AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -inarP_synecho_opreg_100.orf -g0.48 -x5 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 = 0 Input sequences: #1 ccsA 186 c-type cytochrome synthesis protein #2 narB 300 nitrate reductase #3 1653591 298 hypothetical protein #4 1001440 300 beta transducin-like protein #5 1001146 273 hypothetical protein #6 cysG 195 uroporphyrin-III C-methyltransferase #7 1001796 300 hypothetical protein Motif number 1 AGTGATAGCCCAAGCAAATGCCAGACTGGCGA 1 88 1 CAGCAAAGCC 0.98406 -99 AAATGCCAGACTGGCGATCGCCGTTGCCGGAA 1 103 1 CGGCGATGCC 0.959409 -84 TAAACAAGATTAAGCAAATGGGCTTTTTACTA 1 153 0 TAGCAAAGGG 0.771551 -34 TCCAGCGGCCCTGGGATAAGGCTTACCGTCGG 3 52 0 CGGGATAGGC 0.958889 -247 AATGGCCGGGCTAGCAAAGGGCAGTTTGGTGA 3 96 0 CAGCAAAGGC 0.981883 -203 AGAATGGAGACAATGAAATGGCCGGGCTAGCA 3 112 0 CATGAAAGGC 0.673792 -187 TTTGCTCAACTCGGCGATCGCCCTAGCCCCAG 3 183 1 TGGCGATGCC 0.79731 -116 CTGCCAGGGACGGGGATAGGGGGGACTAAATC 4 111 0 CGGGATAGGG 0.897264 -190 TCAAAAATAGCGAGGAAAGCCCTAGGCGTTAG 4 177 0 CAGGAAACCC 0.802343 -124 CAATTATGGGCAGGGAAAAGCCTATTCGACCT 4 263 0 CGGGAAAGCC 0.989981 -38 TTGTAACGATTGGGGATATGGGCTAGTTTGGG 5 100 0 TGGGATAGGG 0.592419 -174 GAGAATTACTCCGGCGATCGCCATAATCTCAT 7 26 0 CGGCGATGCC 0.959409 -275 CCCTACCATTCTGGCAAATAGCTTAACAATTT 7 91 0 CGGCAAAAGC 0.937335 -210 CAATTGAAACCGGGCAAAAGCGAAGATCCCTA 7 167 1 CGGCAAAGCG 0.98212 -134 CTTACTTTGCCTAGCAATAACCCTGGGGCAAT 7 201 1 CAGCAATACC 0.732076 -100 * ****** *** Masking position 4 Map Score: 15.0729 Number of sites scoring better than the average of aligned sites = 3651 Number in coding regions = 3329 Number in noncoding regions = 322 Number of orfs with sites within 600 bp upstream = 323 Fraction of orfs with sites within 600 bp upstream = 0.0518792 Motif number 2 ATCACTAGAGCAAAGCCAATCAGAATCAAAG 1 63 0 CAAAGCCATC 0.966689 -124 TAGGATAGTAAAAAGCCCATTTGCTTAATCT 1 148 1 AAAAGCCATT 0.975457 -39 GCGATAGTAGCAAAGCTGATTATCACTGTCA 2 53 0 CAAAGCTATT 0.975494 -248 TGGAATAAGGAAAAACTGATTTTTCCTGGCG 2 126 1 AAAAACTATT 0.858918 -175 ATGGGCAGGGAAAAGCCTATTCGACCTGTAA 4 259 0 AAAAGCCATT 0.974378 -42 ACCTTAAAATAAAAGCTCATATTTTTTGCTC 5 15 0 AAAAGCTATA 0.86521 -259 TTAGTAATACCAAAGTTTATTTAGATTGATT 5 138 0 CAAAGTTATT 0.796009 -136 AGCCTGTTTTAAAAGCCCCTCTGGCCCCTCA 6 129 0 AAAAGCCCTC 0.840422 -67 TTTCAATTGCCAAAACTAATTAGTTTATTAA 7 145 0 CAAAACTATT 0.886857 -156 ******* *** Masking position 4 Map Score: 5.76367 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 275 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 AAACTCAACAGCGGCTAGGATAGTAAAAAGCC 1 133 1 GCGGCGGATA 0.895961 -54 ATTATTGATGGCACCTGGAATAAGGAAAAACT 2 111 1 GCACCGAATA 0.842845 -190 TTATCCCAGGGCCGCTGGAACTGGTTAAAACT 3 65 1 GCCGCGAACT 0.956747 -234 TTAAACGTTGGCCGCAATGATTGGCAGATCAA 