AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i094_tpal_bbur_100.orf -o094_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 RTP01005 28 AE000520 #2 RTP00862 75 AE000520 #3 RBB00366 86 3615 #4 RBB00362 41 3615 #5 RBB00361 300 3615 #6 RBB00360 40 3615 #7 RBB00359 24 3615 #8 RBB00358 67 3615 #9 RBB00356 82 3615 #10 RBB00355 70 3615 #11 RBB00352 51 3615 #12 RBB00351 23 3615 #13 RBB00808 108 3615 #14 RBB00084 242 3615 Motif number 1 TTTTATACTTAAAAATAAAATATATAAATTG 3 20 0 AAAATAAAAT 0.955201 -67 TTTATTTTTAAGTATAAAAAACACATTGGTT 3 32 1 ATATAAAAAA 0.760037 -55 TTTTGTTTGAATAATTGAAATGGAGAAGTGC 3 61 1 AAATTGAAAT 0.766183 -26 ACATCTTTAAAGAATTAAAAAGATTTTTCAC 5 20 0 AAATTAAAAA 0.967701 -281 TCAAATTACAACAATTAAAAAACCCTTTAAA 5 51 0 AAATTAAAAA 0.967701 -250 TACTTCTAGCATTAATAAAAACACAGTAGTA 5 150 0 ATAATAAAAA 0.870638 -151 TTTAAAAGGGATTATTAAAATTTTATTTTAT 5 185 1 ATATTAAAAT 0.888221 -116 ATTTTATTTTATAAATAAAGAATACTACTTG 5 204 1 AAAATAAAGA 0.927725 -97 AAATTTTTTAAAAATTAAAATATTAACTTTA 5 244 0 AAATTAAAAT 0.964944 -57 GGCATATAAACAAAAAAAGACACCTTAAAA 6 21 0 AAAAAAAAGA 0.823916 -20 TCTTGAAACTATTAATAAAATGGTAGCAAAT 8 29 0 ATAATAAAAT 0.860623 -39 AAAATTAAAAATATATCAAAG 9 1 1 AAATTAAAAA 0.967701 -82 GCATGCACTCAAAAATTAAGACTAACACTGT 10 15 0 AAAATTAAGA 0.832384 -56 AGCTCCCATTAGTATTAAATT 11 1 0 ATATTAAATT 0.633142 -51 ACCTGTTGTTAGAATTAAAGTGAGGCTTTAA 13 87 1 AAATTAAAGT 0.938366 -22 AAATAAAAGAATAAATAAATTATTACAAAAG 14 19 0 AAAATAAATT 0.821741 -224 AATTAATGTTAAAATAAAAGAATAAATAAAT 14 30 0 AAATAAAAGA 0.857968 -213 AAAAATGCTTAAAATATAAAAACCTTAATAA 14 69 0 AAATATAAAA 0.808624 -174 TTAATTGCTAATAAATAAAAATGCTTAAAAT 14 85 0 AAAATAAAAA 0.958691 -158 AATTATCTATAAAAATTAATTGCTAATAAAT 14 100 0 AAAATTAATT 0.640735 -143 ATTTTAATAAACAAAATAAATTATCTATAAA 14 118 0 AAAAATAAAT 0.750439 -125 TTTGTTTATTAAAATTTAAAATGCTATTGAA 14 134 1 AAATTTAAAA 0.920579 -109 AATGCTATTGAAAATATAAATTTTAAGCTTT 14 153 1 AAATATAAAT 0.795166 -90 * ********* Masking position 4 Map Score: 31.8733 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 168 Number in noncoding regions = 483 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 CAGCCATCCCAAAAAATCCATA 1 17 1 AAAAAACCAT 0.889638 -12 ATAAAGAATCAATTTATATATTT 3 3 1 AAAGAACAAT 0.443001 -84 TTTAAGTATAAAAAACACATTGGTTTTGTTT 3 38 1 AAAAACCATT 0.952796 -49 TACAACAATTAAAAAACCCTTTAAAACATCT 5 45 0 AAAAAACCTT 0.977252 -256 TAGCATTAATAAAAACACAGTAGTAGGAAAA 5 144 0 AAAAACCAGT 0.761016 -157 ATCCCTTTTAAAAAAATACTTCTAGCATTAA 5 166 0 AAAAAAACTT 0.821793 -135 ATAAAATTTTAATAATCCCTTTTAAAAAAAT 5 180 0 AATAATCCTT 0.801519 -121 AAAGACACCTTTTTAAGGTGT 6 1 1 AAAGACCCTT 0.986488 -40 ATAAACAAAAAAAGACACCTTAAAAAGGTGT 6 15 0 AAAGACCCTT 0.986488 -26 CGACATGCGGAATAACAACTTTGATATATTT 9 19 0 AATAACACTT 0.83228 -64 TAAAAGACTCCTTTTTTAAGACA 9 70 0 AAAGACCCTT 0.985908 -13 ATTAACTCCTTATATATTTTC 10 60 0 ATTAACCCTT 0.931159 -11 TCCTTATGGTAGTAACGCCTTCAAAGCTCCC 