AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_aful_mthe_300.orf -o056_aful_mthe_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG48429 192 Archaeoglobus_fulgidus #2 RAG21207 31 Archaeoglobus_fulgidus #3 RAG50420 80 Archaeoglobus_fulgidus #4 RAG21288 173 Archaeoglobus_fulgidus #5 RAG22420 300 Archaeoglobus_fulgidus #6 RAG45771 182 Archaeoglobus_fulgidus #7 RAG45588 64 Archaeoglobus_fulgidus #8 RAG35664 297 Archaeoglobus_fulgidus #9 RAG49289 45 Archaeoglobus_fulgidus #10 RTH00661 61 M.thermo #11 RTH01407 25 M.thermo #12 RTH01538 300 M.thermo #13 RTH01353 75 M.thermo #14 RTH00151 64 M.thermo #15 RTH00311 135 M.thermo #16 RTH01312 127 M.thermo #17 RTH02147 135 M.thermo #18 RTH02014 144 M.thermo #19 RTH00569 142 M.thermo Motif number 1 GAGCTAAGTAGGGGCGGAATTAAAAAAGGT 2 12 0 GGGGCGGAAT 0.858811 -20 CAAACAAAAATTGGAGGGATTT 3 3 0 TTGGAGGGAT 0.89635 -78 TTTCCGTCAAGGGAAGAGATTTT 3 68 1 GGGAAGAGAT 0.685784 -13 GGGAGAGTGAGGGAAGGTATTAAACTTTAA 4 14 1 GGGAAGGTAT 0.779388 -160 CAGCAAAAATTAGGAGGGATAGTAGGCTGA 4 66 0 TAGGAGGGAT 0.959387 -108 AATCGTAAACGTGACGGGATTTGCATCATT 5 165 0 GTGACGGGAT 0.78357 -136 ATGCTGGTGGTGGGAGTGATGAAAAAGTTC 6 97 1 TGGGAGTGAT 0.888418 -86 TATAAAAAATGAGTAGGGATATAAACCAAA 8 91 1 GAGTAGGGAT 0.919474 -207 TCAAATCCGGGAGGCGGGACTTGAATGCTT 8 119 0 GAGGCGGGAC 0.967768 -179 TTTTATAGACGGGGCGTGATATTATTAATC 12 23 0 GGGGCGTGAT 0.943639 -278 CGCAGGCCCTCAGGAGGGATCG 15 3 0 CAGGAGGGAT 0.951418 -133 ATGATTTCATCAGTAGGGACCAGTTCCAGC 16 22 0 CAGTAGGGAC 0.621887 -106 TAGATTCCACTGGGAGGGTCAAATATGAGG 18 38 0 TGGGAGGGTC 0.708463 -107 CCCCCATGTTGAGGAGGTATGTCTGTCGAG 18 119 0 GAGGAGGTAT 0.905168 -26 CCTCAACATGGGGGAGTGAC 18 135 1 GGGGAGTGAC 0.943639 -10 ********** Masking position 6 Map Score: 12.4973 Number of sites scoring better than the average of aligned sites = 1029 Number in coding regions = 964 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 CCAGTTTTAAGGCTAAAGCCACCGATTTAAAAACC 1 6 1 TTGCGCACCA 0.844591 -187 ATAAATAAAATTCTCGGCAACTGCTACAAATCAAATACGT 1 101 0 TCGCGCACAA 0.833795 -92 GTAAATCGTTTTCGGTGCCTTAGATAACAATTTATCGAAA 1 140 0 TCGCGAAACA 0.892601 -53 CAATAATAGCTACAAAGCCTATGCTGAAGGACATTGCAAA 5 100 1 TCGCGCGAAG 0.985551 -201 GCAGTGCAATTACCTTGCCTGGGCGAACCAAAACTTTTTA 6 51 1 TCGCGCAACA 0.982484 -132 TTGTGGAATTTGAAGAGGGTTCGCTGAAAGGCGAAAAGAG 8 25 0 TAGGGCGAAG 0.73338 -273 GATCTCCGCCTGCCGCGGAGTGGCGGACTACAGTCCCACG 8 163 1 TCGGGCGACA 0.979996 -135 CGATCCCTCCTGAGGGCCTGCGGCCTGACAGATGATG 15 8 1 TCGGGCGCCG 0.992087 -128 CGAGAAACCATTCATAGGTATAGCCAACAGTTACACTGAC 15 52 1 TCGGGCAACG 0.985427 -84 ACTGACATAGTTCCCGGCCACATCCACCTGAGGGAACTTG 15 86 1 TCGCTCACCG 0.916571 -50 CATCATAACATCCCCCGCCGGTGCTGCATGGTGGACATCA 17 15 0 TCGCGCGCAG 0.987323 -121 TGTCGAGGGCTGCAATGCATCTGATGACCGTGCCATGCCC 18 86 0 TCGCGAGACG 0.967099 -59 * * ** ** *** * Masking position 1 Map Score: 10.1997 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 260 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 GTTCTATTTGAAAAAAGGTTTTTAAATCGGT 1 31 0 AAAAAAGTTT 0.820101 -162 TTGACGGAAATAATAAGCTTTTTGGTTTGAA 3 47 0 TAATAAGTTT 0.942528 -34 CCGGTGGATTAAAAAAGTTATCAGCTTTCCT 4 140 0 AAAAAAGTAT 0.756878 -34 CTTCATTATTTTTTAAGTTTTGGTTGGATGG 5 267 0 TTTTAAGTTT 0.756918 -34 GCATGCGCTTTAAAAAGTTTTGGTTCGCCCA 6 70 0 TAAAAAGTTT 0.942526 -113 TCCTGAAAACTAATAAGTTATTACTATATAT 12 65 1 TAATAAGTAT 0.918043 -236 AATACTTTGATAATAAGATTTAAATATATAG 12 88 0 TAATAAGTTT 0.942526 -213 TAAATAGTTCTTTAAAGATATCTTACTGCAT 16 59 0 TTTAAAGTAT 0.680193 -69 GGGTTATAACTTATAAGATATAACTTATAAC 19 46 1 TTATAAGTAT 0.884409 -97 TGGGCTACAATTAAAAGCTTTTACACACAGT 19 79 0 TTAAAAGTTT 0.918044 -64 ******* *** Masking position 6 Map Score: 4.68934 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 36 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 TGCTGACATTAGGCTAAGCTGTAAATCGTTT 1 169 0 AGGTAAGCTG 0.84648 -24 ATAGCTACAAAGCCTATGCTGAAGGACATTG 5 105 1 AGCTATGCTG 0.943623 -196 AACTTTTTAAAGCGCATGCTGGTGGTGGGAG 6 82 1 AGCCATGCTG 0.970488 -101 TTAGAAAAGAAGTAAAAGCTGTACTACAATG 6 141 0 AGTAAAGCTG 0.652704 -42 TCTACCTCTGAGCTAAGGCGGGTTCGATAGC 8 204 1 AGCAAGGCGG 0.942801 -94 AAGTATTTATAGGGCCGGGTGAAAATATAGA 12 112 1 AGGCCGGGTG 0.906434 -189 ATCCCTCCTGAGGGCCTGCGGCCTGACAGAT 15 13 1 AGGCCTGCGG 0.922113 -123 TCCACCATGCAGCACCGGCGGGGGATGTTAT 17 20 1 AGCCCGGCGG 0.974256 -116 AGGAGTATTGAGTATAGGGTGAGTTGATGTT 17 76 1 AGTTAGGGTG 0.833519 -60 TGGAGTATTGAGTACAGGGTGATGGG 17 120 1 AGTCAGGGTG 0.907721 -16 ATTCTTCAATAGCGTATGCGGGCATGGCACG 18 67 1 AGCTATGCGG 0.939951 -78 *** ******* Masking position 1 Map Score: 6.69206 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 349 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 GTCATGTAAACCCTTATTTTTCAGCCTACTATC 4 46 1 CCCTATTTTA 0.797045 -128 CTACTATCCCTCCTAATTTTTGCTGCCCCACCA 4 71 1 TCCTATTTTC 0.797045 -103 GCTTTCCTTTCCGGAATTTTGACATGCAAAAGC 4 115 0 CCGGATTTTC 0.968543 -59 AGTCCGGTTGCTCTTATTTGTCCGGATGTATTG 5 17 1 CTCTATTTGC 0.919802 -284 AGTCCCGCCTCCCGGATTTGAACCGGGGACCAT 8 128 1 CCCGATTTGC 