AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imodE_ecoli_opreg_300.orf -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 b0762 128 orf, hypothetical protein #2 modA 166 molybdate-binding periplasmic protein; permease #3 moaA 300 molybdopterin biosynthesis, protein A #4 moaB 21 molybdopterin biosynthesis, protein B #5 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A Motif number 1 TTTGCGTGGCGTTCGTTTTCCGTCACAATAAGACTT 1 27 0 GGTTTTCGTC 0.98558 -102 CTTTTGTGCGGTCAGCTTTGCGTGGCGTTCGTTTTC 1 43 0 GGCTTTCGTC 0.990942 -86 CACAAAAGGGGAGTGCTTTTCTGTGCTTAGCGGTTA 1 71 1 GGCTTTCTGC 0.967367 -58 TTTCTCAACTTCCTGCTTTTCCTGCCGATATTTTTT 2 45 1 TGCTTTCCTC 0.911581 -122 TTTTCCTGCCGATATTTTTTCTTATCTACCTCACAA 2 61 1 GTTTTTCTTC 0.969291 -106 AATTTTCCCAGCAGTTATTGCTAACCTTTGTGAGGT 2 88 0 GTTATTCTAC 0.683096 -79 AAAGGACGATGCACGCTATGCCTCCCTGATGATGTA 3 20 1 GGCTATCCTC 0.943261 -281 AAGGGAAAATGGCGGTTTTACTTTGATATACATCAT 3 48 0 GGTTTTCTTA 0.906442 -253 GCGTGTAAATGAGATTTTTACCATCCACACTTTCGC 3 133 0 GTTTTTCCAC 0.959925 -168 CGCCCTGGTGGCAATCTTTACGAGCATTGTCACGGC 3 233 0 GTCTTTCGAA 0.802234 -68 GCGCCTGCGGGCGCTTTTTTTGTCTCCCTTTGAT 5 9 1 GGCTTTTTTC 0.888989 -292 GCCGATCGCTGTCGTTTTTACCAAACCACGGCGACT 5 266 0 GTTTTTCCAC 0.959934 -35 * ***** *** * Masking position 9 Map Score: 8.85791 Number of sites scoring better than the average of aligned sites = 1260 Number in coding regions = 1156 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 2 CGCAAAGCTGACCGCACAAAAGGGGAGTGCT 1 57 1 ACCGCAAAAA 0.834722 -72 TTTCTTATCTACCTCACAAAGGTTAGCAATA 2 78 1 ACCTCAAAAG 0.967993 -89 TCTACCTCTAAAGGACGATGCACG 3 4 1 ACCTCTAAGG 0.964937 -297 ACTTTGATATACATCATCAGGGAGGCATAGC 3 34 0 ACATCACAGG 0.971873 -267 CTATTTCGCTACAGAATAAGGGAAAATGGCG 3 70 0 ACAGAAAAGG 0.840965 -231 GAGCATTGTCACGGCCAAAGCACCGTATCAG 3 217 0 ACGGCCAAGC 0.886885 -84 AACGTCAAAAGGAGAGATCAG 4 2 1 ACGTCAAAGG 0.984803 -20 AGCAGCCAATACCGCATCAGGGATTTTCGTT 5 229 0 ACCGCACAGG 0.993903 -72 ACGGCGACTCACCTCAGCAGCCAATACCGCA 5 244 0 ACCTCACAGC 0.978132 -57 ****** **** Masking position 9 Map Score: 7.73198 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 645 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 TCCGAGTTAGTCGTTATATTGTCGCCTACA 2 123 1 TCGTTATATT 0.897513 -44 CCTTAATGTAACGTTATGTAGGCGACAATA 2 139 0 ACGTTATGTA 0.940379 -28 CACGATCATGACGCTATATACATGATTACA 3 101 1 ACGCTATATA 0.977203 -200 ATCCACACTTTCGCTATGTAATCATGTATA 3 117 0 TCGCTATGTA 0.98514 -184 TTCAAATTATTCGATGTATACAAGCCTATA 5 116 1 TCGATGTATA 0.880391 -185 CTATAGCAGTTCGCTATATAGGCTTGTATA 5 132 0 TCGCTATATA 0.987648 -169 ********** Masking position 5 Map Score: 4.89806 