AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifis_ecoli_bsub_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 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 secF 125 protein-export membrane protein #10 yrvB 38 yrvB #11 yrzD 115 yrzD #12 yrbF 33 similar to hypothetical proteins #13 tgt 26 tRNA-guanine transglycosylase #14 queA 222 S-adenosylmethionine tRNA ribosyltransferase #15 ruvB 250 Holliday junction DNA helicase #16 ruvA 138 Holliday junction DNA helicase #17 bofC 47 bofC #18 csbX 70 alpha-ketoglutarate permease #19 yrbE 237 similar to opine catabolism Motif number 1 AAGGCGTTTACGCCGCATCCGGCATCTCAATA 6 10 0 CGCCATCGGC 0.999347 -224 GCGGCGTAAACGCCTTATCCGGCCTACGGCTCG 6 27 1 CGCCATCGGC 0.999347 -207 GACGCTGGCGCGTCTTATCAGGCCTACAAACCG 6 58 0 CGTCATCGGC 0.997977 -176 GACGCGCCAGCGTCGCATCAGGCTCCGGGTGCC 6 77 1 CGTCATCGGC 0.997977 -157 AAGGCGTTCACGCTGCATCCGGCACCCGGAGCC 6 97 0 CGCTATCGGC 0.995775 -137 GCAGCGTGAACGCCTTATCCGGCCTACGGCTCG 6 114 1 CGCCATCGGC 0.999347 -120 GACGCTGGCGCGTCTTATCAGGCCTACAAATCC 6 146 0 CGTCATCGGC 0.997977 -88 GACGCGCCAGCGTCGCATCAGGCACAGGATGCG 6 165 1 CGTCATCGGC 0.997977 -69 AGGCATTTTACGCCGCATCCTGTGCCTGATGCG 6 178 0 CGCCATCTGT 0.967248 -56 CGGCGTAAAATGCCTTATCCGGCATTAAACTCC 6 196 1 TGCCATCGGC 0.990972 -38 AGCCTGAGGCCGCAAAATCTGGCACAGTATATC 15 78 1 CGCAATCGGC 0.992574 -173 AGACAGGAGACGCTGGATCATGTTCTTCTGTAC 15 165 1 CGCTATCTGT 0.819814 -86 **** *** *** Masking position 7 Map Score: 44.9627 Number of sites scoring better than the average of aligned sites = 808 Number in coding regions = 238 Number in noncoding regions = 570 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 GGGAGAGCGCCCCGGCACTAGACTACCCGCCT 1 47 1 CCCGGCACTA 0.801245 -46 TTACGCCGCATCCGGCATCTCAATA 6 4 0 TCCGGCATCA 0.985594 -230 AAACGCCTTATCCGGCCTACGGCTCGGTTTGT 6 34 1 TCCGGCCTAG 0.988632 -200 GCGCGTCTTATCAGGCCTACAAACCGAGCCGT 6 52 0 TCAGGCCTAA 0.954093 -182 TCACGCTGCATCCGGCACCCGGAGCCTGATGC 6 91 0 TCCGGCACCG 0.97724 -143 GAACGCCTTATCCGGCCTACGGCTCGGATTTG 6 121 1 TCCGGCCTAG 0.988632 -113 GCGCGTCTTATCAGGCCTACAAATCCGAGCCG 6 140 0 TCAGGCCTAA 0.954093 -94 CAGCGTCGCATCAGGCACAGGATGCGGCGTAA 6 172 1 TCAGGCACAA 0.885086 -62 AGGCACAGGATGCGGCGTAAAATGCCTTATCC 6 184 1 TGCGGCGTAA 0.776402 -50 AAATGCCTTATCCGGCATTAAACTCCCAACAG 6 203 1 TCCGGCATTA 0.940429 -31 TTTTGATGAGGCCTCCTGTTCTCAAA 13 9 0 TGAGGCCTCG 0.890727 -18 AAAAATATCTCCCGGCATCTTGCCGACAAAAT 14 70 0 CCCGGCATCG 0.969375 -153 TGCCAGATTTTGCGGCCTCAGGCTTTGCTCTA 15 70 0 TGCGGCCTCG 0.969118 -181 GGCCGCAAAATCTGGCACAGTATATCGGGCAG 