AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifis_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 queA 92 synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase #2 tgt 55 tRNA-guanine transglycosylase #3 yajC 22 orf, hypothetical protein #4 secD 27 protein secretion; membrane protein, part of the channel #5 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #6 nrdB 233 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #7 yhdG 300 putative dehydrogenase #8 fis 25 site-specific DNA inversion stimulation factor; DNA-binding protein; a trans activator for transcription #9 HI0240 69 protein-export membrane protein (secD) #10 HI0241 107 conserved hypothetical protein #11 HI0244 300 tRNA-guanine transglycosylase (tgt) #12 HI0245 123 queuosine biosynthesis protein (queA) #13 HI0979 148 nitrogen fixation protein (nifR3) #14 HI1659 179 ribonucleoside-diphosphate reductase, alpha chain (nrdA) #15 HI1660 141 ribonucleoside diphosphate reductase, beta chain (nrdB) Motif number 1 AAGGCGTTTACGCCGCATCCGGCATCTCAATA 6 10 0 CGCCATCGGC 0.999527 -224 GCGGCGTAAACGCCTTATCCGGCCTACGGCTCG 6 27 1 CGCCATCGGC 0.999527 -207 GACGCTGGCGCGTCTTATCAGGCCTACAAACCG 6 58 0 CGTCATCGGC 0.998892 -176 GACGCGCCAGCGTCGCATCAGGCTCCGGGTGCC 6 77 1 CGTCATCGGC 0.998892 -157 AAGGCGTTCACGCTGCATCCGGCACCCGGAGCC 6 97 0 CGCTATCGGC 0.99461 -137 GCAGCGTGAACGCCTTATCCGGCCTACGGCTCG 6 114 1 CGCCATCGGC 0.999527 -120 GACGCTGGCGCGTCTTATCAGGCCTACAAATCC 6 146 0 CGTCATCGGC 0.998892 -88 GACGCGCCAGCGTCGCATCAGGCACAGGATGCG 6 165 1 CGTCATCGGC 0.998892 -69 AGGCATTTTACGCCGCATCCTGTGCCTGATGCG 6 178 0 CGCCATCTGT 0.941597 -56 CGGCGTAAAATGCCTTATCCGGCATTAAACTCC 6 196 1 TGCCATCGGC 0.99461 -38 **** *** *** Masking position 7 Map Score: 39.9648 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 56 Number in noncoding regions = 551 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 2 GGTTTAAAACGTTGGACTGTTTTTCTGACGTAGTGGAG 2 23 1 GTTTTTTTCA 0.882598 -33 CGTACCTGTTTTTGGAATTCTTTCCGCAATAGTTTCAT 5 267 0 TTTTCTTTCA 0.985295 -34 GCGGCGTATATTACGCATTTTTTGCACGAGATGAAAGG 7 241 0 TTATTTTTCG 0.738006 -60 GAATAACATTAAATTATTTTCCAGAGCCACGCATT 9 8 1 ATTTTTTTCA 0.927621 -62 AGTTTTCCTTTTCTTTTCTAACGCACAGAGC 9 49 0 TTTTCTTTCA 0.985298 -21 AATGAAGCAATTTATGGTATTTTACGCAAAATTTTTAA 10 57 1 TTTTTTTTCA 0.973008 -51 GTTGGTCATCATTATTCTACTTTGCCTGTTATTGAAAA 11 64 0 ATTTCTTTCG 0.945934 -237 AATACGGCATTTTGCCTTGCTTTGCAAAGTGAAATTTG 13 48 0 TTTTCTTTCA 0.984893 -101 TTTACGTTCCTTTCCTAGCAAGCCTAAA 13 131 0 TTTTCTTTCG 