AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_tpal_bbur_300.orf -o231_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 RTP00221 300 AE000520 #2 RTP01008 135 AE000520 #3 RBB00489 275 3615 #4 RBB00148 300 3615 #5 RBB00146 23 3615 Motif number 1 AGGAAAAACGCGTAGGAACAGGACAGCACGCCGTTCCCGCCCC 1 17 0 CGGGGAGCCG 0.955248 -284 CTGGGCAAACGGCTGGTATCGCGCGAAATCCTGTCCCGGCGCG 1 92 1 GGGGGGATCG 0.970697 -209 GAAATCCTGTCCCGGCGCGGGGGATGTGCCCCGTGTCTTTGCG 1 116 1 CCGCGGGCCG 0.996919 -185 CCGTGTCTTTGCGCGCTCAGGGGAGGTTTTCCCTTCAGGAGCC 1 146 1 GCGCGGGTCC 0.977446 -155 CCCTTCAGGAGCCCGGGGACGGGGTGCTCTCCGTGAAGGTGTC 1 176 1 GCGGGGGCCG 0.999285 -125 GGCAGGAGCAGCGTGCACCTGCGGATCACACGGCGACACCTTC 1 210 0 GCGCGGTCCG 0.996229 -91 GCTTGACGAGGCAAGGAGACGTATTTCCCTCAGTCTCAGGCAG 1 248 0 GCGGGATCCG 0.989982 -53 CGCTCATTGCGCGCTGCGTTGCGCTGTTTGCGGCACAGGATAC 2 24 0 GCTGGGGTCG 0.988642 -112 CGAATGGCGTGCAATGCTGCGTGTATATCGCAGAGCACCGTTT 2 99 1 GCTGGGTCCG 0.993672 -37 TATGAAGTATGCCAGGAGTGGTGGAATTGGCAGACACGCTAGA 4 102 1 GCGGGGAGCG 0.994026 -199 GGATCTAGTGCCTTTGGCGTGTGGGTTCGACTCCCACCTTCTG 4 149 1 CCTGGGTGCC 0.840221 -152 TAGAGTGTCACCTTGCCAAGGTGGAAGTCGCGGGTTCAAATCC 4 217 1 CCGCGGACCG 0.993016 -84 ** ** * * * * * * Masking position 21 Map Score: 20.0856 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 189 Number in noncoding regions = 495 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 CACGCCGTTCCCGCCCCCCCCCA 1 1 0 CCCCCCCCCA 0.988891 -300 CAAAGGGAAAACACCCCACCCGAAGTGAGGAAA 1 54 0 ACCCCCCCGA 0.996413 -247 CGGGGCACATCCCCCGCGCCGGGACAGGATTTC 1 116 0 CCCCCCCGGG 0.99199 -185 CCTGAAGGGAAAACCTCCCCTGAGCGCGCAAAG 1 152 0 AACCCCCTGA 0.967723 -149 CACGGAGAGCACCCCGTCCCCGGGCTCCTGAAG 1 178 0 ACCCTCCCGG 0.988207 -123 TCACACGGCGACACCTTCACGGAGAGCACCCCG 1 195 0 ACCCTACGGA 0.830363 -106 CCGCAGGTGCACGCTGCTCCTGCCTGAGACTGA 1 229 1 ACCTCCCTGC 0.888434 -72 GGGAAATACGTCTCCTTGCCTCGTCAAGCCCGA 1 262 1 TCCCTCCTCG 0.839987 -39 GCAGCATTGCACGCCATTCGGCACCATATGCAA 2 86 0 ACCCTCGGCA 0.882366 -50 TCTGCCAATTCCACCACTCCTGGCATACTTCAT 4 103 0 CCCCCCCTGG 0.992147 -198 GTGGGAGTCGAACCCACACGCCAAAGGCACTAG 4 153 0 AACCCCGCCA 0.809309 -148 GCAAGGTGACACTCTACCCCTGAGTTACTTTCG 4 200 0 ACCTCCCTGA 0.967723 -101 ** ** * ***** Masking position 4 Map Score: 14.228 Number of sites scoring better than the average of aligned sites = 1447 Number in coding regions = 430 Number in noncoding regions = 1017 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 CTTCTCTAGAATTCATTTTTAATCGATTTTTCA 3 14 1 ATTCATTTAT 0.759471 -262 TTTTTCAAGGATTATTCTTTACTAACTTCACCA 