AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i251_tpal_bbur_300.orf -o251_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00897 300 AE000520 #2 RTP00899 21 AE000520 #3 RTP00159 29 AE000520 #4 RTP00160 86 AE000520 #5 RTP00981 170 AE000520 #6 RTP00980 169 AE000520 #7 RTP00594 46 AE000520 #8 RBB00689 187 3615 #9 RBB00430 43 3615 #10 RBB00429 50 3615 #11 RBB00336 248 3615 #12 RBB00335 32 3615 #13 RBB00191 207 3615 #14 RBB00188 64 3615 #15 RBB00152 70 3615 #16 RBB00097 42 3615 #17 RBB00094 70 3615 #18 RBB00092 67 3615 #19 RBB00089 39 3615 Motif number 1 TAAGCATACTAATAATTTAACTACTAAATT 8 29 1 AATAATTTAA 0.895904 -159 AAGGTTTTTGTTTATTTTAATTTATTTGCA 11 89 0 TTTATTTTAA 0.938907 -160 TATAAGTAATTTTATTATAAGACATAGGTT 11 125 0 TTTATTATAA 0.80208 -124 AAATTGTAAAATTAATATAAGTAATTTTAT 11 140 0 ATTAATATAA 0.759561 -109 ACCTAAGAGATTTATTATAAATAGGCAATA 11 191 1 TTTATTATAA 0.80208 -58 CTTTTTTATATTAAATTTAATTTAACCTAC 13 17 1 TTAAATTTAA 0.495671 -191 AATTCTATCTTATAATTTAAGGTAGAAAGT 13 48 0 TATAATTTAA 0.930385 -160 AATAAAAAACATAATTTTAACAGAATTCTA 13 71 0 ATAATTTTAA 0.821192 -137 TAGAAGTTAATAAAATTTAATTTACCAAAA 13 103 0 TAAAATTTAA 0.75348 -105 CCCCTTTGAATGTAATTTAAATCGCAAATA 13 183 0 TGTAATTTAA 0.809536 -25 TATTATATTTTAATATTTTTAAC 14 52 0 TATATTTTAA 0.916941 -13 TAAATAATATATAATTTTAATATTACAAC 15 52 1 ATAATTTTAA 0.821192 -19 ATGATTATTATAATTTAATTATAAGGAT 16 9 1 TATAATTTAA 0.930385 -34 TTTTTATTAGTAAAATTTAATTTA 17 5 0 TAAAATTTAA 0.75348 -66 AGCTTTACATATTAATTTAAAC 18 3 0 ATTAATTTAA 0.923802 -65 ACTATTTCCTATTATTTTAATATGTAAAGC 18 46 0 ATTATTTTAA 0.908839 -22 ********** Masking position 6 Map Score: 18.8554 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 56 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 GGAATGACTGAAATTTTTGTGTTTGATCAAACAC 1 96 0 AAATTTTTTT 0.956565 -205 CCTTAATTTTTGGGGTTGAAACCACTG 4 70 0 TAATTTTGTT 0.857564 -17 GAAATAAAGAAAATTATTGATTTTTTCGCCGCCG 5 85 0 AAATTTTTTT 0.951035 -86 TAATTTTCTTTATTTCTTGGATTTTCTTCTGAGC 5 103 1 TATTTTTTTT 0.51306 -68 TTTAGTAGTTAAATTATTAGTATGCTTACTTATT 8 23 0 AAATTTTATG 0.749226 -165 TTTAACTACTAAATTATCACAATTGAAAAATTAT 8 44 1 AAATTTCATT 0.879192 -144 CACAATTGAAAAATTATTGCAATTGAAATATCTA 8 61 1 AAATTTTATT 0.961192 -127 TAGAAATGTAAAATTTTTTTAGTTCTATAATACT 8 113 0 AAATTTTGTT 0.914502 -75 CAAATTAATCAAATTGTTATAAACA 9 2 1 AAATTATATT 0.594855 -42 TTACTTATATTAATTTTACAATTTTTTTTCAAAA 11 146 1 TAATTTATTT 0.651881 -103 GGAACCTGCTTAATTCTTCTCTTTATAAATAAGT 11 220 0 TAATTTTTTT 0.924907 -29 TGTTAACTTTTTTATATTAAATTTAATT 13 5 1 AACTTTTATT 0.760736 -203 AATTCTGTTAAAATTATGTTTTTTATTGTTTTTG 13 74 1 AAATTTGTTT 0.776871 -134 TATTATAATTTAATTATAAGGATTTTAAAAGTAA 16 16 1 TAATTTAATT 0.724329 -27 TTTCGTTTTTTAATTATTTTTATTAGTAAAATTT 17 17 0 TAATTTTATT 0.933343 -54 ATCTTTTATAAAATTTTCGTTTTTTAATTATTTT 17 31 0 AAATTTCTTT 0.864993 -40 TATGAAAAAAATTCTTTTTATTAGAAGAGAGA 19 9 1 AAATTTTATT 0.961673 -31 ***** ** *** Masking position 5 Map Score: 14.8669 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 117 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 AGGAAGTCATCCCCCTTGTGCCCGCCAACCCCTAA 1 14 1 CCCGTGCCGC 