AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -inarL_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 frdA 175 succinate dehydrogenase flavoprotein subunit #4 sdhB 293 succinate dehydrogenase iron- sulphur protein subunit #5 1653267 249 hypothetical protein #6 1653591 298 hypothetical protein #7 1001440 300 beta transducin-like protein #8 1001146 273 hypothetical protein #9 cysG 195 uroporphyrin-III C-methyltransferase #10 sdhB 166 succinate dehydrogenase iron-sulfur protein #11 1001796 300 hypothetical protein Motif number 1 CAACGATTTTTGCCCTGGGGTCGGTCCCCCACTAG 1 19 1 TCCGGGGCGT 0.933439 -168 TTGAGTTTCCGGCAACGGCGATCGCCAGTCTGGCA 1 106 0 GCAGGCGTGC 0.956008 -81 TAGTTAATTTGTCCTGAGGGCTAGCCCAAAATAAT 2 164 0 GCCAGGGTGC 0.946802 -137 ACAATGACAATCCCTAGGGGCCTGCCTTCCCTAAT 3 130 0 TCCGGGGCGC 0.995325 -46 CATGGGTTAATGCCCAGGGGGCAGCGAATGATTTG 4 53 0 TCCGGGGCGC 0.995325 -241 CCACTAAAATTCCCAAGGCGATCGCCCCTAAAATC 4 120 0 TCCGGCGTGC 0.996087 -174 ATAGGCACAATTCTAGGGGGTTCTCGACAAAAAAA 4 198 1 TCTGGGGTTC 0.925979 -96 AGGAAATACCCTGGGAAAAGCAATATGGGCG 4 273 0 TCCGGGAAGC 0.922918 -21 AGATTTCCCTGCCCTAGGCGATTGATTTAGTTGAG 5 149 0 GCCGGCGTGA 0.969761 -101 ACCAACACTCTCCCCAGGGGAAAGAAAACTTGGCT 5 213 0 TCCGGGGAGA 0.893116 -37 ACGATGCTGGGGCTAGGGCGATCGCCGAGTTGAGC 6 186 0 GCTGGCGTGC 0.986223 -113 CCCTATCCCCGTCCCTGGCAGTGTCAACGCTGACA 7 122 1 GCCGGCATTC 0.884348 -179 AGCGAGGAAAGCCCTAGGCGTTAGCTTCAATTCTA 7 166 0 GCCGGCGTGC 0.99639 -135 ATAAATATCATCCTTAGGGAACTTCGATAGAAAAT 8 182 0 TCTGGGACTC 0.604545 -92 CTCCGAGAATTACTCCGGCGATCGCCATAATCTCA 11 27 0 TCTGGCGTGC 0.985056 -274 * ** **** * ** Masking position 8 Map Score: 24.9225 Number of sites scoring better than the average of aligned sites = 2521 Number in coding regions = 2331 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 2 TGCCCTCAACGATTTTTGCCCTGGGGTCGGTCC 1 13 1 GTTTTGCCTG 0.928036 -174 TCGCCAGTCTGGCATTTGCTTGGGCTATCACTA 1 87 0 GATTTGCTGG 0.944308 -100 AGGAAAAACTGATTTTTCCTGGCGAACAGTTAT 2 133 1 GTTTTCCTGC 0.942442 -168 AGAATTGTGCCTATTTTCCCAAGTCTTTGACAC 4 179 0 CTTTTCCCAG 0.698242 -115 CCGCCCATATTGCTTTTCCCAGGGTATTTCCT 4 272 1 TTTTTCCCGG 0.82036 -22 AGATTTACTTCAGATTTCCCTGCCCTAGGCGAT 5 162 0 CATTTCCCGC 0.931259 -88 CCGACGGTAAGCCTTATCCCAGGGCCGCTGGAA 6 52 1 GTTATCCCGG 0.814339 -247 TCACCAAACTGCCCTTTGCTAGCCCGGCCATTT 6 96 1 GCTTTGCTGC 0.889512 -203 TGAACGGTGACAGTTTTGCTAGCGTTGTCTGGA 6 145 0 CTTTTGCTGC 0.947314 -154 CTCATTATCCCGAATTTGCCATCAAACCAGGCG 7 62 0 CATTTGCCTC 0.750893 -239 CTAACGCCTAGGGCTTTCCTCGCTATTTTTGAC 7 177 1 GCTTTCCTGC 0.838002 -124 AGGTCGAATAGGCTTTTCCCTGCCCATAATTGT 