AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i206_nucleases_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ptr 175 protease III #2 ygdB 38 orf, hypothetical protein #3 ppdA 183 prepilin peptidase dependent protein A #4 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #5 ygdP 300 putative invasion protein #6 HI1316 300 H. influenzae predicted coding region HI1316 #7 HI1317 81 conserved hypothetical protein #8 HI1318 267 translation initiation factor 3 (infC) #9 HI1319 138 ribosomal protein L35 (rpL35) #10 HI1320 66 ribosomal protein L20 (rpL20) #11 HI1321 112 exodeoxyribonuclease V, beta chain (recB) Motif number 1 ACCGCGAAAAGGGTGTTTCGTCACTGGC 2 8 1 AAAGGGTGTT 0.948902 -31 AGGCGCTCCAAAGGTGCGAATAATAGCACAA 4 63 0 AAGGTGCGAT 0.920357 -88 CTATCCACAGAAAAGGTGAATAAAAACGGCT 5 131 1 AAAAGGTGAT 0.947807 -170 TAAACAGAGGAAGGGGTGGATAGCCGTTTTT 5 152 0 AAGGGGTGAT 0.967169 -149 TATCCTGGTAGTGGCGTATATAAAAATTT 6 9 1 TAGTGGCGAT 0.766051 -292 TGGTTAGAAGAAAAGGGGTATGAAATCCCAG 6 83 1 AAAAGGGGAT 0.891074 -218 CTTGTACCCGTAAATGCGGATTATCTCCAAA 6 131 0 TAAATGCGAT 0.695769 -170 ATGATGAAATAAGGGATGGTTTGATCTTTTG 6 186 0 AAGGGATGTT 0.633098 -115 AATACAAGGCGTATGCGGCCCCCA 6 287 0 ACAAGGCGAT 0.898785 -14 AGTCGTAGATTAAGGGCGTATCTGATACGCC 7 15 1 TAAGGGCGAT 0.97557 -67 CAGAGATAACAAAGGGCGTATCAGATACGCC 7 29 0 AAAGGGCGAT 0.992015 -53 ACTGCTTTTGAAAAGGCGATTTAATTTGCCT 9 101 1 AAAAGGCGTT 0.963039 -38 AAGTGCAAAAAAAGGACGCTTTTCAGCGTCC 11 40 0 AAAGGACGTT 0.879068 -73 ******** ** Masking position 11 Map Score: 12.402 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 673 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 2 GAATTTAATCTTGTGCTGCACGAGTCAGCC 1 90 0 TTGTGCTGCA 0.917549 -86 GTTCTTGTTATTTCGCTGAAAGAGAACAGC 4 119 0 TTTCGCTGAA 0.978904 -32 GAATATATTTTTTCGCTTCATCAATGATGA 6 210 0 TTTCGCTTCA 0.938849 -91 ATTTTGTTGCATAAGTGGTGT 8 2 1 TTTTGTTGCA 0.903655 -266 GTAAAAATCTTTTCGCTAAAAATAAAAGAT 8 87 0 TTTCGCTAAA 0.86803 -181 GAATTTTGCTGAGATTTTTCAGC 9 4 1 TTTTGCTGAG 0.930979 -135 AAACAAAAAGATTTGCTGAAAAATCTCAGC 9 18 0 ATTTGCTGAA 0.901005 -121 CAGCAAATCTTTTTGTTTAAGTTTGACTTA 9 30 1 TTTTGTTTAA 0.816332 -109 TAATCGTACGTTTTGCTTAAATAACGGC 10 9 0 TTTTGCTTAA 0.957057 -58 ********** Masking position 7 Map Score: 6.07292 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 504 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 GTGCTGTATAAAAATTGCGCAATCTATCC 1 6 1 GTAAAAATCG 0.89951 -170 ATTTAACGGAGGGTAAAAAAACCGACGCACACTG 3 39 0 GTAAAAAACG 0.957658 -145 TCCTGCAACGGCGTAAATAGTCCGGAAGATGCGC 