AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_excinuclease_abc_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 uvrB 300 DNA repair; excision nuclease subunit B #2 uvrA 253 excision nuclease subunit A #3 HI0249 153 excinuclease ABC, subunit A (uvrA) #4 HI1247 300 excinuclease ABC, subunit B (uvrB) Motif number 1 TTTTTTAACTGGTTAGATAAATG 1 1 1 TTTTTTCGGT 0.976066 -300 GTGATGACAGTTTTATGGCAAGAGATGCCTGTT 1 49 0 TTTTATCAGA 0.750827 -252 GATGAACTGTTTTTTTATCCAGTATAATTTGTT 1 213 1 TTTTTTCAGT 0.957097 -88 ATTCAGAACGATTTTTTTCAGGAGACACGAAC 2 10 0 ATTTTTCGGA 0.976066 -244 TCTGGCCAGGTTTGTTTCCCGGAACCGAGGTCA 2 93 0 TTTGTTCGGA 0.890877 -161 GATTAAACGCTTTTTTGCCCGGTGGCATGGTGC 2 219 0 TTTTTTCGGT 0.976066 -35 AAAAACCTCATTTTTTATCTAAAAAAGTGCGGT 3 13 1 TTTTTTCAAA 0.885966 -141 AAAGTGCGGTTATTTTGCCTGAAATTTTTTAAA 3 36 1 TATTTTCGAA 0.879747 -118 TTTGCCTGAAATTTTTTAAAAGATCTATATATT 3 49 1 ATTTTTAAGA 0.811384 -105 AAGATCTATATATTTTAACTGGATATTTGCACA 3 68 1 TATTTTCGGA 0.96874 -86 GGATCCGCAAAATTTTAAAAAGTTAATCCACAA 4 36 0 AATTTTAAGT 0.646517 -265 AAAAACTTTAAATTTTTACTAGACAAAACTTAA 4 143 0 AATTTTCAGA 0.919936 -158 AAATTTAAAGTTTTTTTAATGAATTTGTGACAT 4 161 1 TTTTTTAGAA 0.769667 -140 TAAAACTTAGATTTTTGCCTGATCAATTTTACA 4 221 1 ATTTTTCGAT 0.86711 -80 TTGCCTGATCAATTTTACACAGTAAATATGCTA 4 235 1 AATTTTAAGT 0.647688 -66 ****** * *** Masking position 6 Map Score: 16.8175 Number of sites scoring better than the average of aligned sites = 1251 Number in coding regions = 982 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 2 CGTCGTACTTAATTATGCCAACAAATTATACTG 1 232 0 AATATGCACA 0.985979 -69 ACAAACGGTTAATTATGACACAAATTGACCTGA 2 175 0 AATATGAAAA 0.980617 -79 ACAGATATTAAAATATGCGATAATGATCGCAAA 3 98 1 AATATGCAAA 0.990521 -56 AATAAATGTAAATTTTGCGATCATTATCGCATA 3 111 0 AATTTGCACA 0.935894 -43 AATAACTCAAAAGTATGAAATAAATGTAAATTT 3 129 0 AATATGAAAA 0.980611 -25 TTTACACAGTAAATATGCTAAAATAGGCATTAT 4 248 1 AATATGCAAA 0.99052 -53 CATTATTCAAAACTATCAAAAAACCGACCGCAC 4 275 1 AATATCAAAA 0.906737 -26 ** ***** * ** Masking position 10 Map Score: 8.15769 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 13 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 GCCACAGAGTAAATTTTGCTCATGATTGAC 1 149 1 AAATTTTGCT 0.970019 -152 TTATGCCAACAAATTATACTGGATAAAAAA 1 223 0 AAATTATACT 0.870873 -78 TCGTCGTACTTAATTATGCCAACAAATTAT 1 236 0 TAATTATGCC 0.957371 -65 GGCAGGTATGTAATTTTACTCGTCGTACTT 1 255 0 TAATTTTACT 0.870873 -46 CACAAACGGTTAATTATGACACAAATTGAC 2 179 0 TAATTATGAC 0.775779 -75 AAAAGTGCGGTTATTTTGCCTGAAATTTTT 3 35 1 TTATTTTGCC 0.772258 -119 CACAGATATTAAAATATGCGATAATGATCG 3 97 1 AAAATATGCG 0.868796 -57 AAATAAATGTAAATTTTGCGATCATTATCG 3 115 0 AAATTTTGCG 0.969431 -39 TAACTTTTTAAAATTTTGCGGATCCCTTGT 4 44 1 AAATTTTGCG 0.969431 -257 GCCTAAAATTAAATTTTAATTTAAAATCAA 4 109 1 AAATTTTAAT 0.552513 -192 TTTTACACAGTAAATATGCTAAAATAGGCA 4 247 1 TAAATATGCT 0.850411 -54 ********** Masking