7 263 1 GTTTTCCCGC 0.976131 -38 GGCTAATTTGCTGGGACTAATGGGG 10 3 1 CATTTGCTGG 0.922864 -164 TTGATCTATGGAATTTTGCCGGGACCAGGAATA 10 73 1 GTTTTGCCGG 0.989035 -94 AAGGTCGAGCCTTTTTTGCCCTGTTGATTTCCT 10 138 1 CTTTTGCCTG 0.900983 -29 AAATTGTTAAGCTATTTGCCAGAATGGTAGGGG 11 91 1 GATTTGCCGA 0.769416 -210 TAGGGATCTTCGCTTTTGCCCGGTTTCAATTGC 11 166 0 CTTTTGCCGG 0.984531 -135 ATTGCCCCAGGGTTATTGCTAGGCAAAGTAAGG 11 200 0 GTATTGCTGG 0.732131 -101 * ******* ** Masking position 7 Map Score: 20.186 Number of sites scoring better than the average of aligned sites = 1309 Number in coding regions = 1183 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 3 TGCTCTAGTGATAGCCCAAGCAAATGCCAG 1 82 1 ATAGCCCAAG 0.850647 -105 TTTTACTATCCTAGCCGCTGTTGAGTTTCC 1 131 0 CTAGCCGCTG 0.74061 -56 GCTGTAATTTATTGCCACTATTGCGATAGT 2 76 0 ATTGCCACTA 0.831267 -225 GTCCTGAGGGCTAGCCCAAAATAATAACTG 2 159 0 CTAGCCCAAA 0.877451 -142 GCTTCAATTAACTGCCAATATTTTA 2 286 1 ACTGCCAATA 0.622949 -15 TCCCAAGGCGATCGCCCCTAAAATCCAATC 4 115 0 ATCGCCCCTA 0.761332 -179 CATCACTAAGCCTGCCACTAAAATTCCCAA 4 139 0 CCTGCCACTA 0.859447 -155 TACTCCCATGATAGCCACAAGAATAACTTC 5 30 1 ATAGCCACAA 0.703039 -220 TTCAGATTTCCCTGCCCTAGGCGATTGATT 5 157 0 CCTGCCCTAG 0.674237 -93 GCCAAGTTTTCTTTCCCCTGGGGAGAGTGT 5 214 1 CTTTCCCCTG 0.685092 -36 GGCGATCGCCCTAGCCCCAGCATCGTACTG 6 195 1 CTAGCCCCAG 0.954701 -104 TAGGCTTTTCCCTGCCCATAATTGTACTAA 7 271 1 CCTGCCCATA 0.91111 -30 CACTTTAATTCCTGCCCATGTACTCACCCA 8 74 1 CCTGCCCATG 0.936351 -200 CTCACCCAAACTAGCCCATATCCCCAATCG 8 96 1 CTAGCCCATA 0.901181 -178 AATAAAAATTATTGCCCCCGGCCCTTCCGT 10 102 1 ATTGCCCCCG 0.835263 -65 CCCGGTTTCAATTGCCAAAACTAATTAGTT 11 151 0 ATTGCCAAAA 0.653479 -150 AAAAATCAGAATTGCCCCAGGGTTATTGCT 11 213 0 ATTGCCCCAG 0.950221 -88 ********** Masking position 5 Map Score: 13.1465 Number of sites scoring better than the average of aligned sites = 2981 Number in coding regions = 2663 Number in noncoding regions = 318 Number of orfs with sites within 600 bp upstream = 337 Fraction of orfs with sites within 600 bp upstream = 0.0541279 Motif number 4 AAAAGCCAGCAACGGGGTCTTAATCTAAACT 4 229 1 AAGGGGTCTT 0.876563 -65 CGTCCTAAAAAAAGGGGAATCTGAAGGAAAA 6 13 1 AAGGGGAATC 0.869033 -286 AACGTTTAAGATGGGGGCATTGTTTTAGTCC 6 251 1 ATGGGGCATT 0.908323 -48 GGACGGGGATAGGGGGGACTAAATCACCACT 7 105 0 AGGGGGACTA 0.893914 -196 GATTGTAACGATTGGGGATATGGGCTAGTTT 8 103 0 ATGGGGATAT 0.8758 -171 GTCCCCCATTATTGGGGAATTTAGGGGGCGG 9 74 0 ATGGGGAATT 0.958423 -122 TTCCCCAATAATGGGGGACTTTCACTCAGTA 9 86 1 ATGGGGACTT 0.973378 -110 TTGAGGGGCCAGAGGGGCTTTTAAAACAGGC 9 