0.980084 -18 TTTACCGCACTTTTTCTTATTTTTCTAAATAAAAAATT 14 44 1 TTTTTTTTCA 0.973008 -136 AAATAAAAAATTTTAATTTTTATTCTCACAAAAACCGT 14 70 1 TTTTTTATCA 0.793224 -110 GACATAACGAATTAGGATACTTTCCTCAGTCTTTGATA 15 52 1 ATTTCTTTCA 0.959721 -90 GAACTTATCATTTATTTAGCTTTCCCTGTTTATCAGGG 15 95 0 TTTACTTTCG 0.839664 -47 *** * **** * * Masking position 11 Map Score: 15.3722 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 52 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 3 GTCTAGTGCCGGGGCGCTCTCCCTGCAACCTTTACC 1 34 0 GGCCTCCCGC 0.98562 -59 GAAGGAAAAAGTGGCTTTCGCGCACCTTAGGTCAGA 5 108 0 GGCTTCGCCC 0.995675 -193 TAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATC 6 17 0 AGCTTCGCGC 0.741852 -217 GGAGCCTGATGCGACGCTGGCGCGTCTTATCAGGCC 6 67 0 GGCCTCGCTC 0.98494 -167 TAGGCCGGATAAGGCGTTCACGCTGCATCCGGCACC 6 104 0 AGCTTCGCGC 0.992286 -130 TGTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCC 6 155 0 GGCCTCGCTC 0.98494 -79 ATGCCGGATAAGGCATTTTACGCCGCATCCTGTGCC 6 185 0 AGATTCGCGC 0.984287 -49 TGATTTTTATGAGTAATTATCGCACCACGCTCATTT 7 159 1 GGATTCGCCC 0.987758 -142 TGCAAAAAATGCGTAATATACGCCGCCTTGCAGTCA 7 253 1 GGATACGCGC 0.967012 -48 * * * ** *** ** Masking position 11 Map Score: 14.1968 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 410 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 AGGCGGGTAGTCTAGTGCCGGGGCGCTCTCCC 1 47 0 TCGTGCCGGG 0.966861 -46 TATTGAGATGCCGGATGCGGCGTAA 6 4 1 TGATGCCGGA 0.972043 -230 ACAAACCGAGCCGTAGGCCGGATAAGGCGTTT 6 34 0 CCAGGCCGGA 0.993833 -200 ACGGCTCGGTTTGTAGGCCTGATAAGACGCGC 6 52 1 TTAGGCCTGA 0.961582 -182 GCATCAGGCTCCGGGTGCCGGATGCAGCGTGA 6 91 1 CCGTGCCGGA 0.989337 -143 CAAATCCGAGCCGTAGGCCGGATAAGGCGTTC 6 121 0 CCAGGCCGGA 0.993833 -113 CGGCTCGGATTTGTAGGCCTGATAAGACGCGC 6 140 1 TTAGGCCTGA 0.961582 -94 TTACGCCGCATCCTGTGCCTGATGCGACGCTG 6 172 0 TCGTGCCTGA 0.973174 -62 CTGTTGGGAGTTTAATGCCGGATAAGGCATTT 6 203 0 TTATGCCGGA 0.983421 -31 ** ******** Masking position 8 Map Score: 11.8408 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 211 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 AACAGTTATTTTTAACAAATTTTTCTCTTCCC 5 54 1 TTACAAATTT 0.960994 -247 TTCCTGAGTTATCCACAAAGTTATGCACTTGC 5 141 1 ATCCAAAGTT 0.873641 -160 TGCGTAAATAATCGGCAAATTTACGTGCCTTT 7 33 0 ATGCAAATTT 0.91503 -268 TGCCGATTATTTACGCAAATTTGCGTGCCAAA 7 48 1 TTCCAAATTT 0.980726 -253 AATTGAGAACTTACTCAAATTTCTTTGAGTGT 7 99 1 TTCCAAATTT 0.980726 -202 TCTCAGAGGATTGGTCAAAGTTTGGCCTTTCA 7 216 1 TTGCAAAGTT 0.94984 -85 TTATGGTATTTTACGCAAAATTTTTAACTTAA 10 