AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i156_HYP_operon_synecho_reg_300.orf -o156_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY13429 300 Synechocystis #2 RCY10985 60 Synechocystis #3 RCY44593 75 Synechocystis #4 RCY02841 300 Synechocystis #5 RCY12071 48 Synechocystis #6 RCY11225 52 Synechocystis #7 RCY27445 138 Synechocystis #8 RCY51708 50 Synechocystis #9 RCY52667 189 Synechocystis #10 RCY03223 273 Synechocystis #11 RCY25232 300 Synechocystis #12 RCY02659 52 Synechocystis #13 RCY51148 105 Synechocystis #14 RCY12836 110 Synechocystis #15 RCY33021 45 Synechocystis #16 RCY30918 138 Synechocystis Motif number 1 TTTTTATTCCCCAGGCAATGGCTCCAAATAA 1 86 0 CCAGGCATGG 0.89586 -215 AAAAAACGAACTAGGGTGGGGGTGGGCAAAG 1 112 1 CTAGGGGGGG 0.969253 -189 TAGGGTGGGGGTGGGCAAAGAGCCATTATTC 1 123 1 GTGGGCAAGA 0.870283 -178 TCTTATGGAGGAGGGCTAGGGAAATTTGACA 1 210 1 GAGGGCAGGG 0.97862 -91 TTTAGTCTCGGTGGGTTAGGGC 2 2 0 GTGGGTAGGG 0.817524 -59 TCATCCCTAGCTAGGGTAGGGGATATTGTTT 4 96 1 CTAGGGAGGG 0.981574 -205 TCCTGGTGATGTGGGGAATGGCTGGTCCGAG 4 140 1 GTGGGGATGG 0.955713 -161 CGAAAATTGTCCAGGCCGTGATTTTGTTAAG 7 56 0 CCAGGCGTGA 0.698539 -83 AAAACCAAACCTGGGCCATGGTTCAACT 8 8 0 CTGGGCATGG 0.978715 -43 TTAAGTCTCCCTAGGGAGGGAAATTTCTGCC 9 23 1 CTAGGGGGGA 0.934845 -167 AAAGGGTAAGCAGGGGGGAGATCAAAAATTT 9 117 0 CAGGGGGAGA 0.883054 -73 GGAATCGTGTTGGCGATGGATTTTTGTCG 9 171 0 GTTGGCATGG 0.826504 -19 AATCAATCGCCTAGGGCAGGGAAATCTGAAG 10 139 1 CTAGGGAGGG 0.981573 -135 ACACTCTCCCCAGGGGAAAGAAAACTTGGCT 10 195 0 CAGGGGAAGA 0.927328 -79 ACGATGGGGGCAAGGGGGGGAGAAAAACCCC 10 248 0 CAAGGGGGGA 0.927572 -26 ACTATTGCCATGGGCAGGGTAAATTGATT 11 9 1 CATGGGAGGG 0.955615 -292 GGCCAACCAGAGCAAGGATTTTTTTTGA 12 8 1 CAGAGCAGGA 0.662105 -45 GAAAAAACCGGAGGGCAAAGAACCGAAC 13 8 0 GAGGGCAAGA 0.856907 -98 CGTGCTTATGCATGGCCATGGTTTACCGGAT 16 66 1 CATGGCATGG 0.900591 -73 ****** **** Masking position 5 Map Score: 23.8621 Number of sites scoring better than the average of aligned sites = 4354 Number in coding regions = 3931 Number in noncoding regions = 423 Number of orfs with sites within 600 bp upstream = 403 Fraction of orfs with sites within 600 bp upstream = 0.0647286 Motif number 2 ATGGGTAGTAAGGATAATTTTTTGAACTGA 1 152 0 AGGATAATTT 0.942214 -149 GAGGAGGGCTAGGGAAATTTGACATCACTT 1 217 1 AGGGAAATTT 0.972893 -84 GGTTAACGAAAATTTTCAGTAACAG 1 286 0 ACGAAAATTT 0.774689 -15 TTTAAACCATAGCGAAAATTGTCCAGGCCG 7 69 0 AGCGAAAATT 0.782945 -70 CTCCCTAGGGAGGGAAATTTCTGCCGTTGC 9 29 1 AGGGAAATTT 0.972893 -161 CTTAAAATTCAGGAAAAATTTTTGATCTCC 9 