AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i154_Hydrogenase_1_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 hyaA 300 hydrogenase-1 small subunit #2 b2997 188 putative hydrogenase subunit #3 b2998 118 orf, hypothetical protein #4 b3000 205 orf, hypothetical protein Motif number 1 GGGGATGTTTAGCCGGTTGCTAAACGAGTAA 1 25 0 AGCGGTTGCT 0.895465 -276 TTTTTCTTTTGGCCGGGCGGTGGGGATGTTT 1 46 0 GGCGGGCGGT 0.987244 -255 TCTGCACTGGCGCACGTCGCCAGAAAGTATT 1 157 0 CGCCGTCGCC 0.979462 -144 CCTTGCTACAGGGACGTCGCTTGCCGACCAT 1 233 1 GGGCGTCGCT 0.987827 -68 ACCGGCAGGACACCGGGCGCTTATGGTCGGC 1 255 0 CACGGGCGCT 0.965762 -46 ATCGCACGTCTCTCCTCCTTGCG 1 288 0 CGCCGTCTCT 0.97156 -13 ATGATACTGCGGCGGGGCGCTAAAACGAAGG 2 60 0 GGCGGGCGCT 0.972637 -129 TGTGGTAAATGGCGCATCGATCGCATTATTG 2 114 1 GGCCATCGAT 0.923986 -75 GATACGCGCTGGCGAATCGCTAAACTAGAAA 4 47 0 GGCAATCGCT 0.873543 -159 *** ******* Masking position 11 Map Score: 9.20826 Number of sites scoring better than the average of aligned sites = 2199 Number in coding regions = 2115 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 TTTTTCTTTTGGCCGGGCGGTGGGGATGTT 1 47 0 GGCCGGGCGG 0.978469 -254 TCTGCACTGGCGCACGTCGCCAGAAAGTAT 1 158 0 CGCACGTCGC 0.99434 -143 CCTTGCTACAGGGACGTCGCTTGCCGACCA 1 233 1 GGGACGTCGC 0.948719 -68 ACCGGCAGGACACCGGGCGCTTATGGTCGG 1 256 0 CACCGGGCGC 0.941964 -45 ATCGCACGTCTCTCCTCCTTGC 1 289 0 CGCACGTCTC 0.952122 -12 ATGATACTGCGGCGGGGCGCTAAAACGAAG 2 61 0 GGCGGGGCGC 0.997105 -128 TGTGGTAAATGGCGCATCGATCGCATTATT 2 114 1 GGCGCATCGA 0.931968 -75 GATACGCGCTGGCGAATCGCTAAACTAGAA 4 48 0 GGCGAATCGC 0.952914 -158 ********** Masking position 8 Map Score: 6.27908 Number of sites scoring better than the average of aligned sites = 3345 Number in coding regions = 3209 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 3 CCACCGCCCGGCCAAAAGAAAAATAGGTCCATTTT 1 54 1 GCAAAGAAAA 0.971968 -247 CATTTTTATCGCTAAAAGATAAATCCACACAGTTT 1 83 1 GCAAAGAAAC 0.990346 -218 TGAAACTTTTGCACAAAACAATACAAACTGTGTGG 1 107 0 GCAAAACAAA 0.971968 -194 CACGTGAGATGCTGAAAACGAAAGCTCATCCTTCT 1 185 0 GCAAAACAAC 0.990344 -116 TCTTAAACAAGCATGAAAAAATAGCGTGCGCAAAA 3 36 1 GCGAAAAAAC 0.978382 -83 CTTATGCTTTGCTTAAAAAAACACCAACTGAGGAG 4 125 1 GCAAAAAAAC 0.991985 -81 ** ***** * * * Masking position 7 Map Score: 4.65289 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 64 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 TCTGGCGACGTGCGCCAGTGCAGAAGGATG 1 164 1 TGCGCCAGTG 0.991265 -137 TGGTTTGCCTTGCTACAGGGACGTCGCTTG 1 226 1 TGCTACAGGG 0.894387 -75 CTCTCCTCCTTGCGACACCGGCAGGACACC 1 272 0 TGCGACACCG 0.978339 -29 ATCATGATACTGCGGCGGGGCGCTAAAACG 2 64 0 TGCGGCGGGG 0.956119 -125 ATGCGATCGATGCGCCATTTACCACACATT 2 110 0 TGCGCCATTT 0.843448 -79 ATGCCAGGTCTTCGCAACGGAATAACTATA 2 168 1 