68 1 TTCCAAAATT 0.901174 -40 AATCATAAATTTAGTCATATTTTTATCCTTAG 11 104 1 TTGCATATTT 0.844986 -197 AGTGTATTTTTTAAACAAATTTCACTTTGCAA 13 33 1 TTACAAATTT 0.960994 -116 CGGTGAAAAATTCAACAAATTTTTACCGCACT 14 23 1 TTACAAATTT 0.960994 -157 ** * ******* Masking position 7 Map Score: 10.9124 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 44 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 AATTCCCTTAGGGAAAAATTTTAA 4 5 0 GGGAAAAATT 0.915857 -23 TCAATGGGAAGAGAAAAATTTGTTAAAAAT 5 61 0 GAGAAAAATT 0.951147 -240 TAACTCAGGAAGGAAAAAGTGGCTTTCGCG 5 122 0 AGGAAAAAGT 0.719123 -179 TTCATTCATAAAGAAAAATTGAGAACTTAC 7 83 1 AAGAAAAATT 0.91417 -218 ATTAATTTAAGTTAAAAATTTTGCGTAAAA 10 76 0 GTTAAAAATT 0.744444 -32 AAAAAAGCCTGTTAAAAAATACAGGCTTTG 11 241 0 GTTAAAAAAT 0.65052 -60 CCCCTCGGGGAAGATAAAATAACCAGCAAT 12 33 0 AAGATAAAAT 0.54153 -91 AAATGATCTCAAGAAAAAATCTCCCCTCGG 12 55 0 AAGAAAAAAT 0.87189 -69 CGAGCAGTTCGATATAAATTAGATTTAGGC 13 108 1 GATATAAATT 0.587115 -41 TCAAAGTGCGGTGAAAAATTCAACAAATTT 14 15 1 GTGAAAAATT 0.873771 -165 GAAAAAGTGCGGTAAAAATTTGTTGAATTT 14 30 0 GGTAAAAATT 0.820806 -150 TTAGAAAAATAAGAAAAAGTGCGGTAAAAA 14 42 0 AAGAAAAAGT 0.820779 -138 TATTTTTCTAAATAAAAAATTTTAATTTTT 14 61 1 AATAAAAAAT 0.741205 -119 TTTTTGTGAGAATAAAAATTAAAATTTTTT 14 74 0 AATAAAAATT 0.817587 -106 TAATGTGTTTGAGAAAAGATCGCAAGTAAT 14 156 0 GAGAAAAGAT 0.627975 -24 ********** Masking position 6 Map Score: 12.7408 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 420 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 7 TTCCGCGGCGCTGGTTTAAAACGT 2 5 1 GCGGCGCTGG 0.994061 -51 GGAGCCTGATGCGACGCTGGCGCGTCTTAT 6 73 0 GCGACGCTGG 0.992958 -161 TGTGCCTGATGCGACGCTGGCGCGTCTTAT 6 161 0 GCGACGCTGG 0.992958 -73 GCCACAATGCGTGGCTCTGGAAAATAATTT 9 21 0 GTGGCTCTGG 0.99171 -49 GCCACGCATTGTGGCTCTGTGCGTTAGAAA 9 36 1 GTGGCTCTGT 0.948749 -34 TTATTGAAAAGTAGCACTGGCTATTAGTAG 11 44 0 GTAGCACTGG 0.912971 -257 ********** Masking position 8 Map Score: 9.17841 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 728 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 ACTCAGACTAAAATAAGAGGCGGGTAGTCTA 1 65 0 AAATAAAGGC 0.907165 -28 AAATTTGCGTAAATAATCGGCAAATTTACGT 7 39 0 AAATAACGGC 0.975278 -262 ACAGAAATAAAGAGCTGACAGAACT 8 5 1 AAATAAGAGC 0.831881 -21 CATCAACTACTAATAGCCAGTGCTACTTTTC 11 38 1 TAATAGCAGT 0.705494 -263 TGCTACTTTTCAATAACAGGCAAAGTAGAAT 11 58 1 CAATAAAGGC 0.695412 -243 TTGCTCCAACGAATAAACAGTTCGAAGATTT 11 278 0 GAATAACAGT 0.782683 -23 TTAATCCCAAATGACCAGCATAATTGCTG 12 9 1 AAATGACAGC 0.92189 -115 