AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_tpal_bbur_100.orf -o207_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 Purged sequences: RBB00392 26 3615 Input sequences: #1 RTP00323 174 AE000520 #2 RTP00235 300 AE000520 #3 RTP00092 41 AE000520 #4 RTP00091 24 AE000520 #5 RTP00090 84 AE000520 #6 RTP00984 143 AE000520 #7 RBB00708 44 3615 #8 RBB00707 79 3615 #9 RBB00462 198 3615 Motif number 1 CTATTTTTTTCTTACCTCTTTGTCGCGGTTTTTGTTT 1 87 1 CTCCTTCGCG 0.935284 -88 TTACACAAGGCGCGCGTATGCACTGCTGGCAAATATA 1 146 1 CCCGTCTGCT 0.992338 -29 ACAGTGTGGTCCTGTGCATCGACTGCGCGTAGGTCTG 2 56 0 CTTGTCTGCG 0.97281 -245 CACTGTACACCACGCCGGTCTGCTGCGCCCGGAGATT 2 87 1 CCCCTCTGCG 0.998817 -214 AAGCGGGGTCCCCACCCGTCATCTGCGTTACACAGCA 2 233 0 CCCCTCTGCG 0.999184 -68 ACGGGTGGGGACCCCGCTTTGCCTGCGAAGCGCAGAA 2 251 1 ACCGTCTGCG 0.992427 -50 AAAAGACGCGCACTCCGTTTTTCTGCGCTTCGCAGGC 2 271 0 CCCCTCTGCG 0.999245 -30 * * ** * ***** Masking position 9 Map Score: 9.73768 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 11 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 TTATTAGTTTTTTATAGTTATAAA 7 5 1 TAGTTTTTTA 0.868718 -40 TAGTTTTTTATAGTTATAAAATAGTTTTTA 7 15 1 TAGTTATAAA 0.63982 -30 AGTTATAAAATAGTTTTTAAGGAATATTT 7 26 1 TAGTTTTTAA 0.94322 -19 CTTAAGGCTTTTGCTTTAAATTGTTGAATG 8 28 1 TTGCTTTAAA 0.689023 -52 CTGTGTAATATAATTTATAATTTAATTAT 8 61 1 TAATTTATAA 0.826676 -19 TATGACATTTTAATTTTATATTTGTTTTTT 9 23 1 TAATTTTATA 0.805809 -176 AATTATTAAATTGTTTAAAAAAACAAATAT 9 40 0 TTGTTTAAAA 0.824112 -159 AACAATTTAATAATTTATTATTAAAAATAA 9 55 1 TAATTTATTA 0.658185 -144 CCTTTTCGGGTTATTTTTAATAATAAATTA 9 65 0 TTATTTTTAA 0.912025 -134 ATTGCTTTTGTTATTTTTAAGAAAAAATAT 9 99 1 TTATTTTTAA 0.912025 -100 ATCGTAGTAGTTATTTTAAATTATGGCAAG 9 137 1 TTATTTTAAA 0.897598 -62 ********** Masking position 10 Map Score: 7.25198 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 121 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TTTCAGTGCGGATCGCACTACCCATGAC 1 6 1 GTGGGACGCC 0.569506 -169 GTTCCCTGGTGTGCGTATAGCACCTGTTTGTCT 2 189 0 GTGGTAAGCC 0.903243 -112 TATACGCACACCAGGGAACGCACGATACACTGC 2 203 1 CCAGGACGCC 0.940103 -98 CGATACACTGCTGTGTAACGCAGATGACGGGTG 2 225 1 CTGGTACGCG 0.934319 -76 CAGATGACGGGTGGGGACCCCGCTTTGCCTGCG 2 245 1 GTGGGACCCC 0.676 -56 CCCGCTTTGCCTGCGAAGCGCAGAAAAACGGAG 2 263 1 CTGGAACGCG 0.798429 -38 CTCGTAATACGTGCAGAAAGCGGTATCATCTCT 6 22 0 GTGAGAAGCG 0.892102 -122 GATGCATTGCGTATGGAACGCTCTTACAAAAAG 6 71 1 GTAGGACGCC 0.991682 -73 *** *** *** * Masking position 7 Map Score: 7.94471 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 55 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 GCTATATTTGCCAGCAGTGCATACGCGCGC 1 155 0 TCCAGCAGGC 0.980643 -20 AGCTCGACAGTTCCAGAACCACTGGTGTTGCA 2 15 0 TCCAGAACAC 0.944466 -286 GTCTGCAAGCTGCCAGCTCGACAGTTCCAGAA 2 29 0 TCCAGCTCAC 0.957769 -272 GCCCGGAGATTGCCATCATGACTCCCATTATG 2 113 1 TCCATCATAC 0.943451 -188 CCATCATGACTCCCATTATGGCTGACCATCAA 2 125 1 TCCATTATGC 0.973875 -176 CATATCCGCATACCAGTTTTGATGGTCAGCCA 2 143 0 TCCAGTTTGA 0.775569 -158 CCACGTAGCTTTCCATATCCGCATACCAGTTT 2 