AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_tpal_bbur_300.orf -o078_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 RTP00424 300 AE000520 #2 RBB00315 172 3615 #3 RBB00314 240 3615 #4 RBB00313 90 3615 #5 RBB00312 91 3615 #6 RBB00307 45 3615 Motif number 1 CCCGACAACATAAATGCAAAATCCTGCACGG 1 167 0 TAAATCAAAA 0.950406 -134 TACATTAAAAAAAAAATAATATCTATTACAT 2 40 1 AAAAATAATA 0.787435 -133 ATTACATAGGAAATACCAAAAACTTTTAAAA 2 64 1 AAATACAAAA 0.732783 -109 AAAACTTTTAAAAATTCACAAACAATTTAGA 2 82 1 AAAATCACAA 0.838093 -91 AGTATAGTGCTAAAACCAACAAGGACAAAAA 2 151 1 TAAAACAACA 0.925436 -22 ACTTAATTGAAGAATCAAAAATTATTTTAA 3 10 1 AAGAACAAAA 0.813029 -231 TAATTTATCAAAAATACAACAAAAAAACAAC 3 55 1 AAAATCAACA 0.971155 -186 AAATACAACAAAAAAACAACCTACAATTTAA 3 66 1 AAAAACAACC 0.806557 -175 CATATAGTATTAAATACAATTAAACAATCAA 3 115 1 TAAATCAATT 0.856518 -126 ATAAAAAATAAAAATACAAAATCCACAAAAT 3 179 1 AAAATCAAAA 0.976087 -62 TTATTAAGATAAAATGTAATAGAATATATAA 3 211 1 AAAATTAATA 0.825113 -30 AGCTTATTTTAATATTCAAAATAGCATTAAT 4 19 0 AATATCAAAA 0.788879 -72 ACCACAATGCAAAAAACAATATTGAATAAAC 4 57 0 AAAAACAATA 0.973773 -34 GTATAGCATATAAATGCAATTGTCAATAATA 5 12 0 TAAATCAATT 0.856518 -80 GCTCCTCCATTAAAAACAATTTTATGCTGCC 5 68 0 TAAAACAATT 0.824164 -24 ATTCCTCTTTAAAATTCAATACAAAGCAAGC 6 19 0 AAAATCAATA 0.97929 -27 ***** ***** Masking position 8 Map Score: 17.289 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 222 Number in noncoding regions = 493 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 CATTATATAGTATAATGTTAAATTAGGATTC 2 115 0 TATAATGTAA 0.965185 -58 CATTATACTATATAATGTTAAAAGTATAGTG 2 129 1 TATAATGTAA 0.965185 -44 ATGTTAAAAGTATAGTGCTAAAACCAACAAG 2 143 1 TATAGTGTAA 0.984243 -30 TGCAAGTAAATATCTTGTTAAATTGTAGGTT 3 83 0 TATCTTGTAA 0.949122 -158 ACTTGCATCATATAGTATTAAATACAATTAA 3 107 1 TATAGTATAA 0.967993 -134 TTTATAGATATATAGTAGTAATAGTAGTAAG 3 153 0 TATAGTATAA 0.967993 -88 TATTACATTTTATCTTAATAAGATTTTGTGG 3 201 0 TATCTTATAA 0.900323 -40 ******* *** Masking position 2 Map Score: 8.35683 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 3 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 CCAAAAACTTTTAAAAATTCACAAACAATT 2 79 1 TTAAAAATTC 0.867696 -94 AGAATCCTAATTTAACATTATACTATATAA 2 114 1 TTTAACATTA 0.958962 -59 GCACTATACTTTTAACATTATATAGTATAA 2 131 0 TTTAACATTA 0.958962 -42 CCTTGTTGGTTTTAGCACTATACTTTTAAC 2 145 0 TTTAGCACTA 0.826623 -28 GGTTCAATTGTTTAAAATAATTTTTGATTC 3 22 0 TTTAAAATAA 0.746906 -219 TTTAATTGTATTTAATACTATATGATGCAA 3 109 0 TTTAATACTA 0.873521 -132 TTAAATACAATTAAACAATCAAACAGTAGC 3 124 1 TTAAACAATC 0.727896 -117 AAAAGCTTATTTTAATATTCAAAATAGCAT 4 23 0 TTTAATATTC 0.856356 -68 AAGCTACAAATTAAACACTAACATGGTATA 5 38 0 TTAAACACTA 0.937214 -54 CGCTCCTCCATTAAAAACAATTTTATGCTG 5 70 0 TTAAAAACAA 0.653396 -22 ATTATTCCTCTTTAAAATTCAATACAAAGC 6 23 0 TTTAAAATTC 0.917514 -23 ********** Masking position 4 Map Score: 8.96229 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 