AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_aquae_reg_100.orf -o199_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RAA00965 16 Aquifex_aeolicus RAA01021 18 Aquifex_aeolicus RAA00750 52 Aquifex_aeolicus Input sequences: #1 RAA00972 117 Aquifex_aeolicus #2 RAA00975 61 Aquifex_aeolicus #3 RAA00976 45 Aquifex_aeolicus #4 RAA01018 36 Aquifex_aeolicus #5 RAA01019 65 Aquifex_aeolicus #6 RAA01777 60 Aquifex_aeolicus #7 RAA01036 44 Aquifex_aeolicus #8 RAA01520 85 Aquifex_aeolicus #9 RAA01531 33 Aquifex_aeolicus #10 RAA01538 152 Aquifex_aeolicus #11 RAA00385 55 Aquifex_aeolicus #12 RAA00617 40 Aquifex_aeolicus #13 RAA01771 33 Aquifex_aeolicus #14 RAA00587 196 Aquifex_aeolicus #15 RAA01715 300 Aquifex_aeolicus #16 RAA01774 118 Aquifex_aeolicus #17 RAA01722 212 Aquifex_aeolicus #18 RAA01723 41 Aquifex_aeolicus #19 RAA01143 70 Aquifex_aeolicus #20 RAA01147 29 Aquifex_aeolicus Motif number 1 ATTAAGGACAAATCTCAGAGGGACGGATATAAACCTA 1 36 1 ACAGAGGGGA 0.892073 -82 GAAGAAGAAATTATGCAGGCTGCAAAGGAGGGCTAAG 2 33 1 TTAGGTGAAG 0.574831 -29 CTGCGGGGAGACCTTAAAAAGGCCAGGAGGTGAAGT 5 40 1 ATAAAGGAGG 0.854164 -26 AGTTGAAAAAGGCAAGGACTTAGGTTA 6 1 1 ATAAAGGAGG 0.854164 -60 TATAATAAAGTTCTCTCGGAGGTAGAAGA 7 3 0 TTCGGGGGAA 0.905566 -42 ACTAATAATTTGCCTTAAAAGGAGGAAGCGA 8 65 1 TCAAAGGGAA 0.786184 -21 GGGAAAAATTATAAGGGGAAAGAAGAGAAAAGA 9 11 0 ATAAGGGAGA 0.900616 -23 ATACACTATTTTGCTAAAGAGGCTAAATTCTATTAAT 10 15 0 TCAAGGGAAA 0.88519 -138 TGTAAACCTTAATAGGAGGTGGGTAAG 10 136 1 AAAGGGGAAG 0.887501 -17 TTTTACGAGAACTTCAAGGAGGCGGAA 11 1 0 ATAGGGGGAA 0.964188 -55 TAAAATACTTAGCTTCAGGAGGTAAAGTTAGGT 13 11 1 ATAGGGGAAG 0.973326 -23 GTAAATTTTTTATTTGCAGAGGTCAGGGA 14 3 0 TTCAGGGAGG 0.876137 -194 TGCCTTACTCTAATTAAAGGGGTGAAAAGCC 14 176 1 TTAAGGGAAA 0.898309 -21 CCGCTCAGTAATATGGAGGGGGCAGGATTCGAACCTG 15 15 0 ATAGGGGGGA 0.969795 -286 TGAGCGGGCGTAGCTCAGTTGGTAGAGCAGCGGCCTT 15 45 1 TCAGTGGGAG 0.912357 -256 TAAGCCCAGGTAGCTCAGTCGGTAGAGCGCACCCTTG 15 150 1 TCAGTGGGAG 0.912357 -151 TTGTTACCTCAAAATTCGGAGGTAGGAA 15 283 1 AACGGGGGGA 0.680209 -18 AGTGGGGCTGTAGCTCAATTGGCAGAGCGCGGGACTC 16 21 1 TCAATGGGAG 0.826105 -98 GCGGGACTCCAAATCCCGTGGGTGGGGGTTCGAGTCC 16 49 1 ATCGTGGGGG 0.789438 -70 ACCTCTGGAAAGTTTTAAGTGGCGGGGCTGGGAGGAC 16 82 0 ATAAGGGGGG 0.969795 -37 AGCAAAAGTGTAAAGGAAAAGGAAAAGAAGGAG 17 7 0 TAAAAGGAAG 0.552448 -206 