AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_tpal_bbur_100.orf -o017_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 RTP00193 63 AE000520 #2 RTP00194 66 AE000520 #3 RTP01039 60 AE000520 #4 RTP00195 72 AE000520 #5 RTP00196 111 AE000520 #6 RTP00024 300 AE000520 #7 RBB00632 156 3615 #8 RBB00123 129 3615 #9 RBB00036 16 3615 #10 RBB00034 263 3615 Motif number 1 CAGGGTGGATTCGGCCTGGCGGAAAAGGTATAC 1 27 0 TCGGCGCGGA 0.753117 -37 CCAGGCCGAATCCACCCTGCGCGGCTAGCTGCG 1 41 1 TCCACGCGCG 0.981719 -23 CGCGCGGGTGTCGGCAGCGTGCGGTACAGGGGG 5 67 0 TCGGCGTGCG 0.992826 -45 CGCCGAGAATTCAGCGACGCGCGGGTGTCGGCA 5 84 0 TCAGCGCGCG 0.996783 -28 GACGGTAGCTTTGGCCGTGCGTGTGTTCCTTCA 6 48 1 TTGGCGCGTG 0.991594 -253 TTCGAGCGTATCAGCAATGAGCGTGTTGACAGT 6 171 0 TCAGCGAGCG 0.979202 -130 CCGTCCAGATTCCGCATCGCGTGATCTATCTCA 6 227 0 TCCGCGCGTG 0.976808 -74 TTATTGATTTTTGGCTAAGCGTGTTTATAGCTT 10 64 0 TTGGCGCGTG 0.991594 -200 ***** ***** Masking position 1 Map Score: 12.7241 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 10 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 GTGTGCGGTATGGCACTCTTTTTAAGGTGAGTGT 5 30 0 TGGTTTTTTA 0.735765 -82 CTTTACTTTTTAGGGGTGATTATTATTTTGTA 7 9 0 TAGTATTATT 0.76511 -148 TTCTTGATATTAACTTTGTTAATATTTATACTTT 7 39 0 TAATTTAATA 0.860714 -118 AAAAAACATTTAACAATTTTTATTATTTTAATTC 7 70 0 TAATTTTATT 0.952863 -87 TATTATAGCTTAAAACTTTTTTTAAAAAAAACAT 7 95 0 TAATTTTTTA 0.931692 -62 AAAATTGATTTAACAATATTAATAAGTTAAGTAT 7 128 1 TAATTTAATA 0.852391 -29 TATTATATACTAGTTTTGTTTATAAAAAAATGAT 8 17 1 TAGTTTTATA 0.906689 -113 AAGCTCAAATTAAATATCATTTTTTTATAAACAA 8 32 0 TAATATTTTT 0.839159 -98 ATATTTAATTTGAGCTTAATTTTTGTCTGCTAAT 8 49 1 TGATATTTTT 0.688249 -81 CTAATCTTTATGAATATGTTTTTTGTGATATATA 8 78 1 TGATTTTTTT 0.852793 -52 TTTATTTGTGTAAAACTGTTTAAAACAATTTGAA 10 14 0 TAATTTTAAA 0.677818 -250 TTAATTGTTTTAAACTTTTTTATTTGTGTAAAAC 10 32 0 TAATTTTATT 0.952865 -232 GATTTTTGGCTAAGCGTGTTTATAGCTTAATTGT 10 58 0 TAATTTTATA 0.958302 -206 TGTAAAATTATAACAATAATTTTACACTATAACA 10 184 1 TAATATTTTA 0.674419 -80 AATCAACCCATAACATTATTAATTCTTATGCACT 10 217 1 TAATTTAATT 0.844558 -47 *** * ****** Masking position 7 Map Score: 12.7076 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 74 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 AGCGCACCTAAGAGCACACTCACCTTAAAAAGAG 5 15 1 AAGCACCACC 0.993633 -97 AGAGTGCCATACCGCACACCGACCCCCTGTACCG 5 45 1 ACGCACCACC 0.99412 -67 GACCCCCTGTACCGCACGCTGCCGACACCCGCGC 5 65 1 ACGCACCCCG 0.969869 -47 CGCCCCTGAAGGAACACACGCACGGCCAAAGCTA 6 53 0 GAACACCACG 