3 105 1 GTAAATAGCG 0.948145 -79 ATGGAGCGAGGAGAAAAAAAGACGAGGGCCAGTT 3 151 0 GAAAAAAACG 0.977333 -33 AAGGTGCAGAGATAACAAAGGGCGTATCAGATAC 7 32 0 GAACAAAGCG 0.962647 -50 TATTAAAACCGTAAAAAAAGCACCGGCAGTAAAT 8 142 1 GAAAAAAGCC 0.941269 -126 AGAGATTCGTGTAAAAGAAGTTCGTTTAATTGAC 8 196 1 GAAAGAAGCG 0.966994 -72 TCCATCATAAGGCAAATTAAATCGCCTTTTCAAA 9 107 0 GAAATTAACG 0.709443 -32 AGTCATAAGTGCAAAAAAAGGACGCTTTTCAGCG 11 43 0 GAAAAAAGCG 0.991016 -70 * ******* ** Masking position 9 Map Score: 5.39869 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 246 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 TATAAAAATTGCGCAATCTATCCGCTTACTTTATG 1 17 1 GCCATTACGC 0.816603 -159 TTTTCTCCTCGCTCCATACTGCCGGC 3 168 1 GCCATCTCGG 0.97541 -16 AATGCGCGCCGCAGGTTTCAGGCGCTCCAAAGGTG 4 78 0 GCGTTCACGC 0.980862 -73 AACCTGCGGCGCGCATTTCAATCGCTGTTCTCTTT 4 96 1 GCCTTCACGC 0.978264 -55 GGGGTGGATAGCCGTTTTTATTCACCTTTTCTGTG 5 136 0 GCGTTTACAC 0.813905 -165 CAAAGTAGGCGCGGCTTACTTCTGGGATTTCATAC 6 100 0 GCGTTCTTGG 0.909362 -201 CAAGAACTTTGCGGTTTACTCTCAGGCGCAAAAGA 6 158 1 GCGTTCTCAG 0.957794 -143 TATCTGATACGCCCTTTGTTATCTCTGCACCTTAT 7 33 1 GCCTTTTCTC 0.818113 -49 GCGAGACTTTGCTCGTTCCTTGCGGGCAACAAATT 8 48 1 GCCTTCTCGG 0.993035 -220 TACGGTTTGGGCGATTTACTGCCGGTGCTTTTTTT 8 154 0 GCATTCTCGG 0.956371 -114 ** * ** ** *** Masking position 7 Map Score: 7.18178 Number of sites scoring better than the average of aligned sites = 1179 Number in coding regions = 1118 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 TTGCCGGATACCGTTAAAAGATATGTATATGATCCGCG 4 11 0 CTTAAGAGTT 0.955802 -140 TTCACCTTTTCTGTGGATAGAGTTGTGAAGAACTACGG 5 113 0 CTGAAGAGTA 0.990771 -188 CTGTTTATAACTCTGCACATAACTGTGAGTTATTCAAT 5 176 1 CTGAATAGTA 0.932998 -125 GTGTGTAATGCCCTGCAGAGAGTGGTTTACCGTCTTCC 5 222 1 CTGAAGAGTT 0.992897 -79 ACACTCTAATCGTTATAAAGAATGGTTAGAAGAAAAGG 6 61 1 CTAAAGAGTA 0.943207 -240 AGAAGTTTATCCATGCAAAGAACGGCTTGCCTTCATCT 6 250 0 CTGAAGAGCT 0.977279 -51 CAAACCGTATCAATGAAGAGATTCGTGTAAAAGAAGTT 8 180 1 CTGAAGAGTT 0.992897 -88 * ** * *** ** * Masking position 9 Map Score: 4.07208 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 19 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 TAAGCGGATAGATTGCGCAATTTTTATACAGCAC 1 7 0 GATTGAATAA 0.850928 -169 TGATAATGAATATTTTAAAATGTCTATATCGGGCTTAT 5 44 1 TATTAAATAA 0.974309 -257 CGAAAAAATATATTCAAGAATCATTAGATGAAGGCAAG 6 225 1 TATTAAATAA 0.974325 -76 GTTTATTCCTATTTTAAAAGATAAATAAGGTGCAGAG 7 55 0 TATTAAAAAA 0.918594 -27 GTATTCCTTCTATTGGTTAATAGTAAAAATCTTTTCGC 8 