TTCGCAACGG 0.857557 -21 GAAACATTGTTTCGAAATTGAACGGTGGAA 4 21 0 TTCGAAATTG 0.63198 -185 AGTTTAGCGATTCGCCAGCGCGTATCCCGT 4 52 1 TTCGCCAGCG 0.983189 -154 GGCGGTTAAACGCGGCATCGTTGCACTCCT 4 155 0 CGCGGCATCG 0.911942 -51 ********** Masking position 3 Map Score: 4.46846 Number of sites scoring better than the average of aligned sites = 4359 Number in coding regions = 4121 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 5 TTTAGCAACCGGCTAAACATCCCCACCGCC 1 32 1 GGCTAAACAT 0.977868 -269 TATCTTTTAGCGATAAAAATGGACCTATTT 1 74 0 CGATAAAAAT 0.805383 -227 CCTGTAGCAAGGCAAACCATCGCTTCACGT 1 215 0 GGCAAACCAT 0.915855 -86 ATCATGATATCGATAACCATAATAAATGTG 2 86 1 CGATAACCAT 0.903011 -103 TTGCGATTGAGGCAAAATATATGCCAGGTC 2 148 1 GGCAAAATAT 0.924379 -41 CCTAAAATATCGCTATATATGACAATATAT 3 82 1 CGCTATATAT 0.943614 -37 TCACCTCATTCGCTATATATTGTCATATAT 3 96 0 CGCTATATAT 0.943614 -23 CGCGTTTAACCGCCAAAGATTTCCCACAAG 4 171 1 CGCCAAAGAT 0.907451 -35 ********** Masking position 5 Map Score: 4.02251 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 494 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 6 ACCTATTTTTCTTTTGGCCGGGCGGTGGGG 1 52 0 CTTTTGGCCG 0.953779 -249 CGTAGTGAAACTTTTGCACAAAACAATACA 1 117 0 CTTTTGCACA 0.985527 -184 AAAGCTCATCCTTCTGCACTGGCGCACGTC 1 170 0 CTTCTGCACT 0.975246 -131 TACACTAATGCTTCTTCCCTTCGTTTTAGC 2 43 1 CTTCTTCCCT 0.932124 -146 CAAAGAACGACTTTTGCGCACGCTATTTTT 3 52 0 CTTTTGCGCA 0.982828 -67 TAAGCACGTATTTTTGCCCAGTTTTTCGTC 4 99 0 TTTTTGCCCA 0.959573 -107 ********** Masking position 5 Map Score: 3.4109 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 275 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 TAAACGAGTAAAAGAGAAGGAATTC 1 6 0 AAAGAGAAGG 0.890252 -295 CCGGCCAAAAGAAAAATAGGTCCATTTTTA 1 61 1 GAAAAATAGG 0.835707 -240 TATTGTTAATAAAGCGTAGTGAAACTTTTG 1 131 0 AAAGCGTAGT 0.83249 -170 TGAGATGCTGAAAACGAAAGCTCATCCTTC 1 186 0 AAAACGAAAG 0.884971 -115 CATCTCACGTGAAGCGATGGTTTGCCTTGC 1 209 1 GAAGCGATGG 0.969055 -92 ACGAAGGGAAGAAGCATTAGTGTAATTAAT 2 37 0 GAAGCATTAG 0.893392 -152 GCGGGGCGCTAAAACGAAGGGAAGAAGCAT 2 50 0 AAAACGAAGG 0.947445 -139 AAACAAGCATGAAAAAATAGCGTGCGCAAA 3 40 1 GAAAAAATAG 0.597218 -79 CGCTAAACTAGAAACATTGTTTCGAAATTG 4 31 0 GAAACATTGT 0.680373 -175 TTTTTTAAGCAAAGCATAAGCACGTATTTT 4 115 0 AAAGCATAAG 0.884971 -91 ********** Masking position 3 Map Score: 4.4463 Number of sites scoring better than the average of aligned sites = 2523 Number in coding regions = 2300 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 8 ********** No masking Map Score: -9.56801e-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: -9.56801e-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 10 ********** No masking Map Score: -9.56801e-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