0.980204 -170 TTTTTATCACCCCCAATTTTGGCTTTAAC 8 279 1 CCCCATTTTC 0.957209 -19 TTCTGATGTCCCCATATGTTCACTGGATAACTG 12 183 0 CCCAATGTTC 0.834181 -118 GTTAAAGAGGCTCTAATTTTCACAGACTGCCCC 12 217 1 CTCTATTTTC 0.948217 -84 CCGGTCTGATCCGGAATTTTTCCGCATTGAGCA 13 11 0 CCGGATTTTC 0.968546 -65 GGCAGCACACCTCATATTTGACCCTCCCAGTGG 18 29 1 CTCAATTTGC 0.860082 -116 TCCCCGTGGTCTGGCATTTTATCTGCTTAAATT 19 114 0 CTGGATTTTC 0.918787 -29 **** ***** * Masking position 6 Map Score: 6.15852 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 197 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TGAAAAAAGGTTTTTAAATCGGTGGCTTTA 1 24 0 TTTTTAAATC 0.610206 -169 AACCTTTTTTAATTCCGCCCCTACT 2 6 1 TTTTTAATTC 0.863869 -26 TAAACCCTTATTTTTCAGCCTACTATCCCT 4 52 1 TTTTTCAGCC 0.947984 -122 GCTGATAACTTTTTTAATCCACCGGCTGTT 4 146 1 TTTTTAATCC 0.894914 -28 GGTGGAGTTCTTTTTACTTCCTGTTTATGG 5 59 0 TTTTTACTTC 0.708925 -242 GCTTCATTATTTTTTAAGTTTTGGTTGGAT 5 269 0 TTTTTAAGTT 0.567594 -32 TCCAGAGAACTTTTTCATCACTCCCACCAC 6 103 0 TTTTTCATCA 0.829848 -80 AGTTTAAAATTTTTTCATTCATTTAATGAT 7 14 0 TTTTTCATTC 0.894914 -51 AGGCACAAGATTTTTAAGCAGATTCGCTCA 8 239 0 TTTTTAAGCA 0.852825 -59 TTCAGACGAGTTTTTCAGTATGAAGGCGAA 12 150 1 TTTTTCAGTA 0.852845 -151 TGATCCGGAATTTTTCCGCATTGAGCA 13 8 0 TTTTTCCGCA 0.74906 -68 ********** Masking position 5 Map Score: 5.35763 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 211 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 TTTTTGCTGCCCCACCATGATGGTATATGC 4 87 1 CCCACCATGA 0.893202 -87 TAAAAAGAACTCCACCACCCGTACCGGCAA 5 73 1 TCCACCACCC 0.988592 -228 TATTGTTCTTCACACCATCCAACCAAAACT 5 253 1 CACACCATCC 0.906339 -48 TTTCATCACTCCCACCACCAGCATGCGCTT 6 91 0 CCCACCACCA 0.98066 -92 GCATTCAAGTCCCGCCTCCCGGATTTGAAC 8 121 1 CCCGCCTCCC 0.957441 -177 GGGACTGTAGTCCGCCACTCCGCGGCAGGC 8 170 0 TCCGCCACTC 0.883603 -128 ACCTTGATGTCCACCATGCAGCACCGGCG 17 10 1 TCCACCATGC 0.934611 -126 CCCATCACCCTGTACTCAAT 17 126 0 CCCATCACCC 0.961174 -10 ********** Masking position 6 Map Score: 5.90137 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 319 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GTTCCTTATAACTGTTTTTGCAATGTCCTTC 5 125 0 ACTGTTTTGC 0.574557 -176 ACTACAATGAACTCTTTTCCAGAGAACTTTT 6 119 0 ACTCTTTTCA 0.853552 -64 ACCACCTCTAACTCCTTTAGAAAAGAAGTAA 6 157 0 ACTCCTTTGA 0.934141 -26 CCTCAAGCAGCCTCTTTTCGCCTTTCAGCGA 8 14 1 CCTCTTTTGC 0.948082 -284 AAAATTAGAGCCTCTTTAACCTTCTGATGTC 12 206 0 CCTCTTTACC 0.922876 -95 CTTCTATCCTCCTTTAGCAGAATAATTG 12 283 0 CCTCCTTTGC 