3 228 0 GCCGCTGATT 0.927705 -71 TGCGGAAAAAGCCGCCCGAATTTGTTTGGTAA 4 21 1 GCCGCGAATT 0.99066 -280 TAAAAACTTTGCCGCCTGGTTTGATGGCAAAT 4 50 1 GCCGCGGTTT 0.969645 -251 GTTTTATTCCGCCCCCTAAATTCCCCAATAAT 6 66 1 GCCCCAAATT 0.954308 -130 AGCCCCTCTGGCCCCTCAAATTAGGAGGAATA 6 115 0 GCCCCAAATT 0.954308 -81 TTTTTAACTAGCTCCGAGAATTACTCCGGCGA 7 41 0 GCTCCGAATT 0.922144 -260 AATCAGAATTGCCCCAGGGTTATTGCTAGGCA 7 208 0 GCCCCGGTTA 0.935333 -93 ***** ***** Masking position 5 Map Score: 8.60682 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 514 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 GCCAGACTGGCGATCGCCGTTGCCGGAAAC 1 107 1 CGATCGCCGT 0.996433 -80 AGCTTTGCTACTATCGCAATAGTGGCAATA 2 67 1 CTATCGCAAT 0.956761 -234 GGTCGATATTTGATCGCAGTGAAAAACTTT 2 201 0 TGATCGCAGT 0.946072 -100 CTCAACTCGGCGATCGCCCTAGCCCCAGCA 3 187 1 CGATCGCCCT 0.987551 -112 TTAGTCCCCCCTATCCCCGTCCCTGGCAGT 4 114 1 CTATCCCCGT 0.962965 -187 CCTTTATTTTCTATCGAAGTTCCCTAAGGA 5 177 1 CTATCGAAGT 0.89467 -97 ATTACTCCGGCGATCGCCATAATCTCATTA 7 24 0 CGATCGCCAT 0.989516 -277 ********** Masking position 3 Map Score: 7.45196 Number of sites scoring better than the average of aligned sites = 3644 Number in coding regions = 3336 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 5 TTTGATCCTAGTGGGGGACCGACCCCAGGG 1 31 0 GTGGGGGACC 0.971335 -156 AACGTTTAAGATGGGGGCATTGTTTTAGTC 3 251 1 ATGGGGGCAT 0.960505 -48 GGTAATTACAATGGTGGACTAAAACAATGC 3 267 0 ATGGTGGACT 0.961997 -32 GGACGGGGATAGGGGGGACTAAATCACCAC 4 106 0 AGGGGGGACT 0.990983 -195 GGGAATTTAGGGGGCGGAATAAAACTTTTT 6 61 0 GGGGCGGAAT 0.891339 -135 GTCCCCCATTATTGGGGAATTTAGGGGGCG 6 75 0 ATTGGGGAAT 0.911297 -121 TTCCCCAATAATGGGGGACTTTCACTCAGT 6 86 1 ATGGGGGACT 0.993918 -110 ********** Masking position 6 Map Score: 5.76033 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 284 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 GGAATCTGAAGGAAAAAAATGTCACCGACG 3 28 1 GGAAAAAAAT 0.924791 -271 CGCTGGAACTGGTTAAAACTCACCAAACTG 3 77 1 GGTTAAAACT 0.951213 -222 GAATTTGTTTGGTAAAAACTTTGCCGCCTG 4 38 1 GGTAAAAACT 0.930177 -263 TAACTTATCATCATAAAAATATTAATATCC 5 221 0 TCATAAAAAT 0.731042 -53 TGTCAACGGTTAAAAATTAGTTTGCCT 5 257 0 GGTTAAAAAT 0.947374 -17 TCTGGTAAAATGTTAAAAATTTGACGTGAA 6 13 1 TGTTAAAAAT 0.884826 -183 TTAGGGGGCGGAATAAAACTTTTTAAACAC 6 55 0 GAATAAAACT 0.816884 -141 TAAAACAGGCTCTAAAAACTGTTGAATATT 6 149 1 TCTAAAAACT 0.667929 -47 AGCAAGTATTTGAAAAAAATTGTTAAGCTA 7 75 1 TGAAAAAAAT 0.839936 -226 CCAGTATCATGAATAAAAATCAGAATTGCC 7 227 0 GAATAAAAAT 0.804594 -74 ********** Masking position 5 Map Score: 5.22355 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 515 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 7 GGGACCGACCCCAGGGCAAAAATCGTTGAG 1 17 0 CCAGGGCAAA 0.986233 -170 ATTGATGGCACCTGGAATAAGGAAAAACTG 