CTTTACACTTTTGCTCAGGAGGCAGGAACGCTCTGTA 17 29 1 TCAGGGGGGA 0.970216 -184 CTTTTATGTTTCTTAAAGAAGGCGGAATGAAGCAATA 17 171 0 TTAGAGGGAA 0.902259 -42 TCTTTAAGAAACATAAAAGAGGAGAGGTATAAAA 17 189 1 ATAAGGGAGG 0.952056 -24 TTTAATTTTTGAGAAGGGGAAGATACCCCTTC 18 20 0 TTAGAGGAAG 0.925987 -22 ATTTAAACCTTCGCAAAGGAGGTAAAGG 19 53 1 TCAGGGGAAG 0.9737 -18 * * *** ** *** Masking position 12 Map Score: 32.9897 Number of sites scoring better than the average of aligned sites = 1823 Number in coding regions = 1636 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 2 TAAAATTAAAGGCAATTAAAACCCCTTTTCAGGA 8 19 0 GGATTAAACC 0.911566 -67 GGGGTTTAAAGCCCAACTGCCGGC 12 1 1 GGGTTAAGCC 0.911982 -40 TGCGCAGGTTCGAATCCTGCCCCCTCC 15 4 1 GCGTTGAACC 0.992572 -297 CCCGCGACCTGCGGCTTGGAAGGCCGCTGCTCTA 15 67 0 GCGTTGAAGC 0.951019 -234 GCCGCAGGTCGCGGGTTCGAGTCCCGTCGCCCGC 15 86 1 GCGTTGAGCC 0.997553 -215 GGGTGAGGGCGCCGGTTCGAGTCCGGTCCTGGGC 15 191 1 GCGTTGAGCC 0.997553 -110 ATTTTTATCAGGGAAGTGGAGCCCAGGACCGGAC 15 211 0 GGAGTGAGCC 0.974794 -90 CCCCACCCACGGGATTTGGAGTCCCGCGCTCTGC 16 42 0 GGATTGAGCC 0.993879 -77 TCCCGTGGGTGGGGGTTCGAGTCCTCCCAGCCCC 16 62 1 GGGTTGAGCC 0.99802 -57 ** * ** *** ** Masking position 7 Map Score: 17.3511 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 25 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 CTCCGAGAGAACTTTATTATATTAAAATCTT 7 19 1 ATTTATTATA 0.968254 -26 TTATCATAAAACTTTATAAAATTGTATTAAG 10 62 0 ATTTATAAAA 0.894495 -91 TTATTGCAAAAATTTTTAAAAGGAATATAAT 10 96 1 ATTTTTAAAA 0.728036 -57 TTTACATATAATTTTATTATATTCCTTTTAA 10 111 0 ATTTATTATA 0.968254 -42 ACACAGGGTAAATTTTTTATTTGCAGAGGTC 14 16 0 ATTTTTTATT 0.728036 -181 AAGAAGTGTTAATTTATTATAGTTTGCGGTG 14 85 1 ATTTATTATA 0.968252 -112 TTCTAACATAAATTTGTTATAATATCAATTT 14 146 1 ATTTGTTATA 0.890122 -51 TAAAAGAAATAATTTATAATATTTTGTTACC 15 260 1 ATTTATAATA 0.968184 -41 TTTAGACATTAGTTTATAATAAGTAGCGTT 19 10 0 ATTTATAATA 0.968252 -61 GGCGAATAGAGTTTATAATTTAAAGCATA 20 10 1 ATTTATAATT 0.894416 -20 * ********* Masking position 5 Map Score: 10.3163 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 6 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 CAACCTCGTTTCCCCGCCCTGCGGGGAGAC 5 22 1 TCCCCGCCCT 0.992619 -44 TCCCTGACCTCTGCAAATAA 14 1 1 TCCCTGACCT 0.820756 -196 AACTGAGCTACGCCCGCTCAGTAATATGGA 15 35 0 CGCCCGCTCA 0.952178 -266 GCTTGGAAGGCCGCTGCTCTACCAACTGAG 