AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_fts_cell_wall_tpal_reg_300.orf -o250_tpal_300.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00409 181 AE000520 #2 RTP00881 18 AE000520 #3 RTP00885 152 AE000520 #4 RTP01136 83 AE000520 #5 RTP01045 27 AE000520 #6 RTP00239 45 AE000520 #7 RTP01008 135 AE000520 #8 RTP00560 30 AE000520 #9 RTP00559 134 AE000520 #10 RTP00558 177 AE000520 #11 RTP01173 118 AE000520 #12 RTP00700 135 AE000520 Motif number 1 GGAAAGAACACGCGCTGGTACTGTAACACCTTT 1 105 0 CGCGCTGCTG 0.99761 -77 TCGAGGAACTTGCGCTCAAGCTTTTCT 4 67 1 TGCGCTCCTT 0.976209 -17 CGCGCTGCGTTGCGCTGTTTGCGGCACAGGATA 7 25 0 TGCGCTGGCG 0.937514 -111 ATGCGCAGAATGCGCTCATTGCGCGCTGCGTTG 7 46 0 TGCGCTCGCG 0.954969 -90 CCCCGCTGGCGCACCAAAATCGAA 9 2 1 CCCGCTGCAC 0.854578 -133 CGGTGGTCAGCACGCTCGTGCTGGTTCGATTTT 9 26 0 CACGCTCCTG 0.994062 -109 GGATTAGAATCGCGCCCGTTCTTAGATCCACTG 9 83 1 CGCGCCCCTT 0.95424 -52 CGGTACACTGCGCGCTGCATCTTCCCCCAATAC 10 71 1 CGCGCTGCTT 0.990863 -107 AGGGCAAGCTCGCGCTGGTATTGGGGGAAGATG 10 88 0 CGCGCTGTTG 0.964957 -90 AGCGCGAGCTTGCCCTCAAGCTGTGCGCCATAC 10 105 1 TGCCCTCCTG 0.958014 -73 CCATACTTTTCCCGCACATGCTGCACCGTCTCG 10 132 1 CCCGCACCTG 0.977578 -46 CGGTGCAAAGCCCGCTCTCGGTCCATCGCCCAC 11 13 0 CCCGCTCGTC 0.966758 -106 ACCTGGCCAACAAGCTCAATCTGCGCAACAAGA 11 67 0 CAAGCTCCTG 0.894184 -52 TCGTACACACTACGCTGGACCTGTATCACCTGG 11 94 0 TACGCTGCTG 0.969773 -25 AACTCTGGTGCCCGCTCCGCCTTAGTAGAA 12 8 0 CCCGCTCCTT 0.985926 -128 CGGTCTTTTTCGCCCTGGTAGTGGGCGTGGGGG 12 86 1 CGCCCTGGTG 0.953572 -50 ACGGTAACGCCACGCACCAACCCCCACGCCCAC 12 106 0 CACGCACCCC 0.771042 -30 ******* *** Masking position 5 Map Score: 30.0327 Number of sites scoring better than the average of aligned sites = 1280 Number in coding regions = 1194 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 CCGAACCCATGTCCGTTGCGACGCTACCCTATG 1 11 0 GCCGTGCGCG 0.996145 -171 ACGTACCGATGTCCGCGACAAAGATCCCCGAAC 1 38 0 GCCGGACAAG 0.975819 -144 TACCCTCGGGGACCGTTACATATGAGGTGTTAA 3 53 0 GCCGTACAAT 0.898305 -100 GAGACACTCAGCCAGATACGGAGTGA 5 4 0 GCAGTACGAG 0.935698 -24 TGCGCTCATTGCGCGCTGCGTTGCGCTGTTTGC 7 36 0 GGCGTGCGTG 0.993367 -100 ATATGCAAGAGGCAGATGCGCAGAATGCGCTCA 7 61 0 GCAGTGCGAG 0.973417 -75 ACGCGTGCCAGTGCGGTACACTGCGCGCTGCAT 10 58 1 GGCGTACATG 0.954719 -120 TTTCGTATACTGCCGAGACGGTGCAGCATGTGC 10 145 0 TCCGGACGTG 0.917386 -33 GAGTGGGCGATGGACCGAGAGCGGGCT 11 5 1 GGCGTGGACG 0.903327 -114 CACCTGCCCTGCCCGGTGCAAAGCCCGCTCTCG 11 