AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icytR_ecoli_hinf_100.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 tsx 298 nucleoside channel; receptor of phage T6 and colicin K #2 cdd 129 cytidine/deoxycytidine deaminase #3 udp 298 uridine phosphorylase #4 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #5 deoC 257 2-deoxyribose-5-phosphate aldolase #6 deoA 126 thymidine phosphorylase #7 deoB 51 phosphopentomutase #8 deoD 56 purine-nucleoside phosphorylase #9 HI0280 214 uridine phosphorylase (udp) #10 HI0518 83 purine-nucleoside phosphorylase (deoD) #11 HI0519 98 transport protein, putative #12 HI0521 212 conserved hypothetical protein #13 HI1116 110 deoxyribose-phosphate aldolase (deoC) #14 HI1350 273 cytidine deaminase (cdd) Motif number 1 TCAAAAATGCGCGACGCATCGCAAATT 2 5 0 GCCGATCGCA 0.973371 -125 TAATTAATGAGATTCAGATCACATATAAAGCCA 2 58 1 GACAATCACA 0.994072 -72 TAGTCAGCATGCAACAAATCACATTGCCTGAAT 3 92 1 GCCAATCACA 0.986321 -207 CACCAAAAGTGATGCAAATCACATAAATCACCC 3 158 0 GACAATCACA 0.994072 -141 GCGTCATGGTGATGAGTATCACGAAAAAATGTT 3 213 1 GAAGATCACG 0.875398 -86 TGAATTTTTCGATCCGCCTCGCATCGTGAGCGG 4 12 0 GACGCTCGCA 0.946605 -144 TGAATTATTTGAACCAGATCGCATTACAGTGAT 5 115 1 GACAATCGCA 0.991694 -143 AACACACTTCGATACACATCACAATTAAGGAAA 5 165 0 GACAATCACA 0.994072 -93 TTGAAAACGTGAGGAAGATCACAGTTTTAGAAA 12 133 0 GAAAATCACA 0.979302 -80 TCAAATAAGTGATCAAGATCACAGTTTTAATGA 14 164 1 GAAAATCACA 0.979302 -110 ** ** ****** Masking position 9 Map Score: 16.1485 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 23 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 2 CGGTTTAGTCAGAAGAAGCAAAAAGACACTTTA 3 257 0 AAAAAGAAAA 0.979661 -42 CCTTCGGCATAAAAGGAAAAGAAG 5 2 0 AAAGAAAGAA 0.785749 -256 TTGTTATGTCACAAAAAGGATAAAACA 8 40 1 AAAAAGATAA 0.836752 -17 AATTTTTTCTAGAACAAGCGAAAAATAAA 9 7 0 AAAAAGGAAA 0.867288 -208 CTGATAACGAATAATAAGTAAAAAAAGAAGTGC 9 79 0 AAAAAGAAAA 0.979661 -136 TATCAGAAAAACAAAAAAGAAATAATGAAAATG 9 106 1 AAAAAAAAAT 0.80531 -109 TGAAAATGTTTGAAAGAGAAAAAAATTTTCTAA 9 131 1 TAAGAGAAAA 0.783619 -84 TATTTTCAAGAAAAGAAATAAAATATTTTTAGA 9 159 0 AAAAAAAAAA 0.938962 -56 CTTATTTTTAATAATGAATAAAAATGAATAAAG 10 53 0 AAAGAAAAAA 0.926658 -31 TTCATTATTAAAAATAAGGAAAAATT 10 68 1 AAAAAGAAAA 0.979661 -16 TTTTCATAAGAAAACAAGTAGAATAAGCCGAAT 11 45 1 AAAAAGAGAA 0.933248 -54 TCTCAACAAGATAAGGAATAAATAAA 13 4 0 AAAGAAAAAT 0.772589 -107 AATTTTTGCTACAATAGGTAAAACATAAATAAA 13 