AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00580_ecoli_reg_100.orf -o00580_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 glpT 272 sn-glycerol-3-phosphate permease #2 ugpA 21 sn-glycerol 3-phosphate transport system, integral membrane protein #3 BIME167 47 BIME #4 ugpB 238 sn-glycerol 3-phosphate transport system; periplasmic binding protein #5 pldA 146 outer membrane phospholipase A #6 pldB 300 lysophospholipase L(2) Motif number 1 AACATGAATTGTTTGATTTCGCGCATATTCGCT 1 56 1 GTTGATCGCG 0.936199 -217 TCAAAATGACGCATGAAATCACGTTTCACTTTC 1 97 0 GCTGAACACG 0.960315 -176 ATGATTAACAGCCTGATTCAGTGAGAGAACCTG 1 220 0 GCTGATAGTG 0.926816 -53 CGCTTATCTGACCTGGCATCGCGT 3 34 1 ACTGGACGCG 0.941973 -14 GGGAGATGGGGCACGGATAAGCGGGAAAATATA 4 52 0 GCCGGTAGCG 0.976651 -187 GGCGGTGACGGCGTGGGTGAGGGAAAATGGGAG 4 80 0 GCTGGTAGGG 0.989952 -159 AGCATAAAACGCGTGAATTCGCGCATTCGGTAC 4 199 1 GCTGATCGCG 0.994659 -40 GTGCTGGTTGGCGTGGGGTTGGGACGCT 6 6 0 GCTGGGTGGG 0.932282 -295 GCCGCGATAACCGTGGTTGAGCGAGGTGGTCAT 6 87 1 CCTGGTAGCG 0.966397 -214 TTGCACCAGAGCCTGGCGACAGGCTTAAAATGA 6 128 1 GCTGGGCAGG 0.956604 -173 TTTTTAGCGTGCCTGACACAACGCTGCGACAGT 6 242 0 GCTGAAAACG 0.938057 -59 ** *** * **** Masking position 5 Map Score: 12.4596 Number of sites scoring better than the average of aligned sites = 1275 Number in coding regions = 1210 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 AATTGTTTGATTTCGCGCATATTCGCTCAT 1 62 1 TTTCGCGCAT 0.986262 -211 TTTCGCGCATATTCGCTCATAATTCGAAAG 1 72 1 ATTCGCTCAT 0.978377 -201 TTAAATGTGAATTGCCGCACACATTATTAA 1 148 0 ATTGCCGCAC 0.888821 -125 GTCGGATGCGTTTCGCTTATCTGACCTGGC 3 21 1 TTTCGCTTAT 0.85817 -27 CCTTCTATATTTTCCCGCTTATCCGTGCCC 4 47 1 TTTCCCGCTT 0.938597 -192 CATCTCCCATTTTCCCTCACCCACGCCGTC 4 77 1 TTTCCCTCAC 0.949704 -162 TTTTTCTGTAATTCGAGCATGTCATGTTAC 4 163 1 ATTCGAGCAT 0.934732 -76 AAACGCGTGAATTCGCGCATTCGGTACAAC 4 205 1 ATTCGCGCAT 0.886273 -34 ********** Masking position 3 Map Score: 9.36837 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 635 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 TTACTATGGCTAAATGGTAAAAAACGAACTTCAGAGG 1 18 0 TGAAAAACGA 0.843272 -255 TACCATTTAGCCATAGTAAAAACATGAATTGTTTGAT 1 36 1 CTAAACATGA 0.934888 -237 ATAAGATTTACAAAATGTTCAAAATGACGCATGAAAT 1 111 0 CGTAAAATGA 0.975103 -162 GCGTTTTATGCTCGCGGGGTAACATGACATGCTCGAA 4 174 0 CGGAACATGA 0.978325 -65 TGAATTCGCGCATTCGGTACAACAAGAGAGATAAACG 4 212 1 CGAAACAAGA 0.968208 -27 ATCAATAATTCGTTACGGAGAACACGACCG 5 127 1 