AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_tpal_bbur_100.orf -o150_tpal_bbur_100.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 RTP00149 141 AE000520 #2 RTP00108 94 AE000520 #3 RTP00103 300 AE000520 #4 RTP00098 140 AE000520 #5 RBB00641 21 3615 #6 RBB00640 85 3615 #7 RBB00638 183 3615 Motif number 1 GTGCAGTACCTTCATACACACGCACCACGTGCCCTTGCACACA 1 30 0 TCTACCCGCC 0.95885 -112 CCCCTGCTATTTTCCCCTCCCCAGGTACACACCGTGCAGTACC 1 63 0 TTCCCCCACC 0.989702 -79 CACTCTTCCTACCCGTCTGTCGCTACTCAATACGGA 1 116 0 TTCCCCCGAC 0.990166 -26 AGACTTATAATCCCCATTCGCGGTCCACGGCTCCCACAAAACA 2 15 1 TCCACCCGTC 0.988595 -80 ACGTGGGATTTACGCCGGAGCTCATTAAGATTCTGCAGGACAA 3 13 0 TCCCACAGTC 0.80113 -288 ATCAAAAAGATTTTCTGCCGCACGACGCGTGTCAGTGTACACA 3 90 1 TTCTCCCGTC 0.99153 -211 TTCACATCGATATTCCAGTCCACAAGCCGATTCGCTAAACGCA 3 160 1 TTCCTCCGTC 0.961692 -141 CAAACCTTGCTTTCCTATCGCGATAGACAGCTGGCTTTCAGCA 3 207 1 TTCTCCCATG 0.786589 -94 TGCAGAACGCTTCTCCTCATCAAGTACCACGACGTTCAGCACC 3 261 1 TCCCACCAAC 0.86176 -40 TCTGCGCGGATATGCTCCCCCAATTTGCGCACCCTTAACTGAC 4 20 1 TTCTCCCGCC 0.990948 -121 CTGACTTACCTGTTTCATCCCTGTAAGCGCGCCGCATCGGAAA 4 58 1 TTTCCCCGCC 0.988458 -83 ATCCTTCAGTTTCCTCGACACCTCCTTCATCTCCGCGCATTCA 4 108 1 TCTCCCCATC 0.976083 -33 TAACTAAGTTTCCATTAACTCCAACGACTTTTCCTTTTGTATT 6 27 0 TCTTCCCTTC 0.82006 -59 * * ** * * ** ** Masking position 1 Map Score: 13.4373 Number of sites scoring better than the average of aligned sites = 986 Number in coding regions = 308 Number in noncoding regions = 678 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 TCTCTGTGATTGTGTGCAAGGGCACGTGGTGCGTGTGTATGAAGG 1 20 1 TGGGGGGGGG 0.998217 -122 ATGAAGGTACTGCACGGTGTGTACCTGGGGAGGGGAAAATAGCAG 1 58 1 TGAGGTGGGG 0.995488 -84 TAGCAGGGGCTGTGCGTACTCCGTATTGAGTAGCGACAGACGGGT 1 97 1 TGGGCTGAGG 0.985074 -45 TGCTGTTTTGTGGGAGCCGTGGACCGCGAATGGGGATTATAAGTC 2 16 0 TGGGGGGAGG 0.993729 -79 AAGAGATGGATGTGTACACTGACACGCGTCGTGCGGCAGAAAATC 3 98 0 TGGAGGGTGG 0.906067 -203 GGAATATCGATGTGAAGACAGAGAGTCAGTTTGAAGAGATGGATG 3 131 0 TGGAGTAGGA 0.779273 -170 AAGGTTTGAACGTGCGTTTAGCGAATCGGCTTGTGGACTGGAATA 3 170 0 CGGGGTGGGG 0.991179 -131 GCTGAGGTGCTGAACGTCGTGGTACTTGATGAGGAGAAGCGTTCT 3 264 0 TGAGGTGAGA 0.939097 -37 GTAAGTCAGTTAAGGGTGCGCAAATTGGGGGAGCATATCCGCGCA 4 22 0 TAGGCTGGGA 0.82031 -119 GTTTCATCCCTGTAAGCGCGCCGCATCGGAAAGAGCGGCATCCTT 4 69 1 TGAGCTGGGG 0.988497 -72 TGAATGCGCGGAGATGAAGGAGGTGTCGAGGAAAC 4 116 0 TGAGGGAGGG 0.969501 -25 ** * * * * ** * * Masking position 23 Map Score: 12.5788 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 154 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 