0.975884 -287 CCGACTACATCCATGCTCCGCACGCGTTACCCTGG 1 133 1 CCTCCGCCGC 0.982838 -168 TAATAATTCCCCGTCAAGCCCTCTTCCATCCAGTA 4 34 0 CCTGCCCCTT 0.843544 -53 CTCGACCTGACCGACGTGCGCACGCTGATCCGAGT 5 39 0 CCAGCGCCGC 0.995157 -132 TTGCCGATGCCCTAGCAGAGCTCGCTCAGAAGAAA 5 125 0 CCAGAGCCGC 0.963938 -46 GCAAGCACTTCCTTAAACCGCACGT 5 156 1 CCTCCGCCGT 0.993469 -15 GGAGTAGATACCGTTCGCCGCCTGCACACTCAGTT 6 27 1 CCTCCGCTGC 0.993102 -143 GAAGGAGATGCCGTTCTGCGCGTTTGTAGACGCCT 6 120 1 CCTGCGCTTT 0.924015 -50 CCTTGGTCTGCGTGCAGGAAATATT 7 1 1 CCTCTGCTGC 0.972001 -46 ** * **** *** Masking position 11 Map Score: 8.67849 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 36 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 CGGCGGCGAAAAAATCAATAATTTTCTTTAT 5 85 1 AAAATAATAA 0.793224 -86 CTAAATTATCACAATTGAAAAATTATTGCAA 8 52 1 ACAATGAAAA 0.962531 -136 AATAAGAATTATAATGAAAAAGTATAATAAA 10 11 1 ATAATAAAAA 0.902501 -40 TATTAAATCGACATTTGAAAACATTTTTTCC 11 30 1 ACATTGAAAA 0.701643 -219 CAAATAAATTAAAATAAACAAAAACCTTTTT 11 91 1 AAAATAACAA 0.763276 -158 TTTTTGAAAAAAAATTGTAAAATTAATATAA 11 150 0 AAAATGTAAA 0.702377 -99 TAACAAGAATAAAATGGGAAAAAAGTAACG 12 13 1 AAAATGGAAA 0.865537 -20 AATTAAATTTAATATAAAAAAGTTAACA 13 8 0 AATATAAAAA 0.651741 -200 TTTACCAAAAACAATAAAAAACATAATTTTA 13 82 0 ACAATAAAAA 0.959483 -126 AGAAAATAGAAAATAGAAAATGC 14 3 1 AAAATGAAAA 0.956853 -62 TTTAACCTTTAAAACCAAAAAGCTGCATTTT 14 27 0 AAAACAAAAA 0.735007 -38 TAATTACAATACAATTAAAAAGGAGCCATTT 15 13 0 ACAATAAAAA 0.959483 -58 ATTGTAATTAACAATCAATAAATAATATATA 15 34 1 ACAATAATAA 0.816304 -37 ACTAATAAAAATAATTAAAAAACGAAAATTT 17 24 1 ATAATAAAAA 0.902501 -47 ACATATTAAAATAATAGGAAATAGTAT 18 51 1 ATAATGGAAA 0.744553 -17 ***** ***** Masking position 10 Map Score: 12.102 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 56 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 ATTAGTATGCTTACTTATTAAAGGTTGTTTT 8 11 0 TTACTATTAA 0.866458 -177 TGAAAAATTATTGCAATTGAAATATCTAACT 8 67 1 TTGCATTGAA 0.418094 -121 ATTTTATACCTTTAAATCTGTTTATA 9 28 0 ATACTTTAAA 0.830718 -16 ACACTTTATTATACTTTTTCATTATAATTCT 10 15 0 ATACTTTTCA 0.368757 -36 TCGATTTAATATGCATTTTAAAAAGATCAA 11 10 0 ATGCTTTTAA 0.640914 -239 TAGGCAATACTTATTTATAAAGAGAAGAATT 11 212 1 TTATTATAAA 0.566937 -37 GAATTCTATCTTATAATTTAAGGTAGAAAGT 13 48 0 TTATATTTAA 0.626128 -160 AGCATTCTATTTGCGATTTAAATTACATTCA 13 176 1 TTGCATTTAA 0.754609 -32 GCGATTTAAATTACATTCAAAGGGGCGTTT 13 188 1 TTACTTCAAA 0.643339 -20 TTAATATTTTTAACCTTTAAAACCAAAAAGC 14 35 0 TAACTTTAAA 0.548981 -30 TATTATATTTTAATATTTTTAAC 14 52 0 TTATTTTTAA 0.750441 -13 GTTAATTACAATACAATTAAAAAGGAGCCAT 15 15 0 ATACATTAAA 0.732466 -56 TTTAAAATCCTTATAATTAAATTATAATAAT 16 14 0 TTATATTAAA 0.628653 -29 AAATTACTTTTAAAATCCTTATAA 16 29 0 TTACTTTAAA 0.938078 -14 AAATTAAATTTTACTAATAAAAATAATTAAA 17 12 1 TTACAATAAA 0.784782 -59 TTAGGTAGCTTTACATATTAATTTAAAC 18 8 0 TTACTATTAA 0.865324 -60 AAGGTTTGCTTTACATATTAAAATAATAGGA 18 39 1 TTACTATTAA 0.865324 -29 **** ****** Masking position 11 Map Score: 7.56026 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 91 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ACCCCTAAACGGGTTCCTGCTTTCATTACG 