AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i348_tpal_bbur_300.orf -o348_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 RTP00571 18 AE000520 #2 RTP00570 33 AE000520 #3 RTP00569 105 AE000520 #4 RTP00568 122 AE000520 #5 RTP00567 266 AE000520 #6 RBB00559 83 3615 Motif number 1 TTCTGAAAGGTCAAGGACCTGTGCTAACACG 3 13 0 TCAAGGACCG 0.950665 -93 AAAGAAGTGAGCGCGCGCGGTGCGGAATTTT 3 58 0 GCGCGCGCGT 0.885025 -48 ATTAAGCGCTTCAAGCGCCAGGTGGAGAAGG 4 43 0 TCAAGCGCCG 0.968051 -80 TCAGGGGAGGGTCGGTGGCTC 4 112 0 TCAGGGGAGG 0.988105 -11 AGGATCAgTCGCAGGCAACATTTTGTGGTAA 5 13 0 GCAGGCAACT 0.952784 -254 ATCCTGTGCTGCAGGGGCGAGCGTGTGCCGC 5 39 1 GCAGGGGCGG 0.997532 -228 GTCGAGCTGAACACGGGACTGCGCAAGAATG 5 153 1 ACACGGGACG 0.963259 -114 GGAGATGGATGCAGGGGACATTCTTGCGCAG 5 171 0 GCAGGGGACT 0.993835 -96 GGCGATTTTAGCGGGGGACTGCGAGACGGGT 5 225 0 GCGGGGGACG 0.995946 -42 TAAAATCGCCGCAGGGACCGGTGTACTCCCT 5 246 1 GCAGGGACCG 0.996123 -21 ********* * Masking position 2 Map Score: 16.944 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 336 Number in noncoding regions = 782 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 CTGAAAGGTCAAGGACCTGTGCTAACACGTG 3 11 0 AAGGACCGTG 0.91165 -95 GAGGTAAAAGAAGTGAGCGCGCGCGGTGCGG 3 64 0 AAGTGAGGCG 0.884739 -42 TCAGGGGAGGGTCGGTGGCTCAC 4 110 0 AGGGGAGGTC 0.990483 -13 CCTGTGCTGCAGGGGCGAGCGTGTGCCGCTC 5 41 1 AGGGGCGGCG 0.997142 -226 TACAGAGACTACTGGCGCGCTTCTTTCTCGT 5 120 0 ACTGGCGGCT 0.827855 -147 CGAGCTGAACACGGGACTGCGCAAGAATGTC 5 155 1 ACGGGACGCG 0.994974 -112 AGATGGATGCAGGGGACATTCTTGCGCAGTC 5 169 0 AGGGGACTTC 0.900919 -98 TCACCAATGTACTGGAGCGTCACACCCGTCT 5 202 1 ACTGGAGGTC 0.917074 -65 CGATTTTAGCGGGGGACTGCGAGACGGGTGT 5 223 0 GGGGGACGCG 0.985328 -44 AAATCGCCGCAGGGACCGGTGTACTCCCT 5 248 1 AGGGACCGTG 0.974244 -19 ******* *** Masking position 1 Map Score: 10.1069 Number of sites scoring better than the average of aligned sites = 1379 Number in coding regions = 445 Number in noncoding regions = 934 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 GGGAGTATAGCCTGCGTC 1 2 0 TAGCCTGCGT 0.964323 -17 GAAAGGTCAAGGACCTGTGCTAACACGTG 3 10 0 GGACCTGTGC 0.982357 -96 TAAAAGAAGTGAGCGCGCGCGGTGCGGAAT 3 61 0 GAGCGCGCGC 0.93046 -45 TCAGGGGAGGGTCGGTGGCTCACATAAC 4 105 0 GGGTCGGTGG 0.91431 -18 CCACAAAATGTTGCCTGCGAcTGATCCTGT 5 16 1 TTGCCTGCGA 0.823003 -251 GCCTGCGAcTGATCCTGTGCTGCAGGGGCG 5 28 1 GATCCTGTGC 0.953263 -239 CTGCAGGGGCGAGCGTGTGCCGCTCAACAC 5 47 1 GAGCGTGTGC 0.979982 -220 GATGATGTTTTAGTCGGTGTTGAGCGGCAC 5 63 0 TAGTCGGTGT 0.738622 -204 AGCTGAACACGGGACTGCGCAAGAATGTCC 5 157 1 GGGACTGCGC 0.988661 -110 ATTTTAGCGGGGGACTGCGAGACGGGTGTG 5 222 0 GGGACTGCGA 0.959872 -45 ATCGCCGCAGGGACCGGTGTACTCCCT 5 250 1 GGACCGGTGT 0.940524 -17 ********** Masking position 7 Map Score: 9.92841 Number of sites scoring better than the average of aligned sites = 1784 Number in coding regions = 518 Number in noncoding regions = 1266 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 ACAAGATATTGAAGAAAAATTCCGCACCGC 3 43 1 GAAGAAAAAT 0.94136 -63 TCTTTTACCTCAAGAAAAAAATGAGTGAAA 3 84 1 CAAGAAAAAA 0.984865 -22 TTCGCGAGTGGAAGAAAAAAGAA 4 4 0 GAAGAAAAAA 0.984865 -119 AGCGCCAGGTGGAGAAGGAAGGTATTATTC 4 31 0 GGAGAAGGAA 0.942373 -92 CAAAGACAAACGAGAAAGAAGCGCGCCAGT 5 111 1 CGAGAAAGAA 0.978129 -156 TATTATAACACAATAAAAAAGACAAAATTG 6 20 1 CAATAAAAAA 0.909638 -64 ********** Masking position 5 Map Score: 5.14902 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 70 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TCCTTGACCTTTCAGAACAAGATATTGAAGA 3 27 1 TTCAGAACAG 0.892379 -79 TGAAGAAAAATTCCGCACCGCGCGCGCTCAC 3 52 1 TTCCGCACGC 0.979278 -54 TTCTTTTTTCTTCCACTCGCGAATAATACCT 4 11 1 TTCCACTCCG 0.882137 -112 CGCTCGCCCCTGCAGCACAGGATCAgTCGCA 5 31 0 TGCAGCACGG 0.979454 -236 GGCGAGCGTGTGCCGCTCAACACCGACTAAA 5 54 1 TGCCGCTCAC 0.993153 -213 CTTTGGTGGCTGCCGATCTTGTGGATGATGT 5 85 0 TGCCGATCTG 0.942549 -182 CAGTCCCGTGTTCAGCTCGACGGTACAGAGA 5 143 0 TTCAGCTCAC 0.972786 -124 GAGACGGGTGTGACGCTCCAGTACATTGGTG 5 203 0 TGACGCTCAG 0.963441 -64 ******** ** Masking position 1 Map Score: 6.0356 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 213 Number in noncoding regions = 445 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CCACTCGCGAATAATACCTTCCTTCTCCAC 4 23 1 ATAATACCTT 0.969455 -100 TTATTGTGTTATAATACATTAAAGT 6 6 0 ATAATACATT 0.967107 -78 TAAAAAAGACAAAATTGATTTGTAAATATG 6 33 1 AAAATTGATT 0.861854 -51 AAATATGTTTATAATAGCTTATAATTAATT 6 56 1 ATAATAGCTT 0.969455 -28 ATAATAGCTTATAATTAATTTCATAAAA 6 66 1 ATAATTAATT 0.882711 -18 ********** Masking position 5 Map Score: 1.44626 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 16 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ********** No masking Map Score: -1.26233e-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 8 ********** No masking Map Score: -1.26233e-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 9 ********** No masking Map Score: -1.26233e-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