15 85 1 TCTGGCACAA 0.70406 -166 GTACGGGCCGCCCGGACTCGGAAAAACAACGC 15 194 1 CCCGGACTCA 0.725783 -57 ********* * Masking position 5 Map Score: 18.2911 Number of sites scoring better than the average of aligned sites = 1446 Number in coding regions = 1031 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 CTCAGACTAAAATAAGAGGCGGGTAGTCTAG 1 64 0 AAAAGAGGCG 0.788209 -29 CAACGTTTTAAACCAGCGCCGCGGAA 2 6 0 AACAGCGCCG 0.987855 -50 TCAGGCCTACAAACCGAGCCGTAGGCCGGAT 6 43 0 AACCGAGCCG 0.987855 -191 TAGGCCTGATAAGACGCGCCAGCGTCGCATC 6 65 1 AAACGCGCCA 0.980079 -169 CAGGCCTACAAATCCGAGCCGTAGGCCGGAT 6 130 0 AACCGAGCCG 0.987855 -104 TAGGCCTGATAAGACGCGCCAGCGTCGCATC 6 153 1 AAACGCGCCA 0.980079 -81 TTTTCGACTAGATCAGCACCGT 9 2 0 GACAGCACCG 0.827869 -124 ATAATAAGCAAAACAGCACCAAGAATCATAA 14 25 0 AACAGCACCA 0.842466 -198 TGCTTCACTTGAGACGAGCCGTTCATCCATG 15 20 0 GAACGAGCCG 0.958785 -231 CGCATCTATAAACACGCGCAAATTTTCTTTT 15 125 0 AAACGCGCAA 0.794934 -126 ACTGTTCAGGAAAAAGAGCCTAATTCTAGTG 19 64 1 AAAAGAGCCT 0.805207 -174 ** ******** Masking position 2 Map Score: 12.0255 Number of sites scoring better than the average of aligned sites = 1512 Number in coding regions = 1392 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 GTCTAGTGCCGGGGCGCTCTCCCTGCAACCTTTACC 1 34 0 GGCGCTCCCC 0.964269 -59 GAAGGAAAAAGTGGCTTTCGCGCACCTTAGGTCAGA 5 108 0 GGCTTTCGCC 0.988502 -193 TAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATC 6 17 0 AGCGTTCGCC 0.600931 -217 GGAGCCTGATGCGACGCTGGCGCGTCTTATCAGGCC 6 67 0 GGCGCTCGCC 0.982679 -167 TAGGCCGGATAAGGCGTTCACGCTGCATCCGGCACC 6 104 0 AGCGTTCGCC 0.988972 -130 TGTGCCTGATGCGACGCTGGCGCGTCTTATCAGGCC 6 155 0 GGCGCTCGCC 0.982679 -79 ATGCCGGATAAGGCATTTTACGCCGCATCCTGTGCC 6 185 0 AGATTTCGCC 0.88131 -49 TGATTTTTATGAGTAATTATCGCACCACGCTCATTT 7 159 1 GGAATTCGCC 0.977245 -142 TGCAAAAAATGCGTAATATACGCCGCCTTGCAGTCA 7 253 1 GGAATACGCC 0.904128 -48 AGTTTGTTTAGCGCCGTTTTCGACTAGATCAGCACC 9 13 0 GGCGTTCGAA 0.818587 -113 TCATGCTTGGACGACATATACGCATATCTTTATTGT 11 49 0 AGCATACGCA 0.661458 -67 AGCGTCTCCTGTCTCATTTTCGCCGCATCTATAAAC 15 143 0 GCCATTCGCC 0.950303 -108 * * **** *** * Masking position 11 Map Score: 15.4197 Number of sites scoring better than the average of aligned sites = 1337 Number in coding regions = 994 Number in noncoding regions = 343 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 5 TTCCGCGGCGCTGGTTTAAAACGT 2 5 1 GCGGCGCTGG 0.992643 -51 TATTGAGATGCCGGATGCGGCGTA 6 5 1 GAGATGCCGG 0.949692 -229 GGAGCCTGATGCGACGCTGGCGCGTCTTAT 6 73 0 GCGACGCTGG 0.995655 -161 