3 40 1 ATTATTTTAT 0.972181 -236 CCATAGATTAATTAATTTTAAGTAGTAGTTATT 3 70 1 ATTAATTTAT 0.973681 -206 AATTATGACCATTAATTTGGATTATAGTAAAAA 3 142 0 ATTAATTGAT 0.920203 -134 TTCTCATTTTATTATTTTATAATAAAAAAAATT 3 188 1 ATTATTTAAT 0.844747 -88 AATAAAAAAAATTATTATTAAATGAATTTCCAT 3 208 1 ATTATTTTAT 0.971924 -68 TGAGTGCGAAATTATTATTTATTTAGTAGATTA 4 25 1 ATTATTTTAT 0.972181 -276 TAATGCCTCAATTAAATTTTATTGATAATTATT 4 275 0 ATTAAATTAT 0.728645 -26 ****** ** * * Masking position 11 Map Score: 7.49458 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 18 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 GGTGGGGTGTTTTCCCTTTGAAGAACTGGG 1 67 1 TTTCCCTTTG 0.922694 -234 TACCAGCCGTTTGCCCAGTTCTTCAAAGGG 1 80 0 TTGCCCAGTT 0.913415 -221 CCCCGTGTCTTTGCGCGCTCAGGGGAGGTT 1 144 1 TTGCGCGCTC 0.971745 -157 AGGAGACGTATTTCCCTCAGTCTCAGGCAG 1 248 0 TTTCCCTCAG 0.795336 -53 GCGCGCTGCGTTGCGCTGTTTGCGGCACAG 2 29 0 TTGCGCTGTT 0.963839 -107 AATGCGCTCATTGCGCGCTGCGTTGCGCTG 2 41 0 TTGCGCGCTG 0.980269 -95 TAAATAATAATTTCGCACTCAGCAGGAGTC 4 16 0 TTTCGCACTC 0.961861 -285 CCTGAGTTACTTTCGCATTTTTACAGAAGG 4 185 0 TTTCGCATTT 0.936423 -116 AAATCCCGTCTTTCGCTTTTTAATAATTAT 4 254 1 TTTCGCTTTT 0.950443 -47 ********** Masking position 2 Map Score: 6.0426 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 72 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TGAGGAAAAACGCGTAGGAACAGGACAGCA 1 32 0 CGCGTAGGAA 0.895192 -269 CGTTTTTCCTCACTTCGGGTGGGGTGTTTT 1 50 1 CACTTCGGGT 0.789537 -251 GCACATCCCCCGCGCCGGGACAGGATTTCG 1 115 0 CGCGCCGGGA 0.959344 -186 TGTCTTTGCGCGCTCAGGGGAGGTTTTCCC 1 149 1 CGCTCAGGGG 0.991067 -152 CCCTCAGTCTCAGGCAGGAGCAGCGTGCAC 1 235 0 CAGGCAGGAG 0.900105 -66 GCGCTCATTGCGCGCTGCGTTGCGCTGTTT 2 38 0 CGCGCTGCGT 0.84615 -98 CTGCGATATACACGCAGCATTGCACGCCAT 2 102 0 CACGCAGCAT 0.923477 -34 TGTTATAATTAGCTTAGGAGATTTCAAGTT 3 254 1 AGCTTAGGAG 0.772411 -22 AATAATTTCGCACTCAGCAGGAGTCGAACC 4 11 0 CACTCAGCAG 0.950883 -290 ATGCGAAAGTAACTCAGGGGTAGAGTGTCA 4 197 1 AACTCAGGGG 0.923249 -104 ********** Masking position 7 Map Score: 5.48413 Number of sites scoring better than the average of aligned sites = 1330 Number in coding regions = 369 Number in noncoding regions = 961 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 GAAAAATCGATTAAAAATGAATTCTAGAGA 3 16 0 TTAAAAATGA 0.809687 -260 ATAACTACTACTTAAAATTAATTAATCTAT 3 72 0 CTTAAAATTA 0.842302 -204 TTAAGTAGTAGTTATTATGCTTATTATCGA 3 87 1 GTTATTATGC 0.60985 -189 TTGGATTATAGTAAAAATTACAATCCGCTA 3 129 0 GTAAAAATTA 0.957539 -147 AATTTTAACAGTTAAAATTATGACCATTAA 3 160 