AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_tpal_bbur_300.orf -o293_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 RTP00005 105 AE000520 #2 RTP00906 121 AE000520 #3 RTP00907 59 AE000520 #4 RTP00138 102 AE000520 #5 RTP00552 92 AE000520 #6 RTP00770 34 AE000520 #7 RTP00771 204 AE000520 #8 RBB00505 32 3615 #9 RBB00504 148 3615 #10 RBB00429 50 3615 #11 RBB00736 178 3615 #12 RBB00735 61 3615 #13 RBB00734 56 3615 #14 RBB00725 54 3615 #15 RBB00716 39 3615 #16 RBB00693 115 3615 #17 RBB00686 63 3615 Motif number 1 ACCTCTAATAAAATCAAAAAGAAAT 8 3 0 AAATAAAAAA 0.919623 -30 ATGTTACTAATAATAGTAAAAAAGAGGAAAA 9 9 0 TAATTAAAAA 0.881315 -140 TTATTAATGATAATGTTAAATATATTACACCAT 9 43 0 TAATTAAAAT 0.817475 -106 ATTAATACTATCATATAAAATTATTAATGATAA 9 63 0 TCATAAAATA 0.777941 -86 TTCCAAAAAATAATACAAAAAAATTAATACTAT 9 85 0 TAATAAAAAA 0.978724 -64 ATAAGAATTATAATGAAAAAGTATAATAAAGTG 10 12 1 TAATAAAATA 0.965672 -39 CTAGACAAAAAAATATAAAATTAAGCAAAAACA 11 33 0 AAATAAAATA 0.833479 -146 TTTATCTTAATAATTAAAATTATAAAATAAGTT 11 69 1 TAATAAATAT 0.819664 -110 GTAAGGCAGCTAATTTAAAAATTAGCCACAAAC 11 112 0 TAATAAAATT 0.868916 -67 CTTACATGAGTAATTTAAAAAAAGAGCTATAAT 11 140 1 TAATAAAAAA 0.97114 -39 TTGGTCTTGATATTTGAAAAATATATAAACATA 12 20 1 TATTAAAATA 0.701555 -42 ATTGTAAATTTAATAAAAAAGAAAAGTCAAGCA 13 16 0 TAATAAAAAA 0.978726 -41 TTTTAATTGAAAAGATTGGAGATTTT 14 4 1 TAATAAAAAT 0.965695 -51 TTTTTGGTTTTAATTGAAAAATTGGAGAAAGT 14 33 1 TAATAAAATT 0.943425 -22 TTACTTAGTTTAATTAAAATTAATTAAAAAAAC 16 11 1 TAATAAATAA 0.881302 -105 TACATAACTTAAATCTAAAATATTTTCTATTTT 16 72 0 AAATAAAAAT 0.874805 -44 **** **** ** Masking position 8 Map Score: 23.3133 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 36 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 ATTCAGTCAAGACCCAACCATATCTACGCTAACGACGCAGATGCTC 1 44 1 GCCCATCGAC 0.906935 -62 CCTTAACGATCTGCACACACCATCTCTCCAAAACGCTTAGGCGTAT 2 23 1 CCCACCCCAC 0.997673 -99 TAGGCGTATGGTCCACCCCCCCCCCACGGGAAAATCAATTGTGTAT 2 60 1 GCCCCCCGAC 0.996505 -62 ACGTGCACGCGCTCTATCCCCTCCATCGAAAGCGGCATCTGCCGCT 4 45 1 GCCCCCCGAC 0.996714 -58 ATTCCCCACCTGCACCCCCGTGCCCATTTCATCAGCAACCG 5 6 1 CCCACCCCAA 0.985085 -87 ATTTCATCAGCAACCGACACTGCCGTGCGCAGGAGCGACCAGCTTG 5 36 1 CCCACTCCAC 0.992933 -57 ACGGCCAGCAGTGTCAATGATAAGTACGTCATTG 6 2 1 CCCAGTCGAC 0.969232 -33 ACAGATTTCCCCGCCCTCCGCTTCTTTCAAAACGCACCTACT 7 7 0 CCCCGCCCAA 0.97109 -198 ACCTTCTTTTCTACGATCACCGACCAACAGATTTCCCCGCCCTCCG 7 33 0 CCCACCCCAC 0.997673 -172 CGAAATCTCCCCACATCCCCGCACACAGAAACCCACCGTGCTGCTC 