AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i197_tpal_bbur_300.orf -o197_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 Purged sequences: RBB00316 172 3615 Input sequences: #1 RTP00800 242 AE000520 #2 RTP00803 126 AE000520 #3 RTP00764 108 AE000520 #4 RTP00766 42 AE000520 #5 RTP00767 126 AE000520 #6 RTP00768 96 AE000520 #7 RTP00769 125 AE000520 #8 RTP00770 34 AE000520 #9 RTP00771 204 AE000520 #10 RBB00315 172 3615 #11 RBB00314 240 3615 Motif number 1 AGGCGCAGTAGGGTGCTGTGCGTCGTATCCTC 1 60 0 GGGCTGTGCG 0.965069 -183 GCGTCGCGTACCTGAAGGCGCAGTAGGGTGCT 1 75 0 CCTAGGCGCA 0.83438 -168 AATTTCTCTTGCGATGTGTGCGTCGCGTACCT 1 94 0 GCGGTGTGCG 0.983837 -149 GCGGTTGTGGGGGAAAGGTGCGATGCAAGACT 1 138 0 GGGAGGTGCG 0.960511 -105 GGGCAGCGGACCGTCCTGCAGGCAAGCGGTTG 1 163 0 CCGCTGCAGG 0.845635 -80 CGCGCAGTGTCCGGTGTGGGCAGCGGACCGTC 1 180 0 CCGGTGGGCA 0.885666 -63 GTATCCGGCTGGGCAATGCGCGCAGTGTCCGG 1 198 0 GGGATGCGCG 0.985958 -45 GACACCTCAGGTGCAGGGTGCAC 1 230 1 GTGGGGTGCA 0.772418 -13 GGGAACTGCGGATACCGAGGCG 2 1 1 GGGCTGCGGA 0.93758 -126 ACGAATCTTCCCGTAGCGCGGGTGGATGAGCA 2 78 1 CCGGCGCGGG 0.953192 -49 TCTGCGTCTTGCGGCAGGCACGCTGGTGAACG 3 20 1 GCGAGGCACG 0.893846 -89 GGTGCTATCCTTTCGGCGCGAGACACACAG 5 107 0 CCTCGGCGCG 0.952156 -20 CGTCTGGGCGGAGCAAGGCCAC 6 1 1 CGTGGGCGGA 0.818698 -96 CCGGCGGGTGTGCACGGCCATG 7 1 1 CCGGGGTGTG 0.842008 -125 CGGGTGTGCACGGCCATGCGCACTCCTTCTGC 7 15 1 CGGATGCGCA 0.966697 -111 TTGGGTGATCGTGCTGTGCGCGCTCATCTTTT 7 49 0 GTGGTGCGCG 0.966492 -77 CCAGTGTACCCGGTAGTGCGCACGTACTATGC 7 93 0 CGGGTGCGCA 0.985716 -33 TTTGAAAGAAGCGGAGGGCGGGGAAATCTGTT 9 22 1 GCGGGGCGGG 0.991387 -183 CAGAAACCCACCGTGCTGCTCGCCTTTGACTC 9 90 0 CCGCTGCTCG 0.86958 -115 TTTCTGTGTGCGGGGATGTGGGGAGATTTCGT 9 116 1 CGGATGTGGG 0.921544 -89 *** ******* Masking position 8 Map Score: 27.6718 Number of sites scoring better than the average of aligned sites = 1288 Number in coding regions = 406 Number in noncoding regions = 882 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 GGTGCTGTGCGTCGTATCCTCGCGAAGGCGA 1 50 0 GTCGTATCCC 0.991737 -193 CACCTGAGGTGTCGTATCCGGCTGGGCAATG 1 212 0 GTCGTATCCG 0.952131 -31 TGAGCATGACGTGGTATACCTGAGTGAAGAA 2 104 1 GTGGTATACT 0.827635 -23 CAAGCGCGCAGTGGTATTCTTGTCTCTTGGT 3 59 1 GTGGTATTCT 0.894374 -50 GTCGTTCCGGGTCGTTTTCACCTGTTGGGGG 5 17 1 GTCGTTTTCC 0.916285 -110 GGGAGTATCTGTGGTTTGCTCAGGGCAACAC 5 45 1 GTGGTTTGCC 0.952679 -82 GGTGCTATCCTTTCGGCGCGAG 5 115 0 GTGCTATCCT 0.963903 -12 CCACTGCATTGGCGTATCCACCTTTAGTGGA 6 29 1 GGCGTATCCC 0.953391 -68 TTGGGTGATCGTGCTGTGCGCGCTCATCTTT 7 50 0 GTGCTGTGCC 0.897495 -76 TAGTGCGCACGTACTATGCGCGCATGAGAGA 7 81 0 GTACTATGCC 0.85291 -45 CCTACCCGCGATCCTTTCCTCACCCGTGCCT 9 148 0 ATCCTTTCCC 0.712578 -57 TGCTTCTTCCGTCCTATCCCTACCCGCGATC 9 166 0 GTCCTATCCT 0.969576 -39 ********* * Masking position 5 Map Score: 10.0457 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 85 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 AGACACAGGATTTTGCACAATA 3 97 1 TTTTGCAATA 0.880256 -12 AGAATCCTAATTTAACATTATACTATATAATG 10 114 1 TTTAACAATA 0.980134 -59 GCACTATACTTTTAACATTATATAGTATAATG 10 129 0 TTTAACAATA 0.980134 -44 CCTTGTTGGTTTTAGCACTATACTTTTAACAT 10 143 0 TTTAGCAATA 0.971744 -30 CAACCTACAATTTAACAAGATATTTACTTGCA 11 82 1 TTTAACAATA 0.981374 -159 TTTAATTGTATTTAATACTATATGATGCAAGT 11 107 0 TTTAATAATA 0.916874 -134 TAAGATAAAATGTAATAGAATATATAAGGAGG 11 215 1 TGTAATAATA 0.81532 -26 ******* *** Masking position 7 Map Score: 5.68582 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 2 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 CAAGACTTTTTGAGGCGGCAATTTCTCTTGC 1 114 0 TGAGGCGGAA 0.955102 -129 GGCAAGCGGTTGTGGGGGAAAGGTGCGATGC 1 144 0 TGTGGGGGAA 0.991084 -99 TTTATAAACTTGAGGTGGTAGTTTTGCCGAC 2 49 1 TGAGGTGGAG 0.956166 -78 TGGGTCTGCGTCTTGCGGCAGGCACGCTGGT 3 16 1 TCTTGCGGAG 0.941349 -93 CCTCAAGTCATTTGGGGGAAAGGGGAG 4 26 1 TTTGGGGGAA 0.955136 -17 CGTTTTCACCTGTTGGGGGAGTATCTGTGGT 5 29 1 TGTTGGGGAG 0.975807 -98 CGTCTGGGCGGAGCAAGGCCACT 6 3 1 TCTGGGCGAG 0.956934 -94 GCGCGCCCCTTCTGGTGGGAACCCCCTTGAG 6 73 0 TCTGGTGGAA 0.966217 -24 ******** ** Masking position 10 Map Score: 6.61752 Number of sites scoring better than the average of aligned sites = 1020 Number in coding regions = 308 Number in noncoding regions = 712 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 TAAAATTTATAAACTTGAGGTGGTAGTTTTGCC 2 44 1 AACTAGGTGG 0.971063 -83 AGGTTCCTCAAGTCATTTGGGGGAAAGGGGAG 4 21 1 AGCATGGGGG 0.926401 -22 GGGTCGTTTTCACCTGTTGGGGGAGTATCTGTG 5 25 1 CACTTGGGGG 0.984394 -102 TCTGGTAACTCCACTAAAGGTGGATACGCCAAT 6 36 0 CCCTAGGTGG 0.912231 -61 GTTACCAGACAGTCTCAAGGGGGTTCCCACCAG 6 60 1 AGCTAGGGGG 0.977676 -37 TCGGCGCGCCCCTTCTGGTGGGAACCCCCTT 6 76 0 CCCTTGGTGG 0.93401 -21 CTTATCATTGACACTGCTGGCCGT 8 2 0 ACCTTGGCCG 0.931004 -33 AGGGCGGGGAAATCTGTTGGTCGGTGATCGTAG 9 36 1 AACTTGGTCG 0.950175 -169 ** ** ****** Masking position 9 Map Score: 4.74038 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 119 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TTGCCTGCAGGACGGTCCGCTGCCCACACC 1 170 1 GACGGTCCGC 0.917465 -73 GCAATGCGCGCAGTGTCCGGTGTGGGCAGC 1 188 0 CAGTGTCCGG 0.980687 -55 ACCTCAGGTGCAGGGTGCAC 1 