AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___hpyl_reg_300.orf -o190_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01302 205 AE000511 #2 RHP00112 171 AE000511 #3 RHP00113 39 AE000511 #4 RHP01571 153 AE000511 #5 RHP00114 300 AE000511 Motif number 1 AAGAAGCAGTATTTTAGCTTTTTAATCCTTTAAAA 1 55 1 ATTGTTTTAA 0.964999 -151 AACTTCAATTTTTCAGTATTTTTAAAGGATTAAAA 1 74 0 TTTTTTTTAA 0.944688 -132 ATACTGAAAAATTGAAGTTTTTTAAAATTTGGAGT 1 90 1 ATTGTTTTAA 0.964954 -116 TTTTTTAAAATTTGGAGTTTTTTCTGGCTTTTAGG 1 107 1 TTTGTTTTCT 0.932969 -99 TTTTCTGGCTTTTAGGGGGTTTTAAATTCTTTTAA 1 126 1 TTTGTTTTAA 0.992646 -80 TTTAAATTCTTTTAAGGTATTCTAACAAGACTATA 1 146 1 TTTGTTCTAA 0.954897 -60 GACTATATCATTGAGATAGTTTTAAGGAAATTAAG 1 174 1 TTGTTTTTAA 0.843621 -32 GAGAATAAGTTTTAAAGTTTTTTAATTTTTTTATA 2 41 0 TTTGTTTTAA 0.991198 -131 CTTTTCTTTTTCTTAAGTTTTTTATTGATACAATT 2 101 1 TCTGTTTTAT 0.897018 -71 TTGAATTAAATCGTTTGTTTTTTAAATTTGGAATT 2 132 0 TCGGTTTTAA 0.930908 -40 ATGATTAATATTTTAGGATTTTTCATTATTCAAAC 4 14 0 TTTGTTTTCA 0.985538 -140 AAGGCTAGAATTTTGCGTTTTTTCATTTTTTTAAT 5 201 0 TTTGTTTTCA 0.985538 -100 TTAAACTCATTTTAGGGAATTTTAACATGCCTTAT 5 268 0 TTTGTTTTAA 0.992641 -33 *** * ****** Masking position 10 Map Score: 24.7909 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 450 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 TTTTAGCTTTTTAATCCTTTAAAAATACTGAA 1 66 1 TATCCTTTAA 0.97602 -140 AGGGGGTTTTAAATTCTTTTAAGGTATTCTAA 1 139 1 AATCTTTTAA 0.793435 -67 TTTGTTCCTTAATTTCCTTAAAACTATCTCAA 1 184 0 ATTCCTTAAA 0.969469 -22 TTTAACCCAAATGTCATTAAATGGAGGGGGT 2 10 1 ATTCATTAAA 0.918336 -162 AATTTGGAATTGTATCAATAAAAAACTTAAGA 2 111 0 TTTCAATAAA 0.627133 -61 AATTTTTCCTTAAATTTGAATTAA 2 158 0 TTTCCTTAAA 0.981088 -14 CCCATCACCTTGACTCATTTAAGA 3 3 0 TATCATTTAA 0.935177 -37 TGAATAATGAAAAATCCTAAAATATTAATCAT 4 17 1 AATCCTAAAA 0.730969 -137 TCCTAAAATATTAATCATTTACTTTAATCATT 4 31 1 TATCATTTAC 0.646588 -123 ATCATTTACTTTAATCATTTAATTTGTGTAAA 4 44 1 TATCATTTAA 0.935158 -110 CTAGCGTCAATCTCTCTTTAAACGCTCCTAAT 5 119 0 TTTCTTTAAA 0.888804 -182 TGCCCTTTAATATGCCCTTTAATGAGCGCTGA 5 162 0 TTCCCTTTAA 0.916222 -139 TTAATCCTCATTTGCCCTTTAATATGCCCTTT 5 174 0 TTCCCTTTAA 0.916222 -127 AACGCAAAATTCTAGCCTTAAATCTTTGATGA 5 217 1 TTGCCTTAAA 0.883292 -84 AGGCATGTTAAAATTCCCTAAAATGAGTTTAA 5 271 1 AATCCCTAAA 0.811619 -30 TAAAATCCTTAAACTCATTTTAG 5 288 0 AATCCTTAAA 0.969469 -13 * * ******** Masking position 11 Map Score: 18.4791 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 624 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 3 CAGTATTTTTAAAGGATTAAAAAGCTAAAAT 1 65 0 AAAGATTAAA 0.979864 -141 TAAAAATACTGAAAAATTGAAGTTTTTTAAA 1 85 1 GAAAATTGAA 0.827513 -121 GAATACCTTAAAAGAATTTAAAACCCCCTAA 1 137 0 AAAAATTTAA 0.961192 -69 AGGGGGTATAAAAAAATTAAAAAACTTTAAA 2 35 1 AAAAATTAAA 0.973162 -137 TTGTATCAATAAAAAACTTAAGAAAAAGAAA 2 103 0 AAAAACTTAA 0.823453 -69 TTTAAAAAACAAACGATTTAATTCAAATTTA 2 141 1 AAAGATTTAA 0.970793 -31 TTTGTTTGAATAATGAAAAATCCTAAAA 4 8 1 GAAAATGAAA 0.856817 -146 TGATTAAAGTAAATGATTAATATTTTAGGAT 4 30 0 AAAGATTAAT 0.860783 -124 TACACAAATTAAATGATTAAAGTAAATGATT 4 43 0 AAAGATTAAA 0.979864 -111 ATGAGGATTAAAAAAATGAAAAAACGCAAAA 5 195 1 AAAAATGAAA 0.932962 -106 TTCGTTTCATCAAAGATTTAAGGCTAGAATT 5 224 0 CAAGATTTAA 0.885921 -77 *** ******* Masking position 6 Map Score: 12.6994 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 285 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 ATTAAAAAGCTAAAATACTGCTTCTTTATT 1 51 0 TAAAATACTG 0.94457 -155 TTAATCCTTTAAAAATACTGAAAAATTGAA 1 76 1 AAAAATACTG 0.626473 -130 CTCCAAATTTTAAAAAACTTCAATTTTTCA 1 94 0 TAAAAAACTT 0.91923 -112 TAAAACCCCCTAAAAGCCAGAAAAAACTCC 1 120 0 TAAAAGCCAG 0.906241 -86 TAGAATACCTTAAAAGAATTTAAAACCCCC 1 140 0 TAAAAGAATT 0.863183 -66 ATAAAAAAATTAAAAAACTTTAAAACTTAT 2 42 1 TAAAAAACTT 0.91923 -130 ATTGTATCAATAAAAAACTTAAGAAAAAGA 2 105 0 TAAAAAACTT 0.91923 -67 TAAATTTGAATTAAATCGTTTGTTTTTTAA 2 142 0 TTAAATCGTT 0.650775 -30 ACAACCCTATTAAAAGCGTTGTTATAGATC 4 113 0 TAAAAGCGTT 0.940604 -41 TCGTCATCACTAAAATCAATGACGGGGCTA 5 31 1 TAAAATCAAT 0.584573 -270 GGGCTAAAACTAAAAGCGTGAGCAGGGCGA 5 55 1 TAAAAGCGTG 0.950609 -246 TTAGGAGCGTTTAAAGAGAGATTGACGCTA 5 120 1 TTAAAGAGAG 0.465157 -181 AAATGAGGATTAAAAAAATGAAAAAACGCA 5 193 1 TAAAAAAATG 0.796029 -108 TAAAATCCTTAAACTCATTT 5 291 0 TAAAATCCTT 0.94457 -10 ********** Masking position 5 Map Score: 14.2009 Number of sites scoring better than the average of aligned sites = 1280 Number in coding regions = 1134 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 CTTTAAAAATACTGAAAAATTGAAGTTTTTT 1 82 1 ACGAAAAATT 0.859094 -124 AGCCAGAAAAAACTCCAAATTTTAAAAAACT 1 105 0 AATCCAAATT 0.955145 -101 TTAATAGAACAAATCCAACTTGAACTTTTCT 2 77 1 AATCCAACTT 0.868537 -95 AACTTAAGAAAAAGAAAAGTTCAAGTTGGAT 2 89 0 AAGAAAAGTT 0.889242 -83 TTATTGATACAATTCCAAATTTAAAAAACAA 2 122 1 AATCCAAATT 0.954115 -50 CAAACGATTTAATTCAAATTTAAGGAAAAAT 2 150 1 AATCAAATTT 0.842863 -22 ATTCAAATTTAAGGAAAAATT 2 161 1 AAGAAAAATT 0.963078 -11 TTGTTTGAATAATGAAAAATCCTAAAATATT 4 12 1 AAGAAAAATC 0.859094 -142 AAAATGAAAAAACGCAAAATTCTAGCCTTAA 5 207 1 AAGCAAAATT 0.980853 -94 ** ******** Masking position 7 Map Score: 5.90378 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 303 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 TTTGTTCCTTAATTTCCTTAAAACTATC 1 188 0 CCTTATTCCT 0.987026 -18 TTTAACCCAAATGTCATTAAATGGAGG 2 6 1 CCCAATTCAT 0.938017 -166 AAACTTTAAAACTTATTCTCATTAATAGAACA 2 56 1 ACTTATTCAT 0.968594 -116 TTGTAACCACCCTTAATGTCATCGCCCTGCTC 5 74 0 CCTTATTCAT 0.991232 -227 TTTAAACGCTCCTAATGATCCTAAACAGCTTG 5 103 0 CCTAAGTCCT 0.923671 -198 TTATAATTTGACTTCGTTTCATCAAAGATTTA 5 235 0 ACTTCTTCAT 0.904669 -66 TAAAATCCTTAAACTCATTTTAGGGAAT 5 283 0 CCTTAATCAT 0.965388 -18 ***** * **** Masking position 9 Map Score: 4.58639 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 77 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ********** No masking Map Score: -3.30951e-14 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: -3.30951e-14 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: -3.30951e-14 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