AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i303_tpal_bbur_300.orf -o303_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 RTP00417 194 AE000520 #2 RTP00981 170 AE000520 #3 RTP00980 169 AE000520 #4 RTP00594 46 AE000520 #5 RTP00593 104 AE000520 #6 RTP00592 140 AE000520 Motif number 1 AGCGGAACTCGACCATCAGTGAAAAT 1 2 1 GCGGACCGCT 0.984213 -193 GATCATGTGTGCGGATTGCTTCCCGATCGGCGGGT 1 95 0 GCGGATCTCG 0.835238 -100 CACGTGGAAGGAGCGTGTGGGGCAGGTGATTGTTC 1 138 0 GAGCGGGGCG 0.920723 -57 GAAAACGAAAAAGAGCTCGAGCCCTTTTACCGCA 1 171 0 AAAGACCGCC 0.693924 -24 CAATCTTTTCGCAAACTCGGATCAGCGTGCGCACG 2 25 1 GCAAATGGCG 0.845555 -146 GGATCAGCGTGCGCACGTCGGTCAGGTCGAGGGGC 2 43 1 GCGCAGCGCG 0.996047 -128 AGGTCGAGGGGCGCAACCGCGGCGGCGAAAAAATC 2 66 1 GCGCACGCCG 0.974711 -105 CGATGCCCTAGCAGAGCTCGCTCAGAAGAAAATCC 2 121 0 GCAGACCGCG 0.996745 -50 TATCTACTCCGCAGAAGACCGTCTCT 3 2 0 GCAGAGCCCC 0.975557 -168 AACTGAGTGTGCAGGCGGCGAACGGTATCTACTCC 3 27 0 GCAGGGCGCG 0.991633 -143 CGTTTTTACAGGAGACCACCGACGTTATCCAGCGC 3 69 0 GGAGACCCCT 0.782025 -101 CCTGAATGAAGGAGATGCCGTTCTGCGCGTTTGTA 3 113 1 GGAGAGCGCG 0.989165 -57 GGTTCAAACCACGGATCTGGCTCCG 3 155 1 ACGGACGGCG 0.957096 -15 AGGAACAACACGCTCACTGATAATATT 4 30 0 GAACACCGCC 0.948217 -17 GCAGATGTGGTGCGCGGTGGTACGG 5 1 1 GCAGAGGGCC 0.976815 -104 ATTCACGGGCGGACATGAGGAACCTGCGCGGGCGG 5 58 1 GGACAGGGCT 0.911596 -47 TGAGGAACCTGCGCGGGCGGAGACGTCACGTACTT 5 73 1 GCGCGGGGAG 0.765212 -32 GCGGAAACAGGCACAATGGGTACGCAAGCCCGCAT 6 39 1 GCACATGGCC 0.961461 -102 ***** * ** * * Masking position 13 Map Score: 25.3227 Number of sites scoring better than the average of aligned sites = 1811 Number in coding regions = 536 Number in noncoding regions = 1275 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 GATAGATCTGCAACCCGCCGATCGGGAAGCA 1 83 1 CAACCCGCGA 0.953423 -112 ATCACCTGCCCCACACGCTCCTTCCACGTGC 1 143 1 CCACACGCCC 0.916658 -52 AGCCCTTTTACCGCACGTGGAAGGAGCGTGT 1 155 0 CCGCACGTGA 0.986741 -40 TGACCGACGTGCGCACGCTGATCCGAGTTTG 2 36 0 GCGCACGCGA 0.99411 -135 CGCCGCGGTTGCGCCCCTCGACCTGACCGAC 2 59 0 GCGCCCCTGA 0.900854 -112 TGCCCTAGCAGAGCTCGCTCAGAAGAAAATC 2 122 0 GAGCTCGCCA 0.838304 -49 ATACCGTTCGCCGCCTGCACACTCAGTTCGC 3 34 1 CCGCCTGCCA 0.989817 -136 ACGTTATCCAGCGCATTCGCGAACTGAGTGT 3 52 0 GCGCATTCCG 0.559451 -118 AAAAACGCCTCCGCAACCTGAATGAAGGAGA 3 97 1 CCGCAACCGA 0.874233 -73 ATAATATTTCCTGCACGCAGACCAAGG 4 7 0 CTGCACGCGA 0.970009 -40 AGGAACAACACGCTCACTGATAATAT 4 31 0 CAACACGCCA 0.927302 -16 TTCCTCATGTCCGCCCGTGAATGTTTTAAAA 5 49 0 CCGCCCGTAA 0.919883 -56 CGTGACGTCTCCGCCCGCGCAGGTTCCTCAT 5 72 0 CCGCCCGCCA 0.997956 -33 ACCGTCTTACCCGCCTTCCGGACAACCATGC 6 70 0 CCGCCTTCGG 0.830184 -71 ******** ** Masking position 4 Map Score: 18.5185 Number of sites scoring better than the average of aligned sites = 1276 Number in coding regions = 357 