTTAAAATTAATTCACTCTTCTAA 4 39 1 AAATTAATTC 0.571913 -68 CATCCGCAGAAAACTGACAACTTTTAGGAAT 5 33 0 AAATGACAAC 0.940004 -129 AAACCCAGCAAAAATGACTACTATGGGAAGA 6 16 1 AAATGACTAC 0.940003 -24 AGATACGGTGAATATGAAATCATTGTCGAAA 11 144 1 AATTGAAATC 0.806643 -147 AATCAGTCTTAATTTGAACTCCACATATCAG 12 34 0 AATTGAACTC 0.737341 -23 TAATCTAGGTAAAGTGACTACCTTTAAACAA 14 14 0 AAATGACTAC 0.939985 -261 GCCATCTAGCATAATGACTACACGTACATGC 14 171 0 ATATGACTAC 0.665637 -104 ATGGGCGCATAAAATGAATTCACTAGATTTG 15 64 1 AAATGAATTC 0.949025 -25 TCTCATTTATAAATTGAAATCACTATCAATA 17 132 0 AAATGAAATC 0.949002 -29 *** ******* Masking position 7 Map Score: 8.04176 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 129 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 GGGGTCAGCCAGAAAATCTAACCACATCAA 3 64 0 AGAAAATCTA 0.973504 -56 GTCGCCAACAAGAAGATCTAA 11 280 1 AGAAGATCTA 0.975407 -11 ATAATAATCTAGATAATCTAGGTAAAGTGA 14 28 0 AGATAATCTA 0.917813 -247 TAGAGTTTGAAGCAGATCTACAAGATGGTG 14 101 1 AGCAGATCTA 0.977177 -174 TTAGCAAATCTAGTGAATTCAT 15 77 0 AGCAAATCTA 0.975407 -12 ********** Masking position 6 Map Score: 3.89199 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 68 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 GGTTGAACAGTTGAACAATGGCGATCGCCAA 2 101 1 TTGAAAATGG 0.976015 -71 GTGAATTAATTTTAACAATTGGTTTTCATTT 4 31 0 TTTAAAATTG 0.941275 -76 TGATTAAGAATTGAACAATTATTTTTTTGGC 5 89 1 TTGAAAATTA 0.602729 -73 TCAAAAAAGTTTTTATAATTGTTGGTAAATT 9 11 1 TTTTAAATTG 0.816702 -40 TTACGTCATGTTTTAGAATGGCATGATTTAC 11 216 1 TTTTAAATGG 0.912592 -75 CTTGGGGATATTGAATAATGGGGCGGCCTAG 13 177 0 TTGAAAATGG 0.976015 -26 GCAACATTGATTGATGAATGGCATGATCCCT 14 244 1 TTGATAATGG 0.918775 -31 ATTTAAGATTGGCAAAAGTATT 15 2 1 TTTAAATTGG 0.840889 -87 GGAATTCTCATTTATAAATTGAAATCACTAT 17 137 0 TTTATAATTG 0.816702 -24 GTCAAGCAAGGTTAAGAATGGTATGCTCTAG 19 22 1 GTTAAAATGG 0.886787 -73 ***** ***** Masking position 7 Map Score: 6.78433 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 278 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 AAAGTAAGCTACCCATTAAAATAGGATTAT 2 130 1 ACCCATTAAA 0.969478 -42 GGCTGACCCCATCCAATAAAAAGAGTGACT 3 84 1 ATCCAATAAA 0.896533 -36 AACAAAAACCCAGCAAAAATGACTACT 6 8 1 ACCCAGCAAA 0.926131 -32 AATTCAGTGAATCCATTAGACTCTTTTAAA 13 33 1 ATCCATTAGA 0.853603 -170 TGAACGATGTACGCAATAGAGTTTGAAGCA 14 85 1 ACGCAATAGA 0.900191 -190 TCTTGAAGAAACCCATTAAA 18 1 0 ACCCATTAAA 0.969478 -38 GACAATGGCCACGCAACAAACAATT 19 80 1 ACGCAACAAA 0.900191 -15 ********** Masking position 5 Map Score: 2.08373 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 96 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 GTTGTCAGTTTTCTGCGGATGAGTTACTAAAT 5 43 1 TTCGCGGAGA 0.993144 -119 CATAGCTGGCCTCAGCGGTGGAGTTCTCCACT 10 69 0 CTCGCGGTGA 0.990925 -83 GGTTATTTATTTCAGAGGTAGAA 12 2 0 TTCGAGGTGA 0.978258 -55 GGCATGATCCCTCCGAGGATGA 14 263 1 CTCGAGGAGA 0.985836 -12 GCCATGGCAGTTCAGCGAATGATTAAAATAAA 17 30 1 TTCGCGAAGA 0.965309 -131 *** ***** ** Masking position 2 Map Score: 1.83007 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 20 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 GGCGATCGCCAAAGTAAGCTACCCATTAAA 2 120 1 AAAGTAAGCT 0.811305 -52 CTAACCAGATAGCGTAAGCTTACCAGACAA 5 121 0 AGCGTAAGCT 0.902599 -41 GCGGAATTTAGACATAAACTAA 10 3 0 GACATAAACT 0.856563 -149 CTTAACGGGGAAAATAAACTGCT 10 139 1 AAAATAAACT 0.841119 -13 AAAAGTATTCAGCATAAACTGTTGATCACC 15 24 1 AGCATAAACT 0.950955 -65 