156 0 TCCATATCGC 0.920927 -145 GGATGATTGTTGTCAGTACTGCTATCCCTCTT 5 59 0 TTCAGTACGC 0.907626 -26 CTGCACGTATTACGAGCATCGCCGATGTATAT 6 39 1 TCGAGCATGC 0.947206 -105 GCAACTCCTATACCATTATAGCAAAGCTCTAA 9 174 0 TCCATTATGC 0.973876 -25 * ******* ** Masking position 5 Map Score: 6.99593 Number of sites scoring better than the average of aligned sites = 1036 Number in coding regions = 307 Number in noncoding regions = 729 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 GTGCATACGCGCGCCTTGTGTAAAACTTTA 1 139 0 GCGCCTTGTG 0.994813 -36 CCGGTCTGCTGCGCCCGGAGATTGCCATCA 2 101 1 GCGCCCGGAG 0.992592 -200 TGTGCGTATAGCACCTGTTTGTCTGCCACG 2 183 0 GCACCTGTTT 0.841938 -118 AACGGAGTGCGCGTCTTTTGGT 2 289 1 GCGTCTTTTG 0.909298 -12 CCGGATGGCGCCTGGAGCCATAAT 4 8 1 GCGCCTGGAG 0.993851 -17 TTTTGATTATGCACCCTGTGCTCTTGCA 5 9 0 GCACCCTGTG 0.981727 -76 ********** Masking position 5 Map Score: 6.22558 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 37 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 AGGTAAGAAAAAAATAGCAACCCCATTACC 1 74 0 AAAATAGCAA 0.916001 -101 GAATACGTCGAAAACAAAAACCGCGACAAA 1 105 0 AAAACAAAAA 0.950635 -70 TCCCAGAGAAAAAATAGAAAGAGGGATAGC 5 41 1 AAAATAGAAA 0.917528 -44 ATAACTATAAAAAACTAATAA 7 2 0 AAAACTAATA 0.814627 -43 AAACAAATATAAAATTAAAATGTCATAATA 9 20 0 AAAATTAAAA 0.877936 -179 ATTGTTTAAAAAAACAAATATAAAATTAAA 9 31 0 AAAACAAATA 0.923101 -168 TTTTTTCTTAAAAATAACAAAAGCAATTTA 9 96 0 AAAATAACAA 0.950635 -103 GCCATAATTTAAAATAACTACTACGATAGA 9 134 0 AAAATAACTA 0.923101 -65 ********** Masking position 4 Map Score: 6.54787 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 66 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 GTCATGTCGTCATGGGTAGTGCGATCCGCACT 1 15 0 CATGGAGTGC 0.971802 -160 AAGAGGTAGGTAATGGGGTTGCTATTTTTTTC 1 66 1 TAAGGGTTGC 0.949682 -109 GTTCCAGAACCACTGGTGTTGCAGGCG 2 6 0 CACGGGTTGC 0.990342 -295 CCCCACCCGTCATCTGCGTTACACAGCAGTGT 2 229 0 CATTGGTTAC 0.849111 -72 GCATCATATACATCGGCGATGCTCGTAATACG 6 44 0 CATGGGATGC 0.993391 -100 AAGAGCGTTCCATACGCAATGCATCATATACA 6 64 0 CATCGAATGC 0.903858 -80 GCTATAATGGTATAGGAGTTGCTTT 9 184 1 TATGGGTTGC 0.987097 -15 *** ** ***** Masking position 2 Map Score: 3.03932 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 105 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 GAGGTAGGTAATGGGGTTGCTATTTTTTTCT 1 68 1 ATGGGTTGCT 0.937818 -107 CATAGAGAGTTGTCAATCCGATTC 3 28 0 AGAGGTTGTC 0.884529 -14 TCTTACAAAAAGGGATTTTCTCATGAACAAA 6 92 1 AGGGTTTTCT 0.94756 -52 TTTTTACTTAAGGCTTTTGCTTTAAATTGTT 8 22 1 AGGCTTTGCT 0.964237 -58 AATTATGGCAAGAGGTTTGTTAGAGCTTTGC 9 155 1 AGAGTTTGTT 0.961933 -44 GAGGTTTGTTAGAGCTTTGCTATAATGGTAT 9 166 1 AGAGTTTGCT 0.986798 -33 **** ****** Masking position 7 Map Score: 0.294985 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 100 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: 1.73616e-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: 1.73616e-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 11 ********** No masking Map Score: 1.73616e-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