AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i036_tpal_bbur_100.orf -o036_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 RTP00413 137 AE000520 #2 RTP00194 66 AE000520 #3 RTP01039 60 AE000520 #4 RTP00195 72 AE000520 #5 RTP00196 111 AE000520 #6 RBB00167 154 3615 #7 RBB00847 84 3615 #8 RBB00136 96 3615 Motif number 1 AAAGGACGCCCTATCAGCACCTGCTGCGCACCCAACTCCC 1 13 1 CACACCGCGA 0.98976 -125 CTGCTGCGCACCCAACTCCCGTGCTGCGCACAAATGCGCA 1 33 1 CCCCCGGCGA 0.970154 -105 ACCGTCTACCCACACTTCACCGGCACAGCGCGCTAACTCT 1 87 1 CCCACCGCGG 0.907493 -51 ACCTGACCGTACCCCTGCTGGATAGTGTCTTTCA 2 5 1 GCCCCCGCAA 0.996325 -62 GTCGTGTACCCACTGCTACCCAGCCGTGAAAGACACTATC 2 31 0 CCACCCGCGA 0.998107 -36 TCTCCATCGTCCATCTTACCCCGCAGGAAATACAGGA 3 34 1 CAACCCGCAA 0.953407 -27 TAATGCTTTTGTCCAGACCCCTGCTCAGTATTTGCCAGAA 4 20 1 GCCCCCGCGA 0.998853 -53 CCATACCGCACACCGACCCCCTGTACCGCACGCTGCCGAC 5 51 1 CCCCCCGTGA 0.995583 -61 ACCGCACGCTGCCGACACCCGCGCGTCGCTGAATTCTCGG 5 75 1 GCCCCGGCGT 0.984207 -37 * * **** ** * * Masking position 10 Map Score: 16.988 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 132 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 CACCGTATTCAAAAAGAAAG 1 128 1 AAAAAGAAAG 0.974396 -10 CAACAATATACAGAAAGCCGGGGTCTC 3 8 1 ATACAGAAAG 0.983296 -53 TATTAATAGCATAAAAAAAGGGAAAACTGA 6 11 0 ATAAAAAAAG 0.990659 -144 CACACTCCTTATAATAAAAGAATATTTATA 6 130 0 ATAATAAAAG 0.950016 -25 AAAATCATGTATGAAAAAAGATTTTTTATT 7 34 1 ATGAAAAAAG 0.965718 -51 TTGATAATGCATAAAAAAAGACATTTTAAA 7 63 0 ATAAAAAAAG 0.990659 -22 CACATTATATATAAAGAAAGTAATAATACC 8 32 1 ATAAAGAAAG 0.990472 -65 TAAATTAATTAAACAAAAAGGTAAAAA 8 80 1 AAACAAAAAG 0.956496 -17 ********** Masking position 7 Map Score: 16.5212 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 13 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 3 GCACGGGAGTTGGGTGCGCAGCAGGTGCTGAT 1 25 0 TGGTGCGCGC 0.98331 -113 GTTATGCGCATTTGTGCGCAGCACGGGAGTTG 1 45 0 TTGTGCGCGC 0.98404 -93 CGGTGGAGAGTTAGCGCGCTGTGCCGGTGAAG 1 101 0 TAGCGCGCGT 0.977152 -37 AGTGTGCTCTTAGGTGCGCTCTTT 5 3 0 TGGTGCGCCT 0.993534 -109 CTTTTTAAGGTGAGTGTGCTCTTAGGTGCGCT 5 15 0 TAGTGTGCCT 0.980623 -97 GTACAGGGGGTCGGTGTGCGGTATGGCACTCT 5 45 0 TGGTGTGCGT 0.994732 -67 GCGGGTGTCGGCAGCGTGCGGTACAGGGGGTC 5 65 0 GAGCGTGCGT 0.948712 -47 * ******* ** Masking position 6 Map Score: 10.4142 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 13 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 CTTTCTTTTTGAATACGGTGGAGAG 1 123 0 TTTTTGAATA 0.821243 -15 ATCCTATCCATATTACAATATTAATAGCAT 6 29 0 TATTACAATA 0.898336 -126 TAGGATATTTTTTTTCAATATCTTTTACAA 6 53 1 TTTTTCAATA 0.888144 -102 TTTCAATATCTTTTACAAAAATTCTTTCAA 6 65 1 TTTTACAAAA 0.891084 -90 TTACAAAAATTCTTTCAAAAGCAATTCAAT 6 77 1 TCTTTCAAAA 0.882901 -78 TTATATCATTTTTTACAAAAAAGCCAAAAT 6 105 0 TTTTACAAAA 0.891084 -50 AAAAAAGACATTTTAAAATAAAAAATCTTT 7 50 0 TTTTAAAATA 0.73437 -35 ********** Masking position 7 Map Score: 6.95571 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 28 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TTCCCTTTTTTTATGCTATTAATATTGTAATATGG 6 17 1 TTATTATTAT 0.849449 -138 TTGAAAAAAAATATCCTATCCATATTACAATATTA 6 36 0 ATATTATTAT 0.930139 -119 AAAAAAGCCAAAATTGAATTGCTTTTGAAAGAATT 6 84 0 AAATAATTTT 0.869138 -71 TTTTTGTAAAAAATGATATAAATATTCTTTTATTA 6 114 1 AAATTATTAT 0.896924 -41 GAAATATTTAATTTTTATAATTGAAAAT 7 4 1 ATATAATTAT 0.82549 -81 ACATTTTAAAATAAAAAATCTTTTTTCATACATGA 7 38 0 ATAAAATTTT 0.728879 -47 TACTTTCTTTATATATAATGTGTTTAGGTTTTGAG 8 19 0 ATATAATTTT 0.93511 -78 TAGTATAATAATATACTATAGGTATTATTACTTTC 8 47 0 ATATTATTAT 0.967728 -50 **** *** *** Masking position 8 Map Score: 4.35935 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 8 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 ********** No masking Map Score: 1.65857e-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: 1.65857e-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: 1.65857e-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