15 58 0 CCGCTGCTCT 0.914622 -243 GGGACTCGAACCCGCGACCTGCGGCTTGGA 15 81 0 CCCGCGACCT 0.973379 -220 CGAGTCCCGTCGCCCGCTCCAATATAAAAA 15 103 1 CGCCCGCTCC 0.968559 -198 CGGACTCGAACCGGCGCCCTCACCCTTACC 15 186 0 CCGGCGCCCT 0.982267 -115 GATTTGGAGTCCCGCGCTCTGCCAATTGAG 16 34 0 CCCGCGCTCT 0.989042 -85 AGGACTCGAACCCCCACCCACGGGATTTGG 16 57 0 CCCCCACCCA 0.938454 -62 GTTCGAGTCCTCCCAGCCCCGCCACTTAAA 16 76 1 TCCCAGCCCC 0.894805 -43 ********** Masking position 9 Map Score: 10.6161 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 197 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TGCATAATTTCTTCTTCAATTTTCTTGAGG 2 20 0 CTTCTTCAAT 0.95131 -42 CACCTCCTGGCCTTTTTAAGGTCTCCCCGC 5 42 0 CCTTTTTAAG 0.801923 -24 AAGTCCTTGCCTTTTTCAACT 6 2 0 CTTTTTCAAC 0.763814 -59 TTCCGCCTCCTTGAAGTTCTCGTAAA 11 7 1 CTCCTTGAAG 0.933523 -49 TACAAACCTCCTTCAAGCCGGCAGTTG 12 24 0 CTCCTTCAAG 0.98398 -17 TAAATTAACACTTCTTTAAGCCAGTATTGA 14 71 0 CTTCTTTAAG 0.966142 -126 GGCTTTTCACCCCTTTAATTAGAGTAAGG 14 178 0 CCCCTTTAAT 0.863216 -19 TAAAAATCCCTTCCTTCAATAAATAAGCCC 15 127 1 TTCCTTCAAT 0.673853 -174 TCAAGTATTCCTTTTTCAATTCCCTAACCG 17 93 0 CTTTTTCAAT 0.877734 -120 TTCATTCCGCCTTCTTTAAGAAACATAAAA 17 177 1 CTTCTTTAAG 0.966142 -36 TATACCTCTCCTCTTTTATGTTTCTTAAAG 17 190 0 CTCTTTTATG 0.64269 -23 ********** Masking position 8 Map Score: 8.17572 Number of sites scoring better than the average of aligned sites = 865 Number in coding regions = 810 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 CCCTCTGAGATTTGTCCTTAATCCTTAACT 1 28 0 TTTGTCCTTA 0.741449 -90 GTCTTGCCTTTAGGGGAGAATA 1 106 0 CTTGCCTTTA 0.878852 -12 TCTCAACTGTTTTTCCCTTATAACCGTCAA 3 15 0 TTTTCCCTTA 0.96888 -31 AGGGGTTTTAATTGCCTTTAATTTTAGCAT 8 27 1 ATTGCCTTTA 0.952015 -59 TATACTAATAATTTGCCTTAAAAGGAGGAA 8 62 1 ATTTGCCTTA 0.921156 -24 TTTTCTCTTCTTTCCCCTTATAATTTTTCC 9 13 1 TTTCCCCTTA 0.905481 -21 TATAATATCAATTTGCCTTACTCTAATTAA 14 163 1 ATTTGCCTTA 0.921156 -34 ATTATAAATTATTTCTTTTACGTTTGTAAA 15 250 0 ATTTCTTTTA 0.677569 -51 CTTCTTTTCCTTTTCCTTTACACTTTTGCT 17 14 1 TTTTCCTTTA 0.951275 -199 AAATTATACTACTTCCTTTAGACATTAGTT 19 27 0 ACTTCCTTTA 0.833782 -44 ********** Masking position 3 Map Score: 6.05621 Number of sites scoring better than the average of aligned sites = 755 Number in coding regions = 705 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 CAATAGCCATACTCAGGTACGCCCACATAT 