128 1 AGGGGGCTTT 0.863214 -68 TGCTGGGACTAATGGGGATAAAATTTAAGGG 10 19 1 AAGGGGATAA 0.707171 -148 GATAAAATTTAAGGGGGACATCCTCCTACAA 10 35 1 AAGGGGACAT 0.947209 -132 TCCATAGATCAATGGGGAATTGTAGGAGGAT 10 54 0 AAGGGGAATT 0.965986 -113 ** ******** Masking position 1 Map Score: 8.57828 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 304 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 GGAAAAACCTTCAAAGAAGC 3 166 0 GGAAAAACCT 0.780591 -10 GGAATCTGAAGGAAAAAAATGTCACCGACG 6 28 1 GGAAAAAAAT 0.914931 -271 CGCTGGAACTGGTTAAAACTCACCAAACTG 6 77 1 GGTTAAAACT 0.918754 -222 GAATTTGTTTGGTAAAAACTTTGCCGCCTG 7 38 1 GGTAAAAACT 0.885381 -263 TGTCAACGGTTAAAAATTAGTTTGCCT 8 257 0 GGTTAAAAAT 0.876996 -17 TTAGGGGGCGGAATAAAACTTTTTAAACAC 9 55 0 GAATAAAACT 0.914225 -141 GGACTAATGGGGATAAAATTTAAGGGGGAC 10 24 1 GGATAAAATT 0.89406 -143 CCGGGACCAGGAATAAAAATTATTGCCCCC 10 91 1 GAATAAAAAT 0.870461 -76 GCAAGTATTTGAAAAAAATTGTTAAGCTAT 11 76 1 GAAAAAAATT 0.710981 -225 CCAGTATCATGAATAAAAATCAGAATTGCC 11 227 0 GAATAAAAAT 0.870461 -74 ********** Masking position 5 Map Score: 6.23465 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 426 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 GTTGACCACTAATTGACCAAAAGATGAATA 2 245 0 AATTGACCAA 0.951963 -56 GAATTTGATTAGTTGACCACTAATTGACCA 2 256 0 AGTTGACCAC 0.837643 -45 CTAGGTGATTAATTGATCAACGAATTAACT 3 19 0 AATTGATCAA 0.927597 -157 GGGCAAAAAAAATTGATCAATCACCAAAAA 3 91 1 AATTGATCAA 0.927597 -85 TCTTTGACACCATTGAGCAACATCACTAAG 4 159 0 CATTGAGCAA 0.90967 -135 AGTTGCGTGGAGGTGAGCAATACACTTAAG 5 85 0 AGGTGAGCAA 0.908011 -165 GCGATCGCCGAGTTGAGCAAAATGATTGAA 6 174 0 AGTTGAGCAA 0.973797 -125 GCCCACCGTCAATTAAGCAAAATGTTACAG 7 235 1 AATTAAGCAA 0.808941 -66 ********** Masking position 6 Map Score: 4.2734 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 232 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 ATTAAGCAAATGGGCTTTTTACTATCCTAG 1 147 0 TGGGCTTTTT 0.781025 -40 CGCTGCCCCCTGGGCATTAACCCATGGAAA 4 62 1 TGGGCATTAA 0.882912 -232 GCGATCGCCTTGGGAATTTTAGTGGCAGGC 4 130 1 TGGGAATTTT 0.824907 -164 GTTTAAGATGGGGGCATTGTTTTAGTCCAC 6 254 1 GGGGCATTGT 0.974587 -45 ACGGGGATAGGGGGGACTAAATCACCACTA 7 104 0 GGGGGACTAA 0.837928 -197 TAATTGACGGTGGGCACTGTGACAAGACTG 7 220 0 TGGGCACTGT 0.909356 -81 CCCCATTATTGGGGAATTTAGGGGGCGGAA 9 72 0 GGGGAATTTA 0.915189 -124 CCCCAATAATGGGGGACTTTCACTCAGTAT 9 88 1 GGGGGACTTT 0.907885 -108 AGGGGCCAGAGGGGCTTTTAAAACAGGCTC 9 131 1 GGGGCTTTTA 0.890942 -65 ATAGATCAATGGGGAATTGTAGGAGGATGT 10 52 0 GGGGAATTGT 0.926303 -115 GGAAGGGCCGGGGGCAATAATTTTTATTCC 10 100 0 GGGGCAATAA 0.786236 -67 ********** Masking position 8 Map Score: 5.18273 Number of sites scoring better than the average of aligned sites = 1838 Number in coding regions = 1541 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 8 GAGCAAAGCCAATCAGAATCAAAGGTTTTGA 1 56 0 AATCAGAATA 0.890823 -131 CCTAAAATCCAATCTAAATTAGCCGTATTTT 4 98 0 AATCTAAATA 0.933563 -196 ACGGGGTCTTAATCTAAACTGTGAGGTAGCC 4 240 1 AATCTAAACG 0.781875 -54 AGGGCAGGGAAATCTGAAGTAAATCTAAAGA 5 169 1 AATCTGAAGA 0.964177 -81 ATCTGAAGTAAATCTAAAGAATATTGATGCT 5 180 1 AATCTAAAGA 0.944348 -70 AAAAAAGGGGAATCTGAAGGAAAAAAATGTC 6 20 1 AATCTGAAGA 0.964177 -279 TCCTCTAATCAATCTAAATAAACTTTGGTAT 8 132 1 AATCTAAATA 0.933563 -142 CATGAATAAAAATCAGAATTGCCCCAGGGTT 11 219 0 AATCAGAATG 0.822078 -82 ********* * Masking position 7 Map Score: 2.90896 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 42 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 9 AGCCCAAGCAAATGCCAGACTGGCGATCGCCGTTGC 1 94 1 AAGATGGCGA 0.990187 -93 TACCCTGGGAAAAGCAATATGGGCGGAGGCTACCTC 4 262 0 AAGAGGGCGG 0.987949 -32 TCCCCAGGGGAAAGAAAACTTGGCTACAGCATCAAT 5 202 0 AAGATGGCTA 0.964942 -48 CGGGCTAGCAAAGGGCAGTTTGGTGAGTTTTAACCA 6 86 0 AAGATGGTGA 0.929017 -213 AGTTTTTACCAAACAAATTCGGGCGGCTTTTTCCGC 7 22 0 AACAGGGCGG 0.940344 -279 CTTTTATTTTAAGGTCATCAGGGCTAATCATTGTAT 8 31 1 AAGAGGGCTA 0.970794 -243 TTTTCTAGCTAATGAGATTATGGCGATCGCCGGAGT 11 15 1 AAGATGGCGA 0.990187 -286 ** * * ****** Masking position 7 Map Score: 2.75768 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 116 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GCAATAGTGGCAATAAATTACAGCAGATAATT 2 82 1 CAATAATACA 0.877714 -219 GATTAGTTGACCACTAATTGACCAAAAGATGA 2 248 0 CCACAATGAC 0.825168 -53 AATTAGTGGTCAACTAATCAAATTCGCTTCAA 2 261 1 CAACAATAAA 0.877714 -40 ATTAATTGATCAACGAATTAACTGAATTTTG 3 10 0 CAACAATAAC 0.969117 -166 ATTCGTTGATCAATTAATCACCTAGCTAATCC 3 24 1 CAATAATACC 0.969117 -152 GACTAAATCACCACTAATAACCCGGCTCATTA 7 88 0 CCACAATACC 0.965737 -213 TTAGATGGCACAATTAATAAACTAATTAGTTT 11 132 1 CAATAATAAC 0.951886 -169 CTTAACGTAACAATTAATTACCCCC 11 286 1 CAATAATACC 0.969117 -15 **** *** *** Masking position 6 Map Score: 3.20386 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 109 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 GTGAGGTAGCCTCCGCCCATATTGCTTTTC 4 260 1 CTCCGCCCAT 0.967697 -34 TAACCAGTTCCAGCGGCCCTGGGATAAGGC 6 62 0 CAGCGGCCCT 0.902896 -237 CCCTTTGCTAGCCCGGCCATTTCATTGTCT 6 107 1 GCCCGGCCAT 0.965605 -192 TCCCCCCTATCCCCGTCCCTGGCAGTGTCA 7 118 1 CCCCGTCCCT 0.982511 -183 TCACAGTGCCCACCGTCAATTAAGCAAAAT 7 228 1 CACCGTCAAT 0.715271 -73 ATAGGCTTTTCCCTGCCCATAATTGTACTA 7 270 1 CCCTGCCCAT 0.90826 -31 AAATTATTGCCCCCGGCCCTTCCGTAATAG 10 107 1 CCCCGGCCCT 0.994021 -60 CCGAGAATTACTCCGGCGATCGCCATAATC 11 30 0 CTCCGGCGAT 0.916797 -271 ********** Masking position 10 Map Score: 4.50339 Number of sites scoring better than the average of aligned sites = 860 Number in coding regions = 787 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 12 CTGTGTATATTTTTCTAACTATTTTCAACTA 3 57 0 TTTTCTACTA 0.976999 -119 TATTCCTTTATTTTCTATCGAAGTTCCCTAA 8 173 1 TTTTCTACGA 0.950335 -101 TGTTGAATATTTTTCTATCTCTATAATTTCT 9 168 1 TTTTCTACTC 0.950335 -28 CTAGTTTTCTAGCTAATGAGATTAT 11 5 1 TTTTCTACTA 0.976999 -296 ATACTTGCTTTTTTTTAACTAGCTCCGAGAA 11 53 0 TTTTTTACTA 0.890582 -248 ******* *** Masking position 6 Map Score: 0.846877 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 5 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 TGACAGTGATAATCAGCTTTGCTACTATCG 2 53 1 AATCAGCTTT 0.88475 -248 CGCCAGGAAAAATCAGTTTTTCCTTATTCC 2 127 0 AATCAGTTTT 0.961455 -174 CCTAATGCTGAATCATTTTTGGTGATTGAT 3 106 0 AATCATTTTT 0.923358 -70 GTCACCGTTCAATCATTTTGCTCAACTCGG 6 167 1 AATCATTTTG 0.890448 -132 AACGGTTAAAAATTAGTTTGCCTTGGACTT 8 250 0 AATTAGTTTG 0.850141 -24 GGCCGGGGGCAATAATTTTTATTCCTGGTC 10 95 0 AATAATTTTT 0.695446 -72 TTAATAAACTAATTAGTTTTGGCAATTGAA 11 145 1 AATTAGTTTT 0.893953 -156 ********** Masking position 5 Map Score: 1.17757 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 128 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 CCACGCAACTACATGTAACCGGTTAAATACC 5 105 1 ACTGTAACCG 0.966236 -145 TGAAGGAAAAAAATGTCACCGACGGTAAGCC 6 34 1 AATGTCACCG 0.983523 -265 ACGCTAGCAAAACTGTCACCGTTCAATCATT 6 153 1 AATGTCACCG 0.983523 -146 AATTGTACTAACTTCACACCG 7 290 1 ACTCACACCG 0.927431 -11 TAGTTTTGGCAATTGAAACCGGGCAAAAGCG 11 158 1 AATGAAACCG 0.94872 -143 ** ******** Masking position 4 Map Score: 0.144361 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 TCAGCATTAGGGAAGGCAGGCCCCTAGGGATT 3 125 1 GGAAGGCAGC 0.939745 -51 GATTTGGATGGGTAACCATGACTACTTTTCAC 4 27 0 GGTAACCAGC 0.932007 -267 TAAACTGTGAGGTAGCCTCCGCCCATATTGCT 4 254 1 GGTAGCCTCC 0.953075 -40 ACTGCCCTTTGCTAGCCCGGCCATTTCATTGT 6 103 1 GCTAGCCCGC 0.979044 -196 TGACAGTTTTGCTAGCGTTGTCTGGAGAGAAT 6 139 0 GCTAGCGTGC 0.939138 -160 ACAAGACTGGGCAAGCCTAGTCAAAAATAGCG 7 197 0 GCAAGCCTGC 0.984075 -104 ATTAAACGTGGGAAGCCATGACCCAGTATCAT 11 247 0 GGAAGCCAGC 0.987824 -54 ******** * * Masking position 4 Map Score: 0.762817 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 237 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357