7 101 0 CCCCCGCGAC 0.995882 -104 CCGCGATCCTTTCCTCACCCGTGCCTACGAAATCTCCCCACATCCC 7 128 0 TCCCCGCCAC 0.969892 -77 * * **** * * * * Masking position 21 Map Score: 17.1491 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 148 Number in noncoding regions = 343 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 TTGGAGAGATGGTGTGTGCAGATCGTTAAGGG 2 22 0 GGGTGGCAGA 0.95011 -100 TTGATTTTCCCGTGGGGGGGGGGTGGACCATA 2 66 0 CGGGGGGGGG 0.997025 -56 GCTTTTTCCGCGTGGGAGTAGTGACCATTTTG 3 33 0 CGGGGGTAGT 0.909048 -27 ATGCCGCTTTCGATGGAGGGGATAGAGCGCGT 4 51 0 CGTGGGGGGA 0.983582 -52 GAAATGGGCACGGGGGTGCAGGTGGGGAAT 5 9 0 CGGGGGCAGG 0.990852 -84 ACCAGCTTGCCGTGGGCGCAAAGTGCATGC 5 73 1 CGGGGGCAAA 0.974556 -20 TGAAAGAAGCGGAGGGCGGGGAAATCTGTTGG 7 24 1 GGGGGGGGGA 0.995235 -181 GGTGGGTTTCTGTGTGCGGGGATGTGGGGAGA 7 110 1 TGGTGGGGGA 0.955762 -95 TTCGTAGGCACGGGTGAGGAAAGGATCGCGGG 7 143 1 CGGTGGGAAA 0.95449 -62 AGGAAAGGATCGCGGGTAGGGATAGGACGGAA 7 159 1 CGGGGAGGGA 0.983582 -46 ** *** ***** Masking position 6 Map Score: 14.3182 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 185 Number in noncoding regions = 428 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 GATACAGCATCAAAAAATCATC 2 110 1 CAAAAATCAT 0.542365 -12 CTAAACCTCTAATAAAATCAAAAAGAAAT 8 9 0 AAAAAATCAA 0.904986 -24 AAAATAATACAAAAAAATTAATACTATCATA 9 81 0 AAAAAATTAA 0.855808 -68 ATAACAATTAATTGGCCTGTT 11 1 1 ATACAATTAA 0.67438 -178 AATTATTAAGATAAAAACCTAGACAAAAAAA 11 53 0 ATAAAACCTA 0.755992 -126 TATCTTAATAATTAAAATTATAAAATAAGTT 11 71 1 ATAAAATTAT 0.727087 -108 TCCTCCTTAAAACCAAATTATAGCTC 11 163 0 CTAAAACCAA 0.954281 -16 TTTTTCAAATATCAAGACCAAAAGCCAAAT 12 10 0 ATAAGACCAA 0.821171 -52 CAATTTTTCAATTAAAACCAAAAATCTCCAA 14 26 0 ATAAAACCAA 0.969211 -29 AAAGCCCACAATAAAAATCAATTTTA 15 6 0 ATAAAATCAA 0.957952 -34 GTCTTAAAAATAAAAAGCCCACA 15 27 0 CTAAAAATAA 0.627849 -13 ACTTAGTTTAATTAAAATTAATTAAAAAAAC 16 13 1 ATAAAATTAA 0.9342 -103 AAAATTAATTAAAAAAACTAAAAATATCATA 16 26 1 AAAAAACTAA 0.891305 -90 AAGTACATAACTTAAATCTAAAATATTTTCT 16 77 0 CTAAATCTAA 0.56143 -39 ** ******** Masking position 4 Map Score: 7.78985 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 201 Number in noncoding regions = 466 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 GCTTAGGCGTATGGTCCACCCCCCCCCCACGGGA 2 57 1 ATTCCACCCC 0.943854 -65 ACCCGCACGAATGCGGCACAGTCAAAATGGTCAC 3 11 1 ATGGCACACA 0.880783 -49 CGAAAGCGGCATCTGCCGCTAACAGCAAGTGAGT 4 71 1 ATGCCGCTCA 0.942292 -32 ATTCCCCACCTGCACCCCCGTGCC 5 1 1 ATCCCACCCA 