AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_tpal_bbur_100.orf -o222_tpal_bbur_100.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 RTP00346 190 AE000520 #2 RTP00620 147 AE000520 #3 RTP00631 32 AE000520 #4 RTP00632 52 AE000520 #5 RTP00633 162 AE000520 #6 RTP00737 87 AE000520 #7 RBB00769 20 3615 #8 RBB00550 22 3615 #9 RBB00549 89 3615 #10 RBB00245 77 3615 #11 RBB00243 91 3615 #12 RBB00242 19 3615 #13 RBB00867 165 3615 Motif number 1 TGACGAATAGGACGCACGCGCGGGTGTGGTT 1 63 1 GACGCCGCGC 0.994689 -128 GAAAAAGGCAGACGAACGCGCACGCTTTATC 1 167 0 GACGACGCGC 0.981431 -24 TTTTTTGAAAAAGGACGCCGCATCACTGCGC 2 61 1 AAGGAGCCGC 0.751761 -87 TTAGACGATCACGTTGAGGTGCAC 4 4 1 GACGACACGT 0.912555 -49 CGATCACGTTGAGGTGCACATACGGAGCGAA 4 16 1 GAGGTCACAT 0.777 -37 CACCGCCCTCGAGGCGCGCGTGCAGGAAGTA 5 72 1 GAGGCCGCGT 0.993688 -91 CAACGTCAAAGACTCCCCCATACTTCCTGCA 5 92 0 GACTCCCCAT 0.854671 -71 GGGAGTCTTTGACGTTGCCGCATACGAGGCG 5 106 1 GACGTGCCGC 0.975526 -57 TGCCGCATACGAGGCGCGCATAGCAACGCTT 5 121 1 GAGGCCGCAT 0.978384 -42 AGCAACGCTTGAGGCTGCTGCAGCAGCGCCT 5 142 1 GAGGCGCTGC 0.951993 -21 ACAGTTCAAAGACTCGGCCGTCTCCTGAACC 6 13 1 GACTCGCCGT 0.928373 -75 TGAACCCCACGGGGCTGCCGCCCGTGCTCAG 6 38 1 GGGGCGCCGC 0.892687 -50 ATAAATATTTGAGGTGCGTATTTTTACGTAA 13 87 1 GAGGTCGTAT 0.617744 -79 ***** ***** Masking position 2 Map Score: 14.375 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 236 Number in noncoding regions = 445 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 TTAATAAAAAAGTTTTTGATAAAGCGTGCGCGT 1 150 1 AGTTTTTTAA 0.956793 -41 GCAGCTTTCTCTTTTTTTTGAAAAAGGACGCCG 2 48 1 CTTTTTTGAA 0.959987 -100 GAATCAGTTTTTTGAAGAGTTTGAATGC 6 70 0 AGTTTTTAAA 0.82135 -18 TTAATAATTAATTTTATTATACATTCACTAAAA 9 28 0 ATTTTATTAA 0.879971 -62 ACACCTCTTTATTTATTCCGATATTTCCATTAT 10 48 0 ATTTATTGAA 0.888181 -30 AATCGGTGTGCTTTTTTGTTAAATAAAATATAT 11 23 1 CTTTTTTTAA 0.956795 -69 TTATAGTCAAATTTTTAGCGATAAGTTTAAAAA 11 55 1 ATTTTTAGAA 0.939434 -37 TCTTATCTCTATTTTTTTAGAAAATTTTTTTGT 13 35 1 ATTTTTTGAA 0.984246 -131 TTTTTAGAAAATTTTTTTGTATATTTTAATTTA 13 48 1 ATTTTTTTAA 0.982964 -118 TGAGGTGCGTATTTTTACGTAAAAGTGATGAGT 13 96 1 ATTTTTATAA 0.934712 -70 GTGAATTTTAATTTTTTAATAAAAAGCGAAAGG 13 129 1 ATTTTTTTAA 0.982891 -37 ******* ** * Masking position 11 Map Score: 12.8725 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 42 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 3 GAATAGGACGCACGCGCGGGTGTGGTTGTC 1 67 1 CACGCGCGGG 0.833801 -124 TTTGATAAAGCGTGCGCGTTCGTCTGCCTT 1 164 1 CGTGCGCGTT 0.756303 -27 CAAACAGTTTTGAGCGCACGAGTGTTGTTC 2 15 0 TGAGCGCACG 0.713531 -133 CAAAACTGTTTGTACGCAGCTTTCTCTTTT 2 33 1 TGTACGCAGC 0.872388 -115 GAACTAATGTCGTGCGCAGTGATGCGGCGT 2 75 0 CGTGCGCAGT 0.950366 -73 TCTCTTCTTTTGTGTGCACCAGCAACGAAC 2 101 0 TGTGTGCACC 0.91999 -47 CTTCGCTCCGTATGTGCACCTCAACGTGAT 4 18 0 TATGTGCACC 0.840379 -35 ACGCGCGCCTCGAGGGCGGTGATTTGTGGA 5 63 0 CGAGGGCGGT 0.867067 -100 ATACTTCCTGCACGCGCGCCTCGAGGGCGG 5 74 0 CACGCGCGCC 0.855519 -89 ATGCGCGCCTCGTATGCGGCAACGTCAAAG 5 112 0 CGTATGCGGC 0.903994 -51 CAAGCGTTGCTATGCGCGCCTCGTATGCGG 5 123 0 TATGCGCGCC 0.969588 -40 ATGCCCTGAGCACGGGCGGCAGCCCCGTGG 6 44 0 CACGGGCGGC 0.959243 -44 ********** Masking position 7 Map Score: 10.2823 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 145 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GCGAGACTGCTAAGAAATCTTAATAAAAAAGT 1 131 1 TAGAAATCTA 0.615469 -60 GAAATCTTAATAAAAAAGTTTTTGATAAAGCG 1 144 1 TAAAAAGTTT 0.678062 -47 GCGTCCTTTTTCAAAAAAAAGAGAAAGCTGCG 2 47 0 TAAAAAAAAA 0.706162 -101 TTCAAACTCTTCAAAAAACTGATTC 6 73 1 