0.845126 -248 AACGGCCTTGAGAACACCCTTACCGTTATAGCGC 6 134 0 AAACACCACC 0.989884 -167 ACCCTGGTTGAGCGCATCCATACCTTCGAGCGTA 6 194 0 ACGCATCACC 0.978778 -107 GACGCCAAGCATAGCATTCGCACCAAGCTTTGAC 6 272 0 AAGCATCACC 0.977048 -29 TACAAAATAATAATCACCCCTAAAAAGTAA 7 7 1 AAATAACCCC 0.727513 -150 TACCCTTAAAATCAAAAACATACCATCATCCACC 10 100 1 ACAAAACACC 0.802474 -164 ATTTTACACTATAACAATCAACCCATAACATTAT 10 202 1 AAACAACCCC 0.964582 -62 * ***** * *** Masking position 6 Map Score: 9.79055 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 80 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 TACAAAATAATAATCACCCC 7 1 1 TACAAAATAA 0.679263 -156 AATATCAAGAATTAAAATAATAAAAATTGT 7 62 1 ATTAAAATAA 0.877827 -95 TAAAACTTTTTTTAAAAAAAACATTTAACA 7 89 0 TTTAAAAAAA 0.841197 -68 ACAAAACTAGTATATAATAAGGAGA 8 6 0 TATATAATAA 0.867673 -124 ACTAGTTTTGTTTATAAAAAAATGATATTT 8 25 1 TTTATAAAAA 0.858967 -105 TTTTTTGTGATATATAATAAATTGACCAGA 8 96 1 TATATAATAA 0.867673 -34 ATCATAATAAAGAGGT 9 1 1 ATCATAATAA 0.766189 -16 TGTAAAACTGTTTAAAACAATTTGAAGCT 10 10 0 TTTAAAACAA 0.940077 -254 AATAAAAAAGTTTAAAACAATTAAGCTATA 10 42 1 TTTAAAACAA 0.940077 -222 ATAGTGTAAAATTATAACAATAATTTTACA 10 180 1 ATTATAACAA 0.916611 -84 ATAATTTTACACTATAACAATCAACCCATA 10 199 1 ACTATAACAA 0.744877 -65 ********** Masking position 6 Map Score: 7.21639 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 55 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 CGCAGCTAGCCGCGCAGGGTGGATTCGG 1 46 0 TGCCGCGCGG 0.995474 -18 ACCTGACCGTACCCCTGCTGGATAGTGTCTT 2 10 1 TCCCCTGCGG 0.879809 -57 AGATGGACGATGGAGACCCCGGCTTTCTGTAT 3 18 0 TGAGACCCGG 0.927082 -43 ATCGTCCATCTTACCCCGCAGGAAATACAGGA 3 39 1 TACCCCGCGG 0.871027 -22 AATGCTTTTGTCCAGACCCCTGCTCAGTATTT 4 21 1 TCAGACCCTG 0.468462 -52 GAAGACGAGTTTGAGGCGCAGAACGA 4 57 1 TGAGGCGCGA 0.92802 -16 TGTCGGCAGCGTGCGGTACAGGGGGTCGGTGT 5 60 0 GGCGGTACGG 0.809306 -52 CGAGAATTCAGCGACGCGCGGGTGTCGGCAGC 5 82 0 GGACGCGCGG 0.983531 -30 ACGGTAGCTTTGGCCGTGCGTGTGTTCCTTCA 6 49 1 TGCCGTGCTG 0.965758 -252 AACTCTCcGGTAGACGCCCCTGAAGGAACACA 6 69 0 TGACGCCCTG 0.964899 -232 ACCgGAGAGTTCGAGGCGCTCGAAATGCGTGA 6 90 1 TGAGGCGCCG 0.936718 -211 CTTACCGTTATAGCGCTCCTTGTCTCCATCAC 6 118 0 TGCGCTCCTG 0.872238 -183 CTTATTGTCAGTGCCGTCCAGATTCCGCATCG 6 241 0 GGCCGTCCGA 0.801261 -60 * ******* ** Masking position 9 Map Score: 8.71846 Number of sites scoring better than the average of aligned sites = 2562 Number in coding regions = 812 Number in noncoding regions = 1750 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 