66 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 CACAAGAGGATAGCACCCTCGTTATGAAC 1 10 0 TAGCACCCTC 0.92971 -291 ACAGACCCTTCCTCACGCTCTACTGCATGC 1 86 0 CCTCACGCTC 0.857677 -215 GACAGACAGGAAACACGCGCACAGACCCTT 1 106 0 AAACACGCGC 0.853948 -195 CACGGATGAAACGCTCACTCACTTCACGCA 1 142 0 ACGCTCACTC 0.956868 -159 AAGTCACGCACAGCACCCCCGACAACATAA 1 185 0 CAGCACCCCC 0.986757 -116 CTTGCAACTGACGCTCCCCCTGAGCGTGTG 1 246 1 ACGCTCCCCC 0.99268 -55 TAAAAAGCATACGCACACGCTCAGGGGGAG 1 259 0 ACGCACACGC 0.978566 -42 AACGCTCCTCCATTAAAAACA 5 81 0 ACGCTCCTCC 0.930046 -11 ATTCAATACAAAGCAAGCCCATTAAT 6 7 0 AAGCAAGCCC 0.907551 -39 ********** Masking position 4 Map Score: 6.637 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 186 Number in noncoding regions = 410 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 GACAGGAAACACGCGCACAGACCCTTCCTC 1 102 0 ACGCGCACAG 0.992131 -199 AAATGCAAAATCCTGCACGGATGAAACGCT 1 157 0 TCCTGCACGG 0.946614 -144 CAGGAGAAAGTCACGCACAGCACCCCCGAC 1 192 0 TCACGCACAG 0.99362 -109 AAGCATACGCACACGCTCAGGGGGAGCGTC 1 255 0 ACACGCTCAG 0.985494 -46 TATGCTTTTTAGACGCACGGTTCCTACTGG 1 278 1 AGACGCACGG 0.985599 -23 ********** Masking position 5 Map Score: 3.30673 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 9 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 GTGAATTTTTAAAAGTTTTTGGTATTTCCT 2 71 0 AAAAGTTTTT 0.741875 -102 GGATTCTATCTAAATTGTTTGTGAATTTTT 2 91 0 TAAATTGTTT 0.971703 -82 TGAAGAATCAAAAATTATTTTAAACAATTG 3 18 1 AAAATTATTT 0.920091 -223 ATTATTTGGTTCAATTGTTTAAAATAATTT 3 29 0 TCAATTGTTT 0.95113 -212 GTATTTTTGATAAATTATTTGGTTCAATTG 3 42 0 TAAATTATTT 0.920697 -199 AGGTTTATTCAATATTGTTTTTTGCATTGT 4 55 1 AATATTGTTT 0.8603 -36 ATCAATTTTTTATACCACAAT 4 80 0 TCAATTTTTT 0.86799 -11 TTGGCAGCATAAAATTGTTTTTAATGGAGG 5 66 1 AAAATTGTTT 0.971062 -26 ********** Masking position 4 Map Score: 7.72815 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 40 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 CTGCATGCTCGTTTTTTTCTAACAACAATG 1 64 0 GTTTTTTTCT 0.873946 -237 GCAGGATTTTGCATTTATGTTGTCGGGGGT 1 171 1 GCATTTATGT 0.934431 -130 TTTTAATGTAGAATTTATCTGTGTCTAGAT 2 20 0 GAATTTATCT 0.863522 -153 AATTGTTTGTGAATTTTTAAAAGTTTTTGG 2 79 0 GAATTTTTAA 0.774887 -94 TTTTTTTGTTGTATTTTTGATAAATTATTT 3 52 0 GTATTTTTGA 0.9099 -189 ATTGTAGGTTGTTTTTTTGTTGTATTTTTG 3 63 0 GTTTTTTTGT 0.909901 -178 TGTGGATTTTGTATTTTTATTTTTTATAGA 3 176 0 GTATTTTTAT 0.946073 -65 ATTGACAATTGCATTTATATGCTATACCAT 5 16 1 GCATTTATAT 0.900634 -76 ********** Masking position 5 Map Score: 3.55103 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 93 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 ********** No masking Map Score: 1.60115e-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: 1.60115e-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 10 ********** No masking Map Score: 1.60115e-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