AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i200_ecoli_bsub_300.orf -o200_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 uvrC 62 excinuclease ABC, subunit C; repair of UV damage to DNA #2 uvrY 300 putative 2-component transcriptional regulator #3 uvrC 135 excinuclease ABC (subunit C) #4 trxA 300 thioredoxin Motif number 1 GGTTACGGTTTTTAAAAACGCTTTTGCGTCA 1 21 0 TTTAAAACGC 0.96121 -42 TCAGCAAAAATGAAAATCAGCCCGCTGAATA 2 58 0 TGAAAATAGC 0.812134 -243 CAAAAACGAGAGAAAAATCGAATACCCACCA 2 191 1 AGAAAAACGA 0.829097 -110 CTTTGAAACGTTAAAAATGGTGGGTATTCGA 2 208 0 TTAAAAAGGT 0.855011 -93 CAAAGTTGCAATAAAAACCGCTAATATACGA 2 234 1 ATAAAAACGC 0.97152 -67 CAATTGGCGAATAAAAAAAGCGATCCCTCAA 3 44 0 ATAAAAAAGC 0.976391 -92 TTTTAAAACCTGAAAAAGAGCGCCGGCATG 4 10 0 TGAAAAAAGC 0.971447 -291 TTTTTCAGGTTTTAAAACAGCTCCGGCAGGG 4 24 1 TTTAAAAAGC 0.967785 -277 CCCAATAATCATTAAAATGGTACGAAGCATA 4 94 0 ATTAAAAGGT 0.810737 -207 GATTTGTGTTTTAAAAAAAGAGCATATCCCA 4 153 1 TTAAAAAAGA 0.877291 -148 TATAAAAATGAGTAAACCGGCTGTGATCAGG 4 192 1 AGTAAACGGC 0.793343 -109 ATTTGTAAGCATTAAAATAGCGTGAACGAAT 4 231 1 ATTAAAAAGC 0.967785 -70 ******* *** Masking position 6 Map Score: 12.4839 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 641 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 2 CAATTTTTGTCACATTTCATCGTAGGGCTTACT 2 96 1 CCATTCACGT 0.935652 -205 GGCTTACCGGATCGTTTCACAGTAAGCCCTACG 2 116 0 ACGTTCAAGT 0.977994 -185 CACCATTTTTAACGTTTCAAAGTTGCAATAAAA 2 217 1 ACGTTCAAGT 0.977994 -84 TACATGCCAGAGCGATTCCGATTGAGGGATCGC 3 23 1 ACGATCCATT 0.928005 -113 AGCATAAGATCACATCTCCTCTTCACTGTCATG 4 67 0 CCATTCCCTT 0.959235 -234 TTAAAAAAAGAGCATATCCCATTCAACCATATA 4 163 1 ACATTCCATT 0.986556 -138 TTTTTAGTATAGCATCTCCCATTCGTTCACGCT 4 249 0 ACATTCCATT 0.986556 -52 ACTAAAAATCATCATTTCACATTGGAGGAATTC 4 274 1 ACATTCAATT 0.97884 -27 * *** *** *** Masking position 7 Map Score: 8.38509 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 58 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 TCACCAACGGCTTACCGGATCGTTTCACAGT 2 126 0 CTACCGGATC 0.987444 -175 CCGCTGCTTACATGCCAGAGCGATTCCGATT 3 15 1 CTGCCAGAGC 0.996811 -121 CATGCCGGCGCTCTTTTTCAG 4 1 1 CTGCCGGCGC 0.998625 -300 TTTACCATGCCCTGCCGGAGCTGTTTTAAAA 4 33 0 CTGCCGGAGC 0.998884 -268 * ********* Masking position 3 Map Score: 5.61923 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 83 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 GTTTCACAGTAAGCCCTACGATGAAATGTGAC 2 104 0 AAGCCTACAT 0.949756 -197 AGAAAAATCGAATACCCACCATTTTTAACGTT 2 201 1 AATCCCACAT 0.989534 -100 CGATCACTACAATTGCCCCAATAATCATTAAA 4 109 0 AATGCCCCAT 0.993169 -192 CAAATCTGATAATGGCCCCGATCACTACAATT 4 127 0 AATGCCCCAT 0.993131 -174 TATTGAATTCCTCCAATGTGAAATGAT 4 284 0 AATCCTCCAT 0.989531 -17 *** ***** ** Masking position 2 Map Score: 3.45325 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 19 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 ACATTAATTAACCCGAACAATACGGGCAAAA 2 23 0 ACCCGAACAT 0.957657 -278 ATGAAAATCAGCCCGCTGAATATGTAACATT 2 49 0 GCCCGCTGAT 0.862507 -252 CCAACGGCTTACCGGATCGTTTCACAGTAAG 2 123 0 ACCGGATCGT 0.974779 -178 CTGCTTACATGCCAGAGCGATTCCGATTGAG 3 18 1 GCCAGAGCGT 0.969431 -118 TTCCAGTTTAACACGAACGTTTGTTTTTCTC 3 84 0 ACACGAACGT 0.798841 -52 CATGCCGGCGCTCTTTTTCAGGTT 4 4 1 GCCGGCGCTT 0.969387 -297 ACCATGCCCTGCCGGAGCTGTTTTAAAACCT 4 30 0 GCCGGAGCTT 0.982415 -271 CTGATAATGGCCCCGATCACTACAATTGCCC 4 123 0 CCCCGATCAT 0.950024 -178 ********* * Masking position 11 Map Score: 2.17649 Number of sites scoring better than the average of aligned sites = 1429 Number in coding regions = 1362 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 CCCGAACAATACGGGCAAAAAACATTCATGAT 2 11 0 AGGGCAAAAA 0.978921 -290 CTACGATGAAATGTGACAAAAATTGACTTTAT 2 89 0 AGTGAAAAAA 0.94945 -212 TGGACAATCGAATTGACAAAAACGAGAGAAAA 2 175 1 ATTGAAAAAA 0.957727 -126 AACGTTTCAAAGTTGCAATAAAAACCGCTAAT 2 227 1 ATTGCATAAA 0.950233 -74 ATGGTTCACAATTGGCGAATAAAAAAAGCGAT 3 51 0 ATGGCAATAA 0.932522 -85 TTCGTGTTAAACTGGAAATAAAGGATTAAACA 3 98 1 ATGGAATAAA 0.950233 -38 * **** ***** Masking position 8 Map Score: 1.04459 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 179 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 ********** No masking Map Score: -1.16286e-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 8 ********** No masking Map Score: -1.16286e-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: -1.16286e-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