TGTGCCTGATGCGACGCTGGCGCGTCTTAT 6 161 0 GCGACGCTGG 0.995655 -73 ACGGTGCTGATCTAGTCGAA 9 1 1 ACGGTGCTGA 0.91255 -125 CTAGTCGAAAACGGCGCTAAACAAACTTAT 9 22 1 ACGGCGCTAA 0.757397 -104 ATTAAGCTGAAAGACGCTGATAAATTTGGT 9 82 1 AAGACGCTGA 0.95159 -44 TTTTGTCGGCAAGATGCCGGGAGATATTTT 14 71 1 AAGATGCCGG 0.905735 -152 AATGAGACAGGAGACGCTGGATCATGTTCT 15 161 1 GAGACGCTGG 0.991584 -90 ********** Masking position 7 Map Score: 13.7715 Number of sites scoring better than the average of aligned sites = 1863 Number in coding regions = 1745 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 CAATTCCCTTAGGGAAAAATTTTAA 4 4 0 AGGAAAATTT 0.870488 -24 GTCAATGGGAAGAGAAAAATTTGTTAAAAATA 5 60 0 AGGAAAATTT 0.870488 -241 ATAACTCAGGAAGGAAAAAGTGGCTTTCGCGC 5 121 0 AAGAAAAGTG 0.910667 -180 TCACAAAAGGCACGTAAATTTGCCGATTATTT 7 28 1 CAGAAATTTG 0.910665 -273 AAAATTTTGGCACGCAAATTTGCGTAAATAAT 7 53 0 CAGAAATTTG 0.910667 -248 TTTCTTTATGAATGAAAATTTTGGCACGCAAA 7 67 0 AAGAAATTTT 0.923211 -234 TTTCATTCATAAAGAAAAATTGAGAACTTACT 7 82 1 AAGAAAATTG 0.963717 -219 AATTTCTTTGAGTGTAAATTTTAGTCACTATT 7 116 1 AGGAAATTTT 0.870488 -185 TTGCCGACAAAATGCAAAACTGCTCCGATAAT 14 51 0 AAGAAAACTG 0.847077 -172 TTTTGTAAAAAAAGGAAATGTTACGTTTTTCT 14 98 1 AAGAAATGTT 0.821883 -125 CCAAAAAGATTAAGCAAAATTGATAATACCAC 14 159 0 TAGAAAATTG 0.788913 -64 GCATAAGGTAAAAGAAAATTTGCGCGTGTTTA 15 116 1 AAGAAATTTG 0.963717 -135 ** * ******* Masking position 6 Map Score: 10.3497 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 145 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 CCCTGCAACCTTTACCCCCTTTTGGATAGAA 1 19 0 TTTACCCCTT 0.959419 -74 TAAATTTCCCTCATTATTAATA 3 8 0 TTTCCCTCTT 0.873813 -15 AGTTTGGCCTTTCATCTCGTGCAAAAAATGC 7 234 1 TTCATCTCTG 0.828769 -67 TTTTACCCCCTGCCTTCTCAAA 11 2 1 TTTACCCCTG 0.943924 -114 TTTCACCCCTTTCTGTAAGCCT 12 22 0 TTCACCCCTT 0.982269 -12 GATGATTTCACCTTTATTCTAGTCTTT 14 206 0 TTCACCTTAT 0.755448 -17 CAAATTTTCTTTTACCTTATGCTGCCCGATA 15 107 0 TTTACCTTTG 0.869634 -144 GCAAATTCACCTCTTTGACTGTTCTT 16 123 0 TTCACCTCTT 0.987311 -16 CCTCTACACCTCTTTGCACACGTTT 17 33 0 TACACCTCTT 0.916305 -15 TTCATTCACCTTCTTTGCTCTATTT 19 5 1 TTCACCTTTT 0.956434 -233 ******** ** Masking position 1 Map Score: 7.81498 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 296 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 CCTGCAACCTTTACCCCCTTTTGGATAGAA 1 19 0 TTACCCCCTT 0.870192 -74 AGTGTGAAAATGACCCTCTTGCAAGTGCAT 5 163 0 TGACCCTCTT 0.902976 -138 AGTTCTGTCAGCTCTTTATTTCTGT 8 9 0 TCAGCTCTTT 0.876106 -17 TTTCATGACCTTCTTGGTCACTTCA 9 111 0 