1 79 1 ACTCAGGTAC 0.945831 -39 TAAAATACTTAGCTTCAGGAGGTAAA 13 7 1 ACTTAGCTTC 0.926512 -27 TGCTCTACCAACTGAGCTACGCCCGCTCAG 15 44 0 ACTGAGCTAC 0.993969 -257 CGCTCTACCGACTGAGCTACCTGGGCTTAT 15 149 0 ACTGAGCTAC 0.993969 -152 CGCTCTGCCAATTGAGCTACAGCCCCACTA 16 20 0 ATTGAGCTAC 0.969306 -99 ********** Masking position 5 Map Score: 4.3478 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 8 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 AGAAGAAATCCTCAAGAAAATTGAAGAAGAAAT 2 10 1 CCTAGAAATG 0.917562 -52 ACCGAACCTCCACAATAGCGGAATATCTTA 6 41 0 CCTCCAAAGG 0.995401 -20 GAAGCTCCTCCTGAAAAGGGGTTTTAATTG 8 7 1 CCTCGAAAGG 0.991196 -79 GCGCCCTCACCCTTACCAAGGGTGCGCTCTACCG 15 169 0 CCTACAAGGG 0.991312 -132 GTTCCTGCCTCCTGAGCAAAAGTGTAAAGGAAAA 17 24 0 CCTACAAAGG 0.992788 -189 ATAATTTAAACCTTCGCAAAGGAGGTAAAGG 19 50 1 CCTCCAAGGG 0.994458 -21 *** * *** ** * Masking position 8 Map Score: 5.75124 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 28 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 AGAGGGACGGATATAAACCTAATCAATCAA 1 52 1 ATATAAACCT 0.863019 -66 GGGAATACATTTTAACGTTTAGGTTAGA 4 9 1 ATTTTAACGT 0.869608 -28 ATCACTATTCTAACCTAAACGTTAAA 4 21 0 ATTCTAACCT 0.914617 -16 ATAAAATTATATGTAAACCTTAATAGGAGG 10 125 1 ATGTAAACCT 0.903116 -28 TCGTAAAAACATTTTAACGACTGTAAATTA 11 30 1 ATTTTAACGA 0.777854 -26 AGGGGGCAGGATTCGAACCTGCGCA 15 6 0 ATTCGAACCT 0.862707 -295 GATCTTTTAAATTTAAACCAAAAAAGTACA 17 126 0 ATTTAAACCA 0.948566 -87 AAGTAGTATAATTTAAACCTTCGCAAAGGA 19 43 1 ATTTAAACCT 0.97234 -28 AGAGTTTATAATTTAAAGCATA 20 18 1 ATTTAAAGCA 0.728237 -12 ********** Masking position 6 Map Score: 4.65435 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 87 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 CTTTCAACCTCGTTTCCCCGCCCTGCGGGGA 5 18 1 CGTTTCCCCC 0.942913 -48 GCCTTTTTAAGGTCTCCCCGCAGGGCGGGGA 5 32 0 GGTCTCCCCC 0.911738 -34 TGCGCAGGTTCGAATCCTGCCCCCTCCATAT 15 11 1 CGAATCCTGC 0.943982 -290 GTCGCGGGTTCGAGTCCCGTCGCCCGCTCCA 15 93 1 CGAGTCCCGC 0.996172 -208 GGCGCCGGTTCGAGTCCGGTCCTGGGCTCCA 15 198 1 CGAGTCCGGC 0.986651 -103 CACGGGATTTGGAGTCCCGCGCTCTGCCAAT 16 38 0 GGAGTCCCGG 0.954756 -81 GGTGGGGGTTCGAGTCCTCCCAGCCCCGCCA 16 69 1 CGAGTCCTCC 0.985283 -50 ********* * Masking position 5 Map Score: 3.73436 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 57 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 