GGGGAAGATAAAATAACCAGCAATTATGCTG 12 26 0 AAATAACAGC 0.971473 -98 AGGTTAAATAAAATAGGCGGTAAGTCTAGTT 12 93 0 AAATAGCGGT 0.908947 -31 AATGCCGTATTAATAGCCAGCCTTGTCGGTT 13 75 1 TAATAGCAGC 0.841075 -74 ACTTATTTAAAAATAAACGGTTTTTGTGAGA 14 93 0 AAATAACGGT 0.946968 -87 AAAGCTAAATAAATGATAAGTTCTATTTAAA 15 110 1 AAATGAAAGT 0.569583 -32 ****** **** Masking position 3 Map Score: 7.43204 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 505 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 ACCGAGCCGTAGGCCGGATAAGGCGTTTAC 6 32 0 AGGCCGGATA 0.942431 -202 TCCGAGCCGTAGGCCGGATAAGGCGTTCAC 6 119 0 AGGCCGGATA 0.942431 -115 TCATTGGGAAAGGCGAACTAAGCCCAATAT 10 32 0 AGGCGAACTA 0.829739 -76 CAGTTGCCGCTGTCGGGCTATTTCGTAGAT 11 155 0 TGTCGGGCTA 0.951233 -146 CAGCGGCAACTGGCGGACTATCTTAGTAGA 11 173 1 TGGCGGACTA 0.951511 -128 ACAACCGACAAGGCTGGCTATTAATACGGC 13 78 0 AGGCTGGCTA 0.978745 -71 AATTAGATTTAGGCTTGCTAGGAAAGGAAC 13 124 1 AGGCTTGCTA 0.926965 -25 TAATTCGTTATGTCGTGCTATCTTCCCCAT 15 36 0 TGTCGTGCTA 0.842664 -106 ********** Masking position 10 Map Score: 5.43601 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 396 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 GTGCGAGCAAGCTCACAAAAGGCACGTAAA 7 16 1 GCTCACAAAA 0.960073 -285 TAAAATTTACACTCAAAGAAATTTGAGTAA 7 109 0 ACTCAAAGAA 0.927312 -192 TGCGATAATTACTCATAAAAATCATCATAT 7 153 0 ACTCATAAAA 0.743918 -148 CTCTGAGATGGATCAAAGAATTGCATTTAA 7 194 0 GATCAAAGAA 0.896217 -107 GAAATAAAGAGCTGACAGAACT 8 14 1 GCTGACAGAA 0.771344 -12 ATCCGCCTCTGCTCAAAGAGCATTGAAAAT 11 202 1 GCTCAAAGAG 0.896915 -99 GAAAATATGATATCACAAAGCCTGTATTTT 11 226 1 TATCACAAAG 0.598546 -75 TCTTTTTGTCAATCAAAAAAAGTGTATTTT 13 13 1 AATCAAAAAA 0.834029 -136 TAATTTTTATTCTCACAAAAACCGTTTATT 14 83 1 TCTCACAAAA 0.890413 -97 TCAAGAATCAAATCAAAAAATTTATTACTT 14 133 1 AATCAAAAAA 0.834029 -47 ********** Masking position 5 Map Score: 2.82322 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 198 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 11 CAAGAAATCGCCGAACAGTTATTTTTAACA 5 41 1 CCGAACAGTT 0.96938 -260 GGCCTACAAACCGAGCCGTAGGCCGGATAA 6 41 0 CCGAGCCGTA 0.987179 -193 GCCTACAAATCCGAGCCGTAGGCCGGATAA 6 128 0 CCGAGCCGTA 0.987179 -106 TAAAAAATCTTCGAACTGTTTATTCGTTGG 11 274 1 TCGAACTGTT 0.888493 -27 TTGTCGGTTGTCGAGCAGTTCGATATAAAT 13 97 1 TCGAGCAGTT 0.969379 -52 ********** Masking position 4 Map Score: 2.0973 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 83 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 TTAAAATTTTTCCCTAAGGGAATTG 4 6 1 ATTTTTCCCT 