76 1 AAAAGGAAAA 0.867288 -35 AAACATAAATAAAAGGAGGAAAATA 13 96 1 AAAGAGAAAA 0.975345 -15 TTATTCAACTAGAAAAAGGAAATTATT 14 5 0 AAAAAGAAAT 0.928321 -269 * ** *** **** Masking position 4 Map Score: 16.6652 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 158 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 3 TAGTAAAAGTTTGCAACAAGGGCGAAAGTCAGTA 1 91 1 TCACAAGGCG 0.93862 -208 TCCCTTGCGGGAGTGAAAAAGGCGCAAATTGCGT 1 254 0 GTAAAAGGCG 0.883172 -45 CGTGAAACATACATCAAAAATGCGCGACGCATCG 2 17 0 ATAAAATGCG 0.922361 -113 TCTCCGTACCTTATAAAAATGTTGCGCAATGTTA 3 54 1 TTAAAAGTTG 0.755148 -245 ATGCTGACTATAGTTAACATTGCGCAACATTTTT 3 68 0 TTAACATGCG 0.91595 -231 TACAGAATTTTCATGAAAAGTGTGATGAATATTG 4 43 0 TTAAAATGTG 0.944699 -113 ACGCGCTATCTGCTAAAAATGTTGCCGATGTGAA 4 86 1 TTAAAAGTTG 0.755148 -70 ATCACGAAACTTCTTACAATGGCGCATCACCTTC 5 30 0 TTACAAGGCG 0.973095 -228 TAAGGAAATCTACTTACAAGTTTGCATCACTGTA 5 139 0 TTACAATTTG 0.700155 -119 CCTTTTTGTGACATAACAAAGGCGGAGTCAACGC 8 25 0 ATACAAGGCG 0.913681 -32 TATCTTAATCAATTAAAAAGTGCGGTAAAAAATG 10 13 1 ATAAAATGCG 0.922361 -71 ACGTTTACAAAAAGTGCGGTGAAAATTC 11 5 1 TCAAAATGCG 0.944944 -94 TAATGTTTATTTTCTAAAACTGTGATCTTCCTCA 12 123 1 TCAAAATGTG 0.878387 -90 ATTGTCTATTTTGTTACCATTGCGTACAATACGA 12 167 1 TTACCATGCG 0.899503 -46 GATTAAATATTCATTAAAACTGTGATCTTGATCA 14 173 0 TTAAAATGTG 0.944699 -101 * * **** **** Masking position 6 Map Score: 14.6776 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 601 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 4 AATATTTAGAAACGCAATTTGCGCCTTTTT 1 243 1 AACGCAATTT 0.74539 -56 AATCACATAAATCACCCTTCATTCTGCAGG 3 145 0 ATCACCCTTC 0.773635 -154 AAGAAGCAAAAAGACACTTTACCGAAGGGT 3 248 0 AAGACACTTT 0.722121 -51 TTCAATATTCATCACACTTTTCATGAAAAT 4 41 1 ATCACACTTT 0.96664 -115 TCTACTCCGCAACACACTTCGATACACATC 5 178 0 AACACACTTC 0.933054 -80 TAACTTTTTGACCGCACTTCTTTTTTTACT 9 66 1 ACCGCACTTC 0.974766 -149 GTCATTTTTTACCGCACTTTTTAATTGATT 10 19 0 ACCGCACTTT 0.984045 -65 GTAAAAAATGACCGCACTTTATTCATTTTT 10 37 1 ACCGCACTTT 0.984045 -47 GCGAATTTTCACCGCACTTTTTGTAAACGT 11 11 0 ACCGCACTTT 0.984045 -88 CGTGAGGAAGATCACAGTTTTAGAAAATAA 12 129 0 ATCACAGTTT 0.885689 -84 AGTGATCAAGATCACAGTTTTAATGAATAT 14 171 1 ATCACAGTTT 0.885689 -103 ********** Masking position 1 Map Score: 14.023 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 130 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 GATTGATAGTAAAAGTTTGCAACAAGGGCG 1 85 1 AAAAGTTTGC 0.940741 -214 GTAATGGGATAACAGTTTACGAACCCGTTG 2 91 0 AACAGTTTAC 0.884213 -39 AAAATTCTGTAACCGTTTTCACGCGCTATC 4 66 1 AACCGTTTTC 0.96551 -90 AAATCTACTTACAAGTTTGCATCACTGTAA 5 138 0 ACAAGTTTGC 0.768073 -120 TTGTTCTAGAAAAAATTTACGTGGAATTAT 9 23 1 AAAAATTTAC 0.750404 -192 TCAAAAAGTTAAACGTTTTCGGTTATAATT 9 47 0 AAACGTTTTC 0.962737 -168 TTTCTCTTTCAAACATTTTCATTATTTCTT 9 122 0 AAACATTTTC 0.916745 -93 TGAAAGAGAAAAAAATTTTCTAAAAATATT 9 141 1 AAAAATTTTC 0.870292 -74 TATTTTGAGTAACCGTTTGCATAATGTTTA 12 102 1 AACCGTTTGC 0.964837 -111 TACAATACGAAACCATTTTCAAAGGGGACG 12 191 1 AACCATTTTC 0.922755 -22 ********** Masking position 6 Map Score: 9.87901 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 181 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CATGGATGTAGTACGCCTGACGTGCCAGGCGAGG 4 125 1 GTGCCTGAGG 0.995848 -31 TCTTTTCCTTTTATGCCGAAGGTGATGCGCCATT 5 13 1 TTGCCGAAGG 0.968857 -245 GATGTTCACTTTGATCCTGATGCGTTTGCCACCA 5 61 1 TTTCCTGAGG 0.962631 -197 GTAAGATGCTTTACGCCTGATGCGCTGCGCTTAT 6 11 1 TTGCCTGAGG 0.99499 -116 GATACGTCTCGTAGGCCTGATAAGCGCAGCGCAT 6 30 0 GTGCCTGAAG 0.984944 -97 GTATCTACCCGTAGGCCGGATAAGGCGTAGACGC 6 59 1 GTGCCGGAAG 0.987411 -68 ATGAGGCGGCTTTTGCCGGATGCGTCTACGCCTT 6 80 0 TTGCCGGAGG 0.995819 -47 ** ****** * * Masking position 10 Map Score: 8.21647 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 143 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 TAGAACTGTGAAACGAAACATATTTTTGTGA 1 177 1 AAACGAAAAT 0.954036 -122 GCTCCTCTGTATACGAAATATTTAGAAACGC 1 227 1 ATACGAAAAT 0.903832 -72 ACATCACAATTAAGGAAATCTACTTACAAGT 5 152 0 TAAGGAAACT 0.812335 -106 TTTCTAGAACAAGCGAAAAATAAA 9 4 0 AAGCGAAAAT 0.812335 -211 GTTTTTCTGATAACGAATAATAAGTAAAAAA 9 87 0 TAACGAATAT 0.744935 -128 GATTTCGCCCTTAGGAAAAATCTTATTTTCA 9 184 0 TTAGGAAAAT 0.903832 -31 TTATTAAAAATAAGGAAAAATT 10 72 1 TAAGGAAAAT 0.954036 -12 TTTTATGATAAAACGGAATATAAAAGGTAAT 12 15 0 AAACGGAAAT 0.812335 -198 TTTTATCATAAAAGGAAAGATGCAAAAACAG 12 33 1 AAAGGAAAAT 0.954036 -180 AACATATCCTTAGGAAAAATATTAAAAATT 14 254 0 TTAGGAAAAT 0.903832 -20 ******** ** Masking position 7 Map Score: 6.21054 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 49 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 ACGATTTTGTGCGTCCCGCAACATCTTTCC 1 23 1 GCGTCCCGCA 0.91928 -276 GCGCCTTTTTCACTCCCGCAAGGGATTTTC 1 263 1 CACTCCCGCA 0.948925 -36 AATTTGCGATGCGTCGCGCATTTTTGATGT 2 11 1 GCGTCGCGCA 0.856165 -119 ATCTTTTATGCAGTCCTGCAGAATGAAGGG 3 131 1 CAGTCCTGCA 