1 41 1 GGGTTCCTGC 0.978686 -260 ATACACTGAGGCGATCCTGCACATCGCTTT 1 213 1 GCGATCCTGC 0.966269 -88 CTGCATACACGCGCTCCTGATCCTGCCTTT 1 270 1 GCGCTCCTGA 0.931605 -31 AAAGAGGCTGCTGCAAACTATTCG 3 16 0 AGGCTGCTGC 0.883716 -14 AGCTCTGCTAGGGCATCGGCAAGCACTTCC 5 138 1 GGGCATCGGC 0.887298 -33 AGAGACGGTCTTCTGCGGAGTAGATA 6 7 1 GGTCTTCTGC 0.948769 -163 TAACGTCGGTGGTCTCCTGTAAAAACGCCT 6 77 1 GGTCTCCTGT 0.898019 -93 TTTTGGGAACCTGCTTAATTCTTC 11 235 0 GGGAACCTGC 0.967364 -14 ********** Masking position 7 Map Score: 3.76925 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 138 Number in noncoding regions = 319 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ATTAGTATGCTTACTTATTAAAGGTTGTTT 8 12 0 TTACTTATTA 0.826587 -176 AGCGATTCGTTTTCATACTAGAAATGTAAA 8 135 0 TTTCATACTA 0.834562 -53 TGTTAACTTTTTTATATTAAATTTAATTT 13 10 1 TTTTATATTA 0.89368 -198 TATTATATTTTAATATTTTTAA 14 53 0 TTATATTTTA 0.618287 -12 AATATTAAAATTATATATTATTTATTGATT 15 46 0 TTATATATTA 0.901995 -25 AATATATAATTTTAATATTACAAC 15 57 1 TTTAATATTA 0.769542 -14 TTAGGTAGCTTTACATATTAATTTAAAC 18 9 0 TTACATATTA 0.963355 -59 AAGGTTTGCTTTACATATTAAAATAATAGG 18 39 1 TTACATATTA 0.963355 -29 ATACTATTTCCTATTATTTTAATATG 18 52 0 TTTCCTATTA 0.851515 -16 ********** Masking position 6 Map Score: 5.19022 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 10 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 GCATTCAATACACTGAGGCGATCCTGCACA 1 206 1 CACTGAGGCG 0.971759 -95 GACGTGCGCACGCTGATCCGAGTTTGCGAA 5 32 0 CGCTGATCCG 0.972731 -139 GGGGCGCAACCGCGGCGGCGAAAAAATCAA 5 73 1 CGCGGCGGCG 0.799226 -98 ACACTCAGTTCGCGAATGCGCTGGATAACG 6 52 1 CGCGAATGCG 0.967588 -118 TCATTCAGGTTGCGGAGGCGTTTTTACAGG 6 92 0 TGCGGAGGCG 0.979959 -78 TGGTTCAAACCACGGATCTGGCTCCG 6 154 1 CACGGATCTG 0.848276 -16 ********** Masking position 3 Map Score: 1.9822 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 42 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ATAATTTAACTACTAAATTATCACAATTGAA 8 40 1 TACTAATTAT 0.568964 -148 GATCTCATTCTCCTTTTTTATCCATAGCGAT 8 159 0 TCCTTTTTAT 0.953457 -29 CTCATTAAATTCCTCATTTATTGCTGCAAAT 11 65 1 TCCTATTTAT 0.960542 -184 AATAAACAAAAACCTTTTTATAAACCTATGT 11 103 1 AACCTTTTAT 0.68563 -146 AAATAAGTATTGCCTATTTATAATAAATCTC 11 197 0 TGCCATTTAT 0.74562 -52 AAATAGGCAATACTTATTTATAAAGAGAAGA 11 209 1 TACTATTTAT 0.912193 -40 GTTACTTTTTTCCCATTTTATTCTTGTTAAA 12 11 0 TCCCTTTTAT 0.927696 -22 TGTTAACTTTTTTATATTAAATTTA 13 5 1 AACTTTTTAT 0.776894 -203 GATTAATATTACCTCATATATTGATAAATAC 13 137 0 ACCTATATAT 0.706388 -71 AAAAATGGCTCCTTTTTAATTGTATTGTAA 15 10 1 TCCTTTTAAT 0.722446 -61 CTCCTTATATATATAAATCTTT 17 59 0 TCCTATATAT 0.857956 -12 **** ****** Masking position 10 Map Score: 4.62272 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 61 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 ********** No masking Map Score: 1.51589e-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 11 ********** No masking Map Score: 1.51589e-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 12 ********** No masking Map Score: 1.51589e-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