AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i002_tpal_bbur_300.orf -o002_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 RTP00850 114 AE000520 #2 RTP00506 81 AE000520 #3 RTP00963 233 AE000520 #4 RBB00142 87 3615 Motif number 1 TCCTACTCCCCACAGGAGTGCTGTTTTGTTTTCG 1 57 0 CAAGGGCTGT 0.862411 -58 CTGGTTCGAGGGTGAGTCGGCCTCCTACTCCCCA 1 79 0 GGGGCGCCTC 0.984869 -36 ACCCTCGAACCAGGCGCCGGCTTCC 1 100 1 CAGGCGCTTC 0.705317 -15 GGGGTGTGTGCGTACGTCAACTTCTTGTCCTCTG 2 26 0 CGAGCACTTC 0.875236 -56 GACGTACGCACACACCCCTGCTGCAAGACACGCA 2 42 1 CAACCGCTGC 0.983536 -40 TAGATACGAGCGCTTCTGCGTGTCTT 2 66 0 GAAGGGCTTC 0.970039 -16 CCGCGTGATAGAAAAGCCTGCCGCACGCAGAAAT 3 38 0 GAAGCGCCGC 0.986538 -196 ACGCCTGGTACAGGCGTGTACCGCGTGATAGAAA 3 58 0 CAGGGACCGC 0.965957 -176 CCAGGCGTGTCACTAGTGGGCTTCACGTTGGAAC 3 84 1 CATGGGCTTC 0.980312 -150 GAACTGCTGCCATTGGCGTGCTTCATCGCGTCGC 3 114 1 CATGGGCTTC 0.98031 -120 TTTGATGGTAAAAATGAGCGACGCGATGAAGCAC 3 131 0 AAAGGGACGC 0.698436 -103 TTTACCATCAAACGGCACAGCATCTAGGTAACGG 3 153 1 AAGCCGCATC 0.796443 -81 ATCTAGGTAACGGGACACTGCCTAGCAAGGACTG 3 174 1 CGGCCGCCTA 0.838827 -60 ACTGCCTAGCAAGGACTGAGCCGCACATGCTCAA 3 190 1 AAGCGGCCGC 0.970902 -44 GCTGCTTCTCAGCCTCTTTTTTGAGC 3 218 0 TGTCCGCCTC 0.733125 -16 ** * * * ***** Masking position 11 Map Score: 16.666 Number of sites scoring better than the average of aligned sites = 2154 Number in coding regions = 644 Number in noncoding regions = 1510 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 AACAAAACAGCACTCCTGTGGGGAGTAGGA 1 61 1 CACTCCTGTG 0.877239 -54 GACGTACGCACACACCCCTGCTGCAAGACA 2 42 1 CACACCCCTG 0.961869 -40 ATGTACCTTGCACAACTGTTTGCATTTCTG 3 15 1 CACAACTGTT 0.9003 -219 TCACGCGGTACACGCCTGTACCAGGCGTGT 3 64 1 CACGCCTGTA 0.975522 -170 CAACGTGAAGCCCACTAGTGACACGCCTGG 3 84 0 CCCACTAGTG 0.917701 -150 CGCGATGAAGCACGCCAATGGCAGCAGTTC 3 114 0 CACGCCAATG 0.951113 -120 AATTTCCCACCTGTTATATTTTATT 4 73 0 CCCACCTGTT 0.984702 -15 ********** Masking position 9 Map Score: 5.93701 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 121 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 AAAACAAAACAGCACTCCTGTGGGGAGTAG 1 59 1 AGCACTCCTG 0.9638 -56 GACGTACGCACACACCCCTGCTGCAAGACA 2 42 1 CACACCCCTG 0.992301 -40 CCGCGTGATAGAAAAGCCTGCCGCACGCAG 3 42 0 GAAAAGCCTG 0.959204 -192 TATCACGCGGTACACGCCTGTACCAGGCGT 3 62 1 TACACGCCTG 0.995714 -172 GCCCACTAGTGACACGCCTGGTACAGGCGT 3 75 0 GACACGCCTG 0.998396 -159 ********** Masking position 4 Map Score: 5.60769 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 6 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 AGCAGGGGTGTGTGCGTACGTCAACTTCTT 2 34 0 TGTGCGTACG 0.986811 -48 TACGAGCGCTTCTGCGTGTCTTGCAGCAGG 2 58 0 TCTGCGTGTC 0.987418 -24 TGTTTGCATTTCTGCGTGCGGCAGGCTTTT 3 31 1 TCTGCGTGCG 0.996927 -203 GCCTCTTTTTTGAGCATGTGCGGCTCAGTC 3 203 0 TGAGCATGTG 0.954458 -31 ********** Masking position 7 Map Score: 1.13639 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 1 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 CCACACTGGACCAGAACTACGT 1 2 1 CACCTGGACC 0.993229 -113 GAGGCCGACTCACCCTCGAACCAGGCGCCGG 1 89 1 CACCTCGAAC 0.989302 -26 TGCTGCAAGACACGCAGAAGCGCTCGTATCT 2 60 1 CACCAGAAGC 0.971903 -22 AAGCCTGCCGCACGCAGAAATGCAAACAGTT 3 28 0 CACCAGAAAT 0.922354 -206 TCACGCGGTACACGCCTGTACCAGGCGTGTC 3 64 1 CACCCTGTAC 0.900294 -170 TAGTGGGCTTCACGTTGGAACTGCTGCCATT 3 97 1 CACTTGGAAC 0.980535 -137 *** ******* Masking position 2 Map Score: 1.4563 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 104 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 ********** No masking Map Score: 2.58227e-13 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 7 ********** No masking Map Score: 2.58227e-13 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: 2.58227e-13 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