0.972883 -18 ACCCTCCTTAACAGCCTCTGCAA 15 123 0 CCTCCTTACA 0.948082 -13 TATACTCAATACTCCTTATGAGACCCACGGG 17 61 0 ACTCCTTAGA 0.920082 -75 GACAGACATACCTCCTCAACATGGGGGAGTG 18 122 1 CCTCCTCACA 0.810124 -23 ******** ** Masking position 6 Map Score: 2.49855 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 589 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 TTTAATACCTTCCCTCACTCTCCCTCC 4 4 0 TCCCCCTCCC 0.994986 -170 AACTTTTTCATCACTCCCACCACCAGCATGCGCT 6 92 0 TCACCCACCC 0.959268 -91 GACCATGGGATCTCCGCCTGCCGCGGAGTGGCGG 8 155 1 TCTCGCTGGC 0.915695 -143 CGGACTACAGTCCCACGCTCTACCTCTGAGCTAA 8 186 1 TCCCCCTCCC 0.994986 -112 GCTCTAATTTTCACAGACTGCCCCATGGACCACT 12 226 1 TCACGCTGCC 0.981863 -75 TTTATGGGAGTCCCGGTCTGATCCGGAATTTTTC 13 22 0 TCCCGCTGCC 0.994986 -54 CTGACATAGTTCCCGGCCACATCCACCTGAGGGA 15 87 1 TCCCGCACCC 0.988549 -49 CATCATAACATCCCCCGCCGGTGCTGCATGGTGG 17 21 0 TCCCCCCGGC 0.961578 -115 **** * *** ** Masking position 1 Map Score: 8.26213 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 95 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 AAAATCTCTTCCCTTGACGGAAATAATAAG 3 61 0 CCCTTGACGG 0.964709 -20 AACTCCACCACCCGTACCGGCAATAATAGC 5 80 1 CCCGTACCGG 0.941976 -221 CAGTGCAATTACCTTGCCTGGGCGAACCAA 6 52 1 ACCTTGCCTG 0.863634 -131 TGTATCTCCCTTACTGGTGTTCTATCT 10 45 0 CCCTTACTGG 0.964819 -17 GGTCCCTCACTTGATTAATAATA 12 4 1 CCCTCACTTG 0.893438 -297 CCCCATGGACCACTTGCTGGAACCTTTATG 12 246 1 CACTTGCTGG 0.899584 -55 ATCATAACATCCCCCGCCGGTGCTGCATGG 17 24 0 CCCCCGCCGG 0.9827 -112 TGCATTGCAGCCCTCGACAGACATACCTCC 18 107 1 CCCTCGACAG 0.877298 -38 ********** Masking position 3 Map Score: 2.09844 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 301 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 CCAGTTTTAAGGCTAAAGCCACC 1 3 1 AGTTTAAGGC 0.844915 -190 TTGCAAAAACAGTTATAAGGAACTCAACTGG 5 133 1 AGTTTAAGGA 0.946541 -168 GTGATGAAAAAGTTCTCTGGAAAAGAGTTCA 6 112 1 AGTTTCTGGA 0.965795 -71 ATAACTTATTAGTTTTCAGGAGCTCACCAAG 12 55 0 AGTTTCAGGA 0.984827 -246 TGTCCCCATATGTTCACTGGATAACTGTCTT 12 179 0 TGTTACTGGA 0.842361 -122 GGGGATGTTATGATGACAGGACCCGTGGGTC 17 40 1 TGATACAGGA 0.7183 -96 GCCCAATTAGAGTTATCAGGA 18 1 0 AGTTTCAGGA 0.984827 -144 **** ****** Masking position 4 Map Score: 2.34919 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 101 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 GAGGAGTACACAAACAAAAATTGGAGGGAT 3 13 0 CAAACAAAAA 0.820165 -68 CTCCTCTTTCAAACCAAAAAGCTTATTATT 3 40 1 AAACCAAAAA 0.919106 -41 ATTTTGACAAAAAACAAAACATTTATTTGT 