AATTTTCTTGAGGATTTCTTCT 2 2 0 AGATTTCTTC 0.727679 -60 TGCAGCCTGCATAATTTCTTCTTCAATTTTC 2 26 0 ATATTTCTTC 0.629543 -36 CTCTTAGCCCTCCTTTGCAGCCTGCA 2 46 0 AGCCTCCTTT 0.860984 -16 AAAGGCAATTAAAACCCCTTTTCAGGAGGAG 8 15 0 AAACCCCTTT 0.946116 -71 ATAATTTTATTATATTCCTTTTAAAAATTTT 10 104 0 TAATTCCTTT 0.674966 -49 TACAAACCTCCTTCAAGCCGGCAG 12 27 0 AACCTCCTTC 0.89862 -14 ATAATAAATTAACACTTCTTTAAGCCAGTAT 14 74 0 AAACTTCTTT 0.872565 -123 GGCTTTTCACCCCTTTAATTAGAGTA 14 181 0 TTACCCCTTT 0.640461 -16 CTCCAATATAAAAATCCCTTCCTTCAATAAA 15 119 1 AAATCCCTTC 0.905872 -182 CCCTGATAAAAATCCCTCTTTACAAACGTAA 15 232 1 AACCCTCTTT 0.778873 -69 AATATTATAAATTATTTCTTTTACGTTTGTA 15 252 0 ATATTTCTTT 0.625143 -49 TACACTGTCAAGTATTCCTTTTTCAATTCCC 17 99 0 AGATTCCTTT 0.868405 -114 AGAAGGGGAAGATACCCCTTCTTGCTTCAC 18 10 0 GAACCCCTTC 0.771136 -32 ** ******** Masking position 9 Map Score: 4.39797 Number of sites scoring better than the average of aligned sites = 995 Number in coding regions = 936 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 12 GGGAGAATATGTGGGCGTACCTGAGTATGG 1 85 0 GTGGGCGTAC 0.960092 -33 GGCTGCAAAGGAGGGCTAAGAG 2 50 1 GAGGGCTAAG 0.95752 -12 ATAGTTTGCGGTGGGCTAAAGTGAGCTGTA 14 103 1 GTGGGCTAAA 0.811997 -94 ATATTACTGAGCGGGCGTAGCTCAGTTGGT 15 38 1 GCGGGCGTAG 0.990556 -263 TGGTAGAGCAGCGGCCTTCCAAGCCGCAGG 15 64 1 GCGGCCTTCC 0.860386 -237 TTATATTGGAGCGGGCGACGGGACTCGAAC 15 100 0 GCGGGCGACG 0.992167 -201 TGGTAAGGGTGAGGGCGCCGGTTCGAGTCC 15 185 1 GAGGGCGCCG 0.970564 -116 ********** Masking position 6 Map Score: 3.22691 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 97 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 CCTAAACGTTAAAATGTATTCCC 4 4 0 AAAATGTATT 0.946726 -33 TTATTATATTAAAATCTTTTAAC 7 32 1 AAAATCTTTT 0.882758 -13 TAAAGAGGCTAAATTCTATTAATTGCG 10 8 0 AAATTCTATT 0.927142 -145 AAACTTTATAAAATTGTATTAAGACTTTGT 10 55 0 AAATTGTATT 0.927142 -98 TACAGTCGTTAAAATGTTTTTACGAGAACT 11 25 0 AAAATGTTTT 0.882758 -31 TTTAAATTATAAACTCTATTCGCC 20 5 0 AAACTCTATT 0.91451 -25 ********** Masking position 5 Map Score: 2.50726 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 18 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 ********** No masking Map Score: 2.73092e-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: 2.73092e-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