2 114 1 CCTGGAATAA 0.732953 -187 TAACTGTTCGCCAGGAAAAATCAGTTTTTC 2 135 0 CCAGGAAAAA 0.913997 -166 GGGCTAGCCCTCAGGACAAATTAACTATTA 2 172 1 TCAGGACAAA 0.909252 -129 TTCCAGCGGCCCTGGGATAAGGCTTACCGT 3 55 0 CCTGGGATAA 0.893328 -244 ACTGGGCAAGCCTAGTCAAAAATAGCGAGG 4 194 0 CCTAGTCAAA 0.808599 -107 ACAATTATGGGCAGGGAAAAGCCTATTCGA 4 266 0 GCAGGGAAAA 0.919823 -35 TTTAAGGTCATCAGGGCTAATCATTGTATT 5 38 1 TCAGGGCTAA 0.915747 -236 TAAGTTAAGTCCAAGGCAAACTAATTTTTA 5 244 1 CCAAGGCAAA 0.946653 -30 CCTCTGGTAAAATGTTAAAAAT 6 3 1 TCTGGTAAAA 0.767143 -193 CTTACGTCATTCACGTCAAATTTTTAACAT 6 22 0 TCACGTCAAA 0.592809 -174 CAGGGTTATTGCTAGGCAAAGTAAGGATAG 7 196 0 GCTAGGCAAA 0.82016 -105 ********** Masking position 9 Map Score: 9.94436 Number of sites scoring better than the average of aligned sites = 2724 Number in coding regions = 2447 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 312 Fraction of orfs with sites within 600 bp upstream = 0.0501124 Motif number 8 TTGCTCTAGTGATAGCCCAAGCAAATGCCA 1 81 1 GATAGCCCAA 0.917448 -106 CAGCGGCTAGGATAGTAAAAAGCCCATTTG 1 141 1 GATAGTAAAA 0.906898 -46 TGTCCTGAGGGCTAGCCCAAAATAATAACT 2 160 0 GCTAGCCCAA 0.953835 -141 AAATGGCCGGGCTAGCAAAGGGCAGTTTGG 3 99 0 GCTAGCAAAG 0.888778 -200 TCCAGACAACGCTAGCAAAACTGTCACCGT 3 145 1 GCTAGCAAAA 0.976976 -154 CGCCTGGTTTGATGGCAAATTCGGGATAAT 4 62 1 GATGGCAAAT 0.597495 -239 ACTGGGCAAGCCTAGTCAAAAATAGCGAGG 4 194 0 CCTAGTCAAA 0.545398 -107 CGGTGTGAAGTTAGTACAATTATGGGCAG 4 282 0 GTTAGTACAA 0.572819 -19 AGGGAACTTCGATAGAAAATAAAGGAATAT 5 172 0 GATAGAAAAT 0.626324 -102 AAATTATAGAGATAGAAAAATATTCAACAG 6 167 0 GATAGAAAAA 0.882087 -29 AATCTCATTAGCTAGAAAACTAG 7 4 0 GCTAGAAAAC 0.723689 -297 AATTCTCGGAGCTAGTTAAAAAAAAGCAAG 7 51 1 GCTAGTTAAA 0.718165 -250 TAACAAATTAGATGGCACAATTAATAAACT 7 125 1 GATGGCACAA 0.814581 -176 CAGGGTTATTGCTAGGCAAAGTAAGGATAG 7 196 0 GCTAGGCAAA 0.856947 -105 ********** Masking position 9 Map Score: 5.91305 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 705 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 9 TCTGCCCTCAACGATTTTTGCC 1 2 1 CTGCCCTCAC 0.94809 -185 CTTATTCCAGGTGCCATCAATAATTATCTGC 2 104 0 GTGCCATCAT 0.884417 -197 CTTCAATTAACTGCCAATATTTTA 2 287 1 CTGCCAATTT 0.934294 -14 ACTCACCAAACTGCCCTTTGCTAGCCCGGCC 3 94 1 CTGCCCTTGC 0.865983 -205 TGAAATTGATCTGCCAATCATTGCGGCCAAC 3 223 1 CTGCCAATAT 0.945999 -76 CCAATCATTGCGGCCAACGTTTAAGATGGGG 3 236 1 CGGCCAACTT 0.835878 -63 TCTTGTCACAGTGCCCACCGTCAATTAAGCA 4 223 1 GTGCCCACGT 0.943214 -78 AGGCTTTTCCCTGCCCATAATTGTACTAACT 4 272 1 CTGCCCATAT 0.970862 -29 ACTTTAATTCCTGCCCATGTACTCACCCAAA 5 75 1 CTGCCCATTA 0.895247 -199 TTTATTAATTGTGCCATCTAATTTGTTATCC 7 122 0 GTGCCATCAA 0.707432 -179 TGGGTCATGGCTTCCCACGTTTAATTTAAAA 7 254 1 CTTCCCACTT 0.802096 -47 ******** ** Masking position 5 Map Score: 4.14274 