AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i246_synecho_ctra_300.orf -o246_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 RCY41704 31 Synechocystis #2 RCY18056 198 Synechocystis #3 RCY08755 34 Synechocystis #4 RCY52765 184 Synechocystis #5 RCY48216 97 Synechocystis #6 RCY38762 115 Synechocystis #7 RCY39606 109 Synechocystis #8 RCY28192 204 Synechocystis #9 RCY32608 188 Synechocystis #10 RCY37719 186 Synechocystis #11 RCY15189 19 Synechocystis #12 RCY26294 221 Synechocystis #13 RCY35925 251 Synechocystis #14 RCY00534 35 Synechocystis #15 RCY21204 91 Synechocystis #16 RCY18152 87 Synechocystis Motif number 1 CCGAAAATGCCGTGGGACAAAACCAGGTTAG 4 96 0 CTGGGACAAA 0.846965 -89 CTTCCCGGAGGCAATGGCAATTTTT 5 5 1 CGGAGGCAAT 0.650426 -93 GGGGCGAGACAATGGGGCAAAGAAAAATTGC 5 27 0 ATGGGGCAAA 0.837187 -71 AGCCCTTGGGGGACATATTGACCCT 7 5 1 CTGGGGGACA 0.902892 -105 TCCACTACGATATGGGGGAATTCCATCATAA 7 68 0 TTGGGGGAAT 0.990601 -42 CTCTGGCCAACCTGGGGGGTTTGTAGGTGTA 9 117 1 CTGGGGGGTT 0.914954 -72 TCCCCCAAAGTTTGAGGGATTAAGAAAAACC 10 64 0 TTGAGGGATT 0.825459 -123 TCCCTCAAACTTTGGGGGATTTTGATTAATC 10 76 1 TTGGGGGATT 0.977806 -111 ATAGCTAGGTTCTGGGACAATCTCACCTGAA 10 127 1 TTGGGACAAT 0.921963 -60 TTGGCTTCCTTATGGGGGAAACTTTCTTTGC 12 145 0 TTGGGGGAAA 0.981908 -77 AACAATTATTTCTGGGGCATTGGCTTCCTTA 12 164 0 TTGGGGCATT 0.967402 -58 CCGGATAAGCTTTCGGGGAATACGCAGTCGG 13 74 0 TTCGGGGAAT 0.898359 -178 GACGTAGAGTTAGGGGGGAAATTTCCGGATA 13 98 0 TGGGGGGAAA 0.935784 -154 ACTCTACGTCCATGGGGGGATTACTTTATCT 13 119 1 CTGGGGGGAT 0.962596 -133 CTGCTTTCGGTCTGGGACAATTGTGACTGTT 13 180 0 TTGGGACAAT 0.921963 -72 * ********* Masking position 6 Map Score: 19.6636 Number of sites scoring better than the average of aligned sites = 2448 Number in coding regions = 2050 Number in noncoding regions = 398 Number of orfs with sites within 600 bp upstream = 299 Fraction of orfs with sites within 600 bp upstream = 0.0480244 Motif number 2 AATTTGTTACCCGTGATACCAAGAGCGAGCTAAAACGCCA 4 26 0 CCGTCAGACC 0.978055 -159 AGGCTCAAACCCGCTATTTCCGGGACTTAGTCCGAAAATG 4 118 0 CCTTCCGGCG 0.913207 -67 ATTGTCTCGCCCCCCCTAGCCTGACCTCTGACCAAATTTA 5 45 1 CCCTCCGACG 0.977324 -53 AGCCGTTTTCCCAATTGCTCCTCACCGGGCTGACTTTTTT 8 127 1 CCTGCCCACC 0.989124 -78 TGAATTTTTGCCAACGGGCCCTGATCCAACATCCTAAAAG 9 50 0 CCCGCCGACC 0.991729 -139 GGCAAAAATTCAAGTTGCCCCTCACCCTCCCCAAGGAAGC 9 78 1 CATGCCCACC 0.957498 -111 TACAAACCCCCCAGGTTGGCCAGAGCTTCCTTGGGGAGGG 9 102 0 CCGTCCGACC 0.994464 -87 TCAAGCCAAACCGCATCTAACGCCAAGGGAG 12 2 1 CACACCCACC 0.871599 -220 GCATCTAACGCCAAGGGAGCCCCAACAGGCTCCTTTTTTA 12 23 1 CCGGCCCACC 0.99572 -199 ATCAATCTAACAAGGCTTACACCGACTCAGTTTGGCAAGA 13 