26 0 GCCGTGCAAG 0.991123 -93 AAACTCTGGTGCCCGCTCCGCCTTAGTAGAA 12 9 0 GCCGTCCGCT 0.882594 -127 CAGAGTTTCTTCCCGGGGCGGAGGAAACTGCCT 12 34 1 TCCGGGCGAG 0.970762 -102 CCCTGGTAGTGGGCGTGGGGGTTGGTGCGTGGC 12 98 1 GGCGGGGGTT 0.829763 -38 GTGGGGGTTGGTGCGTGGCGTTACCGTCGGTAC 12 112 1 GGCGGGCGTA 0.914638 -24 * *** **** ** Masking position 5 Map Score: 17.8874 Number of sites scoring better than the average of aligned sites = 1027 Number in coding regions = 961 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 CATAGGGTAGCGTCGCAACGGACATG 1 4 1 AGGAGGTCGC 0.952325 -178 ATGGGTTCGGGGATCTTTGTCGCGGACATCGGT 1 34 1 GGTTTGTCGC 0.806002 -148 TTTCCATCTTGGGAAATAATCGCCGCTTTTAGG 1 75 0 GGAATATCGC 0.907003 -107 ATTTAAGGAGTGAGAAGCATGGCGAAGCAATTG 3 14 0 TGGAGATGGC 0.971884 -139 GATGAAAAGATGTGAAGTGTTGCCAAGAATCTT 3 95 0 TGGAGGTTGC 0.820429 -58 CTCCGTATCTGGCTGAGTGTCTCG 5 14 1 GGTAGGTCTC 0.948832 -14 TCTTGCATATGGTGCCGAATGGCGTGCAATGCT 7 84 1 GGGCGATGGC 0.979102 -52 TGGGGATCATTATCTCTGGGTACACC 8 4 1 GGTATATCTC 0.783686 -27 CAAATACTTCGGATTAGAATCGCGCCCGTTCTT 9 73 1 GGTAGATCGC 0.989178 -62 GGGGGTAGTATGGCTCGAAAGAGA 9 121 0 GGGAGATGGC 0.99599 -14 AGCATGTGCGGGAAAAGTATGGCGCACAGCTTG 10 121 0 GGAAGATGGC 0.979995 -57 CTGCCGAGACGGTGCAGCATGTGCGGGAAAAGT 10 136 0 GGGAGATGTG 0.828627 -42 GGGCGTGGGGGTTGGTGCGTGGCGTTACCGTCG 12 108 1 GTGTGGTGGC 0.789085 -28 ** * ** ***** Masking position 10 Map Score: 12.5553 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 409 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 TCGCAACGGACATGGGTTCGGGGATCTTTG 1 23 1 CATGGGTTCG 0.910017 -159 TTGTCGCGGACATCGGTACGTCTTCCCTAA 1 50 1 CATCGGTACG 0.959818 -132 AAGGCCCAGGATTGGGTGCGTTCATTTTTT 1 148 1 ATTGGGTGCG 0.904815 -34 TAACGGTCCCCGAGGGTACTAAAAAAAAAG 3 68 1 CGAGGGTACT 0.981701 -85 TTAAAAACGGTGCTCTGCGATATA 7 122 0 AAACGGTGCT 0.838057 -14 CGAACCAGCACGAGCGTGCTGACCACCGAA 9 31 1 CGAGCGTGCT 0.925578 -104 TTGATTTTGTCGTGGGTGCGCGCCCT 10 7 0 CGTGGGTGCG 0.995692 -171 ACAAAATCAACGTGTGTACTCCACGAATCG 10 27 1 CGTGTGTACT 0.940208 -151 TATACTGCCGAGACGGTGCAGCATGTGCGG 10 143 0 AGACGGTGCA 0.818997 -35 GGTCCAGCGTAGTGTGTACGAGT 11 106 1 AGTGTGTACG 0.90208 -13 GTGGCGTTACCGTCGGTACT 12 126 1 CGTCGGTACT 0.98142 -10 ********** Masking position 7 Map Score: 10.843 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 532 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 GGCCTTCACCGGCTGAGGAAAGAACACGCGC 1 123 0 GGCGAGGAAA 0.992922 -59 