0.992735 -92 TGCCCATTTCATCAGCAACCGACACTGCCGTGCG 5 31 1 ATGCAACCCA 0.961278 -62 GACCAACAGATTTCCCCGCCCTCCGCTTCTTTCA 7 24 0 TTCCCGCCCC 0.856367 -181 CTTTTCTACGATCACCGACCAACAGATTTCCCCG 7 40 0 ATCCGACCCA 0.957654 -165 TAATTTAAAAATTAGCCACAAACATCATTATACA 11 101 0 ATGCCACACA 0.980713 -78 TTATAAGCCTCCCGCAAAAAGTACAT 16 100 0 ATGCCTCCCA 0.978792 -16 ** ****** ** Masking position 2 Map Score: 4.18436 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 247 Number in noncoding regions = 578 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 TACTCCCACGCGGAAAAAGCATTGA 3 45 1 CGGAAAAGCA 0.989288 -15 CGGCATCTGCCGCTAACAGCAAGTGAGTACG 4 77 1 CGCTAAAGCA 0.977358 -26 TTGCCGTGGGCGCAAAGTGCATGC 5 79 1 CGCAAATGCA 0.976209 -14 CCCACATCCCCGCACACAGAAACCCACCGTG 7 107 0 CGCACAAGAA 0.92527 -98 AGGGATAGGACGGAAGAAGCACATGTGACCG 7 176 1 CGGAAGAGCA 0.97124 -29 ATAAGCCTCCCGCAAAAAGTACATAACTTAA 16 93 0 CGCAAAAGTA 0.971315 -23 ****** **** Masking position 11 Map Score: 3.2968 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 16 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TGCCTAAAAGAGGCGCACAGTTCCTGTATA 1 15 0 AGGCGCACAG 0.961961 -91 GCGGCATCTGCCGCTAACAGCAAGTGAGTA 4 76 1 CCGCTAACAG 0.913744 -27 ACCGACACTGCCGTGCGCAGGAGCGACCAG 5 48 1 CCGTGCGCAG 0.745328 -45 TTTGCGCCCACGGCAAGCTGGTCGCTCCTG 5 65 0 CGGCAAGCTG 0.846294 -28 AGCTTGCCGTGGGCGCAAAGTGCATGC 5 76 1 GGGCGCAAAG 0.786462 -17 ACGGCCAGCAGTGTCAATGAT 6 2 1 CGGCCAGCAG 0.985019 -33 CTACGATCACCGACCAACAGATTTCCCCGC 7 39 0 CGACCAACAG 0.91848 -166 TCCGAGTCAAAGGCGAGCAGCACGGTGGGT 7 87 1 AGGCGAGCAG 0.961838 -118 CCCCACATCCCCGCACACAGAAACCCACCG 7 109 0 CCGCACACAG 0.961817 -96 TCAAATATCAAGACCAAAAGCCAAAT 12 7 0 AGACCAAAAG 0.440553 -55 TATAAGCCTCCCGCAAAAAGTACATAACTT 16 95 0 CCGCAAAAAG 0.870363 -21 ********** Masking position 10 Map Score: 6.53142 Number of sites scoring better than the average of aligned sites = 1185 Number in coding regions = 361 Number in noncoding regions = 824 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 GATCGTAGAAAAGAAGGTAGATGATATCCGAGTCA 7 61 1 AAAAGGATAT 0.872009 -144 GGTGTAATATATTTAACATTATCATTAATAATTTT 9 45 1 ATTAATATAT 0.651473 -104 AATACAAAAAAATTAATACTATCATATAAAATTAT 9 72 0 AATAATATAT 0.922346 -77 AATAAGAATTATAATGAAAAAGTAT 10 1 1 AAAAGTATAT 0.966838 -50 CAATCCCTTTAATACACTTTATTATACTTTTTCAT 10 24 0 AAACATATAT 0.840942 -27 AAACCTAGACAAAAAAATATAAAATTAAGCAAAAA 11 35 0 AAAAATAAAT 0.781146 -144 AAAATTATAAAATAAGTTGTATAATGATGTTTGTG 11 84 1 AAAAGTATAT 0.966838 -95 