29 0 CAGTCACGCG 0.66328 -223 GGGATAATAGCCTTGGTAGCAACAGCAACCCCAGCAATTG 13 210 1 CCGTCACACC 0.981548 -42 ** * * ** ** * * Masking position 10 Map Score: 8.73111 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 716 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 TTAAAAATTATTAAAACAGAATCTTAA 1 15 0 AAATTAAAAC 0.929144 -17 CAGAATTTGGACGAATTGTTAGAAAACGCAAAATT 2 110 0 AAATTAGAAA 0.846728 -89 GCCAACAATCTCAAAAGATTGGCTTAAC 3 17 0 AAATCAAAGA 0.692415 -18 ATCACGGGTAACAAATTTATGGAACGGAGCAGGGT 4 49 1 AAATTGGAAC 0.840371 -136 CCCACCTTTCTCCAATTCTAGAAAACATT 4 166 1 TAATTGAAAA 0.681399 -19 CCCGGTGAGGAGCAATTGGGAAAACGGCTTGGGCT 8 121 0 AAATTAAAAC 0.929144 -84 GTTGCTTAAAACAAATCTGGGAAAAAAGTCAGCCC 8 153 0 AAATCGAAAA 0.938235 -52 CCAAAGTTTGAGGGATTAAGAAAAACCATTTAGAT 10 56 0 AGATTAAAAA 0.732363 -131 TTTGCTTTACAAAAATTTACAAAACTGTTACATTT 12 99 1 AAATTAAAAC 0.929144 -123 AATTCCTACGAGCAATCAAGAAAAACAATTATTTC 12 183 0 AAATCAAAAA 0.929144 -39 TCAGTTTGGCAAGAATTATTGAAAACGAAGAG 13 8 0 AAATTGAAAA 0.948625 -244 TAGCTCCATCAAAAATCAACGAAAATCAACATTAT 16 12 1 AAATCGAAAA 0.938235 -76 * **** ***** Masking position 5 Map Score: 5.73986 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 264 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 CTTTGACCTAAGGCGATCGCCTTACCCCAGACTAACT 2 15 1 AGGTGCTACC 0.911613 -184 CAACAATCTCAAAAGATTGGCTTAACCGAAAC 3 6 0 AAATGCTACC 0.987335 -29 AGAATTGGAGAAAGGTGGGCCTAATCCAGGCTCAAAC 4 148 0 AAAGGCAACC 0.984132 -37 ACTACACCGAAAACTTTTGGCTTATCCACGGCCATTG 6 11 1 AAATGCTACC 0.987335 -105 CCCTGACTGAAAAAAATGGACAAATCCAGAAGGACAT 7 32 1 AAATGCAACC 0.984442 -78 CAAAAATTTCATACCGTCGTCATAGCCCTGTCATACT 8 61 1 ATATGCTACC 0.941806 -144 CTACATTAATAAATGTCAGCCCAAGCCGTTTTCCCAA 8 104 1 AAACGCAACC 0.958568 -101 TTGTAGGTGTAAACCGGTTCCCAATCCTTTTTAACTT 9 137 1 AAAGTCAACC 0.924314 -52 TTGGCAAGTCAGAGACGTTGCATATCCAGATAAAGTA 13 140 0 AGAGTCTACC 0.894936 -112 *** * * * ** ** Masking position 14 Map Score: 6.04857 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 159 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 AATTGTCAGGAAAAGACTGGCATTGACGCAAAA 2 81 0 AAAAATGCAT 0.964764 -118 ATCTTCTTCGATCATACTGCCATATCAGATACA 2 143 0 ATCAATGCAT 0.809705 -56 CAACAATCTCAAAAGATTGGCTTAACCGAAAC 3 10 0 AAAAATGCTT 0.922545 -25 ATGGGGCAAAGAAAAATTGCCATTGCCTCCGGG 5 14 0 GAAAATGCAT 0.9449 -84 GCCCTTGGGGGACATATTGACCCTGACTGAAAA 7 12 1 GACAATGCCC 0.841452 -98 GGGGAATTCCATCATAATGTCCTTCTGGATTTG 7 52 0 ATCAATGCCT 0.845626 -58 ATACAAAAAAAAGCCCTCTAAAACAAT 8 5 1 AAAAAAGCCT 0.897399 -200 AAAGCCCTCTAAAACAATGACCTTGTCCTGAAA 8 20 1 AAAAATGCCT 0.972383 -185 ACCTTGTCCTGAAAAACTGACACAAAAATTTCA 8 39 1 GAAAATGCAC 0.868104 -166 ACAGTTCAGCAAATAAGTGTCATCAAGCC 8 186 1 AAATATGCAT 0.776712 -19 ATTTAGATCAAAAATATAGTCTTGTCTGCTCTG 10 31 0 AAAAAAGCTT 0.747181 -156 **** * ** *** Masking position 6 Map Score: 5.02318 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 276 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 GCGAGCTAAAACGCCAATGGTTGAAGGCGA 4 12 0 ACGCCAATGG 0.952723 -173 TAGTCCGAAAATGCCGTGGGACAAAACCAG 4 101 0 ATGCCGTGGG 0.904529 -84 AAAATTGCCATTGCCTCCGGGAAG 5 5 0 TTGCCTCCGG 0.908561 -93 GATTGCTGCCATGACAATGGCCGTGGATAA 6 32 0 ATGACAATGG 0.827908 -84 TCGGATCTTTATGCCTAGGGCCAGCAATGG 6 60 1 ATGCCTAGGG 0.976892 -56 TGACAGGGCTATGACGACGGTATGAAATTT 8 64 0 ATGACGACGG 0.921891 -141 ACTTGAATTTTTGCCAACGGGCCCTGATCC 9 63 0 TTGCCAACGG 0.958068 -126 ACCGCATCTAACGCCAAGGGAGCCCCAACA 12 20 1 ACGCCAAGGG 0.978451 -202 AACGCCTCCGGTCAATTGCTG 13 241 0 ACGCCTCCGG 0.962874 -11 ********** Masking position 5 Map Score: 7.92256 Number of sites scoring better than the average of aligned sites = 808 Number in coding regions = 759 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 7 CGCTCTTGGTATCACGGGTAACAAATTTATGGAA 4 39 1 ACAGGTAACA 0.987316 -146 TATGGAACGGAGCAGGGTTAACTATAAAGGCTAA 4 66 1 ACAGTTAACA 0.98003 -119 AATCTAAAAAATCAAAGTTAAAAAGGATTGGGAA 9 154 0 ACAGTTAAAA 0.845681 -35 CTCACCTGAAATCCTGGTTCACAATAGTTTTTAT 10 148 1 ACCGTTCACA 0.946202 -39 ATTTTTGTAAAGCAAAGTTGACAAGGAGTTTTTT 12 81 0 ACAGTTGACA 0.970608 -141 CAGGGATAATAGCCTTGGTAGCAACAGCAACCCC 13 208 1 ACCGGTAGCA 0.952974 -44 TCAAATACTAAACAATGGTGACTATTTACACCAT 15 27 0 ACAGGTGACA 0.981266 -65 ATTTGACTGCAACCATGGTAACCAAAATACTGAT 16 45 1 ACCGGTAACA 0.987063 -43 * ** ****** * Masking position 1 Map Score: 5.78436 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 97 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 AATGGTTATGTTAGTTTGATGTAGTCCTAC 6 85 1 TTAGTTTGAT 0.961572 -31 AATTTTAGTTAAATCTAAAAAATC 9 175 0 TTAGTTAAAT 0.940876 -14 GTAAGCCTTGTTAGATTGATATCCTCCGAC 13 49 1 TTAGATTGAT 0.883796 -203 ATTAGTTAGATATTGAATGGT 15 2 1 TTAGTTAGAT 0.972867 -90 GGACGTACCTTTAGTTAAATTACTTGAGCA 15 72 0 TTAGTTAAAT 0.940876 -20 ********** Masking position 6 Map Score: 2.34421 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 17 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GATTGACAACACCTGGCCAGTTAGTCTGGG 2 40 0 ACCTGGCCAG 0.927834 -159 GGTGTTGTCAATCAGATCAGTGATTTTTGC 2 57 1 ATCAGATCAG 0.84378 -142 CTGAAGCTAAATTTGGTCAGAGGTCAGGCT 5 62 0 ATTTGGTCAG 0.976484 -36 ACCATTTGGTCAGGACAGA 11 7 0 ATTTGGTCAG 0.976484 -13 ATTGTTTAGTATTTGATCAGCCTAATCTGC 15 45 1 ATTTGATCAG 0.963515 -47 TAGTTAAATTACTTGAGCAGATTAGGCTGA 15 61 0 ACTTGAGCAG 0.907941 -31 ********** Masking