102 1 AGGAAAAATT 0.918749 -88 AGTTGAGATCGGGAAAATTTGGTATTTAAC 10 108 0 GGGAAAATTT 0.847449 -166 CGCCTAGGGCAGGGAAATCTGAAGTAAATC 10 146 1 AGGGAAATCT 0.947694 -128 TGCCATGGGCAGGGTAAATTGATTTTTTCT 11 16 1 AGGGTAAATT 0.842128 -285 CCATTCAGTCAGGATAATTTTTGCAGTTTT 11 81 1 AGGATAATTT 0.942214 -220 AAAACTTAGAAGCAAAATCTAGCTATTCTT 14 66 0 AGCAAAATCT 0.847705 -45 GGGAAGAGGAAAGTCTATAGTGGCAG 16 7 1 AGGAAAGTCT 0.848882 -132 GGATAAATTCAGCATAGTTT 16 129 1 AGCATAGTTT 0.617244 -10 ********** Masking position 6 Map Score: 13.7068 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 814 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 3 CATTGCCTGGGGAATAAAAAACGAACTAGG 1 97 1 GGAATAAAAA 0.691281 -204 GGGAAAAAAAGCTAATTGAT 4 1 1 GGGAAAAAAA 0.934745 -300 TGGCTGGTCCGAGAGAAACAGGCTAGGCTT 4 158 1 GAGAGAAACA 0.597224 -143 TGTAGCTAGTGGCAAAAATCTTTACAAAGC 4 184 0 GGCAAAAATC 0.878923 -117 GTGGAGCTTTGAGAAAAACCAAACCTGGGC 8 23 0 GAGAAAAACC 0.927688 -28 AAGCAGGGGGGAGATCAAAAATTTTTCCTG 9 111 0 GAGATCAAAA 0.522026 -79 TGGTTACTTCGACAAAAATCCATCGCCAAC 9 162 1 GACAAAAATC 0.659642 -28 CTCTCCCCAGGGGAAAGAAAACTTGGCTAC 10 193 0 GGGAAAGAAA 0.769752 -81 GCAAGGGGGGGAGAAAAACCCCAGTCACCG 10 240 0 GAGAAAAACC 0.927688 -34 ACTGGAAAATGGGATCAAACAACAAGAAAA 11 40 0 GGGATCAAAC 0.880686 -261 CGATCGCCTAGGGATAAACAATAAACGTGT 11 148 1 GGGATAAACA 0.954359 -153 TGTCAATCCAGGGATAAATCCAGGCATATT 11 183 0 GGGATAAATC 0.932712 -118 GACTTAGGGGGGCAAAAACAATGTCAATCC 11 204 0 GGCAAAAACA 0.91632 -97 AAAACCGGAGGGCAAAGAACCGAAC 13 6 0 GGCAAAGAAC 0.712675 -100 AACAATTTCAGGAAAAAACCGGAGGGCAAA 13 20 0 GGAAAAAACC 0.905362 -86 TGATTCCGATGGGATAAACACAATGTAACA 13 46 0 GGGATAAACA 0.954359 -60 TTATCCCATCGGAATCAATCCCAAATCGAG 13 59 1 GGAATCAATC 0.500933 -47 ********** Masking position 4 Map Score: 13.9794 Number of sites scoring better than the average of aligned sites = 2227 Number in coding regions = 1907 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 332 Fraction of orfs with sites within 600 bp upstream = 0.0533248 Motif number 4 CTCCCAAAGGCGATCGCCGATTATTTCAGA 3 48 0 CGATCGCCGA 0.996386 -28 TTTAGTTTGGCGATCGCCGATAAAAAGTAG 4 45 1 CGATCGCCGA 0.996386 -256 CGACAAAAATCCATCGCCAACACGATTCC 9 171 1 CCATCGCCAA 0.974164 -19 TCAACTAAATCAATCGCCTAGGGCAGGGAA 10 132 1 CAATCGCCTA 0.978194 -142 TTGCCCCCGGCGATCGCCTAGGGATAAACA 11 138 1 CGATCGCCTA 0.994421 -163 ********** Masking position 4 Map Score: 8.42942 Number of sites scoring better than the average of aligned sites = 1806 Number in coding regions = 1596 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 