GTTAAATGTTTTTTTTAAAAAAAGTTTTAA 7 90 1 TTTTTTAAAA 0.702846 -67 AATTTTATTATAGCTTAAAACTTTTTTTAA 7 104 0 TAGCTTAAAA 0.881538 -53 TAAACAAAACTAGTATATAATAAGGAGA 8 9 0 TAGTATATAA 0.712745 -121 TATACTAGTTTTGTTTATAAAAAAATGATA 8 22 1 TTGTTTATAA 0.890755 -108 AGCTTCAAATTGTTTTAAACAGTTTTACA 10 10 1 TTGTTTTAAA 0.802943 -254 ACTTTTTTATTTGTGTAAAACTGTTTAAAA 10 23 0 TTGTGTAAAA 0.961186 -241 ACAAATAAAAAAGTTTAAAACAATTAAGCT 10 39 1 AAGTTTAAAA 0.833911 -225 GCTGTTTACATAGTGTAAAATTATAACAAT 10 171 1 TAGTGTAAAA 0.968934 -93 TTGATTGTTATAGTGTAAAATTATTGTTAT 10 193 0 TAGTGTAAAA 0.968934 -71 ********** Masking position 6 Map Score: 6.22614 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 29 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 TTTCCTGCGGGGTAAGATGGACGATGGAGACCCC 3 30 0 GGAAGTGAGA 0.98437 -31 TTTGCCAGAAGACGAGTTTGAGGCGCAGAACGA 4 50 1 GAGAGTGAGC 0.985505 -23 GGCGTCTACCgGAGAGTTCGAGGCGCTCGAAATG 6 83 1 gGGAGTGAGC 0.997188 -218 GCTCAACCAGGGTGAGATAGATCACGCGATGCGG 6 215 1 GGGAGTGACA 0.989397 -86 AAAGATGCTGTGAGAGGTGGATGATGGTATGTTT 10 115 0 TGGAGTGAGA 0.98437 -149 ** *** * ** ** Masking position 8 Map Score: 0.976635 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 11 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 GGATAGTGTCTTTCACGGCTGGGTAGCAGTG 2 30 1 TTTCAGGCTG 0.884341 -37 CCCCTGTACCGCACGCTGCCGACACCCGCGC 5 68 1 GCACGTGCCG 0.952838 -44 TGGATGTCTCGCTCAGTGACGGTAGCTTTGG 6 31 1 GCTCATGACG 0.971157 -270 GTAAGGGTGTTCTCAAGGCCGTTGGAACTGT 6 145 1 TCTCAGGCCG 0.9916 -156 CTGTCAACACGCTCATTGCTGATACGCTCGA 6 172 1 GCTCATGCTG 0.986952 -129 TTTGACTTATTGTCAGTGCCGTCCAGATTCC 6 247 0 TGTCATGCCG 0.974854 -54 ***** ***** Masking position 4 Map Score: 1.29927 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 95 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 CGCAGCTAGCCGCGCAGGGTGGATTCG 1 47 0 AGCCGCGCAG 0.967414 -17 AGTATTTGCCAGAAGACGAGTTTGAGGCGC 4 46 1 AGAAGACGAG 0.923372 -27 AAAGACGCCGAGAATTCAGCGA 5 100 0 AGACGCCGAG 0.995673 -12 ACTCTCcGGTAGACGCCCCTGAAGGAACAC 6 70 0 AGACGCCCCT 0.898738 -231 TGCGTGATGGAGACAAGGAGCGCTATAACG 6 115 1 AGACAAGGAG 0.862981 -186 ATGGAGACGCCAAGCATAGCATTC 6 287 0 AGACGCCAAG 0.983055 -14 ********** Masking position 1 Map Score: 0.686518 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 47 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 8.47978e-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: 8.47978e-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: 8.47978e-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