0.888011 -22 GCGAAAGCCACTTTTTCCTTCCTGAGTTAT 5 123 1 CTTTTTCCTT 0.825377 -178 TAAGTTCTCAATTTTTCTTTATGAATGAAA 7 82 0 ATTTTTCTTT 0.760515 -219 GATTGGTCAAAGTTTGGCCTTTCATCTCGT 7 224 1 AGTTTGGCCT 0.560469 -77 AGTTTTCCTTTTCTTTTCTA 9 60 0 AGTTTTCCTT 0.948533 -10 TATTGGGCTTAGTTCGCCTTTCCCAATGAA 10 33 1 AGTTCGCCTT 0.814399 -75 TGTGTTTTCCTTATTAATTTAA 10 96 0 TGTTTTCCTT 0.805043 -12 TTAGTCATATTTTTATCCTTAGTATGATTA 11 114 1 TTTTATCCTT 0.74468 -187 CCGAGGGGAGATTTTTTCTTGAGATCATTT 12 55 1 ATTTTTTCTT 0.664162 -69 TTAATACGGCATTTTGCCTTGCTTTGCAAA 13 58 0 ATTTTGCCTT 0.962372 -91 TATAAATTAGATTTAGGCTTGCTAGGAAAG 13 120 1 ATTTAGGCTT 0.740318 -29 CTTATCATTTATTTAGCTTTCCCTGTTTAT 15 100 0 ATTTAGCTTT 0.626634 -42 TTTATTTATCCTTTAAATAGAAC 15 129 0 ATTTATCCTT 0.928661 -13 ********** Masking position 4 Map Score: 7.10347 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 578 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 13 AATTGCTTCATTGGGAAAGGCGAACTAAGC 10 39 0 TTGGGAAAGG 0.937758 -69 AAATCTCCCCTCGGGGAAGATAAAATAACC 12 39 0 TCGGGGAAGA 0.983567 -85 TCCCCATAAGTTGGGGAAGACAATAGGGGC 15 13 0 TTGGGGAAGA 0.990296 -129 TCCCCAACTTATGGGGAAGATAGCACGACA 15 26 1 ATGGGGAAGA 0.975838 -116 ********** Masking position 7 Map Score: 0.988737 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 14 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 CAACCTTTACCCCCTTTTGGATAGAATATA 1 15 0 CCCCTTTTGG 0.95166 -78 TATGTCGTACCTGTTTTTGGAATTCTTTCC 5 280 0 CTGTTTTTGG 0.806268 -21 GAGTGTGTCCTGTTGGGAGTTTAATG 6 218 0 GTCCTGTTGG 0.950901 -16 CGGTAACCATCTCTTGTCGGCATCAACTAC 11 18 1 CTCTTGTCGG 0.973721 -283 CCGCCAGTTGCCGCTGTCGGGCTATTTCGT 11 159 0 CCGCTGTCGG 0.979238 -142 TTAATAGCCAGCCTTGTCGGTTGTCGAGCA 13 84 1 GCCTTGTCGG 0.968206 -65 ********** Masking position 5 Map Score: 0.687037 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 229 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 TATTAATAATGAGGGAAATTTA 3 2 1 ATTATAATGA 0.932143 -21 CAAAATTTTCATTCATAAAGAAAAATTGAGA 7 76 1 ATTATAAAGA 0.905542 -225 AAAGAATTGCATTTAAAATGAGCGTGGTGCG 7 179 0 ATTAAAATGA 0.947053 -122 TTTAACTTAAATTAATAAGGAAAACACA 10 90 1 ATTATAAGGA 0.936824 -18 TTTGCCTGTTATTGAAAAGTAGCACTGGCTA 11 51 0 ATTAAAAGTA 0.840444 -250 TCTAGTTTGAATTGAAAATGATCTCAAGAAA 12 69 0 ATTAAAATGA 0.947053 -55 TAGATAACTTATTTAAAAATAAACGGTTTTT 14 99 0 ATTAAAAATA 0.773 -81 *** ******* Masking position 5 Map Score: 2.28872 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 94 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899