5 GTTCGTTTTTTATTCCCCAGGCAATGGCTC 1 93 0 TATTCCCCAG 0.950443 -208 AACAGTTCGTTTCGCCCAAATTAGAGGGTG 1 261 0 TTCGCCCAAA 0.705612 -40 TGTCCACTGTTACTGCCAAGAAACT 2 46 1 TACTGCCAAG 0.970829 -15 CTTGACTAATTATTGCCAAATTGATGGCTC 3 20 1 TATTGCCAAA 0.800042 -56 TTTTACCTCTCCCAAAGGCGATCGCC 3 60 0 CTCTCCCAAA 0.726713 -16 AAACAACAAAATCTGCCCAGGAGTTATTAA 4 266 0 ATCTGCCCAG 0.704939 -35 ATGTAACAGTTACGGCCAAGAAC 5 4 0 TACGGCCAAG 0.948282 -45 AGTTGAACCATGGCCCAGGTTTGGTTTT 8 9 1 CATGGCCCAG 0.865256 -42 TTTAAGCGAGTATTCCCCAACTGGACAAAA 9 78 0 TATTCCCCAA 0.832551 -112 TTACTCCCATGATAGCCACAA 10 2 1 TACTCCCATG 0.907238 -272 CTAACCAACACTCTCCCCAGGGGAAAGAAA 10 203 0 CTCTCCCCAG 0.925748 -71 ACTATTGCCATGGGCAGGGTAA 11 3 1 TATTGCCATG 0.815711 -298 GAAAATCCCTTACTCCCCAGCAATTTCAGC 11 249 1 TACTCCCCAG 0.975971 -52 TCCGGTAAACCATGGCCATGCATAAGCACG 16 66 0 CATGGCCATG 0.452627 -73 ********** Masking position 6 Map Score: 12.8357 Number of sites scoring better than the average of aligned sites = 1897 Number in coding regions = 1702 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 6 AAGATGCCACCAACTAACCCTTCAAATAAGATTTCTC 1 23 1 CAACCTAAAT 0.923222 -278 GGCAAAGAGCCATTATTCAGTTCAAAAAATTATCCTT 1 136 1 CATCATAAAA 0.470452 -165 CGATTCTTGACAAGTGCCCAGTCAAATGGGTAGTAAG 1 170 0 CAACCGAAAT 0.979893 -131 CGGCGATCGCCAAACTAAAGTTTAAAACCTGACATCA 4 27 0 CAAAATAAAA 0.541496 -274 CACGGCGGGACAAAAGCCCGGGAGACTTTAATGACCA 4 212 1 CAACCGGACT 0.836078 -89 AATACTCGCTTAAAATTCAGGAAAAATTTTTGATCTC 9 94 1 TAACAGAAAT 0.61795 -96 ATGATAGCCACAAGAATAACTTCAAATTTAATTCACC 10 19 1 CAAAATAAAT 0.646299 -255 ACTTCAAATTTAATTCACCAGATAAAATAGCTTAAGT 10 37 1 TAACCGAAAA 0.733652 -237 CACGCAACTACATGTAACCGGTTAAATACCAAATTTT 10 88 1 CATCCGAAAT 0.936216 -186 ACTATTGCCATGGGCAGGGTAAATTGATTTTTTC 11 8 1 CCACAGAAAT 0.674754 -293 AAAATGGGATCAAACAACAAGAAAAAATCAATTTACC 11 28 0 CAACAGAAAA 0.922807 -273 GAATGGAAGTCAAAAAGACTGGAAAATGGGATCAAAC 11 50 0 CAAACGAAAT 0.951249 -251 TCAATGTTATCAAAACTCCATAAAAAAACTGCAAAAA 11 98 0 CAACCTAAAA 0.885999 -203 TAGGGATAAACAATAAACGTGTGAACTAATATGCCTG 11 156 1 CAACGGAACT 0.833433 -145 CCTAAGTCAGCAATGACAGAGTTGAAAATCCCTTACT 11 226 1 CAAAGGGAAA 0.372564 -75 ATTCTACTTCCATTAATACTGTTAAATAACCTGCTAT 15 18 0 CATACGAAAT 0.854585 -28 AAACAGAGCTCAAGCTCACCGGAAACTCTGCCACTAT 16 27 0 CAAACGAACT 0.903116 -112 CATGGCCATGCATAAGCACGGCAAACAGAGCTCAAGC 16 49 0 CATACGAACA 0.644711 -90 *** ** * **** Masking position 15 Map Score: 8.6013 Number of sites scoring better than the average of aligned sites = 1539 Number in coding regions = 1340 