AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00780_ecoli_reg_100.orf -o00780_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ybcR 300 orf, hypothetical protein #2 bioA_bioB 86 bioA: 7,8-diaminopelargonic acid synthetase, bioB: biotin synthesis, sulfur insertion? #3 sohB 219 putative protease #4 sppA 160 protease IV, a signal peptide peptidase #5 yegQ 146 orf, hypothetical protein #6 yhbU 208 putative collagenase #7 pepE 211 peptidase E, a dipeptidase where amino-terminal residue is aspartate #8 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #9 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #10 hflK 85 protease specific for phage lambda cII repressor Motif number 1 GCTTAAACCCGCCGTCGAGCGGGTTTTTCCATTTTTT 1 162 1 GGCGCGGTTT 0.986345 -139 CACCCGCTTTGTCTGCGAGGTGGGGTT 1 284 1 GTCGGGGGTT 0.974659 -17 GAGTCCCCACCTTGGTTAAACAACGCT 3 203 0 GTCCCTTGTT 0.933798 -17 TTACGATGCCGGGCGTGGGTTGTTGGCGTCC 5 5 1 GGCGCTGGTT 0.99262 -142 GGCGTGGGTTGTTGGCGTCCGGCGCTTTACCAGAGCC 5 22 1 GGCGCGCGTT 0.980086 -125 ACGCAAAAATGTTAACGAACTGGGATTTTAGTTAACC 6 154 0 GACGCGGGTT 0.991997 -55 CATGGCTCACGATGTCGCACATTGCTTCTGGAAAGTG 7 120 0 GGCGCTTGTT 0.982889 -92 CGCAGTGGTAGCATGCCTCCCGTGATTTCTTACTAAC 7 175 1 GTCCCGTGTT 0.964065 -37 GGTTTCGGGCTGTTTTTTTACACGGGG 9 1 1 GTCGCGTTTT 0.951063 -75 TACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGAT 9 29 1 GACGCTGCTT 0.915155 -47 TTGTTATGCGGTGATCCCTGTTGTCTTTCGACGCCAG 10 44 0 GACCGTGTTT 0.630559 -42 * * ** * *** ** Masking position 16 Map Score: 9.60735 Number of sites scoring better than the average of aligned sites = 850 Number in coding regions = 803 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 GTATTGAAAACACCACTACAAATACATAAG 1 46 0 CACCACTACA 0.927946 -255 TACGTACGTAAACCACTAAATGATATTTGA 1 90 0 AACCACTAAA 0.874151 -211 AACCACTCTTAACAGCATAACCAATTTTTT 1 119 0 AACAGCATAA 0.809379 -182 TACTTCGTCACACAGCTTAAACCCGCCGTC 1 148 1 CACAGCTTAA 0.889816 -153 ACACCGAATTAACAACAAAAAACACGTTTT 2 22 0 AACAACAAAA 0.563385 -65 AGTACACTGGCAGCGCGACAGACAACGTCG 3 24 0 CAGCGCGACA 0.810525 -196 GGGGCGATAACACCGCAAAATGGATACTTT 3 105 1 CACCGCAAAA 0.976948 -115 GAGCCCCCCACAGCGCTACAATGCCCGCCC 5 54 1 CAGCGCTACA 0.932897 -93 GCACTCCCCTAACCGCTTCATCAGGTGAAG 5 95 1 AACCGCTTCA 0.963606 -52 GACAGGTCAGATCCGCTTCACCTGATGAAG 5 110 0 ATCCGCTTCA 0.754103 -37 TGCGCTATCAAAACGCAAAAATGTTAACGA 6 173 0 AAACGCAAAA 0.698193 -36 CAACAGGGATCACCGCATAACAAATATGGA 10 58 1 CACCGCATAA 0.968539 -28 ********** Masking position 10 Map Score: 7.92696 Number of sites scoring better than the average of aligned sites = 1946 Number in coding regions = 1793 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 CCTCGCAGACAAAGCGGGTGTAAATTGAGGGAA 1 271 0 AAAGGGGTAA 0.959753 -30 TGCCTGTTGTAAACTGTGAGCCAAAGCGTTGTT 3 179 1 AAAGTGGCCA 0.975577 -41 GCCCGCCCTTAAAGTGGGGGCACTCCCCTAACC 5 76 1 AAAGGGGCAC 0.990309 -71 ATGATTGTTGAAACAGGGAGTAAAACTC 6 6 0 AAAGGGGTAA 0.959753 -203 GCAATGTGCGACATCGTGAGCCATGTCAGTAAG 7 132 1 ACAGTGGCCA 0.957663 -80 TCGATTCTGAAAAAATTGCGCACGATACGTCTC 8 23 0 AAATTGGCAC 0.901346 -63 CTGTTTTTTTACACGGGGAGCCAGCGATCCTGC 9 20 1 ACAGGGGCCA 