AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_tpal_bbur_300.orf -o127_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 RTP00395 300 AE000520 #2 RTP00396 118 AE000520 #3 RTP01065 39 AE000520 #4 RTP00503 233 AE000520 #5 RTP01180 45 AE000520 #6 RTP01181 77 AE000520 Motif number 1 CCGACGCGCCAGTCACTCCT 1 1 1 CCGACGCGCC 0.939388 -300 AGTCACTCCTCCCCCCTGCTCCACCGCGCG 1 21 1 CCCCCCTGCT 0.888336 -280 CCCCCCTGCTCCACCGCGCGCAAAGACAAC 1 31 1 CCACCGCGCG 0.98259 -270 GCGGTTGGTACACCCCCGCCAGCAGCAATA 1 71 1 CACCCCCGCC 0.965752 -230 TGAGCATTGCCGCCGCCGCTAGCGCCCCTG 1 125 1 CGCCGCCGCT 0.85848 -176 CCGCCGCTAGCGCCCCTGCGCACACGGTCG 1 137 1 CGCCCCTGCG 0.719521 -164 GGATTTGTGGCGACCGTGTGCGCAGGGGCG 1 147 0 CGACCGTGTG 0.719585 -154 TACTACTGCACACACGCGCGGATTTGTGGC 1 166 0 CACACGCGCG 0.832681 -135 CCTCTGCGACCGCCCCTGCGTCTGTTCAGA 1 209 0 CGCCCCTGCG 0.719521 -92 CGCGTGACGCATCCTCTGCGACCGCCCCTG 1 221 0 ATCCTCTGCG 0.83688 -80 TCTCGCATGCAGCACGCGCGTGACGCATCC 1 237 0 AGCACGCGCG 0.729473 -64 GAACGACTTTCACCTGCACGTCCATATGGA 2 12 1 CACCTGCACG 0.860225 -107 CCATATGGAGACGACGTGCCACTTGAGCTA 2 33 1 ACGACGTGCC 0.728607 -86 TTGCTTTTGCAGGAGGCGCGCGGCTACGAT 2 73 0 AGGAGGCGCG 0.838379 -46 TTGTTCCTCCTCCTGCGCGGTGTTCGTTG 2 100 0 CTCCTGCGCG 0.985465 -19 ACACGACAGACCGCGCGCGCAAGATCA 3 8 1 AGACCGCGCG 0.976598 -32 CTCTTTTTTGAGCATGTGCGGCTCAGTCCT 4 24 1 AGCATGTGCG 0.81358 -210 CGTTACCTAGATGCTGTGCCGTTTGATGGT 4 69 1 ATGCTGTGCC 0.663346 -165 ACGCGGTACACGCCTGTACCAGGCGTGTCA 4 159 0 CGCCTGTACC 0.848337 -75 ATAGAAAAGCCTGCCGCACGCAGAAATGCA 4 190 1 CTGCCGCACG 0.914925 -44 ********** Masking position 9 Map Score: 32.5277 Number of sites scoring better than the average of aligned sites = 2031 Number in coding regions = 615 Number in noncoding regions = 1416 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 GGTGGAGCAGGGGGGAGGAGTGACTGGCGCGTCG 1 12 0 GGGGAGGGAC 0.958401 -289 TGCTGCTGGCGGGGGTGTACCAACCGCTTTTGAG 1 64 0 GGGGTGTCAC 0.929612 -237 ACCCCCGCCAGCAGCAATACCAATGAACCGGAAA 1 82 1 GCAGAATCAT 0.939338 -219 GCTAGCGGCGGCGGCAATGCTCACGCCAGGATTT 1 114 0 GCGGAATCAC 0.99378 -187 GCGCGTGTGTGCAGTAGTAAGGACCGCCGTAGTC 1 177 1 GCAGAGTAAC 0.972593 -124 AGTAAGGACCGCCGTAGTCTGAACAGACGCAGGG 1 192 1 GCCGAGTTAC 0.958126 -109 CGAACACCGCGCAGGAGGAGGAACAA 2 103 1 GCAGAGGGAC 0.983773 -16 CACGCCAATGGCAGCAGTTCCAACGTGAAGCCCA 4 121 1 GCAGAGTCAC 0.996305 -113 ATTTCTGCGTGCGGCAGGCTTTTCTATCACGCGG 4 183 0 GCGGAGGTTC 0.939423 -51 CCTGCCGCACGCAGAAATGCAAACAGTTGTGCAA 4 199 1 GCAGAATCAC 0.990149 -35 ACTGCGCTTTGCGGAAATCCTTTTTCTTTCGGTA 5 13 0 GCGGAATCTT 0.859696 -33 **** *** * ** Masking position 4 Map Score: 13.3104 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 133 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 CAGGGGCGCTAGCGGCGGCGGCAATGCTCA 1 125 0 AGCGGCGGCG 0.909869 -176 GGGCGGTCGCAGAGGATGCGTCACGCGCGT 1 224 1 AGAGGATGCG 0.98641 -77 CGCGCGGCTACGATGTTGAGCTGTTAGCTC 2 57 0 CGATGTTGAG 0.872948 -62 GTTTTGATGTTGATCTTGCGCGCGCGGTCT 3 18 0 TGATCTTGCG 0.853637 -22 TGCTCAAAAAAGAGGCTGAGAAGCAGC 4 8 0 AGAGGCTGAG 0.974939 -226 GCCTCTTTTTTGAGCATGTGCGGCTCAGTC 4 22 1 TGAGCATGTG 0.881416 -212 CCCGTTACCTAGATGCTGTGCCGTTTGATG 4 67 1 AGATGCTGTG 0.985293 -167 TGAGCGTGCAAGATGAGGTGAAACAGGATC 6 12 1 AGATGAGGTG 0.947814 -66 TAAATCTGCCAGATCCTGTTTCACCTCATC 6 23 0 AGATCCTGTT 0.72199 -55 GATTTAGTGCCGATGATGCGAACGGAAATA 