AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_aquae_reg_300.orf -o199_aquae_300.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 TAGGTTTATATCCGTCCCTCTGAGATTTGTCCTTAAT 1 36 0 TCCGCCCTGT 0.906191 -82 ACCTCGTTTCCCCGCCCTGCGGGGAGACCTTAAAAAG 5 24 1 CCCGCCCGGA 0.902092 -42 ACTTCACCTCCTGGCCTTTTTAAGGTCT 5 48 0 CTTCCCCTCT 0.741181 -18 TAACCTAAGTCCTTGCCTTTTTCAACT 6 1 0 CCTTCCTTAT 0.905671 -60 TCTTCTACCTCCGAGAGAACTTTATTATA 7 3 1 TTCTCCCGAA 0.828898 -42 TCGCTTCCTCCTTTTAAGGCAAATTATTAGT 8 65 0 TTCCCCTTGA 0.904905 -21 TCTTTTCTCTTCTTTCCCCTTATAATTTTTCCC 9 11 1 TCTTCCTTAT 0.789358 -23 CTTACCCACCTCCTATTAAGGTTTACATATAAT 10 130 0 CACCCCTTGT 0.690585 -23 TTCCGCCTCCTTGAAGTTCTCGTAAAA 11 1 1 TTCCCCCTAT 0.950771 -55 ACCTAACTTTACCTCCTGAAGCTAAGTATTTTA 13 11 0 CTTTCCCTAT 0.938368 -23 TCCCTGACCTCTGCAAATAAAAAATTTAC 14 3 1 CCTGCCTGAA 0.602206 -194 GGCTTTTCACCCCTTTAATTAGAGTAAGGCA 14 176 0 TTTCCCTTAA 0.799955 -21 CAGGTTCGAATCCTGCCCCCTCCATATTACTGAGCGG 15 15 1 TCCTCCCTAT 0.954626 -286 AAGGCCGCTGCTCTACCAACTGAGCTACGCCCGCTCA 15 45 0 CTCTCCCTGA 0.976807 -256 GTTCGAGTCCCGTCGCCCGCTCCAATATAAAAATCCC 15 100 1 CGTCCCCTAA 0.805457 -201 ATATAAAAATCCCTTCCTTCAATAAATAAGCCCAGGT 15 124 1 CCCTCCCAAT 0.768181 -177 CAAGGGTGCGCTCTACCGACTGAGCTACCTGGGCTTA 15 150 0 CTCTCCCTGA 0.976806 -151 GAGTCCCGCGCTCTGCCAATTGAGCTACAGCCCCACT 16 21 0 CTCTCCTTGA 0.942655 -98 GGACTCGAACCCCCACCCACGGGATTTGGAGTCCCGC 16 49 0 CCCCCCCGAT 0.962473 -70 GTCCTCCCAGCCCCGCCACTTAAAACTTTCCAGAGGT 16 82 1 CCCCCCTTAT 0.968948 -37 TACAGAGCGTTCCTGCCTCCTGAGCAAAAGTGTAAAG 17 29 0 TCCTCCCTGA 0.963707 -184 ACATTAATCTTCTTACCGGTTAGGGAATTGAAAAAGG 17 77 1 TCTTCCTTGA 0.825186 -136 TATTGCTTCATTCCGCCTTCTTTAAGAAACATAAAAG 17 171 1 TTCCCCCTAA 0.957356 -42 TTTTATACCTCTCCTCTTTTATGTTTCTTAAAGA 17 189 0 CCTCCCTTAT 0.934383 -24 GAAGGGGTATCTTCCCCTTCTCAAAAATTAAA 18 20 1 CTTCCCCTAA 0.963303 -22 CCTTTACCTCCTTTGCGAAGGTTTAAAT 19 53 0 CTTTCCCTGA 0.950544 -18 **** ** ** * * Masking position 7 Map Score: 32.2943 Number of sites scoring better than the average of aligned sites = 1497 Number in coding regions = 1339 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 2 TAAAATTAAAGGCAATTAAAACCCCTTTTCAGGA 8 19 0 GGATTAAACC 0.902236 -67 GGGGTTTAAAGCCCAACTGCCGGC 12 1 1 GGGTTAAGCC 0.918269 -40 TGCGCAGGTTCGAATCCTGCCCCCTCC 15 4 1 GCGTTGAACC 0.991652 -297 CCCGCGACCTGCGGCTTGGAAGGCCGCTGCTCTA 15 67 0 GCGTTGAAGC 0.945239 -234 GCCGCAGGTCGCGGGTTCGAGTCCCGTCGCCCGC 15 86 1 GCGTTGAGCC 0.997248 -215 GGGTGAGGGCGCCGGTTCGAGTCCGGTCCTGGGC 15 191 1 GCGTTGAGCC 0.997248 -110 