position 9 Map Score: 2.13968 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 121 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 AGATCAGTGATTTTTGCGTCAATGCCAGTCTT 2 70 1 TTTTTGTCAA 0.942156 -129 AATGCCAGTCTTTTCCTGACAATTTTGCGTTT 2 90 1 TTTTCGACAA 0.827184 -109 TCCACGGCCATTGTCATGGCAGCAATCGGATC 6 35 1 TTGTCGGCAG 0.919419 -81 TTTGTCCATTTTTTTCAGTCAGGGTCAATATG 7 24 0 TTTTTGTCAG 0.951781 -86 TTGTGTCAGTTTTTCAGGACAAGGTCATTGTT 8 32 0 TTTTCGACAA 0.827184 -173 CGGTATGAAATTTTTGTGTCAGTTTTTCAGGA 8 45 0 TTTTTGTCAG 0.951781 -160 ATTGTGACTGTTTTCTTGGCAAGTCAGAGACG 13 160 0 TTTTCGGCAA 0.965517 -92 ***** ***** Masking position 11 Map Score: 3.12682 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 76 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 GACGAATTGTTAGAAAACGCAAAATTGTCA 2 106 0 TAGAAAACGC 0.893662 -93 AGGGAAATAAAAAAGGCTGAAGCTAAA 5 81 0 TAAAAAAGGC 0.906042 -17 ATCGTAGTGGAAGAAAAGGAAGTGCAAAAA 7 88 1 AAGAAAAGGA 0.860034 -22 AAAATCAAAGTTAAAAAGGATTGGGAACCG 9 151 0 TTAAAAAGGA 0.916705 -38 CTGGTCGCAATAAAAAAGGAGCCTGTTGGG 12 43 0 TAAAAAAGGA 0.93477 -179 TAAAGCAAAGTTGACAAGGAGTTTTTTTAT 12 78 0 TTGACAAGGA 0.874907 -144 GCAAGAATTATTGAAAACGAAGAG 13 5 0 TTGAAAACGA 0.905583 -247 ********** Masking position 6 Map Score: 1.57401 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 195 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 GTTTCGGTTAAGCCAATCTTTTGAGAT 3 8 1 TTAAGCCAAT 0.510983 -27 AATGACCTTGTCCTGAAAAACTGACACAAA 8 35 1 TCCTGAAAAA 0.619822 -170 CAGATTTGTTTTAAGCAACAGTTCAGCAAA 8 169 1 TTAAGCAACA 0.675952 -36 TAAGCAACAGTTCAGCAAATAAGTGTCATC 8 180 1 TTCAGCAAAT 0.759255 -25 GTTTGAGGGATTAAGAAAAACCATTTAGAT 10 56 0 TTAAGAAAAA 0.883553 -131 ACTAGACAGATTAATCAAAATCCCCCAAAG 10 85 0 TTAATCAAAA 0.796616 -102 CAATGTGAATTCAATAAAAACTATTGTGAA 10 165 0 TCAATAAAAA 0.79672 -22 TCAAGCCAAACCGCATCTAA 12 1 1 TCAAGCCAAA 0.881858 -221 CTACGAGCAATCAAGAAAAACAATTATTTC 12 183 0 TCAAGAAAAA 0.923961 -39 ACGTTGCATATCCAGATAAAGTAATCCCCC 13 133 0 TCCAGATAAA 0.664492 -119 CAGTCTCCTATTCATAAAAATTCCTC 14 7 0 TTCATAAAAA 0.739323 -29 CTAGCTCCATCAAAAATCAACGAAA 16 6 1 TCCATCAAAA 0.87903 -82 ********** Masking position 8 Map Score: 2.55108 Number of sites scoring better than the average of aligned sites = 1466 Number in coding regions = 1206 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 261 Fraction of orfs with sites within 600 bp upstream = 0.041921 Motif number 13 ********** No masking Map Score: 3.98858e-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: 3.98858e-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: 3.98858e-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