AGCCGGTGAAGGCCCAGGATTGGGTGCGTTC 1 140 1 GGCCAGGATT 0.974794 -42 TGAGAAGCATGGCGAAGCAATTGCTG 3 6 0 GGCAAGCAAT 0.95375 -147 CTTTTTTAACGGCAAACAAAAGTTTAATGGG 4 23 1 GGCAACAAAA 0.880001 -61 CGCTGTTTGCGGCACAGGATACTGCCTTTTC 7 15 0 GGCCAGGATA 0.988876 -121 CCCCGCTGGCGCACCAAAATCGAACCAG 9 8 1 GGCCACCAAA 0.978293 -127 TTCTTCCCGGGGCGGAGGAAACTGCCTAATT 12 40 1 GGCGAGGAAA 0.992922 -96 *** ******* Masking position 6 Map Score: 6.40734 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 97 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ATCAAATTACCGCATAATACGATCAACCCT 3 125 1 CGCATAATAC 0.801127 -28 CACGCAGTGCAAGATATACCGT 6 3 1 CGCAGTGCAA 0.858343 -43 GTAGGAAAAGGCAGTATCCTGTGCCGCAA 7 10 1 GGCAGTATCC 0.952725 -126 CGCTGCGTTGCGCTGTTTGCGGCACAGGAT 7 26 0 CGCTGTTTGC 0.877301 -110 GAGGCAGATGCGCAGAATGCGCTCATTGCG 7 56 0 CGCAGAATGC 0.978352 -80 GCGTGTATATCGCAGAGCACCGTTTTTAA 7 117 1 CGCAGAGCAC 0.959906 -19 AGATGCAGCGCGCAGTGTACCGCACTGGCA 10 63 0 CGCAGTGTAC 0.987881 -115 GCACCGTCTCGGCAGTATACGAAATACCCC 10 154 1 GGCAGTATAC 0.967689 -24 ATTCTTGTTGCGCAGATTGAGCTTGTTGGC 11 65 1 CGCAGATTGA 0.857144 -54 CACGGAATTAGGCAGTTTCCTCCGCCCCGG 12 46 0 GGCAGTTTCC 0.939301 -90 ********** Masking position 3 Map Score: 10.1006 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 566 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 CCATGCTTCTCACTCCTTAAATGTAAGGTT 3 25 1 CACTCCTTAA 0.880099 -128 GTAAGGTTAACACCTCATATGTAACGGTCC 3 47 1 CACCTCATAT 0.939018 -106 TTCTTGGCAACACTTCACATCTTTTCATCA 3 99 1 CACTTCACAT 0.905188 -54 ATAATACGATCAACCCTCTTTCCAA 3 138 1 CAACCCTCTT 0.849929 -15 TTAAAAAAGGCACCCCTCATG 4 2 0 CACCCCTCAT 0.987858 -82 ACTTTCTGGACACCCCATTAAACTTTTGTT 4 37 0 CACCCCATTA 0.899896 -47 TCACTCCGTATCTGGCTGAGT 5 2 1 CACTCCGTAT 0.900323 -26 GATCCACTGCCACCTCTCTTTCGAGCCATA 9 107 1 CACCTCTCTT 0.95198 -28 ********** Masking position 2 Map Score: 4.88245 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 192 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 CGCCGCTTTTAGGGAAGACGTACCGATGTC 1 58 0 AGGGAAGACG 0.907179 -124 TTTCCCAAGATGGAAAGGTGTTACAGTACC 1 92 1 TGGAAAGGTG 0.950268 -90 GGTAATTTGATGAAAAGATGTGAAGTGTTG 3 106 0 TGAAAAGATG 0.694283 -47 TTGGAAAGAGGGTTGATCGTA 3 142 0 TGGAAAGAGG 0.929167 -11 CCATATGCAAGAGGCAGATGCGCAGAATGC 7 66 0 GAGGCAGATG 0.900325 -70 GCTGGTATTGGGGGAAGATGCAGCGCGCAG 10 78 0 GGGGAAGATG 0.986219 -100 TGCACCGGGCAGGGCAGGTGGAGGCAATTC 11 39 1 AGGGCAGGTG 0.971206 -80 TTGAGCTTGTTGGCCAGGTGATACAGGTCC 