AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_tpal_bbur_300.orf -o190_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 RTP00381 170 AE000520 #2 RTP00767 126 AE000520 #3 RTP00768 96 AE000520 #4 RTP00769 125 AE000520 #5 RTP00770 34 AE000520 #6 RTP00771 204 AE000520 Motif number 1 GCTTTCAGGCGCTGGCGGATGCGTATTT 1 6 1 CAGCGTGCGG 0.881444 -165 TCACGGTGGTGGAGCGCGAGCGCAGCCACGTCG 1 116 1 GGGCGGGCGC 0.996015 -55 GTCTCGCGCCGAAAGGATAGCACC 2 113 1 GAAGGTGCAC 0.975223 -14 CGTCTGGGCGGAGCAAGGCCACTGCATTGGCG 3 10 1 GGGCAGCCAC 0.769011 -87 GACAGTCTCAAGGGGGTTCCCACCAGAAGGGGC 3 67 1 AGGGGTCCAC 0.925156 -30 GGTTCCCACCAGAAGGGGCGCGCCGA 3 81 1 AGAGGGGCGC 0.997172 -16 CCGGCGGGTGTGCACGGCCATGCGC 4 3 1 GGGGGGGCAC 0.99662 -123 TCTTTTTTGCAGAAGGAGTGCGCATGGCCGTGC 4 22 0 AGAGGGGCGC 0.997172 -104 CCTTCTGCAAAAAAGATGAGCGCGCACAGCACG 4 39 1 AAAGAGGCGC 0.960002 -87 ATGCGCGCATAGTACGTGCGCACTACCGGGTAC 4 87 1 AGACGGGCAC 0.98857 -39 GTTTTGAAAGAAGCGGAGGGCGGGGAAATCTGT 6 20 1 AACGGGGCGG 0.958284 -185 ATATCCGAGTCAAAGGCGAGCAGCACGGTGGGT 6 84 1 CAAGGGGCAG 0.963428 -121 CACGGGTGAGGAAAGGATCGCGGGTAGGGATAG 6 151 1 GAAGGTGCGG 0.970898 -54 ** *** * **** Masking position 11 Map Score: 19.2855 Number of sites scoring better than the average of aligned sites = 1000 Number in coding regions = 268 Number in noncoding regions = 732 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 AAAGCGTTTTCTCCGCCGTGTCCCGGTGTTCTTCTTTGTTCAGG 1 63 0 CTCTGCGGCC 0.999239 -108 GGGGGAGTATCTGTGGTTTGCTCAGGGCAACACCCTGTCGATGG 2 43 1 CTGTGTGGCC 0.978096 -84 GTGGATACGCCAATGCAGTGGCCTTGCTCCGCCCAGACG 3 6 0 CACTGCTGGC 0.942674 -91 TGGGAACCCCCTTGAGACTGTCTGGTAACTCCACTAAAGGTGGA 3 45 0 CTGTGCGTCC 0.992427 -52 GGCGGGTGTGCACGGCCATGCGCACTCCTTCTGCAAAAAAGATG 4 13 1 CACTGGCTCC 0.904724 -113 CAATGACGTACTTATCATTGACACTGCTGGCCGT 5 1 0 CTCTGCTGCT 0.972307 -34 CACCGTGCTGCTCGCCTTTGACTCGGATATCATCTACCTTCTTT 6 70 0 CTCTGCGGCC 0.999239 -135 CGATCCTTTCCTCACCCGTGCCTACGAAATCTCCCCACATCCCC 6 127 0 CTCTGCCGCC 0.998198 -78 TTCCTTACCGGTCACATGTGCTTCTTCCGTCCTATCC 6 178 0 CTCTCCGTCC 0.984256 -27 ** * ** * ** * * Masking position 9 Map Score: 10.1301 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 152 Number in noncoding regions = 371 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 CGGGACACGGCGGAGAAAACGCTTTCGTTTA 1 82 1 CGAGAAAACG 0.940756 -89 AGCGCAGCCACGTCGAGCACATTATCATTAA 1 134 1 CGCGAGCACA 0.990239 -37 ATTAAGGGAACGAAGAATACA 1 160 1 CGAGAATACA 0.782444 -11 CACAGATACTCCCCCAACAGGTGAAAACGAC 2 27 0 CCCCAACAGG 0.976067 -100 GTGTGTCTCGCGCCGAAAGGATAGCACC 2 109 1 CGCGAAAGGA 0.846835 -18 AAGGGGGTTCCCACCAGAAGGGGCGCGCCGA 3 76 1 CCCCAGAAGG 0.945567 -21 AAGATGAGCGCGCACAGCACGATCACCCAAT 4 51 1 CGACAGCACG 0.969071 -75 ACGGCCAGCAGTGTCAATGATA 5 2 1 CGCCAGCAGT 0.954711 -33 CTACGATCACCGACCAACAGATTTCCCCGCC 6 38 0 CGCCAACAGA 0.988721 -167 GGTCGGTGATCGTAGAAAAGAAGGTAGATGA 6 54 1 CGAGAAAAGA 0.922075 -151 GAGTCAAAGGCGAGCAGCACGGTGGGTTTCT 6 90 1 CGGCAGCACG 0.941863 -115 CTCCCCACATCCCCGCACACAGAAACCCACC 6 110 0 CCCGCACACA 0.839323 -95 ** ******** Masking position 1 Map Score: 11.919 Number of sites scoring better than the average of aligned sites = 1013 Number in coding regions = 291 Number in noncoding regions = 722 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 CTGAGCAAACCACAGATACTCCCCCAACAG 2 38 0 CACAGATACT 0.888563 -89 TCGGCGCGCCCCTTCTGGTGGGAACC 3 81 0 CGCCCCTTCT 0.994475 -16 CGGCCATGCGCACTCCTTCTGCAAAAAAGA 4 25 1 CACTCCTTCT 0.966465 -101 ACAGCACGATCACCCAATCTCTCATGCGCG 4 64 1 CACCCAATCT 0.889287 -62 CCCGGTAGTGCGCACGTACTATGCGCGCAT 4 87 0 CGCACGTACT 0.961434 -39 TCTTTCAAAACGCACCTACT 6 1 0 CGCACCTACT 0.988727 -204 TTTCCCCGCCCTCCGCTTCTTTCAAAACGC 6 18 0 CTCCGCTTCT 0.950303 -187 ********** Masking position 10 Map Score: 5.86736 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 89 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 CTCCGCCGTGTCCCGGTGTTCTTCTTTGTT 1 67 0 TCCCGGTGTT 0.9874 -104 TCGTTTAAGATCACGGTGGTGGAGCGCGAG 1 106 1 TCACGGTGGT 0.995805 -65 TTGCAGTCGTTCCGGGTCGTTTTCACCTGT 2 12 1 TCCGGGTCGT 0.971788 -115 ATAGCCATCGACAGGGTGTTGCCCTGAGCA 2 61 0 ACAGGGTGTT 0.947891 -66 CCAGACAGTCTCAAGGGGGTTCCCACCAGA 3 64 1 TCAAGGGGGT 0.93331 -33 GTTCCAGTGTACCCGGTAGTGCGCACGTAC 4 98 0 ACCCGGTAGT 0.959371 -28 AAGGCGAGCAGCACGGTGGGTTTCTGTGTG 6 96 1 GCACGGTGGG 0.970583 -109 ********** Masking position 5 Map Score: 5.67828 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 169 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 GGATGCGTATTTTGAAAACGGATACACGTC 1 27 1 TTTGAAAACG 0.967289 -144 GGGACACGGCGGAGAAAACGCTTTCGTTTA 1 83 1 GGAGAAAACG 0.986623 -88 TCCCCCAACAGGTGAAAACGACCCGGAACG 2 19 0 GGTGAAAACG 0.992784 -108 CTCCACTAAAGGTGGATACGCCAATGCAGT 3 31 0 GGTGGATACG 0.965687 -66 CCTCCGCTTCTTTCAAAACGCACCTACT 6 9 0 TTTCAAAACG 0.87147 -196 TAGGCACGGGTGAGGAAAGGATCGCGGGTA 6 147 1 TGAGGAAAGG 0.899153 -58 ********** Masking position 6 Map Score: 3.90379 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 124 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 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 Motif number 9 ********** 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