AGGTACACACCGTGCAGTACCTTCATACACA 1 53 0 CGTGCAGTAC 0.971035 -89 ATACGGAGTACGCACAGCCCCTGCTATTTTC 1 92 0 CGCACAGCCC 0.909594 -50 CGTTGTCCTGCAGAATCTTAATGAGCT 3 7 1 CCTGCAGAAC 0.926987 -294 TGACACGCGTCGTGCGGCAGAAAATCTTTTT 3 93 0 CGTGCGGCAA 0.920964 -208 AGACAGCTGGCTTTCAGCAACAATGGCAAGT 3 231 1 CTTTCAGCAC 0.935375 -70 TGAGGAGAAGCGTTCTGCACTTGCCATTGTT 3 249 0 CGTTCTGCAT 0.824142 -52 AGTACCACGACGTTCAGCACCTCAGCAG 3 283 1 CGTTCAGCAC 0.982585 -18 GGAGCATATCCGCGCAGAAATAGCGCA 4 7 0 CGCGCAGAAT 0.935681 -134 TCCCTGTAAGCGCGCCGCATCGGAAAGAGCG 4 75 1 CGCGCCGCAC 0.988396 -66 ********* * Masking position 5 Map Score: 6.25373 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 57 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TGATAACGATTATCAAGAAGAGTCTGAGTT 3 64 0 TATCAAGAAG 0.981096 -237 TGATAATCGTTATCAAAAAGATTTTCTGCC 3 79 1 TATCAAAAAG 0.979643 -222 AAGTATATTCTTTAAAGAAGTATTATTGTG 7 40 1 TTTAAAGAAG 0.941464 -144 AAATTTTTAATATCAAAAATTTTACAATAT 7 90 0 TATCAAAAAT 0.902169 -94 CAAACAAAACTTTAAAAAAGCATAAAATAA 7 118 0 TTTAAAAAAG 0.93713 -66 ********** Masking position 5 Map Score: 2.48896 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 13 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 CTATTTTCCCCTCCCCAGGTACACACCGTGCAGTACC 1 63 0 CCCGTCACAC 0.991523 -79 CACTCTTCCTACCCGTCTGTCGCTACT 1 125 0 CTCCTCCCGC 0.965054 -17 TTATAATCCCCATTCGCGGTCCACGGCTCCCACAAAA 2 19 1 CTCGTCACGC 0.995085 -76 CGCACGACGCGTGTCAGTGTACACATCCATCTCTTCA 3 108 1 GTCTTCACAC 0.965881 -193 TTCAAACTGACTCTCTGTCTTCACATCGATATTCCAG 3 141 1 CTCTTCACAC 0.994188 -160 CCTTGCTTTCCTATCGCGATAGACAGCTGGCTTTCAG 3 211 1 CTCGTGACAC 0.97158 -90 CGGATATGCTCCCCCAATTTGCGCACCCTTAACTGAC 4 26 1 CCCTTCGCAC 0.972539 -115 AGAGCGGCATCCTTCAGTTTCCTCGACACCTCCTTCA 4 100 1 CTCTTCTCGC 0.976394 -41 * ** * * **** * Masking position 10 Map Score: 6.27263 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 26 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 CACACGCACCACGTGCCCTTGCACACAATC 1 27 0 ACGTGCCCTT 0.987968 -115 TTTTCTTCATACGTGGGATTTACGCCGGAG 3 36 0 ACGTGGGATT 0.977601 -265 CAAGGTTTGAACGTGCGTTTAGCGAATCGG 3 186 0 ACGTGCGTTT 0.98505 -115 AGCGTTCTGCACTTGCCATTGTTGCTGAAA 3 242 0 ACTTGCCATT 0.96661 -59 ********** Masking position 4 Map Score: 0.647365 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 0 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: -3.50765e-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: -3.50765e-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: -3.50765e-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