11 81 1 TGGCCAGGTG 0.93519 -38 GTTTCTTCCCGGGGCGGAGGAAACTGCCTA 12 38 1 GGGGCGGAGG 0.924186 -98 ********** Masking position 7 Map Score: 5.25594 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 394 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 GTTCATTTTTTACGGTGTTTGAGCG 1 167 1 TACGGTGTTT 0.960099 -15 GATACGGTCTATGCTCGG 2 3 1 TACGGTCTAT 0.923101 -16 ATTTGTTGTTCACGGTATATCTTGCACTGC 6 14 0 CACGGTATAT 0.74757 -32 TTAAAAACGGTGCTCTGCGATATAC 7 121 0 AACGGTGCTC 0.812301 -15 TCTCGGTGTACCCAGAGATAA 8 20 0 CTCGGTGTAC 0.968116 -11 AGTAAAGTTGTTCGGTGGTCAGCACGCTCG 9 41 0 TTCGGTGGTC 0.921528 -94 AAAGCCCGCTCTCGGTCCATCGCCCACTC 11 10 0 CTCGGTCCAT 0.891407 -109 AACTGCCTAATTCCGTGTTCCTCTTTTCGG 12 59 1 TTCCGTGTTC 0.847222 -77 TGTTCCTCTTTTCGGTCTTTTTCGCCCTGG 12 74 1 TTCGGTCTTT 0.947973 -62 ********** Masking position 6 Map Score: 2.91246 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 273 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 TACGTCTTCCCTAAAAGCGGCGATTATTTC 1 66 1 CTAAAAGCGG 0.980512 -116 GGTAATTTGATGAAAAGATGTGAAGTGTTG 3 106 0 TGAAAAGATG 0.7295 -47 TTGGAAAGAGGGTTGATCGTA 3 142 0 TGGAAAGAGG 0.93186 -11 TTGTTTGCCGTTAAAAAAGGCACCCCTCAT 4 12 0 TTAAAAAAGG 0.886586 -72 TTAAAAACGGTGCTCTGCGA 7 126 0 TTAAAAACGG 0.92537 -10 GGCAGTGGATCTAAGAACGGGCGCGATTCT 9 88 0 CTAAGAACGG 0.917607 -47 GGGCGATGGACCGAGAGCGGGCTTTGCACC 11 15 1 CCGAGAGCGG 0.879024 -104 CGAAAAAGACCGAAAAGAGGAACACGGAAT 12 68 0 CGAAAAGAGG 0.974559 -68 ********** Masking position 6 Map Score: 3.45247 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 195 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 ACATGGGTTCGGGGATCTTTGTCGCGGACA 1 32 1 GGGGATCTTT 0.964397 -150 TAGTACCCTCGGGGACCGTTACATATGAGG 3 59 0 GGGGACCGTT 0.967009 -94 TGGGGATCATTATCTCTGGGT 8 2 1 GGGGATCATT 0.93888 -29 GGGGGTAGTATGGCTCGAAA 9 125 0 GGGGGTAGTA 0.956255 -10 CGCTGGTATTGGGGGAAGATGCAGCGCGCA 10 79 0 GGGGGAAGAT 0.865019 -99 CGTGGGGGTATTTCGTATACTGC 10 165 0 GGGGGTATTT 0.972662 -13 TAGTGGGCGTGGGGGTTGGTGCGTGGCGTT 12 104 1 GGGGGTTGGT 0.938413 -32 ********** Masking position 4 Map Score: 3.61574 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 79 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 ********** No masking Map Score: 2.27617e-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: 2.27617e-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: 2.27617e-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