0.957284 -168 TACCCACCAAAAGTGATGCAAATCACATAA 3 165 0 AAGTGATGCA 0.699775 -134 ATACTCATCACCATGACGCAAATGCGTTGC 3 202 0 CCATGACGCA 0.888457 -97 AAACTTCTTACAATGGCGCATCACCTTCGG 5 28 0 CAATGGCGCA 0.902671 -230 CGTTTGCCACCACTGACGCATTCATTTGAA 5 83 1 CACTGACGCA 0.945368 -175 GATCGCATTACAGTGATGCAAACTTGTAAG 5 131 1 CAGTGATGCA 0.954281 -127 TCTCCGTACTCAGTGCTTCAAATTTAAATG 7 28 0 CAGTGCTTCA 0.743094 -24 ********** Masking position 4 Map Score: 3.52549 Number of sites scoring better than the average of aligned sites = 1651 Number in coding regions = 1556 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 9 AATTTGCGATGCGTCGCGCATTTTT 2 6 1 GCGATGCGTC 0.969728 -124 TATGTTTCACGCGTTGCATAATTAATGAGA 2 40 1 GCGTTGCATA 0.982349 -90 GGCGTTGCCTCATAATCATGT 2 119 0 GCGTTGCCTC 0.994859 -11 TGACGCAAATGCGTTGCATAAATTTACCCA 3 189 0 GCGTTGCATA 0.982349 -110 TTTGGGCGGAGCGTTGACTCCGCCTTTGTT 8 15 1 GCGTTGACTC 0.973635 -42 ********** Masking position 5 Map Score: 3.813 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 52 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TAGAACTGTGAAACGAAACATATTTTTGTG 1 177 1 AAACGAAACA 0.722758 -122 AGAAAAACAAAAAAGAAATAATGAAAATGT 9 110 1 AAAAGAAATA 0.9381 -105 TATTTTCAAGAAAAGAAATAAAATATTTTT 9 162 0 AAAAGAAATA 0.9381 -53 ATAATGAATAAAAATGAATAAAGTGCGGTC 10 46 0 AAAATGAATA 0.744718 -38 AAGATGCAAAAACAGAAATAATTTTGTCAG 12 49 1 AACAGAAATA 0.866958 -164 ACGGTTACTCAAAATAAATATGTTTTTGAT 12 88 0 AAAATAAATA 0.933282 -125 ACAGTTTTAGAAAATAAACATTATGCAAAC 12 116 0 AAAATAAACA 0.920243 -97 CAATGGTAACAAAATAGACAATTTTGAAAA 12 159 0 AAAATAGACA 0.706423 -54 ACCATAGTCAAAAATAAAGAATTTTTGCTA 13 57 1 AAAATAAAGA 0.81147 -54 CAATAGGTAAAACATAAATAAAAGGAGGAA 13 87 1 AACATAAATA 0.857443 -24 ********** Masking position 8 Map Score: 5.8611 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 70 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 GATTGTACTGACTTTCGCCCTTGTTGCAAAC 1 99 0 ACTTCGCCCT 0.886931 -200 TAGAAACGCAATTTGCGCCTTTTTCACTCCC 1 249 1 ATTTCGCCTT 0.941624 -50 TGCCGGATGCGTCTACGCCTTATCCGGCCTA 6 70 0 GTCTCGCCTT 0.986853 -57 GCGGAGCGTTGACTCCGCCTTTGTTATGTCA 8 20 1 GACTCGCCTT 0.981268 -37 TGAACGTGATGATTTCGCCCTTAGGAAAAAT 9 194 0 GATTCGCCCT 0.965059 -21 ATAATTGATAGTCTTAGCCTTGTTTGTTAAG 14 111 1 GTCTAGCCTT 0.920713 -163 **** ****** Masking position 4 Map Score: 0.729074 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 169 