AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_excinuclease_abc_ecoli_hinf_reg_100.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 0.980101 -300 GTGATGACAGTTTTATGGCAAGAGATGCCTGTT 1 49 0 TTTTATCAGA 0.784449 -252 GATGAACTGTTTTTTTATCCAGTATAATTTGTT 1 213 1 TTTTTTCAGT 0.964212 -88 ATTCAGAACGATTTTTTTCAGGAGACACGAAC 2 10 0 ATTTTTCGGA 0.980101 -244 TCTGGCCAGGTTTGTTTCCCGGAACCGAGGTCA 2 93 0 TTTGTTCGGA 0.907919 -161 GATTAAACGCTTTTTTGCCCGGTGGCATGGTGC 2 219 0 TTTTTTCGGT 0.980101 -35 AAAAACCTCATTTTTTATCTAAAAAAGTGCGGT 3 13 1 TTTTTTCAAA 0.903687 -141 AAAGTGCGGTTATTTTGCCTGAAATTTTTTAAA 3 36 1 TATTTTCGAA 0.898329 -118 TTTGCCTGAAATTTTTTAAAAGATCTATATATT 3 49 1 ATTTTTAAGA 0.828591 -105 AAGATCTATATATTTTAACTGGATATTTGCACA 3 68 1 TATTTTCGGA 0.973977 -86 GGATCCGCAAAATTTTAAAAAGTTAATCCACAA 4 36 0 AATTTTAAGT 0.687966 -265 AAAAACTTTAAATTTTTACTAGACAAAACTTAA 4 143 0 AATTTTCAGA 0.932782 -158 AAATTTAAAGTTTTTTTAATGAATTTGTGACAT 4 161 1 TTTTTTAGAA 0.801197 -140 TAAAACTTAGATTTTTGCCTGATCAATTTTACA 4 221 1 ATTTTTCGAT 0.887395 -80 TTGCCTGATCAATTTTACACAGTAAATATGCTA 4 235 1 AATTTTAAGT 0.689471 -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 0.983278 -69 ACAAACGGTTAATTATGACACAAATTGACCTGA 2 175 0 AATATGAAAA 0.976908 -79 ACAGATATTAAAATATGCGATAATGATCGCAAA 3 98 1 AATATGCAAA 0.988685 -56 AATAAATGTAAATTTTGCGATCATTATCGCATA 3 111 0 AATTTGCACA 0.924284 -43 AATAACTCAAAAGTATGAAATAAATGTAAATTT 3 129 0 AATATGAAAA 0.976902 -25 TTTACACAGTAAATATGCTAAAATAGGCATTAT 4 248 1 AATATGCAAA 0.988684 -53 CATTATTCAAAACTATCAAAAAACCGACCGCAC 4 275 1 AATATCAAAA 0.890479 -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 0.969273 -152 TTATGCCAACAAATTATACTGGATAAAAAA 1 223 0 AAATTATACT 0.867994 -78 TCGTCGTACTTAATTATGCCAACAAATTAT 1 236 0 TAATTATGCC 0.956324 -65 GGCAGGTATGTAATTTTACTCGTCGTACTT 1 255 0 TAATTTTACT 0.867994 -46 CACAAACGGTTAATTATGACACAAATTGAC 2 179 0 TAATTATGAC 0.771336 -75 AAAAGTGCGGTTATTTTGCCTGAAATTTTT 3 35 1 TTATTTTGCC 0.767767 -119 CACAGATATTAAAATATGCGATAATGATCG 3 97 1 AAAATATGCG 0.865878 -57 AAATAAATGTAAATTTTGCGATCATTATCG 3 115 0 AAATTTTGCG 0.968671 -39 TAACTTTTTAAAATTTTGCGGATCCCTTGT 4 44 1 AAATTTTGCG 0.968671 -257 GCCTAAAATTAAATTTTAATTTAAAATCAA 4 109 1 AAATTTTAAT 0.546235 -192 TTTTACACAGTAAATATGCTAAAATAGGCA 4 247 1 TAAATATGCT 0.847156 -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 TCCCCAAAGCAACGGCTTTTTTAACATTTGT 1 90 0 AACGGCTTTT 0.958881 -211 GTAATGGTACAATCGCGCGTTTACACTTATT 2 40 0 AATCGCCGTT 0.957775 -214 TACCATTACCAATAGCGCTTTTACTATGTTG 2 62 1 AATAGCCTTT 0.919371 -192 TTCCCGGATTAAACGCTTTTTTGCCCGGTGG 2 227 0 AAACGCTTTT 0.95279 -27 AAAAAAACCTCATTTTTTATCTAAAA 3 6 1 AACCTCTTTT 0.931825 -148 CAGGCAAAATAACCGCACTTTTTTAGATAAA 3 26 0 AACCGCCTTT 0.99499 -128 TCAAAAAACCGACCGCACTTT 4 290 1 GACCGCCTTT 0.985334 -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 CAGGCATCTCTTGCCATAAAACTGTCATCA 1 51 1 TTGCCATAAA 0.669561 -250 CTTACCGGGTTATCCCCAAAGCAACGGCTT 1 103 0 TATCCCCAAA 0.846479 -198 GAGTTTTATCTCGCCACAGAGTAAATTTTG 1 137 1 TCGCCACAGA 0.952087 -164 ACGGTTAATTATGACACAAATTGACCTGAA 2 174 0 ATGACACAAA 0.678764 -80 TAACTGGATATTTGCACAGATATTAAAATA 3 83 1 TTTGCACAGA 0.934874 -71 CTATCCACAGAGCCTGTGGAT 4 2 1 TATCCACAGA 0.984114 -299 TCCACAAAGTTATCCACAGGCTCTGTGGAT 4 13 0 TATCCACAGG 0.935382 -288 TTAAAAAGTTAATCCACAAAGTTATCCACA 4 25 0 AATCCACAAA 0.880234 -276 AAATCTAAGTTTTACACAGACTTAGCGATG 4 205 0 TTTACACAGA 0.961443 -96 CCTGATCAATTTTACACAGTAAATATGCTA 4 238 1 TTTACACAGT 0.797692 -63 ********** Masking position 8 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 TTGGGGATAACCCGGTAAGGCCGGAGTTTT 1 114 1 CCCGGTAAGG 0.994183 -187 AGGTTTGTTTCCCGGAACCGAGGTCACAAC 2 89 0 CCCGGAACCG 0.982043 -165 ACACAACACTCCGGGTAATGCATTCCAATA 2 133 1 CCGGGTAATG 0.984356 -121 AGCGTTTAATCCGGGAAAGGTGA 2 241 1 CCGGGAAAGG 0.994038 -13 ********** Masking position 7 Map Score: 2.36329 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 CCCGGTAAGGCCGGAGTTTTATCTCGCCAC 1 124 1 CCGGAGTTTT 0.994691 -177 ATGATTGACAGCGGAGTTTACGCTGTATCA 1 170 1 GCGGAGTTTA 0.965112 -131 AATGCATTACCCGGAGTGTTGTGTAACAAT 2 127 0 CCGGAGTGTT 0.990983 -127 GGCAAAATAACCGCACTTTTTTAGATAAAA 3 25 0 CCGCACTTTT 0.963065 -129 ********** Masking position 5 Map Score: 0.59974 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 80 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 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