AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i211_tpal_bbur_100.orf -o211_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 RTP00856 236 AE000520 #2 RTP01116 118 AE000520 #3 RBB00509 60 3615 #4 RBB00508 79 3615 #5 RBB00505 32 3615 #6 RBB00504 148 3615 Motif number 1 CATAATGGTGTCGTACTCTTTTTTCGAACC 1 152 0 TCGTACTCTT 0.962702 -85 CGTAAGAACTGCTTCCTCTTTCG 1 224 1 GCTTCCTCTT 0.987349 -13 AAAACCTTCCTCTTAATCTTCAAT 3 47 0 CCTTCCTCTT 0.993086 -14 ATTTTCCTCTACGAATTAAAT 4 69 0 TTTTCCTCTA 0.967516 -11 TTTTCCTCTTTTTTACTATT 6 1 1 TTTTCCTCTT 0.993078 -148 TTTTCCTCTTTTTTACTATTATTAGTAACA 6 11 1 TTTTACTATT 0.900101 -138 AATCCCCTTTACTCTTTAAATACCTA 6 133 0 CTTTACTCTT 0.982932 -16 ********** Masking position 4 Map Score: 9.18478 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 53 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 GTGTCGTACTCTTTTTTCGAACCGTCGCAGA 1 144 0 CTTTTTTGAA 0.945955 -93 GCAGTTCTTACGTTTTTTTAATGGGGTAGCC 1 205 0 CGTTTTTTAA 0.752624 -32 ATAAATTGACATTATTTCTAATGTAAATTAA 3 11 1 ATTATTTTAA 0.930451 -50 GGTCAGTGTTTTTTATTAATTAATAATAA 4 9 1 TTTTTTATAA 0.828166 -71 TAAAAATCTACTTATTATTAATTAATAAAAA 4 20 0 CTTATTATAA 0.918815 -60 TAATAAGTAGATTTTTATAAAATCCTTTCTT 4 34 1 ATTTTTAAAA 0.848058 -46 TACGAATTAAATTTTTAAGAAAGGATTTTAT 4 50 0 ATTTTTAGAA 0.966881 -30 CTTTTTTACTATTATTAGTAACATAATGGTG 6 18 1 ATTATTATAA 0.94082 -131 ATCATATAAAATTATTAATGATAATGTTAAA 6 56 0 ATTATTATGA 0.768274 -93 GATAGTATTAATTTTTTTGTATTATTTTTTG 6 84 1 ATTTTTTGTA 0.775737 -65 TTTTTGTATTATTTTTTGGAAAAGTTATGCT 6 97 1 ATTTTTTGAA 0.960912 -52 ******* *** Masking position 11 Map Score: 8.86946 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 89 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 ACCCGTGCAGCACGCTACGCACCAAGGAGCGG 1 23 1 CACGCACCAC 0.961769 -214 GAAGTTCCATAACGCCGCTCCTTGGTGCGTAG 1 37 0 AACGCGCCCT 0.973007 -200 TATGGAACTTCACGAGATTGCCCACGCTCGAG 1 58 1 CACGAATGCC 0.952698 -179 CTCTTCTATCCACGCCTTTGCTCGAGCGTGGG 1 78 0 CACGCTTGCT 0.951257 -159 GAGATGGTCGCACTCTGTGCCCCAGATACCGT 1 107 1 CACTCGTCCC 0.973007 -130 CAAAGTTTGGCGCGCGGCTGCCACAGCAGCTT 2 13 1 CGCGCGCGCC 0.997866 -106 TCGAGTGCATCGCGAAGCTGCTGTGGCAGCCG 2 27 0 CGCGAGCGCT 0.976549 -92 ATCACGCGTGCACGCAGCCCCCTCGCTGCCGT 2 79 0 CACGCGCCCC 0.99879 -40 ***** ** *** Masking position 3 Map Score: 9.05332 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 84 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 ATACCGTCTACGTCTGCGACGGTTCGAAAA 1 132 1 CGTCTGCGAC 0.962927 -105 GTAGCCAAGCCAGCATCCACCATTTTCTGC 1 181 0 CAGCATCCAC 0.960036 -56 GATGCTGGCTTGGCTACCCCATTAAAAAAA 1 194 1 TGGCTACCCC 0.92653 -43 AACGTAAGAACTGCTTCCTCTTTCG 1 222 1 CTGCTTCCTC 0.90173 -15 GTTTGGCGCGCGGCTGCCACAGCAGCTTCG 2 17 1 CGGCTGCCAC 0.99736 -102 GCTGCCACAGCAGCTTCGCGATGCACTCGA 2 29 1 CAGCTTCGCG 0.905642 -90 CTCGCATCAACGGCAGCGAGGGGGCTGCGT 2 70 1 CGGCAGCGAG 0.967865 -49 CTCTACCGGCTAACACATATCACGCG 2 103 0 CGGCTAACAC 0.949286 -16 ********** Masking position 4 Map Score: 5.14221 Number of sites scoring better than the average of aligned sites = 1224 Number in coding regions = 362 Number in noncoding regions = 862 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 CCATTTTCTGCATAATGGTGTCGTACTCTT 1 162 0 CATAATGGTG 0.990629 -75 CCATTATGCAGAAAATGGTGGATGCTGGCT 1 174 1 GAAAATGGTG 0.982553 -63 TTATTAGTAACATAATGGTGTAATATATTT 6 29 1 CATAATGGTG 0.990629 -120 AATTATTAATGATAATGTTAAATATATTAC 6 48 0 GATAATGTTA 0.903592 -101 ********** Masking position 5 Map Score: 2.89249 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 28 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 TACCCCATTAAAAAAACGTAAGAACTGCTTC 1 208 1 AAAAAAGTAA 0.927092 -29 TTACATTAGAAATAATGTCAATTTAT 3 6 0 AATAATTCAA 0.891517 -55 CTTAATCTTCAATAAAGTTTAATTTACATTA 3 29 0 AATAAATTTA 0.834761 -32 AATCCTTTCTTAAAAATTTAATTCGTAGAGG 4 54 1 TAAAAATTAA 0.795105 -26 CTAAACCTCTAATAAAATCAAAAAGAAAT 5 9 0 AATAAATCAA 0.939999 -24 TTATGTTACTAATAATAGTAAAAAAGAGGAA 6 13 0 AATAATGTAA 0.891517 -136 ATAATGGTGTAATATATTTAACATTATCATT 6 40 1 AATATATTAA 0.910123 -109 ACTATCATATAAAATTATTAATGATAATGTT 6 59 0 AAAATTTTAA 0.811574 -90 AAAATAATACAAAAAAATTAATACTATCATA 6 81 0 AAAAAATTAA 0.962869 -68 ****** **** Masking position 4 Map Score: 5.92806 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 110 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 CGTAGCGTGCTGCACGGGTATTCCAGGCAC 1 12 0 TGCACGGGTA 0.951761 -225 TCCACGCCTTTGCTCGAGCGTGGGCAATCT 1 72 0 TGCTCGAGCG 0.764157 -165 AAATGGTGGATGCTGGCTTGGCTACCCCAT 1 186 1 TGCTGGCTTG 0.925212 -51 AGCTTCGCGATGCACTCGAGGTTTTGGAAG 2 40 1 TGCACTCGAG 0.961076 -79 GGGGGCTGCGTGCACGCGTGATATGTGTTA 2 89 1 TGCACGCGTG 0.996505 -30 ********** Masking position 1 Map Score: 0.549814 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 16 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 ********** No masking Map Score: -1.70998e-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: -1.70998e-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: -1.70998e-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