0.983013 -56 ACCGCATAACAAATATGGAGCACAAAC 10 69 1 AAATGGGCAC 0.958972 -17 *** *** **** Masking position 3 Map Score: 6.20668 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 185 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AGTATTGAAAACACCACTACAAATACATAA 1 47 0 ACACCACTAC 0.827636 -254 TTACGTACGTAAACCACTAAATGATATTTG 1 91 0 AAACCACTAA 0.861586 -210 TAACCACTCTTAACAGCATAACCAATTTTT 1 120 0 TAACAGCATA 0.857204 -181 TTACTTCGTCACACAGCTTAAACCCGCCGT 1 147 1 ACACAGCTTA 0.816263 -154 TACACCGAATTAACAACAAAAAACACGTTT 2 23 0 TAACAACAAA 0.719994 -64 TGGGGCGATAACACCGCAAAATGGATACTT 3 104 1 ACACCGCAAA 0.914926 -116 GTCATTACGATAACCACATCTATTGCGCCT 4 109 1 TAACCACATC 0.904758 -52 GGCACTCCCCTAACCGCTTCATCAGGTGAA 5 94 1 TAACCGCTTC 0.937736 -53 ACTGCGAATTTAACCACTTACTGACATGGC 7 151 0 TAACCACTTA 0.930093 -61 ACAACAGGGATCACCGCATAACAAATATGG 10 57 1 TCACCGCATA 0.958412 -29 ********** Masking position 3 Map Score: 5.67004 Number of sites scoring better than the average of aligned sites = 984 Number in coding regions = 907 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 AAACCCGCCGTCGAGCGGGTTTTTCCATTTT 1 166 1 TCGGCGGGTT 0.760233 -135 CTCACAGTTTACAACAGGCATGTTAAGCCGT 3 168 0 ACACAGGCAT 0.956869 -52 AATAAATATCACGACAGGAGTTAATCAA 4 8 0 ACGCAGGAGT 0.884098 -153 CCGGTACTTGTCAGCAGGAATTGCGGACTGT 4 74 0 TCACAGGAAT 0.905271 -87 CACACCTGTCACAGGCGCAATAGATGTGGTT 4 120 0 ACAGCGCAAT 0.870553 -41 CCAACAACCCACGCCCGGCATCGTAA 5 6 0 ACGCCGGCAT 0.971864 -141 ATGTGCGACATCGTGAGCCATGTCAGTAAGT 7 135 1 TCGGAGCCAT 0.94033 -77 GTAAGAAATCACGGGAGGCATGCTACCACTG 7 177 0 ACGGAGGCAT 0.981042 -35 TTGAGACGTATCGTGCGCAATTTTTTCAGAA 8 21 1 TCGGCGCAAT 0.914995 -65 GCGTCGAAAGACAACAGGGATCACCGCATAA 10 47 1 ACACAGGGAT 0.920629 -39 *** ******* Masking position 11 Map Score: 5.05823 Number of sites scoring better than the average of aligned sites = 925 Number in coding regions = 845 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 ACGTAACAGACTCGGAGTCAGTGAATAACT 1 232 0 CTCGGAGTCA 0.959556 -69 AACCCCACCTCGCAGACAAAGCGGGTGT 1 283 0 CTCGCAGACA 0.967092 -18 CGTTGTCTGTCGCGCTGCCAGTGTACTTTA 3 27 1 CGCGCTGCCA 0.965612 -193 CAGAGATGTTATTGCAGCGAAAGTATGACA 3 134 0 ATTGCAGCGA 0.724914 -86 GTTAAGCCGTCTCGCAGAGATGTTATTGCA 3 148 0 CTCGCAGAGA 0.938061 -72 CTGTTGTAAACTGTGAGCCAAAGCGTTGTT 3 182 1 CTGTGAGCCA 0.816731 -38 TTTAGTTAACCTTGCTGCGACAATTTTTGA 6 135 0 CTTGCTGCGA 0.894675 -74 TTTTTTTACACGGGGAGCCAGCGATCCTGC 9 23 1 CGGGGAGCCA 0.974023 -53 GCGTCTGAAGCGTGGAGTCATATCCTCTGG 10 18 1 CGTGGAGTCA 0.904537 -68 ********** Masking position 10 Map Score: 4.08535 Number of sites scoring better than the average of aligned sites = 1384 Number in coding regions = 1327 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 CACTGACTCCGAGTCTGTTACGTTTCGTAGT 1 239 1 GAGTCTGTAC 0.900936 -62 GCATTTCAATCAGCCTGGGGCGATAACACCG 3 89 1 CAGCCTGGGC 0.889904 -131 CACATCTATTGCGCCTGTGACAGGTGTGACC 4 123 1 GCGCCTGTAC 0.98431 -38 CTCTGGTAAAGCGCCGGACGCCAACAACCCA 5 26 0 GCGCCGGAGC 0.529194 -121 AAAGTGATTTGAGCAGGTAACGAATTCAAGC 7 95 0 GAGCAGGTAC 0.88291 -117 TGAAAAAATTGCGCACGATACGTCTCAATTG 8 18 0 GCGCACGAAC 0.939506 -68 