0 GTTAAAATTA 0.965258 -116 AATTTTAACTGTTAAAATTCTCATTTTATT 3 171 1 GTTAAAATTC 0.958188 -105 TATTTGTTTTGTTATAATTAGCTTAGGAGA 3 245 1 GTTATAATTA 0.935791 -31 CCCACCTTCTGTAAAAATGCGAAAGTAACT 4 181 1 GTAAAAATGC 0.938809 -120 CTTTCGCTTTTTAATAATTATCAATAAAAT 4 263 1 TTAATAATTA 0.730142 -38 ********** Masking position 4 Map Score: 5.12691 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 75 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 GTAAAGAATAATCCTTGAAAAATCGATTAA 3 32 0 ATCCTTGAAA 0.940999 -244 ATAATAACTACTACTTAAAATTAATTAATC 3 75 0 CTACTTAAAA 0.910258 -201 AAAACTTGAAATCTCCTAAGC 3 265 0 AAACTTGAAA 0.95898 -11 TAGATTAGGCATACTTGCAAAAGCTTTTAA 4 51 1 ATACTTGCAA 0.940999 -250 TAGTATACAAAAACTTAAAAGCTTTTGCAA 4 65 0 AAACTTAAAA 0.936979 -236 GGCATACTTCATACTCAAAATAGTATACAA 4 85 0 ATACTCAAAA 0.910258 -216 ********** Masking position 5 Map Score: 1.88249 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 14 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 AAAATCGATTAAAAATGAATTCTAGAGAAG 3 14 0 AAAAATGAAT 0.802671 -262 TGAAGTTAGTAAAGAATAATCCTTGAAAAA 3 40 0 AAAGAATAAT 0.911629 -236 TAACTTCACCATAGATTAATTAATTTTAAG 3 62 1 ATAGATTAAT 0.86498 -214 TTTTTTTATTATAAAATAATAAAATGAGAA 3 188 0 ATAAAATAAT 0.903157 -88 TTATAATAAAAAAAATTATTATTAAATGAA 3 204 1 AAAAATTATT 0.842298 -72 ATGAATTTCCATAAAATATTTGTTTTGTTA 3 229 1 ATAAAATATT 0.774822 -47 TCTACTAAATAAATAATAATTTCGCACTCA 4 25 0 AAATAATAAT 0.790926 -276 AATTATCAATAAAATTTAATTGAGGCATTA 4 278 1 AAAATTTAAT 0.729693 -23 ********** Masking position 3 Map Score: 1.17351 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 137 Number in noncoding regions = 406 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 GAAGAACTGGGCAAACGGCTGGTATCGCGC 1 86 1 GCAAACGGCT 0.905113 -215 TCATCGGGCTTGACGAGGCAAGGAGACGTA 1 268 0 TGACGAGGCA 0.831784 -33 GTAGGAAAAGGCAGTATCCTGTG 2 4 1 GGAAAAGGCA 0.988472 -132 GGCACCATATGCAAGAGGCAGATGCGCAGA 2 70 0 GCAAGAGGCA 0.989322 -66 CAGGAGTGGTGGAATTGGCAGACACGCTAG 4 114 1 GGAATTGGCA 0.911609 -187 GAACCCACACGCCAAAGGCACTAGATCCTA 4 147 0 GCCAAAGGCA 0.969109 -154 ********** Masking position 7 Map Score: 1.42882 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 104 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ********** No masking Map Score: 5.35339e-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 11 ********** No masking Map Score: 5.35339e-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 12 ********** No masking Map Score: 5.35339e-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