233 1 CAGGGTGCAC 0.784944 -10 TGATCTGGGTCTGCGTCTTGCGGC 3 5 1 CTGGGTCTGC 0.96356 -104 GTGCAAAATCCTGTGTCTGCAATTCACCAA 3 85 0 CTGTGTCTGC 0.958065 -24 ATTGCAGTCGTTCCGGGTCGTTTTCA 5 7 1 GTCGTTCCGG 0.746548 -120 CCCTTACGCTGTGTGTCTCGCGCCGAAAGG 5 99 1 GTGTGTCTCG 0.701739 -28 ACCCCCTTGAGACTGTCTGGTAACTCCACT 6 54 0 GACTGTCTGG 0.857501 -43 GGTGATCGTGCTGTGCGCGCTCATCTTTTT 7 48 0 CTGTGCGCGC 0.750438 -78 TGCTCCACGTTCCAGTGTACCCGGT 7 111 0 CACGTTCCAG 0.508828 -15 CGGTGGGTTTCTGTGTGCGGGGATGTGGGG 9 109 1 CTGTGTGCGG 0.960428 -96 TAGAATTTATCTGTGTCTAGATTTTAATTA 10 12 0 CTGTGTCTAG 0.886852 -161 ********** Masking position 6 Map Score: 4.99478 Number of sites scoring better than the average of aligned sites = 1688 Number in coding regions = 536 Number in noncoding regions = 1152 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 ATGTAATAGATATTATTTTTTTTTTAATGTAGAATTTA 10 33 0 TTTTTTTTAT 0.929583 -140 TGTTTGTGAATTTTTAAAAGTTTTTGGTATTTCCTATG 10 68 0 TTATTTTTGT 0.946569 -105 AAATTAGGATTCTATCTAAATTGTTTGTGAATTTTTAA 10 89 0 TTATTGTTGT 0.883954 -84 TTTTTTGTCCTTGTTGGTTTTAGCACTA 10 155 0 TTTTTGTTGT 0.917711 -18 GGTTCAATTGTTTAAAATAATTTTTGATTCTTCAATTA 11 14 0 TTTTTTTTAT 0.929577 -227 TTGTTGTATTTTTGATAAATTATTTGGTTCAATTGTTT 11 39 0 TTATATTTGT 0.889157 -202 CTTGTTAAATTGTAGGTTGTTTTTTTGTTGTATTTTTG 11 63 0 TTTTTTTTGT 0.962876 -178 CAACCTACAATTTAACAAGATATTTACTTGCATCATAT 11 82 1 TTATATTTCT 0.645549 -159 ACTGTTTGATTGTTTAATTGTATTTAATACTATATGAT 11 113 0 TTTTATTTAT 0.856683 -128 TTGTGGATTTTGTATTTTTATTTTTTATAGATATATAG 11 169 0 TTTTTTTTAT 0.929583 -72 * * * ***** ** Masking position 11 Map Score: 4.59169 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 54 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 CTATGGCAAAATTCGCCTTCGCGAGGATAC 1 38 1 ATTCGCCTTC 0.908226 -205 CAGCACCCTACTGCGCCTTCAGGTACGCGA 1 74 1 CTGCGCCTTC 0.912613 -169 ATCTGCGTTCACCAGCGTGCCTGCCGCAAG 3 27 0 ACCAGCGTGC 0.666952 -82 CGCGCTTGTAATCTGCGTTCACCAGCGTGC 3 37 0 ATCTGCGTTC 0.957256 -72 GACTTGAGGAACCTGCCTTCCTTC 4 5 0 ACCTGCCTTC 0.972859 -38 GCATTGGCGTATCCACCTTTAGTGGAGTTA 6 34 1 ATCCACCTTT 0.713343 -63 TGCTCCACGTTCCAGTGTACCC 7 114 0 CTCCACGTTC 0.9321 -12 CAACAGATTTCCCCGCCCTCCGCTTCTTTC 9 25 0 CCCCGCCCTC 0.9479 -180 CTCGGATATCATCTACCTTCTTTTCTACGA 9 63 0 ATCTACCTTC 0.903242 -142 TCCTATCCCTACCCGCGATCCTTTCCTCAC 9 156 0 ACCCGCGATC 0.921067 -49 ********** Masking position 6 Map Score: 4.74177 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 129 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 ACTGCGCCTTCAGGTACGCGACGCACACAT 1 83 1 CAGGTACGCG 0.964837 -160 