11 25 0 AGTAACCCTT 0.888097 -27 ATAATCTCCTTATGGTAGTAA 11 41 0 ATAATCCCTT 0.764716 -11 TGCTTAAAATATAAAAACCTTAATAAAGAGA 14 64 0 ATAAAACCTT 0.926325 -179 ****** **** Masking position 1 Map Score: 17.806 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 179 Number in noncoding regions = 455 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 GTTTGAATAATTGAAATGGAGAAGTGCTTTAT 3 65 1 TAAATGGAGA 0.938224 -22 TTTTAAAAAAAATATAAGGAGAGGATTAATT 5 280 1 AATAAGGAGA 0.976202 -21 AAAAGACACCTTAAAAAGGTGTCTTT 6 5 0 TAAAAGGTGT 0.888477 -36 TAATAGTTTCAAGAAAAGGAGAGCGTTGATAA 8 46 1 AAAAAGGAGA 0.980597 -22 TGTTATGTCTTAAAAAAGGAGTCTTTTA 9 65 1 TAAAAGGAGT 0.980597 -18 GAAATGAAAATATATAAGGAGTTAAT 10 55 1 TATAAGGAGT 0.976202 -16 AGGCGTTACTACCATAAGGAGATTAT 11 36 1 AATAAGGAGA 0.976201 -16 AAATAAATTATTACAAAAGAGAGTATT 14 6 0 TCAAAAGAGA 0.815914 -237 TATAAAAACCTTAATAAAGAGAGCAAATTAAT 14 54 0 TATAAAGAGA 0.939017 -189 * ********* Masking position 6 Map Score: 9.00379 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 30 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 TACTTAAAAATAAAATATATAAATTGATTC 3 16 0 TAAAATATAT 0.902792 -71 GGTGATGTAGGAAAAATTATTTTTCCTACT 5 124 1 GAAAAATTAT 0.823743 -177 AGGGATTATTAAAATTTTATTTTATAAATA 5 191 1 AAAATTTTAT 0.646478 -110 TTAATTTTTAAAAAATTTAGAATTTTTAAA 5 257 1 AAAAATTTAG 0.759569 -44 AGAATTTTTAAAAAAAATATAAGGAGAGGA 5 275 1 AAAAAAATAT 0.702427 -26 TAAAATGGTAGCAAATATATCACTTATTTT 8 15 0 GCAAATATAT 0.830512 -53 AAAATTAAAAATATATCAAAGTTGTT 9 7 1 AAAAATATAT 0.931337 -76 ACTGTGAAATGAAAATATATAAGGAGTTAA 10 50 1 GAAAATATAT 0.948057 -21 TCTCTTTTGTAATAATTTATTTATTCTTTT 14 16 1 AATAATTTAT 0.775664 -227 AATAAAGAGAGCAAATTAATGTTAAAATAA 14 44 0 GCAAATTAAT 0.556478 -199 TAAAAATGCTTAAAATATAAAAACCTTAAT 14 71 0 TAAAATATAA 0.635475 -172 AATTATCTATAAAAATTAATTGCTAATAAA 14 101 0 AAAAATTAAT 0.775664 -142 AATTTTTATAGATAATTTATTTTGTTTATT 14 114 1 GATAATTTAT 0.823727 -129 TTTTGTTTATTAAAATTTAAAATGCTATTG 14 133 1 TAAAATTTAA 0.719197 -110 TAATAAAGCTTAAAATTTATATTTTCAATA 14 158 0 TAAAATTTAT 0.93036 -85 ********** Masking position 4 Map Score: 11.2007 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 140 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TATGGATTTTTTGGGATGGCT 1 18 0 ATGGATTTTT 0.935663 -11 AACAAAACCAATGTGTTTTTTATACTTAAA 3 38 0 ATGTGTTTTT 0.821652 -49 AAAGAATTAAAAAGATTTTTCACAAATCAG 5 13 0 AAAGATTTTT 0.858113 -288 TTAATTCTTTAAAGATGTTTTAAAGGGTTT 5 33 1 AAAGATGTTT 0.615346 -268 AGATGTTTTAAAGGGTTTTTTAATTGTTGT 5 45 1 AAGGGTTTTT 0.919944 -256 ATGTAGGAAAAATTATTTTTCCTACTACTG 5 128 1 AATTATTTTT 0.764163 -173 TTAATGCTAGAAGTATTTTTTTAAAAGGGA 5 166 1 AAGTATTTTT 0.93278 -135 TTAAAAAATTTAGAATTTTTAAAAAAAATA 5 264 1 TAGAATTTTT 0.664901 -37 AATCCTCTCCTTATATTTTTTTTAAAAATT 5 277 0 TTATATTTTT 0.606342 -24 AACAACTTTGATATATTTTTAATTTT 9 7 0 ATATATTTTT 0.825954 -76 CTCTCTTTATTAAGGTTTTTATATTTTAAG 14 63 1 TAAGGTTTTT 