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 7 TCTTATTTGAAGGGTTAGTTGGTGGCATCT 1 24 0 AGGGTTAGTT 0.851734 -277 ACTCCTGGGCAGATTTTGTTGTTTAGCTAG 4 272 1 AGATTTTGTT 0.931649 -29 GTCCAGGCCGTGATTTTGTTAAGATGTAGT 7 49 0 TGATTTTGTT 0.791185 -90 ATGGTTTAAAAGGTTTGCTTACCGTTGCCC 7 89 1 AGGTTTGCTT 0.880646 -50 ACCATGGCCCAGGTTTGGTTTTTCTCAAAG 8 17 1 AGGTTTGGTT 0.965027 -34 CCTAGGCGATTGATTTAGTTGAGATCGGGA 10 124 0 TGATTTAGTT 0.791185 -150 AATATTCTTTAGATTTACTTCAGATTTCCC 10 157 0 AGATTTACTT 0.784702 -117 CCCTGGGGAGAGTGTTGGTTAGAATCTGAC 10 211 1 AGTGTTGGTT 0.840405 -63 AAGAATAGCTAGATTTTGCTTCTAAGTTTT 14 66 1 AGATTTTGCT 0.739758 -45 TTTGCTTCTAAGTTTTGGTTTTCCGCCGCA 14 80 1 AGTTTTGGTT 0.924509 -31 ********** Masking position 5 Map Score: 4.69193 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 271 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 GTTAACTTAATCATCCCTAGCTAGGGTAGG 4 86 1 TCATCCCTAG 0.912473 -215 ACCAGGAATCGGAACCCTAGAAACAATATC 4 117 0 GGAACCCTAG 0.773502 -184 CGGGCCTATCTCAACAATGGGGTCTTGGAC 7 21 1 TCAACAATGG 0.752297 -118 GCAAACCTTTTAAACCATAGCGAAAATTGT 7 77 0 TAAACCATAG 0.88563 -62 AGTTGAACCATGGCCCAGGTTTG 8 4 1 TGAACCATGG 0.963586 -47 TTTTGTCGAAGTAACCATAGAGAATCAAAA 9 149 0 GTAACCATAG 0.860509 -41 CCTCAACGATGGGGGCAAGGGG 10 262 0 TCAACGATGG 0.81818 -12 CGTTTATTGTTTATCCCTAGGCGATCGCCG 11 145 0 TTATCCCTAG 0.914064 -156 ATGCCTGGATTTATCCCTGGATTGACATTG 11 186 1 TTATCCCTGG 0.959179 -115 TTTGCCGTGCTTATGCATGGCCATGGTTTA 16 61 1 TTATGCATGG 0.751866 -78 TTCAATCCGGTAAACCATGGCCATGCATAA 16 71 0 TAAACCATGG 0.944774 -68 TATGCTGAATTTATCCATGGGAGCTTTAAC 16 115 0 TTATCCATGG 0.966106 -24 ********** Masking position 3 Map Score: 8.98381 Number of sites scoring better than the average of aligned sites = 983 Number in coding regions = 870 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 9 TGAACTGAATAATGGCTCTTTGCCCACCCC 1 130 0 AATGGCTCTT 0.862589 -171 ATTATTGCCAAATTGATGGCTCTGAAATAA 3 28 1 AATTGATGGC 0.784338 -48 AAAAAAAGCTAATTGATGTCAGGTTTTAAA 4 14 1 AATTGATGTC 0.881522 -287 TGATGTGGGGAATGGCTGGTCCGAGAGAAA 4 146 1 AATGGCTGGT 0.856217 -155 CTGGACAAAAAATGGCAGTTAGTTTAACCG 9 58 0 AATGGCAGTT 0.908029 -132 ATCCTGACTGAATGGAAGTCAAAAAGACTG 11 66 0 AATGGAAGTC 0.968424 -235 CTCTTCTAGTAATGGAACTCGATTTGGGAT 13 76 0 AATGGAACTC 0.940495 -30 AGTGGATCTCCTCTTCTAGT 13 96 0 AGTGGATCTC 0.819807 -10 TAACAGTATTAATGGAAGTAGAATA 15 31 1 AATGGAAGTA 0.825923 -15 ********** Masking position 3 Map Score: 1.947 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 291 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 