6 47 1 CGATGATGCG 0.974308 -31 ********** Masking position 8 Map Score: 8.50372 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 126 Number in noncoding regions = 325 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 CCGACGCGCCAGTCACTCCTCCCCC 1 5 1 CGCGCCAGCA 0.833054 -296 GTTGTCTTTGCGCGCGGTGGAGCAGGGGGGA 1 30 0 CGCGCGGTGA 0.957412 -271 CGCTCAAAAGCGGTTGGTACACCCCCGCCAG 1 62 1 CGGTTGGTCA 0.875529 -239 GGTACACCCCCGCCAGCAGCAATACCAATGA 1 77 1 CGCCAGCACA 0.825546 -224 CCTGCGCACACGGTCGCCACAAATCCGCGCG 1 151 1 CGGTCGCCCA 0.889344 -150 ATGCGTCACGCGCGTGCTGCATGCGAGAAAA 1 239 1 CGCGTGCTCA 0.996058 -62 CGTAGCCGCGCGCCTCCTGCAAAAGCAACGA 2 75 1 CGCCTCCTCA 0.978776 -44 CACGACAGACCGCGCGCGCAAGATCAACATC 3 12 1 CGCGCGCGAA 0.911292 -28 CGTGCTTCATCGCGTCGCTCATTTTTACCAT 4 94 0 CGCGTCGCCA 0.975857 -140 TGCTGCCATTGGCGTGCTTCATCGCGTCGCT 4 106 0 GGCGTGCTCA 0.964145 -128 ACTAGTGACACGCCTGGTACAGGCGTGTACC 4 154 1 CGCCTGGTCA 0.990685 -80 GCTTTTCTATCACGCGGTACACGCCTGTACC 4 169 0 CACGCGGTCA 0.933004 -65 GTGATAGAAAAGCCTGCCGCACGCAGAAATG 4 187 1 AGCCTGCCCA 0.882674 -47 ******** ** Masking position 11 Map Score: 15.1341 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 152 Number in noncoding regions = 375 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 CGCAAAGACAACACGCTCAAAAGCGGTTGG 1 49 1 ACACGCTCAA 0.958391 -252 GCGGCGGCGGCAATGCTCACGCCAGGATTT 1 114 0 CAATGCTCAC 0.972803 -187 GCTAGCGCCCCTGCGCACACGGTCGCCACA 1 142 1 CTGCGCACAC 0.873265 -159 GCATGCGAGAAAACGCACACACTGCCACAA 1 257 1 AAACGCACAC 0.982009 -44 CCTGCAAAAGCAACGAACACCGCGCAGGAG 2 90 1 CAACGAACAC 0.894607 -29 ACTGAGCCGCACATGCTCAAAAAAGAGGCT 4 21 0 ACATGCTCAA 0.921405 -213 CCGCACGCAGAAATGCAAACAGTTGTGCAA 4 203 1 AAATGCAAAC 0.731446 -31 GTGTATGTACCTTGCACAACTGTTTGCAT 4 215 0 CCTTGCACAA 0.804122 -19 ACCTCATCTTGCACGCTCAC 6 1 0 GCACGCTCAC 0.969378 -77 ********** Masking position 9 Map Score: 5.71038 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 116 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 CCGACGCGCCAGTCACTCCT 1 1 1 CCGACGCGCC 0.970054 -300 CCCCCCTGCTCCACCGCGCGCAAAGACAAC 1 31 1 CCACCGCGCG 0.925838 -270 GCGCGCAAAGACAACACGCTCAAAAGCGGT 1 46 1 ACAACACGCT 0.560105 -255 CTTACTACTGCACACACGCGCGGATTTGTG 1 168 0 CACACACGCG 0.889672 -133 TTTCTCGCATGCAGCACGCGCGTGACGCAT 1 239 0 GCAGCACGCG 0.991109 -62 ACGACTTTCACCTGCACGTCCATATGGAGA 2 14 1 CCTGCACGTC 0.917927 -105 GTTAGCTCAAGTGGCACGTCGTCTCCATAT 2 35 0 GTGGCACGTC 0.872678 -84 CAACATCGTAGCCGCGCGCCTCCTGCAAAA 2 69 1 GCCGCGCGCC 0.955711 -50 TGATGTTGATCTTGCGCGCGCGGTCTGTCG 3 14 0 CTTGCGCGCG 0.959942 -26 GCGACGCGATGAAGCACGCCAATGGCAGCA 4 107 1 GAAGCACGCC 0.963191 -127 AAGCCCACTAGTGACACGCCTGGTACAGGC 4 148 1 GTGACACGCC 0.950103 -86 GCAGGCTTTTCTATCACGCGGTACACGCCT 4 174 0 CTATCACGCG 0.851861 -60 AGAAAAGCCTGCCGCACGCAGAAATGCAAA 4 192 1 GCCGCACGCA 0.944174 -42 TTCACCTCATCTTGCACGCTCAC 6 4 0 CTTGCACGCT 0.908879 -74 ********** Masking position 5 Map Score: 19.168 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 65 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: 1.56563e-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 8 ********** No masking Map Score: 1.56563e-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 9 ********** No masking Map Score: 1.56563e-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