AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_tpal_bbur_300.orf -o013_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 RTP00193 63 AE000520 #2 RTP00194 66 AE000520 #3 RTP01039 60 AE000520 #4 RTP00195 72 AE000520 #5 RTP00196 111 AE000520 #6 RTP00024 300 AE000520 #7 RBB00632 156 3615 #8 RBB00123 129 3615 #9 RBB00036 16 3615 #10 RBB00034 263 3615 Motif number 1 GTATACCTTTTCCGCCAGGCCGAATCCACCCTG 1 27 1 TCCGCGCCGA 0.743925 -37 CGCAGCTAGCCGCGCAGGGTGGATTCGGCCTGG 1 41 0 CGCGCGTGGA 0.982821 -23 CCCCCTGTACCGCACGCTGCCGACACCCGCGCG 5 67 1 CGCACGCCGA 0.99344 -45 TGCCGACACCCGCGCGTCGCTGAATTCTCGGCG 5 84 1 CGCGCGCTGA 0.996977 -28 TGAAGGAACACACGCACGGCCAAAGCTACCGTC 6 48 0 CACGCGCCAA 0.99231 -253 ACTGTCAACACGCTCATTGCTGATACGCTCGAA 6 171 1 CGCTCGCTGA 0.980985 -130 TGAGATAGATCACGCGATGCGGAATCTGGACGG 6 227 1 CACGCGCGGA 0.975329 -74 AAGCTATAAACACGCTTAGCCAAAAATCAATAA 10 64 1 CACGCGCCAA 0.99231 -200 ***** ***** Masking position 13 Map Score: 12.7241 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 10 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 CCAACGGCCTTGAGAACACCCTTACCGTTATAGC 6 136 0 TGAAACATTA 0.76397 -165 AAAGTATAAATATTAACAAAGTTAATATCAAGAA 7 39 1 TATAACATTA 0.976454 -118 GAATTAAAATAATAAAAATTGTTAAATGTTTTTT 7 70 1 AATAAAATTA 0.857092 -87 ATGTTTTTTTTAAAAAAAGTTTTAAGCTATAATA 7 95 1 TAAAAAATTA 0.757262 -62 ATACTTAACTTATTAATATTGTTAAATCAATTTT 7 128 0 TATAATATTA 0.85372 -29 ATCATTTTTTTATAAACAAAACTAGTATATAATA 8 17 0 TATAACACTA 0.946046 -113 TGCTAATCTTTATGAATATGTTTTTTGTGATATA 8 76 1 TATAATATTT 0.833539 -54 TTCAAATTGTTTTAAACAGTTTTACACAAATAAA 10 14 1 TTTAACATTA 0.815268 -250 GTTTTACACAAATAAAAAAGTTTAAAACAATTAA 10 32 1 AATAAAATTA 0.857684 -232 ACAATTAAGCTATAAACACGCTTAGCCAAAAATC 10 58 1 TATAACATTA 0.976454 -206 CTTAGCCAAAAATCAATAAATCTACCCTTAAAAT 10 78 1 AATAATACTA 0.803447 -186 AGCATCTTTCAATTAACAAAACTTACAAAATGCT 10 140 1 AATAACACTT 0.708306 -124 TTTTACACTATGTAAACAGCATTTTGTAAGTTTT 10 157 0 TGTAACATTT 0.763971 -107 TGTAAAATTATAACAATAATTTTACACTATAACA 10 184 1 TAAAATATTA 0.764988 -80 AGTGCATAAGAATTAATAATGTTATGGGTTGATT 10 217 0 AATAATATTA 0.905636 -47 *** **** *** Masking position 8 Map Score: 13.0011 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 83 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 TTAGGGGTGATTATTATTTTGTA 7 1 0 TATTTTTTGA 0.925917 -156 TTAACTTTGTTAATATTTATACTTTACTTTTTA 7 31 0 TATATTATAT 0.601066 -126 TTAACAATTTTTATTATTTTAATTCTTGATATT 7 62 0 TATTTTTTAT 0.914899 -95 AATTGTTAAATGTTTTTTTTAAAAAAAGTTTTA 7 86 1 TTTTTTTTAA 0.858185 -71 TCTCCTTATTATATACTAGTTTTGT 8 3 1 TCTTTTATAA 0.823737 -127 AAATTAAATATCATTTTTTTATAAACAAAACTA 8 27 0 TATTTTTTAA 0.94962 -103 TTTTGTCTGCTAATCTTTATGAATATGTTTTTT 8 69 1 TATCTTATGA 0.721922 -61 CAATCTGGTCAATTTATTATATATCACAAAAAA 8 96 0 ATTTTTATAA 0.599251 -34 ACCTCTTTATTATGAT 9 1 0 TTTTTTATGT 0.750864 -16 AGCTTCAAATTGTTTTAAACAGTTTTACA 10 7 1 