101 0 TATTTAAAAA 0.814371 -167 GAAGGAATACGATTATTAAAACCGTAAAAAAAGCACCG 8 129 1 GATTTAATAA 0.871663 -139 GGATTGTTTCTATTCAACAAGCCCTAGAA 8 249 1 TATTAAATAA 0.974325 -19 ATTAGTTCATTNTTAGAAAAATATTACATAGGAGATTA 10 35 1 TNTTAAATAA 0.974316 -32 CTAATGGCATTATTTTACAAAATTTAAAGTCATAAGTG 11 66 0 TATTAAATAA 0.974325 -47 **** * ** ** * Masking position 9 Map Score: 5.48519 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 4 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TACTTTATGATGCGCACCAGTCACGGACTG 1 43 1 TGCGCACCAG 0.969867 -133 GTCCGGAAGATGCGCCGAAGAAATAGAAAC 3 124 1 TGCGCCGAAG 0.982686 -60 GATTGAAATGCGCGCCGCAGGTTTCAGGCG 4 89 0 CGCGCCGCAG 0.991191 -62 TAGTGTGTAATGCCCTGCAGAGAGTGGTTT 5 220 1 TGCCCTGCAG 0.960792 -81 TTTGATCTTTTGCGCCTGAGAGTAAACCGC 6 168 0 TGCGCCTGAG 0.92312 -133 AAGGCGTATGCGGCCCCCAGAAGTTTATCC 6 276 0 CGGCCCCCAG 0.942827 -25 TCAAATTTGTTGCCCGCAAGGAACGAGCAA 8 56 0 TGCCCGCAAG 0.92465 -212 ********** Masking position 9 Map Score: 2.3482 Number of sites scoring better than the average of aligned sites = 1161 Number in coding regions = 1124 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 ACCGCGAAAAGGGTGTTTCGTCACT 2 4 1 GCAAAGGGTG 0.989487 -35 GGTTTCAGGCGCTCCAAAGGTGCGAATAATAG 4 68 0 GCCAAAGGTG 0.964066 -83 AACTCTATCCACAGAAAAGGTGAATAAAAACG 5 127 1 ACAAAAGGTG 0.959654 -174 GTTATAAACAGAGGAAGGGGTGGATAGCCGTT 5 155 0 GAAAGGGGTG 0.94529 -146 AGAATGGTTAGAAGAAAAGGGGTATGAAATCC 6 79 1 GAAAAAGGGG 0.879791 -222 ATTTTGTTGCATAAGTGGTGTGAATACTAT 8 9 1 GCAAGTGGTG 0.97616 -259 CGTTTAATTGACCAAAATGGTGAACAAGCAGG 8 218 1 ACAAATGGTG 0.943181 -50 ** ******** Masking position 6 Map Score: 2.12855 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 242 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 GATGGTTATATAAACATAGGCTGACTCGTG 1 72 1 TAAACATAGG 0.955837 -104 CTCGAAGAATTTAACGGAGGGTAAAAAAAC 3 51 0 TTAACGGAGG 0.96921 -133 TGCAGAGTTATAAACAGAGGAAGGGGTGGA 5 163 0 TAAACAGAGG 0.979906 -138 TATTTATCTTTTAAAATAGGAATAAAC 7 65 1 TTAAAATAGG 0.855965 -17 AGATTTTAACAGATGAGAACTAATG 11 98 0 TTAACAGATG 0.930506 -15 ********** Masking position 4 Map Score: 0.186793 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 38 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 ********** No masking Map Score: 6.87338e-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 11 ********** No masking Map Score: 6.87338e-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 12 ********** No masking Map Score: 6.87338e-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