0.659924 -180 TTTATATTTTAAGCATTTTTATTTATTAGC 14 80 1 AAGCATTTTT 0.829471 -163 TTTATTAGCAATTAATTTTTATAGATAATT 14 101 1 ATTAATTTTT 0.475068 -142 ********** Masking position 6 Map Score: 8.66544 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 234 Number in noncoding regions = 654 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 ATTTTTTTAAAAGGGATTATTAAAATTTTAT 5 180 1 AAGGGATTTT 0.777968 -121 AAAAAATATAAGGAGAGGATTAATT 5 286 1 AGGAGAGGTT 0.967354 -15 TTTCAAGAAAAGGAGAGCGTTGATAA 8 52 1 AGGAGAGCTT 0.953143 -16 TGTCGTTATGATGTGCGGCTTGTTATGTCTT 9 45 1 ATGTGCGGTT 0.774642 -38 ATGTCTTAAAAAAGGAGTCTTTTA 9 69 1 AAAGGAGTTT 0.775593 -14 CATGACAGTGTTAGTCTTAATT 10 2 1 ATGACAGTTT 0.767498 -69 TTTAATACTAATGGGAGCTTTGAAGGCGTTA 11 13 1 ATGGGAGCTT 0.957895 -39 GTTAGAATTAAAGTGAGGCTTTAAA 13 94 1 AAGTGAGGTT 0.950371 -15 ATTATTACAAAAGAGAGTATT 14 1 0 AAGAGAGTTT 0.967235 -242 ******** ** Masking position 10 Map Score: 2.56277 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 119 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 AATTTATATATTTTATTTTTAAGTATAAAA 3 21 1 TTTTATTTTT 0.832537 -66 ACTACTTAAATATAGCTTTGTTTG 4 5 1 CTTAAATATA 0.532637 -37 ATTGTTGTAATTTGAATTTAAATTAATCTT 5 67 1 TTTGAATTTA 0.613586 -234 ATTATTAAAATTTTATTTTATAAATAAAGA 5 195 1 TTTTATTTTA 0.938828 -106 AAAATATTAACTTTATTTTACTAACAAGTA 5 229 0 CTTTATTTTA 0.913502 -72 AAAGTTAATATTTTAATTTTTAAAAAATTT 5 245 1 TTTTAATTTT 0.779 -56 TTTGATATATTTTTAATTTT 9 1 0 TTTTAATTTT 0.779 -82 GGAATAACAACTTTGATATATTTTTAATTT 9 12 0 CTTTGATATA 0.533651 -71 CAGTGTTAGTCTTAATTTTTGAGTGCATGC 10 16 1 CTTAATTTTT 0.459593 -55 TTTTATTATAAGAAGGGTAA 12 1 1 TTTTATTATA 0.903568 -23 AAAGCCTCACTTTAATTCTAACAACAGGTC 13 86 0 TTTAATTCTA 0.418242 -23 AATACTCTCTTTTGTAATAATTTATTTAT 14 10 1 TTTTGTAATA 0.15856 -233 TTATTTATTCTTTTATTTTAACATTAATTT 14 32 1 TTTTATTTTA 0.938828 -211 ATTAAGGTTTTTATATTTTAAGCATTTTTA 14 71 1 TTATATTTTA 0.552176 -172 ATTTTAAGCATTTTTATTTATTAGCAATTA 14 85 1 TTTTTATTTA 0.499123 -158 GCATTTTAAATTTTAATAAACAAAATAAAT 14 128 0 TTTTAATAAA 0.348097 -115 AAATTTTAAGCTTTATTATATTTCATTAGA 14 170 1 CTTTATTATA 0.866011 -73 ********** Masking position 2 Map Score: 8.95202 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 157 Number in noncoding regions = 450 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 CGCTTTCACGCTGAGCTGTTGCAGCGGCTT 2 26 0 CTGAGCTGTT 0.988436 -50 GTTGGAACTACTGACCTATTATTTA 13 6 0 CTGACCTATT 0.982986 -103 CGAATCCCTCCTGACCTGTTGTTAGAATTA 13 74 1 CTGACCTGTT 0.993693 -35 ********** Masking position 4 Map Score: 1.13346 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 6 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 ********** No masking Map Score: -3.06711e-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: -3.06711e-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: -3.06711e-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