5 207 0 AAAACAAAAC 0.952754 -94 TCACACCATCCAACCAAAACTTAAAAAATA 5 262 1 CAACCAAAAC 0.971854 -39 TTGCCTGGGCGAACCAAAACTTTTTAAAGC 6 65 1 GAACCAAAAC 0.949399 -118 GTAGGGATATAAACCAAAGCATTCAAGTCC 8 103 1 AAACCAAAGC 0.927618 -195 ATACTCCAGCAAAACAACACAAACATCAAC 17 98 0 AAAACAACAC 0.861208 -38 ********** Masking position 6 Map Score: 1.96214 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 45 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 CTTTTTTAATCCACCGGCTGTTCAGGTTTC 4 154 1 CCACCGGCTG 0.881101 -20 ACTTTTTAAAGCGCATGCTGGTGGTGGGAG 6 83 1 GCGCATGCTG 0.93608 -100 GGTTCAAATCCGGGAGGCGGGACTTGAATG 8 122 0 CGGGAGGCGG 0.956095 -176 CGCCACTCCGCGGCAGGCGGAGATCCCATG 8 158 0 CGGCAGGCGG 0.763016 -140 CGCCTGCCGCGGAGTGGCGGACTACAGTCC 8 169 1 GGAGTGGCGG 0.837242 -129 AGTATTTATAGGGCCGGGTGAAAATATAGA 12 113 1 GGGCCGGGTG 0.90998 -188 GTGGTCCATGGGGCAGTCTGTGAAAATTAG 12 229 0 GGGCAGTCTG 0.862956 -72 TCCCTCCTGAGGGCCTGCGGCCTGACAGAT 15 14 1 GGGCCTGCGG 0.952077 -122 GAGGGAACTTGCAGAGGCTGTTAAGGAGGG 15 115 1 GCAGAGGCTG 0.916125 -21 CCACCATGCAGCACCGGCGGGGGATGTTAT 17 21 1 GCACCGGCGG 0.964526 -115 TTCTTCAATAGCGTATGCGGGCATGGCACG 18 68 1 GCGTATGCGG 0.77602 -77 ********** Masking position 10 Map Score: 9.37256 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 411 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 AGGCGGAGATCCCATGGTCCCCGGTTCAAA 8 144 0 CCCATGGTCC 0.986675 -154 CACAGACTGCCCCATGGACCACTTGCTGGA 12 237 1 CCCATGGACC 0.967003 -64 CGATCCCTCCTGAGGGCCTGCGGCCTGA 15 9 1 CCTGAGGGCC 0.917515 -127 GATGACAGGACCCGTGGGTCTCATAAGGAG 17 51 1 CCCGTGGGTC 0.973402 -85 TAAGTTATAACCCGGGTTCCCGGGTGCCAG 19 29 0 CCCGGGTTCC 0.938545 -114 CTTGATTCCCCGTGGTCTGGCATTTTAT 19 125 0 CCCGTGGTCT 0.971348 -18 ********** Masking position 6 Map Score: 1.28325 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 = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 CCTCCTAATTTTTGCTGCCCCACCATGATG 4 79 1 TTTGCTGCCC 0.970819 -95 TCTTTAACCTTCTGATGTCCCCATATGTTC 12 195 0 TCTGATGTCC 0.963054 -106 AACCATTCCCTTTGATGTACATATATGTAC 16 100 0 TTTGATGTAC 0.803086 -28 ACCTTGATGTCCACCATGCAGC 17 3 1 CTTGATGTCC 0.954869 -133 AAATATGAGGTGTGCTGCCCAATTAGAGTT 18 18 0 TGTGCTGCCC 0.93745 -127 CTGCAATGCATCTGATGACCGTGCCATGCC 18 87 0 TCTGATGACC 0.911633 -58 CTTGATTCCCCGTGGTCTGG 19 133 0 CTTGATTCCC 0.811865 -10 ********** Masking position 6 Map Score: 0.873093 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 150 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