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 32 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 TTGTGACGGAAAACGAACGCCACGCAAAGC 1 35 1 AAACGAACGC 0.958324 -94 CGCCACGCAAAGCTGACCGCACAAAAGGGG 1 52 1 AGCTGACCGC 0.944978 -77 TTCCCTGAATGCCCGCTTAGTCGGGC 2 7 1 GAATGCCCGC 0.981365 -160 GAGAAAAAGAAAATGCCCGACTAAGCGGGC 2 21 0 AAATGCCCGA 0.949238 -146 CTCTAAAGGACGATGCACGCTATGCCTCCC 3 16 1 CGATGCACGC 0.906329 -285 GAGACAAAAAAAGCGCCCGCAGGCGC 5 7 0 AAGCGCCCGC 0.984531 -294 GGTTTGGTAAAAACGACAGCGATCGGCGGC 5 275 1 AAACGACAGC 0.916203 -26 ********** Masking position 5 Map Score: 2.93192 Number of sites scoring better than the average of aligned sites = 1730 Number in coding regions = 1625 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 TTTTACCATCCACACTTTCGCTATGTAATCA 3 123 0 CACACTTCGC 0.98916 -178 TGGTAAAAATCTCATTTACACGCTAGTATCG 3 146 1 CTCATTTCAC 0.898991 -155 ATAACCACTAAACACTCTAGCCTCTGCACCT 3 179 1 AACACTCAGC 0.881558 -122 ATAATTACTCCTCACTTACACGTAATACTAC 5 53 1 CTCACTTCAC 0.982915 -248 TTCATAATGGCTCACTCAAGCTTGCTCACGA 5 198 0 CTCACTCAGC 0.988983 -103 ACCACGGCGACTCACCTCAGCAGCCAATACC 5 247 0 CTCACCTAGC 0.975364 -54 ******* *** Masking position 4 Map Score: 2.64126 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 241 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 CCGTCACAATAAGACTTTTGCCAGGACATTGTT 1 10 0 AGATTTCCAG 0.993574 -119 ACGACTAACTCGGAATTTTCCCAGCAGTTATTGC 2 103 0 CGATTTCCAG 0.985843 -64 GCGTGTAAATGAGATTTTTACCATCCACACTTTC 3 135 0 GGATTTCCAT 0.915089 -166 AAAGCACCGTATCAGTTGACCCAGGTGCAGAGGC 3 198 0 ACATTACCAG 0.91508 -103 AATGCTCGTAAAGATTGCCACCAGGGCGAAGGAA 3 241 1 AGATGCCCAG 0.98297 -60 AAGCTTGCTCACGATTGATTCCAGTAACAAACCG 5 178 0 AGATGTCCAG 0.992249 -123 * ** ** * **** Masking position 6 Map Score: 0.977724 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 250 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 AGAATAGTCTCATGACTATATCTGGAGTTG 1 106 1 CATGACTATA 0.966655 -23 TCCTGCTTTTCCTGCCGATATTTTTTCTTA 2 55 1 CCTGCCGATA 0.985144 -112 ATAGCACGATCATGACGCTATATACATGAT 3 97 1 CATGACGCTA 0.967139 -204 GTTTAGTGGTTATGCCGATACTAGCGTGTA 3 162 0 TATGCCGATA 0.965633 -139 TCGATGTATACAAGCCTATATAGCGAACTG 5 126 1 CAAGCCTATA 0.952055 -175 ********** Masking position 9 Map Score: 2.25184 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 295 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 ********** No masking Map Score: -5.44113e-14 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: -5.44113e-14 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: -5.44113e-14 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