Number of sites scoring better than the average of aligned sites = 1312 Number in coding regions = 1178 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 10 GCATTTGCTTGGGCTATCACTAGAGCAAAG 1 79 0 GGGCTATCAC 0.906047 -108 AACTCAACAGCGGCTAGGATAGTAAAAAGC 1 134 1 CGGCTAGGAT 0.785302 -53 TTATTATTTTGGGCTAGCCCTCAGGACAAA 2 162 1 GGGCTAGCCC 0.499966 -139 TGAAATGGCCGGGCTAGCAAAGGGCAGTTT 3 101 0 GGGCTAGCAA 0.887944 -198 TACGATGCTGGGGCTAGGGCGATCGCCGAG 3 192 0 GGGCTAGGGC 0.891753 -107 CTAACGCCTAGGGCTTTCCTCGCTATTTTT 4 177 1 GGGCTTTCCT 0.849055 -124 TGACAAGACTGGGCAAGCCTAGTCAAAAAT 4 201 0 GGGCAAGCCT 0.74765 -100 TTGGGGATATGGGCTAGTTTGGGTGAGTAC 5 93 0 GGGCTAGTTT 0.864613 -181 AATAACCCTGGGGCAATTCTGATTTTTATT 7 216 1 GGGCAATTCT 0.776755 -85 ********** Masking position 4 Map Score: 4.85132 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 568 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 11 TTCTGATTGGCTTTGCTCTAGTGATAGCCC 1 69 1 CTTTGCTCTA 0.869401 -118 TAAAAAGCCCATTTGCTTAATCTTGTTTAG 1 156 1 ATTTGCTTAA 0.86011 -31 TGTATTCATCTTTTGGTCAATTAGTGGTCA 2 243 1 TTTTGGTCAA 0.932122 -58 CGTTCAATCATTTTGCTCAACTCGGCGATC 3 172 1 TTTTGCTCAA 0.983263 -127 ACCTGTAACATTTTGCTTAATTGACGGTGG 4 237 0 TTTTGCTTAA 0.952613 -64 AGCTCATATTTTTTGCTCATAA 5 3 0 TTTTGCTCAT 0.936528 -271 ********** Masking position 4 Map Score: 2.25179 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 218 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 12 TTAATTGAAGCGAATTTGATTAGTTGACCA 2 267 0 CGAATTTGAT 0.949418 -34 AAAAGCCGCCCGAATTTGTTTGGTAAAAAC 4 27 1 CGAATTTGTT 0.949418 -274 AGTATTCCTCCTAATTTGAGGGGCCAGAGG 6 113 1 CTAATTTGAG 0.89219 -83 AGTTTTCTAGCTAATGAGATTATGGCGATC 7 13 1 CTAATGAGAT 0.816071 -288 ATTGTGCCATCTAATTTGTTATCCCCTACC 7 116 0 CTAATTTGTT 0.957699 -185 AATTAATAAACTAATTAGTTTTGGCAATTG 7 143 1 CTAATTAGTT 0.923864 -158 ********** Masking position 5 Map Score: 1.72025 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 95 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TGATTATCACTGTCATGGATCGAGTTGCTAG 2 37 0 TGTCATGGTC 0.8752 -264 AGGAAAAAAATGTCACCGACGGTAAGCCTTA 3 37 1 TGTCACCGCG 0.960971 -262 CTAGCAAAACTGTCACCGTTCAATCATTTTG 3 156 1 TGTCACCGTC 0.992299 -143 TCCCTGGCAGTGTCAACGCTGACATATTGTC 4 133 1 TGTCAACGTG 0.957909 -168 TGCCCAGTCTTGTCACAGTGCCCACCGTCAA 4 216 1 TGTCACAGGC 0.940901 -85 TTAAGCAAAATGTTACAGGTCGAATAGGCTT 4 247 1 TGTTACAGTC 0.849574 -54 TGTCAACGGTTAAAAATTAGT 5 263 0 TGTCAACGTT 0.892975 -11 ******** ** Masking position 5 Map Score: 0.091519 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 160 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 ********** No masking Map Score: -6.20771e-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: -6.20771e-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