position 3 Map Score: 9.2824 Number of sites scoring better than the average of aligned sites = 769 Number in coding regions = 628 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 4 ACAAATGTTAAAAAAGCCGTTGCTTTGGGGA 1 90 1 AAAAGCCGTT 0.953034 -211 AATAAGTGTAAACGCGCGATTGTACCATTAC 2 40 1 AACGGCGATT 0.951344 -214 CAACATAGTAAAAGCGCTATTGGTAATGGTA 2 62 0 AAAGGCTATT 0.907658 -192 CCACCGGGCAAAAAAGCGTTTAATCCGGGAA 2 227 1 AAAAGCGTTT 0.945681 -27 TTTTAGATAAAAAATGAGGTTTTTTT 3 6 0 AAAAGAGGTT 0.921808 -148 TTTATCTAAAAAAGTGCGGTTATTTTGCCTG 3 26 1 AAAGGCGGTT 0.994326 -128 AAAGTGCGGTCGGTTTTTTGA 4 290 0 AAAGGCGGTC 0.983022 -11 **** ****** Masking position 2 Map Score: 4.82121 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 367 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 TGATGACAGTTTTATGGCAAGAGATGCCTG 1 51 0 TTTATGGCAA 0.631844 -250 AAGCCGTTGCTTTGGGGATAACCCGGTAAG 1 103 1 TTTGGGGATA 0.823637 -198 CAAAATTTACTCTGTGGCGAGATAAAACTC 1 137 0 TCTGTGGCGA 0.943917 -164 TTCAGGTCAATTTGTGTCATAATTAACCGT 2 174 1 TTTGTGTCAT 0.641535 -80 TATTTTAATATCTGTGCAAATATCCAGTTA 3 83 0 TCTGTGCAAA 0.924422 -71 ATCCACAGGCTCTGTGGATAG 4 2 0 TCTGTGGATA 0.981298 -299 ATCCACAGAGCCTGTGGATAACTTTGTGGA 4 13 1 CCTGTGGATA 0.924589 -288 TGTGGATAACTTTGTGGATTAACTTTTTAA 4 25 1 TTTGTGGATT 0.861593 -276 CATCGCTAAGTCTGTGTAAAACTTAGATTT 4 205 1 TCTGTGTAAA 0.954832 -96 TAGCATATTTACTGTGTAAAATTGATCAGG 4 238 0 ACTGTGTAAA 0.769574 -63 ********** Masking position 3 Map Score: 5.15775 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 499 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 6 GCAGTCACTGAACAGGCATCTCTTGCCATAAAA 1 39 1 AACGCTCTCT 0.97376 -262 CTTGCCATAAAACTGTCATCACTCATCTTGACA 1 60 1 AACGCTCACT 0.991876 -241 AAAATTACATACCTGCCCGCCCAACTCCTTCAG 1 268 1 ACCGCGCCCA 0.974229 -33 TGTTTCCCGGAACCGAGGTCACAACATAGTAAA 2 81 0 AACGGTCACA 0.984572 -173 GCATGGTGCTACCGGCGATCACAAACGGTTAAT 2 195 0 ACCGGTCACA 0.981449 -59 ACTATCAAAAAACCGACCGCACTTT 4 286 1 AACGCGCACT 0.990217 -15 *** * * ***** Masking position 1 Map Score: 3.05399 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 106 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 AAAACTCCGGCCTTACCGGGTTATCCCCAA 1 114 0 CCTTACCGGG 0.981579 -187 TGGCCAGGTTTGTTTCCCGGAACCGAGGTC 2 94 0 TGTTTCCCGG 0.978414 -160 TATTGGAATGCATTACCCGGAGTGTTGTGT 2 133 0 CATTACCCGG 0.985694 -121 TTAAACGCTTTTTTGCCCGGTGGCATGGTG 2 220 0 TTTTGCCCGG 0.962552 -34 TCACCTTTCCCGGATTAAACGCT 2 241 0 CCTTTCCCGG 0.994675 -13 ********** Masking position 4 Map Score: 3.63294 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 216 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 ********** No masking Map Score: -2.71184e-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: -2.71184e-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 10 ********** No masking Map Score: -2.71184e-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