ATTTTTATCAGGGAAGTGGAGCCCAGGACCGGAC 15 211 0 GGAGTGAGCC 0.971736 -90 CCCCACCCACGGGATTTGGAGTCCCGCGCTCTGC 16 42 0 GGATTGAGCC 0.993147 -77 TCCCGTGGGTGGGGGTTCGAGTCCTCCCAGCCCC 16 62 1 GGGTTGAGCC 0.997774 -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 AAGATTTTAATATAATAAAGTTCTCTCGGAG 7 19 0 TATAATAAAT 0.963874 -26 CTTAATACAATTTTATAAAGTTTTATGATAA 10 62 1 TTTTATAAAT 0.881187 -91 ATTATATTCCTTTTAAAAATTTTTGCAATAA 10 96 0 TTTTAAAAAT 0.700791 -57 TTAAAAGGAATATAATAAAATTATATGTAAA 10 111 1 TATAATAAAT 0.963874 -42 GACCTCTGCAAATAAAAAATTTACCCTGTGT 14 16 1 AATAAAAAAT 0.700791 -181 CACCGCAAACTATAATAAATTAACACTTCTT 14 85 0 TATAATAAAT 0.963872 -112 AAATTGATATTATAACAAATTTATGTTAGAA 14 146 0 TATAACAAAT 0.876339 -51 GGTAACAAAATATTATAAATTATTTCTTTTA 15 260 0 TATTATAAAT 0.963813 -41 AACGCTACTTATTATAAACTAATGTCTAAA 19 10 1 TATTATAAAT 0.963872 -61 TATGCTTTAAATTATAAACTCTATTCGCC 20 10 0 AATTATAAAT 0.881119 -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 GTTTTAATTGCCTTTAATTTTAGCATTTTGA 8 31 1 CCTTTAATTT 0.860224 -55 CTTCTTTCCCCTTATAATTTTTCCC 9 19 1 CTTATAATTT 0.939506 -15 TAATTCTTATCATAAAACTTTATAAAATTGT 10 68 0 CATAAAATTT 0.717944 -85 TTAAGGTTTACATATAATTTTATTATATTCC 10 117 0 CATATAATTT 0.811929 -36 TAAATTATTTCTTTTACGTTTGTAAAGAGGG 15 245 0 CTTTTACTTT 0.918871 -56 AGCCCCGCCACTTAAAACTTTCCAGAGGTAT 16 90 1 CTTAAAATTT 0.901544 -29 CTCCTTCTTTTCCTTTTCCTTTACACT 17 7 1 CTTTTCCTTT 0.812975 -206 TTTCCTTTTCCTTTACACTTTTGCTCAGGAG 17 19 1 CTTTACATTT 0.856333 -194 ATTAACTGATCTTTTAAATTTAAACCAAAAA 17 132 0 CTTTTAATTT 0.963424 -81 TACCTCTCCTCTTTTATGTTTCTTAAAGAAG 17 187 0 CTTTTATTTT 0.805914 -26 TATGCTTTAAATTATAAACTCTATT 20 15 0 CTTTAAATAT 0.663675 -15 ******* *** Masking position 3 Map Score: 6.29829 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 380 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 TTATAAGGGAAAAACAGTTGAGAGGTGAAGG 3 22 1 AAAACATTGA 0.882582 -24 GGGAATACATTTTAACGTTTAGGT 4 4 1 AATACATTTA 0.969601 -33 GTTAAAAGATTTTAATATAATAAA 7 31 0 AAAAGATTTA 0.948741 -14 CGCAATTAATAGAATTTAGCCTCTTTAG 10 8 1 AATAGATTTA 0.960453 -145 ACAAAGTCTTAATACAATTTTATAAAGTTTT 10 55 1 AATACATTTT 0.868501 -98 AGTTCTCGTAAAAACATTTTAACGACTGTAA 11 25 1 AAAACATTTA 0.9604 -31 GGCGAATAGAGTTTATAATTTAAAG 20 5 1 AATAGATTTA 0.960097 -25 ****** **** Masking position 6 Map Score: 5.08754 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 19 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TGCCTTAAAAGGAGGAAGCGA 8 75 1 GGAGGAAGCG 0.917236 -11 TATGGAGGGGGCAGGATTCGAACCTGCGCA 15 11 0 GCAGGATTCG 0.975022 -290 CTTCCAAGCCGCAGGTCGCGGGTTCGAGTC 15 79 1 GCAGGTCGCG 0.972403 -222 GGAGCGGGCGACGGGACTCGAACCCGCGAC 15 93 0 ACGGGACTCG 0.982778 -208 GGAGCCCAGGACCGGACTCGAACCGGCGCC 15 198 0 ACCGGACTCG 0.968756 -103 TTGGCAGAGCGCGGGACTCCAAATCCCGTG 16 39 1 GCGGGACTCC 0.975698 -80 GGCGGGGCTGGGAGGACTCGAACCCCCACC 16 69 0 GGAGGACTCG 0.989734 -50 ********** Masking position 5 Map Score: 5.6838 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 78 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 CAATAGCCATACTCAGGTACGCCCACATAT 1 79 1 ACTCAGGTAC 0.947391 -39 TAAAATACTTAGCTTCAGGAGGTAAA 13 7 1 ACTTAGCTTC 0.928587 -27 TGCTCTACCAACTGAGCTACGCCCGCTCAG 15 44 0 ACTGAGCTAC 0.994151 -257 CGCTCTACCGACTGAGCTACCTGGGCTTAT 15 149 0 ACTGAGCTAC 0.994151 -152 CGCTCTGCCAATTGAGCTACAGCCCCACTA 16 20 0 ATTGAGCTAC 0.970212 -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 GAGGGACGGATATAAACCTAATCAATCAAT 1 53 1 TATAAACCTA 0.646667 -65 ATCACTATTCTAACCTAAACGTTAAAA 4 20 0 TTCTAACCTA 0.603366 -17 AATAAATCTTTCAACCTCGTTTCCCCGC 5 9 1 TTTCAACCTC 0.976951 -57 TCTTCTACCTCCGAGAGAACT 7 2 1 CTTCTACCTC 0.845015 -43 CTTACCCACCTCCTATTAAGGT 10 141 0 TACCCACCTC 0.874554 -12 GCAGTTGGGCTTTAAACCCC 12 1 0 TTTAAACCCC 0.833485 -40 TACAAACCTCCTTCAAGCCG 12 31 0 TACAAACCTC 0.934244 -10 TTCCTACCTCCGAATTTTGA 15 291 0 TTCCTACCTC 0.974908 -10 GTACAGAGCGTTCCTGCCTCCTGAGCAAAA 17 37 0 TTCCTGCCTC 0.879761 -176 TTTTATACCTCTCCTCTTTTA 17 202 0 TTTATACCTC 0.947794 -11 AGTAGTATAATTTAAACCTTCGCAAAGGAG 19 44 1 TTTAAACCTT 0.722663 -27 ********** Masking position 7 Map Score: 5.1052 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 430 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 9 CTCCTGAAAAGGGGTTTTAATTGCCTTTAAT 8 18 1 GGGGTTTTAT 0.912075 -68 CTTTAATTTTAGCATTTTGATATACTAATAA 8 42 1 AGCATTTTAT 0.790075 -44 CTCCTTTTAAGGCAAATTATTAGTATATCAA 8 58 0 GGCAAATTTT 0.818776 -28 ATTAGAGTAAGGCAAATTGATATTATAACAA 14 159 0 GGCAAATTAT 0.924992 -38 ATTGAAGGAAGGGATTTTTATATTGGAGCGG 15 116 0 GGGATTTTAT 0.971192 -185 GAGCTACCTGGGCTTATTTATTGAAGGAAGG 15 135 0 GGCTTATTAT 0.874983 -166 TTTGTAAAGAGGGATTTTTATCAGGGAAGTG 15 227 0 GGGATTTTAT 0.971192 -74 TCAGTTAATGGGGATATTATTGCTTCATTCC 17 154 1 GGGATATTTT 0.925047 -59 ******** ** Masking position 7 Map Score: 2.70111 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 71 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 TCTTCAATTTTCTTGAGGATTTCTTCT 2 7 0 TCTTGAGGTT 0.865701 -55 AGTTTTGACGGTTATAAGGGAAA 3 3 1 TTTTGACGTT 0.927935 -43 GGGAATACATTTTAACGTTTAGGTTAGAAT 4 10 1 TTTTAACGTT 0.929262 -27 CTCCTGGCCTTTTTAAGGTCTCCCCGCAGGG 5 38 0 TTTTAAGGCT 0.946578 -28 CGCTTCCTCCTTTTAAGGCAAATTATTAGTA 8 64 0 TTTTAAGGAA 0.807453 -22 ACCCACCTCCTATTAAGGTTTACATATAATT 10 129 0 TATTAAGGTT 0.816081 -24 CGTAAAAACATTTTAACGACTGTAAATTAAA 11 31 1 TTTTAACGCT 0.915902 -25 TACCTCCGAATTTTGAGGTAACAAAATATTA 15 276 0 TTTTGAGGAA 0.804321 -25 ******** ** Masking position 6 Map Score: 0.909029 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 213 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 11 CAGCCTGCATAATTTCTTCTTCAATTTTCT 2 25 0 AATTTCTTCT 0.590708 -37 CTCTTAGCCCTCCTTTGCAGCCTG 2 48 0 TAGCCCTCCT 0.797768 -14 GAAGCTCCTCCTGAAAAGGGGT 8 3 1 AGCTCCTCCT 0.57866 -83 AGGCAATTAAAACCCCTTTTCAGGAGGAGC 8 14 0 AACCCCTTTT 0.916656 -72 TCGCTTCCTCCTTTTAAGGCAAATT 8 71 0 TCCTCCTTTT 0.693523 -15 AATTTTATTATATTCCTTTTAAAAATTTTT 10 103 0 TATTCCTTTT 0.896879 -50 CCAATATAAAAATCCCTTCCTTCAATAAAT 15 121 1 AATCCCTTCC 0.650786 -180 CCCTGATAAAAATCCCTCTTTACAAACGTA 15 232 1 AATCCCTCTT 0.840727 -69 TATTATAAATTATTTCTTTTACGTTTGTAA 15 251 0 TATTTCTTTT 0.611921 -50 CTCCTTCTTTTCCTTTTCCTTTACACT 17 8 1 TTTTCCTTTT 0.660864 -205 CACTGTCAAGTATTCCTTTTTCAATTCCCT 17 98 0 TATTCCTTTT 0.896879 -115 TTTTATACCTCTCCTCTTTTATGTT 17 198 0 TACCTCTCCT 0.788142 -15 AAGGGGAAGATACCCCTTCTTGCTTCAC 18 9 0 TACCCCTTCT 0.968697 -33 AAGGGGTATCTTCCCCTTCTCAAAAATTAA 18 21 1 TTCCCCTTCT 0.873954 -21 ********** Masking position 7 Map Score: 6.42979 Number of sites scoring better than the average of aligned sites = 1389 Number in coding regions = 1304 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 12 ********** 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 13 ********** 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 14 GCCATACTCAGGTACGCCCACATATTCTCCC 1 84 1 GGTCGCCCAC 0.976005 -34 CTTTCAACCTCGTTTCCCCGCCCTGCGGGGA 5 18 1 CGTTCCCCGC 0.98282 -48 GCCTTTTTAAGGTCTCCCCGCAGGGCGGGGA 5 32 0 GGTTCCCCGC 0.978805 -34 AGGTTCGAATCCTGCCCCCTCCATATTACTG 15 16 1 CCTCCCCCTC 0.968979 -285 TACCAACTGAGCTACGCCCGCTCAGTAATAT 15 38 0 GCTCGCCCGC 0.987763 -263 GGTTCGAGTCCCGTCGCCCGCTCCAATATAA 15 99 1 CCGCGCCCGC 0.974281 -202 GACTCGAACCGGCGCCCTCACCCTTACCAAG 15 183 0 GGCCCCTCAC 0.838886 -118 TGGGAGGACTCGAACCCCCACCCACGGGATT 16 60 0 CGACCCCCAC 0.960191 -59 TTCGAGTCCTCCCAGCCCCGCCACTTAAAAC 16 77 1 CCCGCCCCGC 0.962891 -42 *** ******* Masking position 7 Map Score: 8.03851 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 67 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 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