ATTATGAAACGTAAACTAGTT 16 5 0 AACGTAAACT 0.959029 -17 GCAATGTCAGAGCATATACTTGCTTTTAAA 17 78 0 AGCATATACT 0.75088 -83 ********** Masking position 6 Map Score: 1.34322 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 42 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 9 GGTCAATTTTTGCTACGCCCAAAGGCCCATGG 1 10 0 TGACGCCAAA 0.977107 -29 GAGCAACTTGTGCCACGGTCAAACCCAATTCAG 2 67 0 TGACGGCAAA 0.985801 -105 ATGATTTCATTGTAATGGGCAAATTCCTAGGCG 3 18 0 TGATGGCAAA 0.964468 -102 ATAAAGTTTTTAAAACGCCCTAACCAGATAGCG 5 137 0 TAACGCCTAA 0.826576 -25 TTACGGGACTTGGAGCGGACAAAGATATTCAGG 13 82 1 TGGCGGCAAA 0.9752 -121 TATTGAATAATGGGGCGGCCTAGCCATGAATAG 13 167 0 TGGCGGCTAG 0.963582 -36 TTCGCTGAACTGCCATGGCCTACTTGGTTAAAA 17 16 0 TGATGGCTAC 0.908467 -145 AGGTTAAGAATGGTATGCTCTAGGCGAGGCAAC 19 30 1 TGATGCCTAG 0.918212 -65 ** **** **** Masking position 12 Map Score: 2.0614 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 156 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 GGATGAGTTACTAAATCCAGAGTTTTTTCCTGAT 5 59 1 CTAAACGATT 0.953531 -103 CCATACACCTTTAAAGCAAACATTCCTGGAT 7 24 1 TTAAACACTT 0.85272 -21 TAGTTTATGTCTAAATTCCGCGTTTACTACACTA 10 12 1 CTAAATGCTT 0.926318 -140 GTTTTTATTGCTAAATCCCGCATTTACTACACCA 11 13 1 CTAAACGCTT 0.986436 -278 CCCGCATTTACTACACCAAGCCGTTGATCGCCAT 11 29 1 CTACACGCGT 0.915244 -262 TGGGTCATTTCCAAAACGAGCATTACGTCATGTT 11 194 1 CCAAACGCTT 0.938144 -97 TCATGCCATTCTAAAACATGACGTAATGCTCGTT 11 208 0 CTAAACGAGT 0.935939 -83 TTAGACTCTTTTAAATCTCAAGTTGAAGCAAATG 13 48 1 TTAAACAATT 0.620296 -155 CGTTCATTACCTAAAATCGACATTTCTTTATACA 14 57 0 CTAAATACTT 0.780087 -218 TTGTCGACTATTAACCCAAGCTGTTGCCTCGCCT 19 51 0 TTAACCGCGT 0.752897 -44 ***** * ** ** Masking position 3 Map Score: 1.71639 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 396 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 11 ********** No masking Map Score: 3.13593e-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 GGAGGCGAACGATCATTCTAGTACATGCAG 11 101 0 GATCATTCTA 0.883458 -190 TTTCCAAAACGAGCATTACGTCATGTTTTA 11 201 1 GAGCATTACG 0.858259 -90 GGTTGATGTAAATCATGCCATTCTAAAACA 11 224 0 AATCATGCCA 0.840482 -67 TACAATTCCAGATCATTACAAATCTCTGAA 14 135 1 GATCATTACA 0.930424 -140 GGCCTTATCAGATCATTCAGCAACATTGAT 14 225 1 GATCATTCAG 0.836156 -50 TCCTCGGAGGGATCATGCCATTCATCAATC 14 252 0 GATCATGCCA 0.975901 -23 GCCTCGCCTAGAGCATACCATTCTTAACCT 19 30 0 GAGCATACCA 0.909304 -65 ********** Masking position 5 Map Score: 0.199203 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 132 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 ********** No masking Map Score: 3.13593e-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 GCACAAGTTGCTCAGGTTGAACAGTTGAAC 2 87 1 CTCAGGTTGA 0.963579 -85 TGTCAGTTTTCTGCGGATGAGTTACTAAAT 5 45 1 CTGCGGATGA 0.970061 -117 TAGCTGGCCTCAGCGGTGGAGTTCTCCACT 10 69 0 CAGCGGTGGA 0.924716 -83 TGGCTATTAACTCGGGTTGATGTAAATCAT 11 238 0 CTCGGGTTGA 0.92259 -53 TTATTTATTTCAGAGGTAGAA 12 2 0 CAGAGGTAGA 0.872819 -55 TCTTTTAAATCTCAAGTTGAAGCAAATGTT 13 54 1 CTCAAGTTGA 0.747115 -149 CATGATCCCTCCGAGGATGA 14 265 1 CCGAGGATGA 0.923588 -10 CATGGCAGTTCAGCGAATGATTAAAATAAA 17 32 1 CAGCGAATGA 0.735362 -129 ********** Masking position 10 Map Score: 0.317075 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 436 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 15 ********** No masking Map Score: 3.13593e-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