TGGGGGTGGGCAAAGAGCCATTATTCAGTT 1 128 1 CAAAGAGCCA 0.906559 -173 TGGTTTTTCTCAAAGCTCCACTGACTTAT 8 32 1 CAAAGCTCCA 0.991413 -19 GTTACTTCGACAAAAATCCATCGCCAACAC 9 164 1 CAAAAATCCA 0.895848 -26 TCAATGTTATCAAAACTCCATAAAAAAACT 11 105 0 CAAAACTCCA 0.969259 -196 TCGCCGGGGGCAAAGCTCAATGTTATCAAA 11 121 0 CAAAGCTCAA 0.969251 -180 GCACGGCAAACAGAGCTCAAGCTCACCGGA 16 41 0 CAGAGCTCAA 0.90624 -98 ATAGGGGGGTTAAAGCTCCCATGGATAAAT 16 107 1 TAAAGCTCCC 0.821808 -32 ********** Masking position 4 Map Score: 4.18458 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 215 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 CCATTCCTACTTTAGCAATTGAATTTCTTA 1 59 1 TTTAGCAATT 0.870367 -242 TGTCCCGCCGTGTAGCTAGTGGCAAAAATC 4 194 0 TGTAGCTAGT 0.966609 -107 GATTTTGTTGTTTAGCTAGTAACTACCT 4 283 1 TTTAGCTAGT 0.960087 -18 TCATAGGATGTGTAACTAGTCAAACGGGCA 7 114 0 TGTAACTAGT 0.87115 -25 TTCCTGAATTTTAAGCGAGTATTCCCCAAC 9 87 0 TTAAGCGAGT 0.766188 -103 AGCAATACACTTAAGCTATTTTATCTGGTG 10 52 0 TTAAGCTATT 0.849626 -222 ATAAACACAATGTAACAATTTCAGGAAAAA 13 33 0 TGTAACAATT 0.64968 -73 AGAAGCAAAATCTAGCTATTCTTTAGGGTG 14 59 0 TCTAGCTATT 0.872127 -52 ********** Masking position 4 Map Score: 1.17616 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 100 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 TTGACTGGGCACTTGTCAAGAATCGGCCTC 1 182 1 ACTTGTCAAG 0.906382 -119 TTTTTTATTAACTTGTCCACTGTTACTGCC 2 33 1 ACTTGTCCAC 0.87509 -28 TTTGGCAATAATTAGTCAAGTTAAAGTTA 3 10 0 ATTAGTCAAG 0.720544 -66 TCTCCCGGGCTTTTGTCCCGCCGTGTAGCT 4 207 0 TTTTGTCCCG 0.859481 -94 AAACAACAAAATCTGCCCAGGAGTTATTAA 4 266 0 ATCTGCCCAG 0.904408 -35 CCATAGCGAAAATTGTCCAGGCCGTGATTT 7 63 0 AATTGTCCAG 0.939463 -76 AACTGCCATTTTTTGTCCAGTTGGGGAATA 9 68 1 TTTTGTCCAG 0.958383 -122 ATGAGGTGGGATCTGTCCAGATCAAAGCCT 14 22 1 ATCTGTCCAG 0.972693 -89 ********** Masking position 5 Map Score: 2.33706 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 306 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 13 GGCGAAACGAACTGTTACTGAAAATTTTCG 1 275 1 ACTGTTACTG 0.984505 -26 TAACTTGTCCACTGTTACTGCCAAGAAACT 2 41 1 ACTGTTACTG 0.984505 -20 GCAGGATGTAACAGTTACGGCCAAGAAC 5 9 0 ACAGTTACGG 0.954824 -40 TTAGAATCTGACGGTGACTGGGGTTTTTCT 10 229 1 ACGGTGACTG 0.969065 -45 ********** Masking position 5 Map Score: 0.311818 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 28 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ********** No masking Map Score: 5.65125e-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: 5.65125e-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