AATTTTTTAA 0.779594 -257 GTTTATAGCTTAATTGTTTTAAACTTTTTTATT 10 42 0 TATTTTTTAA 0.94962 -222 TAGTGTAAAATTATTGTTATAATTTTACACTAT 10 180 0 TATTTTATAT 0.934029 -84 TGTTATGGGTTGATTGTTATAGTGTAAAATTAT 10 199 0 TATTTTATAT 0.934029 -65 ATAACATTATTAATTCTTATGCACTTATAGTAT 10 226 1 TATTTTATGA 0.942726 -38 * *** ***** * Masking position 7 Map Score: 11.5874 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 46 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 AGGGTGGATTCGGCCTGGCGGAAAAGGTATAC 1 27 0 CGGCCGGCGA 0.956578 -37 CAGGCCGAATCCACCCTGCGCGGCTAGCTGCG 1 42 1 CCACCTGCGG 0.919001 -22 CACTGCTACCCAGCCGTGAAAGACACTATCCA 2 29 0 CAGCCTGAAG 0.932555 -38 GCGCGGGTGTCGGCAGCGTGCGGTACAGGGGG 5 67 0 CGGCACGTGG 0.956027 -45 GCCGAGAATTCAGCGACGCGCGGGTGTCGGCA 5 84 0 CAGCGCGCGG 0.935475 -28 CCAAAGCTACCGTCACTGAGCGAGACATCCAC 6 30 0 CGTCATGAGG 0.935968 -271 ACGGTAGCTTTGGCCGTGCGTGTGTTCCTTCA 6 49 1 TGGCCTGCGG 0.968249 -252 CTCcGGTAGACGCCCCTGAAGGAACACACGCA 6 65 0 CGCCCTGAAG 0.862638 -236 ACAGTTCCAACGGCCTTGAGAACACCCTTACC 6 144 0 CGGCCTGAGA 0.985968 -157 TCGAGCGTATCAGCAATGAGCGTGTTGACAGT 6 171 0 CAGCATGAGG 0.9792 -130 CGTCCAGATTCCGCATCGCGTGATCTATCTCA 6 227 0 CCGCACGCGG 0.977192 -74 GGAATCTGGACGGCACTGACAATAAGTCAAAG 6 247 1 CGGCATGACA 0.827103 -54 ***** **** * Masking position 4 Map Score: 8.9314 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 276 Number in noncoding regions = 671 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 TATCCAGCAGGGGTACGGTCAGGT 2 5 0 GGGTACGGTC 0.964423 -62 CATGTACGCTAATGCTTTTGT 4 2 1 ATGTACGCTA 0.684643 -71 GTGTGCTCTTAGGTGCGCTCTTT 5 4 0 AGGTGCGCTC 0.983879 -108 TTTTTAAGGTGAGTGTGCTCTTAGGTGCGC 5 16 0 GAGTGTGCTC 0.928016 -96 CAGGGGGTCGGTGTGCGGTATGGCACTCTT 5 44 0 GTGTGCGGTA 0.940113 -68 GGTGTCGGCAGCGTGCGGTACAGGGGGTCG 5 64 0 GCGTGCGGTA 0.972505 -48 CTTTGGCCGTGCGTGTGTTCCTTCAGGGGC 6 56 1 GCGTGTGTTC 0.861503 -245 GATGGAGACAAGGAGCGCTATAACGGTAAG 6 120 1 AGGAGCGCTA 0.888537 -181 ATAACGGTAAGGGTGTTCTCAAGGCCGTTG 6 139 1 GGGTGTTCTC 0.876123 -162 TCGAAGGTATGGATGCGCTCAACCAGGGTG 6 199 1 GGATGCGCTC 0.951002 -102 AAAGCTTGGTGCGAATGCTATGCTTGGCGT 6 275 1 GCGAATGCTA 0.642876 -26 ********** Masking position 9 Map Score: 8.16503 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 126 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 AAGATGGACGATGGAGACCCCGGCTTTCTG 3 21 0 ATGGAGACCC 0.95452 -40 AGAAGACGAGTTTGAGGCGCAGAACGA 4 56 1 TTTGAGGCGC 0.973364 -17 CCGAGAATTCAGCGACGCGCGGGTGTCGGC 5 85 0 AGCGACGCGC 0.95077 -27 TACCgGAGAGTTCGAGGCGCTCGAAATGCG 6 89 1 TTCGAGGCGC 0.990067 -212 GCTCGAAGGTATGGATGCGCTCAACCAGGG 6 197 1 ATGGATGCGC 0.981099 -104 ATGGAGACGCCAAGCATAGC 6 291 0 ATGGAGACGC 0.989193 -10 ********** Masking position 5 Map Score: 4.27585 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 24 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 GACACTATCCAGCAGGGGTACGGTCAGGT 2 10 0 AGCAGGGGTA 