AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i193_tpal_bbur_300.orf -o193_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 RTP00420 64 AE000520 #2 RTP00421 246 AE000520 #3 RTP00422 166 AE000520 #4 RBB00205 220 3615 Motif number 1 GTCCAGATTTGTTGCGTGTGGAACAGCCGCGCACCCGACC 2 49 1 GTGGTGAGCC 0.9839 -198 CCGCATCAGGGTCCGGAGAAGGAGAGCACGCTTGCACGGC 2 90 1 GTGGAGAGCG 0.991956 -157 TCGCCGCATTGCGTAGGGTATCGGAGTTGGCCGTGCAAGC 2 119 0 GCGGTTAGTG 0.984829 -128 CCTACGCAATGCGGCGAGGGTAAATGCACGGTAGAAAGAA 2 142 1 GCGGGTTGCG 0.993985 -105 CTCGCGTCTCGCCTTGGCGCGCAATGTTTGAACACGGGTT 2 180 0 GCGCGGTGTG 0.986659 -67 ACCTGCAGGCTCTGGGAAGAGCAGCGTCTGTCGTCTGC 2 219 0 GCGGAGAGCC 0.987223 -28 TATACCCCTTGCAAAGACTTGGTGAGTGTGGCCCTTATCA 3 29 1 GCGCTGAGTG 0.990382 -138 CGGTCCCGCTGCCCAGGCTATGGGAGCCAGACTGTGCGTG 3 72 1 GCGCTTAGCG 0.99362 -95 ATATCTGAAAGTAGTGCGGCGCCGAGCACGCACAGTCTGG 3 98 0 GTGGGGAGCG 0.997265 -69 AGTTTGTATAGTAAAGTCGGTTTTTGCTTGTTAGAATTGT 4 48 0 GTGCGTTGCG 0.97948 -173 ** * ** * *** * Masking position 6 Map Score: 14.9796 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 110 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 2 AGGGTAAAATTTAACATATTCTTTATTA 4 5 1 TAAAATTAAA 0.850319 -216 AATTGTTTGATAAAATAATAAAGAATATGTTAAA 4 20 0 TAAAATATAA 0.969487 -201 ATACAAACTGTAAAATACCACCAAAAATACATGC 4 79 1 TAAAATACAA 0.989477 -142 TGAACATAAATAAAATAGCATGTATTTTTGGTGG 4 96 0 TAAAATACAA 0.989463 -125 ATGTTCAAATTAAAATAATCTTTAAAGAAAAATA 4 123 1 TAAAATATCA 0.905718 -98 ATCTTTAAAGAAAAATATCAATCAAAAAGACAAT 4 140 1 AAAAATACAA 0.943979 -81 TAACGACAATTAAAATATAATTCACATTTTTATA 4 176 0 TAAAATAAAA 0.96075 -45 TCTAGCATATTAAAATATCTTTAACGACAATTAA 4 197 0 TAAAATACTA 0.942699 -24 ******* ** * Masking position 5 Map Score: 8.08222 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 13 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 TGCGGCGGTCGGGTGCGCGGCTGTTCCACA 2 65 0 GGGTGCGCGG 0.983049 -182 GGCCGTGCAAGCGTGCTCTCCTTCTCCGGA 2 101 0 GCGTGCTCTC 0.964603 -146 CTCGCGTCTCGCCTTGGCGCGCAATGTTTG 2 190 0 GCCTTGGCGC 0.931734 -57 AGCGTCTGTCGTCTGCTCGCGTCTCGCCTT 2 205 0 GTCTGCTCGC 0.962103 -42 ACCTGCAGGCTCTGGGAAGAGCAG 2 233 0 GCAGGCTCTG 0.831099 -14 CTACGCGTGCGCCCTTGTTATACC 3 5 1 GCGTGCGCCC 0.867759 -162 GGCTCCCATAGCCTGGGCAGCGGGACCGAC 3 70 0 GCCTGGGCAG 0.959059 -97 GCCAGACTGTGCGTGCTCGGCGCCGCACTA 3 97 1 GCGTGCTCGG 0.977127 -70 ********** Masking position 8 Map Score: 7.82012 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 41 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TGAGCGACAATCCGTGGCAGGTGTTTGCGAACGCCTAT 1 17 0 TGTGGGTTGC 0.941163 -48 CTCCTCTGACGGCCCAGAAGAAGGTTGC 2 1 0 GCCGGGTTGC 0.990505 -246 GGCCGTCAGAGGAGCATATGATGTGTCCAGATTTGTTG 2 25 1 GGCTGGGTCC 0.986383 -222 TCCGGACCCTGATGCGGCGGTCGGGTGCGCGGCTGTTC 2 69 0 GGCGGGGTGC 0.998114 -178 GGTATCGGAGTTGGCCGTGCAAGCGTGCTCTCCTTCTC 2 105 0 TGCGCGGTGC 0.990766 -142 TCTGGGAAGAGCAGCGTCTGTCGTCTGCTCGCGTCTCG 2 209 0 GGCTGGCTGC 0.983598 -38 GTCTTTGCAAGGGGTATAACAAGGGCGCACGCGTAG 3 9 0 GGTTCGGCGC 0.913153 -158 CAGGCTATGGGAGCCAGACTGTGCGTGCTCGGCGCCGC 3 85 1 GCCGTGGTGC 0.983889 -82 * ** * * * **** Masking position 13 Map Score: 5.41141 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 86 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 TTAAGCAGTTGAGCGACAATCCGTGGCAGG 1 34 0 GAGCGACAAT 0.904643 -31 CTCCTCTGACGGCCCAGAAGAAGGTTGC 2 9 0 GGCCCAGAAG 0.914368 -238 GTGCGCGGCTGTTCCACACGCAACAAATCT 2 53 0 GTTCCACACG 0.897237 -194 TTGCGCGCCAAGGCGAGACGCGAGCAGACG 2 196 1 AGGCGAGACG 0.903282 -51 GACCTGATAAGGGCCACACTCACCAAGTCT 3 43 0 GGGCCACACT 0.994641 -124 CAGGCTATGGGAGCCAGACTGTGCGTGCTC 3 85 1 GAGCCAGACT 0.984309 -82 TGCGTGCTCGGCGCCGCACTACTTTCAGAT 3 106 1 GCGCCGCACT 0.955184 -61 ********** Masking position 8 Map Score: 1.58507 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 194 Number in noncoding regions = 495 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 ********** No masking Map Score: 2.93755e-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: 2.93755e-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: 2.93755e-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