AGTAATTTAAAAAAAGAGCTATAATTTGGTTTTAA 11 148 1 AAAAGTATAT 0.966838 -31 TAATTAAAAAAACTAAAAATATCATAAAAACGTGT 16 31 1 AATAATATAT 0.922346 -85 ** *** *** ** Masking position 11 Map Score: 3.24646 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 11 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 CTTTGCGCCCACGGCAAGCTGGTCGCTCCT 5 66 0 ACGGCAAGCT 0.978823 -27 ACGGCCAGCAGTGTCAATGA 6 1 1 ACGGCCAGCA 0.989916 -34 ATCCGAGTCAAAGGCGAGCAGCACGGTGGG 7 86 1 AAGGCGAGCA 0.984486 -119 TAAAAAAGAAAAGTCAAGCATTAAA 13 6 0 AAGTCAAGCA 0.950009 -51 ********** Masking position 7 Map Score: 0.329034 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 12 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: -2.79e-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: -2.79e-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 CAAGACCCAACCATATCTACGCTAACGACG 1 51 1 CCATATCTAC 0.794127 -55 TCTGCACACACCATCTCTCCAAAACGCTTA 2 32 1 CCATCTCTCC 0.960693 -90 GGCGTATGGTCCACCCCCCCCCCACGGGAA 2 62 1 CCACCCCCCC 0.986712 -60 CGTGCACGCGCTCTATCCCCTCCATCGAAA 4 46 1 CTCTATCCCC 0.875084 -57 ATTCCCCACCTGCACCCCCGTGC 5 4 1 CCCCACCTGC 0.969666 -89 AACAGATTTCCCCGCCCTCCGCTTCTTTCA 7 24 0 CCCGCCCTCC 0.965157 -181 CGAAATCTCCCCACATCCCCGCACACAGAA 7 117 0 CCACATCCCC 0.979492 -88 TCCGTCCTATCCCTACCCGCGATCCTTTCC 7 160 0 CCCTACCCGC 0.976737 -45 ********** Masking position 7 Map Score: 6.02684 Number of sites scoring better than the average of aligned sites = 1747 Number in coding regions = 498 Number in noncoding regions = 1249 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 GATGATTTTTTGATGCTGTATCAT 2 108 0 ATTTTTTGAT 0.727575 -14 CGTGCACGTGCTTTTTGGTACGCGTACGTT 4 24 0 CTTTTTGGTA 0.801707 -79 CTTTTTTACTATTATTAGTAACATAATGGT 9 18 1 ATTATTAGTA 0.689718 -131 ATAGTATTAATTTTTTTGTATTATTTTTTG 9 85 1 TTTTTTTGTA 0.766921 -64 TTTTTGTATTATTTTTTGGAAAAGTTATGC 9 97 1 ATTTTTTGGA 0.829838 -52 TAAATTTACAATGTTTAGTTGAGGTAATAT 13 37 1 ATGTTTAGTT 0.727826 -20 AAGATTGGAGATTTTTGGTTTTAATTGAAA 14 22 1 ATTTTTGGTT 0.925123 -33 TTTTTATGATATTTTTAGTTTTTTTAATTA 16 31 0 ATTTTTAGTT 0.919648 -85 AATATTTTCTATTTTTTGTAAACACGTTTT 16 57 0 ATTTTTTGTA 0.94835 -59 ********** Masking position 5 Map Score: 2.20897 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 64 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 ********** No masking Map Score: -2.79e-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 15 ********** No masking Map Score: -2.79e-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