TGTAAAAAAACAGCCCGAAACC 9 2 0 CAGCCCGAAC 0.938215 -74 CGGCGTAGCGTCTGAAGCGTGGAGTCAT 10 8 1 GCGTCTGAGC 0.921077 -78 ******** ** Masking position 7 Map Score: 2.20509 Number of sites scoring better than the average of aligned sites = 1613 Number in coding regions = 1496 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 8 ACAGCTTAAACCCGCCGTCGAGCGGGTTTT 1 159 1 CCCGCCGTCG 0.98761 -142 AACCCCACCTCGCAGACAAAGC 1 289 0 CCCCACCTCG 0.994975 -12 GAGTCCCCACCTTGGTTAAACAAC 3 206 0 CCCCACCTTG 0.985314 -14 ACAACCCACGCCCGGCATCGTAA 5 4 0 CCCGGCATCG 0.980941 -143 TACCAGAGCCCCCCACAGCGCTACAATGCC 5 49 1 CCCCACAGCG 0.969901 -98 CGCTACAATGCCCGCCCTTAAAGTGGGGGC 5 67 1 CCCGCCCTTA 0.918166 -80 ********** Masking position 6 Map Score: 4.01129 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 215 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 CTGGAAATTATTTTTTGGTTATTTGTT 1 8 1 TTATTTTTTG 0.776794 -293 TATTTTTTGGTTATTTGTTGAGATTTGCTT 1 19 1 TTATTTGTTG 0.712469 -282 ACAGCATAACCAATTTTTTACGTACGTAAA 1 108 0 CAATTTTTTA 0.930342 -193 GCGGGTTTTTCCATTTTTTGAGTCTCGATA 1 180 1 CCATTTTTTG 0.922435 -121 CTTGCTGCGACAATTTTTGATTTAAGGCAG 6 125 0 CAATTTTTGA 0.735828 -84 ACGGTATATTCCGTTTTTTACAGGAGAATT 7 12 0 CCGTTTTTTA 0.75043 -200 TCGCTCATGACTATTTTTTATCAACCCAAA 7 45 0 CTATTTTTTA 0.95541 -167 CATGAGCGAACTATTTGTTATTTCCATTGG 7 66 1 CTATTTGTTA 0.938484 -146 GTATCGTGCGCAATTTTTTCAGAATCGAAA 8 28 1 CAATTTTTTC 0.804295 -58 TTTGTGCTCCATATTTGTTATGCGGTGATC 10 65 0 ATATTTGTTA 0.630125 -21 ********** Masking position 5 Map Score: 2.26601 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 311 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 10 ATACTCGGTAGCATTCTCTCAAATATCATTTA 1 72 1 GATTCTCTAA 0.908521 -229 TAAATTGAGGGAATACTACGAAACGTAACAGA 1 252 0 GATACTACAA 0.908521 -49 GGGGCTTCTCCAAAACGTGTTTTT 2 3 1 GCTTCTCCAA 0.990191 -84 AGGTTTACAAGTCTACACCGAATTAACAACAA 2 34 0 GCTACACCAA 0.961396 -53 GGCTACTCCTCAACGACGTTGT 3 1 1 GCTACTCCCA 0.973622 -219 GTATTCTCCCAACTTAAGGTCA 4 149 0 GATTCTCCAA 0.984662 -12 * ******* ** Masking position 4 Map Score: 1.03274 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 42 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 TCTCGATATTAGCTGATAACCCAATACCTGAGTT 1 202 1 AGTGAACCAA 0.933262 -99 TTCGGTGTAGACTTGTAAACCTAAATCTTTTCAA 2 44 1 ACTGTACCAA 0.992299 -43 AATCGACTTGTAAACCAAATTGAAAAGAT 2 68 0 ACTGTACCAA 0.992299 -19 GCCTGTTGTAAACTGTGAGCCAAAGCGTTGTTTA 3 180 1 AATGTACCAA 0.961086 -40 CCCAACCGGTACTTGTCAGCAGGAATTGCGGACT 4 76 0 ACTGTACAGA 0.930511 -85 CGCCTGTGACAGGTGTGACCTTAAGTTGGGAGAA 4 134 1 AGTGTACTAA 0.928103 -27 AGCGGATCTGACCTGTCATCAGAACGAGAGAATT 5 123 1 ACTGTACAAA 0.977544 -24 ** *** * ** ** Masking position 8 Map Score: 3.95286 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 19 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 ********** No masking Map Score: -5.30475e-13 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 13 ********** No masking Map Score: -5.30475e-13 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 14 ********** No masking Map Score: -5.30475e-13 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