TGACCTTCTT 0.918587 -15 TTTCACCCCTTTCTGTAAGCCT 12 22 0 TCACCCCTTT 0.975695 -12 GATGATTTCACCTTTATTCTAGTCTTT 14 206 0 TCACCTTTAT 0.796124 -17 GCAAATTCACCTCTTTGACTGTTCTT 16 123 0 TCACCTCTTT 0.979866 -16 CCTCTACACCTCTTTGCACACGTTT 17 33 0 ACACCTCTTT 0.884687 -15 TTCATTCACCTTCTTTGCTCTATTT 19 6 1 TCACCTTCTT 0.969597 -232 ********** Masking position 3 Map Score: 6.27745 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 298 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 AACCTTTACCCCCTTTTGGATAGAATATAATC 1 12 0 CCCTTTTGTA 0.852787 -81 TTTCATGACCTTCTTGGTCACTTCACCAAA 9 106 0 CCTTCTTGCA 0.947258 -20 ATTCCACGCTCCTTTTTTATTGTTTTTCAAGA 11 92 0 CCTTTTTTTG 0.711994 -24 TTTCACCCCTTTCTGTAAGCCTGTTAT 12 17 0 CCCCTTTCTA 0.766374 -17 CGTAACATTTCCTTTTTTTACAAAAATATCTC 14 91 0 CCTTTTTTCA 0.932019 -132 TGTATTCATGTCTTTTTTTTCGTGAAAGAATG 16 30 1 TCTTTTTTCG 0.515721 -109 GCAAATTCACCTCTTTGACTGTTCTTCATTG 16 118 0 CCTCTTTGTG 0.902646 -21 CCTCTTTGGTCAAACTAATCAT 17 1 1 CCTCTTTGCA 0.980923 -47 CCTCTACACCTCTTTGCACACGTTTATGAT 17 28 0 CCTCTTTGCA 0.980923 -20 TTATAAGTAGCCTTCTTCTTCAAGACCAGATA 19 95 0 CCTTCTTCCA 0.864024 -143 ACGTTCTATGTCTCTTTTATCACAATTCATGC 19 127 0 TCTCTTTTCA 0.753018 -111 GGCTTCTTCCCCCTTGATCATTCACGAAAG 19 218 0 CCCCCTTGCA 0.941419 -20 ******** ** Masking position 6 Map Score: 6.79274 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 517 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 10 CAAGAAATCGCCGAACAGTTATTTTTAACA 5 41 1 CCGAACAGTT 0.973625 -260 GGCCTACAAACCGAGCCGTAGGCCGGATAA 6 41 0 CCGAGCCGTA 0.989255 -193 GCCTACAAATCCGAGCCGTAGGCCGGATAA 6 128 0 CCGAGCCGTA 0.989255 -106 TGCTTATTATCGGAGCAGTTTTGCATTTTG 14 46 1 CGGAGCAGTT 0.968777 -177 TTCACTTGAGACGAGCCGTTCATCCATGAA 15 18 0 ACGAGCCGTT 0.963736 -233 GCTCTTTTTCCTGAACAGTTTATGATTTTC 19 53 0 CTGAACAGTT 0.876143 -185 ********** Masking position 4 Map Score: 4.84053 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 177 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 CCTATTATGCCGTTCAAGAAATCGCCGAAC 5 27 1 CGTTCAAGAA 0.947129 -274 AAGTTATGCACTTGCAAGAGGGTCATTTTC 5 158 1 CTTGCAAGAG 0.895128 -143 TTACGCATTTTTTGCACGAGATGAAAGGCC 7 239 0 TTTGCACGAG 0.86664 -62 TTTTTATTGTTTTTCAAGAAGACTTGTCAT 11 81 0 TTTTCAAGAA 0.943757 -35 CTCTCTCATTCTTTCACGAAAAAAAAGACA 16 38 0 CTTTCACGAA 0.969829 -101 AATCATAAACTGTTCAGGAAAAAGAGCCTA 19 56 1 TGTTCAGGAA 0.835736 -182 TTGTAAGCGCTTTTCAAGAATGGAAATTAA 19 159 0 TTTTCAAGAA 0.943757 -79 CCCCCTTGATCATTCACGAAAGCGCTTTAT 19 210 0 CATTCACGAA 0.888032 -28 ********** Masking position 6 Map