Number in noncoding regions = 919 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 TGGAGAGGTATCCGTGTTGGCATCTAAAACG 1 47 0 TCCGGTTGGC 0.990367 -148 CTTCCCGATCGGCGGGTTGCAGATCTATCTC 1 81 0 GGCGGTTGCA 0.922727 -114 TGATCATGTGTGCGGATTGCTTCCCGATCGG 1 100 0 TGCGATTGCT 0.778473 -95 CGCACGCTGATCCGAGTTTGCGAAAAGATTG 2 25 0 TCCGGTTTGC 0.984736 -146 TTTTTTCGCCGCCGCGGTTGCGCCCCTCGAC 2 68 0 GCCGGGTTGC 0.940156 -103 GATGCCGTTCTGCGCGTTTGTAGACGCCTGG 3 126 1 TGCGGTTTGT 0.982714 -44 CCTTGGTCTGCGTGCAGGAAATATTATCA 4 9 1 TGCGGCAGGA 0.834469 -38 GCAGATGTGGTGCGCGGTGGTACGGATGACT 5 11 1 TGCGGGTGGT 0.98089 -94 GTACCCATTGTGCCTGTTTCCGCCGTTTTCT 6 31 0 TGCCGTTTCC 0.893113 -110 CGGACAACCATGCGGGCTTGCGTACCCATTG 6 52 0 TGCGGCTTGC 0.988003 -89 **** ****** Masking position 3 Map Score: 10.6374 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 104 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 CATATCTCGTTTTAGATGCCAACACGGATA 1 40 1 TTTAGATGCC 0.980356 -155 TTATTGATTTTTTCGCCGCCGCGGTTGCGC 2 76 0 TTTCGCCGCC 0.926182 -95 AGGAAGTGCTTGCCGATGCCCTAGCAGAGC 2 139 0 TGCCGATGCC 0.982084 -32 TCTTCTGCGGAGTAGATACCGTTCGCCGCC 3 19 1 AGTAGATACC 0.924011 -151 ACCTGAATGAAGGAGATGCCGTTCTGCGCG 3 112 1 AGGAGATGCC 0.972674 -58 TCTGCGCGTTTGTAGACGCCTGGTTCAAAC 3 134 1 TGTAGACGCC 0.991884 -36 ********** Masking position 5 Map Score: 3.30999 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 91 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 ATCTACTCCGCAGAAGACCGTCTCT 3 6 0 CAGAAGACCG 0.963166 -164 GTTTTTACAGGAGACCACCGACGTTATCCA 3 73 0 GAGACCACCG 0.987509 -97 ACGCCTGGTTCAAACCACGGATCTGGCTCC 3 149 1 CAAACCACGG 0.97443 -21 TTCCTGCACGCAGACCAAGG 4 1 0 CAGACCAAGG 0.959041 -46 CAAAGTCATCCGTACCACCGCGCACCACAT 5 15 0 CGTACCACCG 0.981278 -90 CCGGAAGGCGGGTAAGACGGTGAGTACCTT 6 80 1 GGTAAGACGG 0.837205 -61 ********** Masking position 4 Map Score: 1.85896 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 111 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ATAGAACGCACAATCTTTTCGCAAACTCGG 2 15 1 CAATCTTTTC 0.866455 -156 CCGACGTGCGCACGCTGATCCGAGTTTGCG 2 34 0 CACGCTGATC 0.979653 -137 AGGGCATCGGCAAGCACTTCCTTAAACCGC 2 147 1 CAAGCACTTC 0.964103 -24 GCCGCCTGCACACTCAGTTCGCGAATGCGC 3 43 1 CACTCAGTTC 0.985871 -127 ATATTTCCTGCACGCAGACCAAGG 4 5 0 CACGCAGACC 0.950717 -42 GCGGAGACGTCACGTACTTCCTTGGC 5 89 1 CACGTACTTC 0.927578 -16 GCTCTCCACTCTTTTCATACCGGGTA 6 125 0 CACTCTTTTC 0.959651 -16 ********** Masking position 2 Map Score: 5.3311 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 30 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ********** No masking Map Score: -1.58918e-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: -1.58918e-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: -1.58918e-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