0.987169 -57 ATATACAGAAAGCCGGGGTCTCCATCGTCC 3 16 1 AGCCGGGGTC 0.996114 -45 GCAAATACTGAGCAGGGGTCTGGACAAAAG 4 25 0 AGCAGGGGTC 0.996737 -48 TTCAGCGACGCGCGGGTGTCGGCAGCGTGC 5 78 0 CGCGGGTGTC 0.974318 -34 ********** Masking position 9 Map Score: 3.30428 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 15 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 CAGCTAGCCGCGCAGGGTGGATTCGGCCTG 1 42 0 CGCAGGGTGG 0.855242 -22 CGCAGCTAGCCGCGCAGGGT 1 54 0 CGCAGCTAGC 0.953185 -10 CATCTTACCCCGCAGGAAATACAGGA 3 45 1 CGCAGGAAAT 0.775049 -16 AAAGAGCGCACCTAAGAGCACACTCA 5 7 1 CGCACCTAAG 0.907896 -105 CCCCCTGTACCGCACGCTGCCGACACCCGC 5 67 1 CGCACGCTGC 0.945919 -45 GAGTTCGAGGCGCTCGAAATGCGTGATGGA 6 96 1 CGCTCGAAAT 0.841378 -205 ACCGTTATAGCGCTCCTTGTCTCCATCACG 6 117 0 CGCTCCTTGT 0.912022 -184 ACTGTCAACACGCTCATTGCTGATACGCTC 6 171 1 CGCTCATTGC 0.804027 -130 ATTGCTGATACGCTCGAAGGTATGGATGCG 6 186 1 CGCTCGAAGG 0.967265 -115 GCATAGCATTCGCACCAAGCTTTGACTTAT 6 268 0 CGCACCAAGC 0.978674 -33 ********** Masking position 3 Map Score: 4.88976 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 153 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GTTAAATGTTTTTTTTAAAAAAAGTTTTAA 7 90 1 TTTTTTAAAA 0.699562 -67 AATTTTATTATAGCTTAAAACTTTTTTTAA 7 104 0 TAGCTTAAAA 0.879683 -53 TAAACAAAACTAGTATATAATAAGGAGA 8 9 0 TAGTATATAA 0.709124 -121 TATACTAGTTTTGTTTATAAAAAAATGATA 8 22 1 TTGTTTATAA 0.889033 -108 AGCTTCAAATTGTTTTAAACAGTTTTACA 10 10 1 TTGTTTTAAA 0.800137 -254 ACTTTTTTATTTGTGTAAAACTGTTTAAAA 10 23 0 TTGTGTAAAA 0.960552 -241 ACAAATAAAAAAGTTTAAAACAATTAAGCT 10 39 1 AAGTTTAAAA 0.831453 -225 GCTGTTTACATAGTGTAAAATTATAACAAT 10 171 1 TAGTGTAAAA 0.968399 -93 TTGATTGTTATAGTGTAAAATTATTGTTAT 10 193 0 TAGTGTAAAA 0.968399 -71 ********** Masking position 6 Map Score: 6.22614 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 29 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 TAAGAGCACACTCACCTTAAAAAGAGTGCCA 5 23 1 CTCCCTTAAA 0.935762 -89 AAATAATAATCACCCCTAAAAAGTAAAGTAT 7 15 1 CACCCTAAAA 0.903978 -142 AAGTTAATATCAAGAATTAAAATAATAAAAA 7 57 1 CAAAATTAAA 0.929214 -100 AAGTTTTAAGCTATAATAAAATTGATTTAAC 7 111 1 CTAAATAAAA 0.848233 -46 AAAAATTAAGCTCAAATTAAATATCATTTTT 8 42 0 CTCAATTAAA 0.932048 -88 GATTAGCAGACAAAAATTAAGCTCAAATTAA 8 53 0 CAAAATTAAG 0.754113 -77 AACAGTTTTACACAAATAAAAAAGTTTAAAA 10 28 1 CACAATAAAA 0.898634 -236 ATCAATAAATCTACCCTTAAAATCAAAAACA 10 89 1 CTACCTTAAA 0.918797 -175 TTTCAATTAACAAAACTTACAAAATGCTGTT 10 146 1 CAAACTTACA 0.797924 -118 *** ******* Masking position 7 Map Score: 2.59041 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 81 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 ********** No masking Map Score: 8.47978e-13 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: 8.47978e-13 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: 8.47978e-13 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