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TTTTGATGTATGTTTCACGCGTTGCATAAT 2 32 1 TGTTTCACGC 0.960036 -98 CAATGTGATTTGTTGCATGCTGACTATAGT 3 88 0 TGTTGCATGC 0.866558 -211 AATCGGCTCATCTTTTATGCAGTCCTGCAG 3 122 1 TCTTTTATGC 0.755888 -177 TAAACATGGATGTAGTACGCCTGACGTGCC 4 121 1 TGTAGTACGC 0.864688 -35 GTAAGATGCTTTACGCCTGATGCGCT 6 7 1 TGCTTTACGC 0.919888 -120 TGTTTTATCCTTTTTGTGAC 8 47 0 TGTTTTATCC 0.700627 -10 TTTATTTTTCGCTTGTTCTAGA 9 3 1 TATTTTTCGC 0.639251 -212 AATGGTTTCGTATTGTACGCAATGGTAACA 12 178 0 TATTGTACGC 0.902646 -35 TTTTGACTATGGTTTTACGCTCAATTACAA 13 40 0 GGTTTTACGC 0.919887 -71 ********** Masking position 10 Map Score: 0.630181 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 628 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 13 AAATGTTAAACCCTTCGGTAAAGTGTCTTT 3 239 1 CCCTTCGGTA 0.972132 -60 TCGTGATGTTCACTTTGATCCTGATGCGTT 5 57 1 CACTTTGATC 0.828057 -201 CTCCGCAACACACTTCGATACACATCACAA 5 174 0 CACTTCGATA 0.934288 -84 GATGATTTCGCCCTTAGGAAAAATCTTATT 9 188 0 CCCTTAGGAA 0.872685 -27 AACGTCCCCTTTGAAAATGGTTTCGT 12 197 0 CCCTTTGAAA 0.954319 -16 CTAATGCCCTCCCTTTGATATGGGTATTAT 14 43 1 CCCTTTGATA 0.974987 -231 ********** Masking position 5 Map Score: 1.06832 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 53 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 AACAAACTCGCAAGGTGAATTTTATTGGCG 5 220 1 CAAGGTGAAT 0.968835 -38 TGGCGACAAGCCAGGAGAATGAA 5 245 1 CCAGGAGAAT 0.963139 -13 CATAAGAAAACAAGTAGAATAAGCCGAATT 11 49 1 CAAGTAGAAT 0.93242 -50 CTTAACTAATCTAGGGGAATCAA 11 86 1 CTAGGGGAAT 0.963139 -13 TTTCCTTTTTCTAGTTGAATAATTGAGCTA 14 16 1 CTAGTTGAAT 0.93242 -258 ********** Masking position 3 Map Score: 0.0903867 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 37 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 GGAGCCTATTATAAAAATCATTGCTCACAA 1 202 0 ATAAAAATCA 0.904839 -97 TCCGTACCTTATAAAAATGTTGCGCAATGT 3 56 1 ATAAAAATGT 0.734901 -243 GATGCAAATCACATAAATCACCCTTCATTC 3 151 0 ACATAAATCA 0.716349 -148 CTTGTCGCCAATAAAATTCACCTTGCGAGT 5 225 0 ATAAAATTCA 0.776832 -33 AGTGCTTCAAATTTAAATGATCAGATCAGT 7 17 0 ATTTAAATGA 0.734911 -35 TTAATAATGAATAAAAATGAATAAAGTGCG 10 49 0 ATAAAAATGA 0.939283 -35 TATGTTTTTGATATAAATGAACTGACAAAA 12 70 0 ATATAAATGA 0.939282 -143 GTTCTATTCAATATAATTGATAGTCTTAGC 14 99 1 ATATAATTGA 0.849923 -175 ********** Masking position 5 Map Score: 1.19882 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 110 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826