Score: 2.95035 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 140 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 ATTGCATTTAAAATGAGCGTGGTGCGATAAT 7 174 0 AAATGAGCTG 0.969135 -127 ATAGCACAACAAATGAGCCAATTGTCACGAT 9 53 1 AAATGAGCAA 0.849055 -73 AAACAATAAAAAAGGAGCGTGGAATTC 11 99 1 AAAGGAGCTG 0.892931 -17 GATGCGGCGAAAATGAGACAGGAGACGCTGG 15 150 1 AAATGAGAAG 0.969472 -101 GTTGCTAATGAAATGGGAGTGGAA 15 237 1 AAATGGGATG 0.918098 -14 TTTCGTGAAAGAATGAGAGAGAAGCGAACAT 16 47 1 GAATGAGAAG 0.947321 -92 AAGCGCTTACAAATGGGATAGTATTAATTTT 19 177 1 AAATGGGAAG 0.947321 -61 GCGCTTTCGTGAATGATCAAGGGGGAAGAAG 19 215 1 GAATGATCAG 0.761064 -23 ******** ** Masking position 3 Map Score: 2.53196 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 150 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 TTTTGGAATTCTTTCCGCAATAGTTTCATGC 5 265 0 CTTTCCGCAT 0.927996 -36 AAATGCAATTCTTTGATCCATCTCAGAGGAT 7 196 1 CTTTGATCAT 0.972076 -105 AAAGGCCAAACTTTGACCAATCCTCTGAGAT 7 215 0 CTTTGACCAT 0.940052 -86 TGAGACGAGCCGTTCATCCATGAACATCACC 15 11 0 CGTTCATCAT 0.869332 -240 CGGCCTCAGGCTTTGCTCTATCACTGATTCA 15 59 0 CTTTGCTCAT 0.982059 -192 CATTCACCTTCTTTGCTCTATTTTATGCAGC 19 13 1 CTTTGCTCAT 0.982059 -225 ******** ** Masking position 4 Map Score: 1.88489 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 60 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 AAAACGTTGGACTGTTTTTCTGACGTAGTG 2 28 1 ACTGTTTTTC 0.966929 -28 CTCCTTTTTTATTGTTTTTCAAGAAGACTT 11 86 0 ATTGTTTTTC 0.869918 -30 GATTCTTGGTGCTGTTTTGCTTATTATCGG 14 29 1 GCTGTTTTGC 0.952076 -194 CGAAGCAAGCGTTGTTTTTCCGAGTCCGGG 15 204 0 GTTGTTTTTC 0.944777 -47 TAAGACTTTGGCTGTTTTTATGGTACAATG 16 93 1 GCTGTTTTTA 0.944777 -46 CACCTCTTTGACTGTTCTTCATTGTACCAT 16 112 0 ACTGTTCTTC 0.88592 -27 ATTTTATGCAGCTGTTTATAGGAAAATCAT 19 32 1 GCTGTTTATA 0.754053 -206 CTAGAATTAGGCTCTTTTTCCTGAACAGTT 19 63 0 GCTCTTTTTC 0.92526 -175 ********** Masking position 5 Map Score: 5.58811 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 773 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 15 CAAAATTTTCATTCATAAAGAAAAATTGAG 7 76 1 ATTCATAAAG 0.851771 -225 AACTACCTGGAATCATATACAATAAAGATA 11 31 1 AATCATATAC 0.893318 -85 CAGCACCAAGAATCATAATGATCTTAGGAA 14 13 0 AATCATAATG 0.851771 -210 TGGTCAAACTAATCATAAACGTGTGCAAAG 17 17 1 AATCATAAAC 0.964956 -31 TTTATAGGAAAATCATAAACTGTTCAGGAA 19 46 1 AATCATAAAC 0.964956 -192 ********** Masking position 5 Map Score: 0.348847 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 25 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