TAAAAAACTA 0.953383 -15 TATACATTCACTAAAAAGTAAATTCTAGGAAT 9 12 0 CAAAAAGTAA 0.885737 -78 AGTGAATGTATAATAAAATTAATTATTAATGT 9 32 1 TATAAAATTA 0.699283 -58 CTAAAAAATATATACTCCTAAA 9 78 0 CAAAAAATAA 0.932732 -12 TTTTATTTAACAAAAAAGCACACCGATTCTCA 11 19 0 CAAAAAGCAA 0.887628 -73 AAACTTATCGCTAAAAATTTGACTATAATATA 11 51 0 CAAAAATTTA 0.81915 -41 AGCGATAAGTTTAAAAAACTCAAGCCATATC 11 71 1 TAAAAAACTA 0.953383 -21 AAAATAGAGATAAGAAAACAAAAACCTGAAAA 13 18 0 TAGAAAACAA 0.830733 -148 AAAAATTTTCTAAAAAAATAGAGATAAGAAAA 13 32 0 TAAAAAATAA 0.938441 -134 TTAAAATATACAAAAAAATTTTCTAAAAAAAT 13 45 0 CAAAAAATTT 0.774098 -121 TCGCTTTTTATTAAAAAATTAAAATTCACACT 13 126 0 TAAAAAATTA 0.952507 -40 * ******** * Masking position 6 Map Score: 9.54909 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 129 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 GTGGTTGTCGAGGCGACATGATCGCATTCC 1 88 1 AGGCGACATG 0.919659 -103 CTCGCATCACAGGCAACAGGAATGCGATCA 1 106 0 AGGCAACAGG 0.962225 -85 CTGGAAAAAGGCAGACGAACG 1 180 0 TGGAAAAAGG 0.883451 -11 TTTCAAAAAAAAGAGAAAGCTGCGTACAAA 2 41 0 AAGAGAAAGC 0.919968 -107 CACACAAAAGAAGAGACATCGTTTACCTTA 2 115 1 AAGAGACATC 0.771945 -33 TTTCTGTGTATGGAGAAAACGC 5 3 0 TGGAGAAAAC 0.705254 -160 ATACACAGAAAGGAAAAGGCAATGGAAATC 5 22 1 AGGAAAAGGC 0.935581 -141 CGTGGGGTTCAGGAGACGGCCGAGTCTTTG 6 19 0 AGGAGACGGC 0.9735 -69 AAAAAGCGAAAGGCAAAAGGTATTGTT 13 149 1 AGGCAAAAGG 0.95189 -17 ********** Masking position 6 Map Score: 3.94081 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 274 Number in noncoding regions = 615 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 ATAATTAACATTAATAATTAATTTTATTAT 9 41 0 TTAATAATTA 0.956629 -49 CCTAAATCAATTAATAATTAACATTAATAA 9 54 0 TTAATAATTA 0.956629 -36 ATAGCAAATATTAGTATTTATGCCAATTAC 10 17 0 TTAGTATTTA 0.930014 -61 ATATTTTAATTTAGTAATTATAAATATTTG 13 68 1 TTAGTAATTA 0.974437 -98 ********** Masking position 5 Map Score: 2.21121 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 TTATTAAGATTTCTTAGCAGTCTCGCATCA 1 127 0 TTCTTAGCAG 0.917809 -64 ACGACATTAGTTCGTTGCTGGTGCACACAA 2 92 1 TTCGTTGCTG 0.953253 -56 ACGATGTCTCTTCTTTTGTGTGCACCAGCA 2 107 0 TTCTTTTGTG 0.926032 -41 CGAAATATCCTTCTTTTCAGAAGCAA 3 7 0 TTCTTTTCAG 0.982015 -26 CCATTGCCTTTTCCTTTCTGTGTATGGAGA 5 17 0 TTCCTTTCTG 0.960933 -146 AAATTTATTTTCAGGTTTTTGTTT 13 5 1 TTATTTTCAG 0.894146 -161 ********** Masking position 5 Map Score: 2.01427 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 58 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 TCATCTTCATATTCAAAATCGTCGTCTTCA 1 15 0 ATTCAAAATC 0.963891 -176 TGCTCAGGGCATTCAAACTCTTCAAAAAAC 6 62 1 ATTCAAACTC 0.986452 -26 AAAAATTAAAATTCACACTCATCACTTTTA 13 115 0 ATTCACACTC 0.983922 -51 ********** Masking position 5 Map Score: 0.121642 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 9 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 CCTGTTGCCTGTGATGCGAGACTGCTAAGA 1 116 1 GTGATGCGAG 0.988546 -75 GTCGTGCGCAGTGATGCGGCGTCCTTTTTC 2 67 0 GTGATGCGGC 0.985263 -81 ACGGAGCGAAGACATGCGGGTAGATA 4 37 1 GACATGCGGG 0.953098 -16 CTCGAGGGCGGTGATTTGTGGACCAAATTC 5 55 0 GTGATTTGTG 0.880099 -108 TTACGTAAAAGTGATGAGTGTGAATTTTAA 13 110 1 GTGATGAGTG 0.974559 -56 ********** Masking position 5 Map Score: 0.0494509 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 65 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ********** No masking Map Score: 3.33488e-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: 3.33488e-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: 3.33488e-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