AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_Ribosomal_Operon___Transcription_bbur_reg_300.orf -o222_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RBB00769 20 3615 #2 RBB00550 22 3615 #3 RBB00549 89 3615 #4 RBB00245 77 3615 #5 RBB00243 91 3615 #6 RBB00242 19 3615 #7 RBB00051 300 3615 #8 RBB00867 165 3615 Motif number 1 ATCTATCTCCTAAAATTATT 1 5 0 TTCCTAAAAT 0.814267 -16 TTTTAGTGAATGTATAATAAAATTAATTATTAA 3 28 1 TTAATAAAAT 0.943977 -62 ATATTTCCATTATAATAGCAAATATTAGTATTT 4 28 0 TTAAGCAAAT 0.830748 -50 ATAATGGAAATATCGGAATAAATAAAGAGGTGT 4 48 1 TTCAATAAAT 0.954591 -30 ATATATTTTATTTAACAAAAAAGCACACCGATT 5 23 0 TTAAAAAAAG 0.91461 -69 TTTTTAAACTTATCGCTAAAAATTTGACTATAA 5 55 0 TTCTAAAAAT 0.95459 -37 CCTAAGAAAGTGTCGCAGAAAATTACCGCCGTA 7 39 1 TTCAGAAAAT 0.97298 -262 TCACCGCTTATTTAGCAATAAATACAGGCAAGA 7 103 1 TTAAATAAAT 0.93833 -198 TATTTTTTTATCGCTAAAAAAATCGTGCGATCT 7 202 0 TGCAAAAAAT 0.936702 -99 ACAAAAAAATTTTCTAAAAAAATAGAGATAAGA 8 35 0 TTCAAAAAAT 0.989452 -131 TAAATTAAAATATACAAAAAAATTTTCTAAAAA 8 48 0 TTAAAAAAAT 0.985488 -118 ACTCATCACTTTTACGTAAAAATACGCACCTCA 8 96 0 TTATAAAAAT 0.938331 -70 CCTTTCGCTTTTTATTAAAAAATTAAAATTCAC 8 129 0 TTAAAAAAAT 0.98548 -37 * ** ******* Masking position 10 Map Score: 18.7299 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 328 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 2 ATATTAAATTAAAGGGGAAGAA 2 7 1 AATAAAGGGA 0.945592 -16 ATTCACTAAAAAGTAAATTCTAGGAATA 3 7 0 AATAAATTTA 0.647707 -83 CTTTTTTGTTAAATAAAATATATTATAGTCAA 5 33 1 AATAAAATTA 0.928908 -59 AAAATTACCGCCGTAAAAGGTAAGGGTGAAAA 7 57 1 CCTAAAAGTA 0.807498 -244 AGCGATAAAAAAATAAGAGAGATGATGGCATA 7 220 1 AATAAGAGGA 0.945592 -81 AATTTCATTGACCTAAAAGAGAGTTTTAA 7 282 1 ACTAAAAGGA 0.981201 -19 AAATTTTCTAAAAAAATAGAGATAAGAAAACA 8 30 0 AAAAATAGGA 0.744213 -136 ATAATTACTAAATTAAAATATACAAAAAAATT 8 57 0 AATAAAATTA 0.928908 -109 GCGTATTTTTACGTAAAAGTGATGAGTGTGAA 8 102 1 ACTAAAAGGA 0.981201 -64 TTTATTAAAAAATTAAAATTCACACTCATCAC 8 120 0 AATAAAATCA 0.854781 -46 TTAATTTTTTAATAAAAAGCGAAAGGCAAAAG 8 136 1 AAAAAAAGGA 0.953869 -30 ** ****** ** Masking position 6 Map Score: 8.17545 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 394 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 AGCAAATACACCTCTTTATTTATTCC 4 62 0 TACACCTCTT 0.868642 -16 AACAAAAAAGCACACCGATTCTCATCAAGG 5 13 0 CACACCGATT 0.846144 -79 GTTTTTTAAACTTATCGCTAAAAATTTGAC 5 60 0 CTTATCGCTA 0.950898 -32 CCTTTTCACCCTTACCTTTTACGGCGGTAA 7 61 0 CTTACCTTTT 0.912523 -240 GAGCTCTTACCTCACCTTTTCACCCTTACC 7 75 0 CTCACCTTTT 0.943296 -226 GAGGTAAGAGCTCACCGCTTATTTAGCAAT 7 92 1 CTCACCGCTT 0.99089 -209 CTCTTATTTTTTTATCGCTAAAAAAATCGT 7 209 0 TTTATCGCTA 0.769996 -92 ACTATGCCATCATCTCTCTTATTTTTTTAT 7 224 0 CATCTCTCTT 0.758277 -77 TTTTTGTTTTCTTATCTCTATTTTTTTAGA 8 26 1 CTTATCTCTA 0.937664 -140 AAAATTCACACTCATCACTTTTACGTAAAA 8 108 0 CTCATCACTT 0.928923 -58 ********** Masking position 9 Map Score: 7.25561 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 115 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 AATAATTAACATTAATAATTAATTTTATTAT 3 41 0 ATTATAATTA 0.96798 -49 TCCTAAATCAATTAATAATTAACATTAATAA 3 54 0 ATTATAATTA 0.96798 -36 AATAGCAAATATTAGTATTTATGCCAATTAC 4 17 0 ATTATATTTA 0.862562 -61 GGTGTGCTTTTTTGTTAAATAAAATATATTA 5 27 1 TTTGTAAATA 0.923046 -65 GCCTGTATTTATTGCTAAATAAGCGGTGAGC 7 101 0 ATTGTAAATA 0.939841 -200 TATATTTTAATTTAGTAATTATAAATATTTG 8 67 1 TTTATAATTA 0.958705 -99 CCTTTCGCTTTTTATTAAAAAATTAAAATTC 8 131 0 TTTATAAAAA 0.785814 -35 **** ****** Masking position 7 Map Score: 4.72726 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 165 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 GCTAGGTAATGCCTAGGGGTTTTAAACCTA 7 13 1 GCCTAGGGGT 0.994356 -288 TTGAGGACATGCTTACGGGTAGATCGCACG 7 182 1 GCTTACGGGT 0.99554 -119 ACAGAACTCGGCTTATGGGTGTCAGCTTAA 7 254 1 GCTTATGGGT 0.993203 -47 ********** Masking position 5 Map Score: 1.91657 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 2 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 ********** No masking Map Score: 1.37435e-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: 1.37435e-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: 1.37435e-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