GACCGTCCTGCAGGCAAGCGGTTGTGGGGG 1 157 0 CAGGCAAGCG 0.960721 -86 CCGGCTGGGCAATGCGCGCAGTGTCCGGTG 1 196 0 AATGCGCGCA 0.945948 -47 TACGACACCTCAGGTGCAGGGTGCAC 1 227 1 CAGGTGCAGG 0.732418 -16 CGTCTTGCGGCAGGCACGCTGGTGAACGCA 3 24 1 CAGGCACGCT 0.977426 -85 ACGCAGATTACAAGCGCGCAGTGGTATTCT 3 49 1 CAAGCGCGCA 0.960864 -60 TTCCCACCAGAAGGGGCGCGCCGA 6 83 1 AAGGGGCGCG 0.94657 -14 TGTGCACGGCCATGCGCACTCCTTCTGCAA 7 19 1 CATGCGCACT 0.834219 -107 CCCAATCTCTCATGCGCGCATAGTACGTGC 7 76 1 CATGCGCGCA 0.984032 -50 ATCCGAGTCAAAGGCGAGCAGCACGGTGGG 9 86 1 AAGGCGAGCA 0.905311 -119 GGAGATTTCGTAGGCACGGGTGAGGAAAGG 9 137 1 TAGGCACGGG 0.808601 -68 ********** Masking position 2 Map Score: 10.3265 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 56 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 TTGGAGCTCAATAAAATTTATAAACTTGAG 2 33 1 ATAAAATTTA 0.807861 -94 TTAATTAAAATCTAGACACAGATA 10 5 1 TTAAAATCTA 0.905161 -168 CTAGACACAGATAAATTCTACATTAAAAAA 10 22 1 ATAAATTCTA 0.943982 -151 TAAAAAAAAAATAATATCTATTACATAGGA 10 45 1 ATAATATCTA 0.820007 -128 AAATATCTTGTTAAATTGTAGGTTGTTTTT 11 77 0 TTAAATTGTA 0.79296 -164 TCTTATTAAGATAAAATGTAATAGAATATA 11 209 1 ATAAAATGTA 0.919805 -32 ATGCCTCCTTATATATTCTATTACATTTTA 11 220 0 ATATATTCTA 0.777717 -21 ********** Masking position 3 Map Score: 1.25217 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 22 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 CTCATGATATCCACTACCCAGTCG 1 5 0 CCACTACCCA 0.694588 -238 CGGTCCGCTGCCCACACCGGACACTGCGCG 1 182 1 CCCACACCGG 0.92997 -61 CTGCGCGCATTGCCCAGCCGGATACGACAC 1 205 1 TGCCCAGCCG 0.959933 -38 TACCACGTCATGCTCATCCACCCGCGCTAC 2 90 0 TGCTCATCCA 0.715 -37 GGCCTTGCTCCGCCCAGACG 6 1 0 CGCCCAGACG 0.717088 -96 CGCATGGCCGTGCACACCCGCCGG 7 5 0 TGCACACCCG 0.968052 -121 GCGCACAGCACGATCACCCAATCTCTCATG 7 60 1 CGATCACCCA 0.894812 -66 TTCTTTTCTACGATCACCGACCAACAGATT 9 46 0 CGATCACCGA 0.768164 -159 CGCGATCCTTTCCTCACCCGTGCCTACGAA 9 143 0 TCCTCACCCG 0.983165 -62 TTCCGTCCTATCCCTACCCGCGATCCTTTC 9 161 0 TCCCTACCCG 0.949022 -44 TTCCTTACCGGTCACATGTGC 9 194 0 TCCTTACCGG 0.849274 -11 ********** Masking position 6 Map Score: 5.7572 Number of sites scoring better than the average of aligned sites = 2106 Number in coding regions = 628 Number in noncoding regions = 1478 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 ********** No masking Map Score: 3.32777e-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: 3.32777e-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 ********** No masking Map Score: 3.32777e-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