CGAAACACGA 0.991803 -20 AACCCCACGCCAACCAGCACAATATGAATCGCCAGTC 6 19 1 CGAAATATGA 0.957794 -282 CAGAGCCTGGCGACAGGCTTAAAATGATCGATGTCAG 6 134 1 CGTAAAATGA 0.975103 -167 AATAGACACACCGGGAGTTCATCATGACCTTAGAATG 6 187 0 CGTATCATGA 0.915447 -114 TTGTGTCAGGCACGCTAAAAAAAACGATTTTACGTGG 6 254 1 CAAAAAACGA 0.857903 -47 * * * ******* Masking position 11 Map Score: 6.5951 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 323 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 TAAGACCACGGGCCACGGAGGCTATCA 1 256 1 GGCCACGGAG 0.987163 -17 ATGACAAGGCGGTGACGGCGTGGGTGAGGG 4 90 0 GGTGACGGCG 0.964385 -149 GATAACTAACGGCTATGGAGTTAAGTATGT 5 68 1 GGCTATGGAG 0.973461 -79 ATCAATAATTCGTTACGGAGAACACGACCG 5 127 1 CGTTACGGAG 0.922265 -20 CAGCAATAGACGCCACCGCGCCGCGATAAC 6 68 1 CGCCACCGCG 0.753863 -233 GCTCAACCACGGTTATCGCGGCGCGGTGGC 6 79 0 GGTTATCGCG 0.942033 -222 TGAGCGAGGTGGTCATAGTGTTGATTGCAC 6 104 1 GGTCATAGTG 0.861356 -197 CCTGTCGCCAGGCTCTGGTGCAATCAACAC 6 121 0 GGCTCTGGTG 0.901245 -180 ACCATTCTAAGGTCATGATGAACTCCCGGT 6 185 1 GGTCATGATG 0.824448 -116 ********** Masking position 2 Map Score: 5.92438 Number of sites scoring better than the average of aligned sites = 2142 Number in coding regions = 2049 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 TGTTATCCCTCTGAAGTTCGTTT 1 4 1 TATCCCTCTG 0.96553 -269 ACCGCCTTGTCATCTTTCTGACACCTTACT 4 107 1 CATCTTTCTG 0.950086 -132 ACAAAAAAGTTATTTTTCTGTAATTCGAGC 4 151 1 TATTTTTCTG 0.975211 -88 CGTTTATCTCTCTTGTTGTACCGA 4 225 0 TATCTCTCTT 0.919065 -14 ATGTTGATTTTATGCTTCTTTGTTGTTGGT 5 22 1 TATGCTTCTT 0.809018 -125 ATAAGGTGAATATTTTTCTGCGGGCTATTT 5 99 0 TATTTTTCTG 0.975211 -48 CCGGTGTGTCTATTTTTGTGCCACAATACG 6 210 1 TATTTTTGTG 0.88322 -91 ********** Masking position 2 Map Score: 3.66626 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 233 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 AAAGAAGCATAAAATCAACATTTCATTAAC 5 13 0 AAAATCAACA 0.892174 -134 TCCTAAAGTAGAAACCAACAACAAAGAAGC 5 35 0 GAAACCAACA 0.980714 -112 CAACCCCACGCCAACCAGCACAATATGAAT 6 18 1 CCAACCAGCA 0.969879 -283 AGGCTCTGGTGCAATCAACACTATGACCAC 6 112 0 GCAATCAACA 0.960573 -189 AGCAGGTAGGCAAACCACCATTCTAAGGTC 6 169 1 CAAACCACCA 0.967562 -132 ********** Masking position 4 Map Score: 0.731887 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 303 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 GTTTCTTGAGTTGCCGCGATGTTAAGAAAACA 1 186 0 TTGCGCGTGT 0.99126 -87 ACCCACGCCGTCACCGCCTTGTCATCTTTCTG 4 95 1 TCACGCCTGT 0.833011 -144 GGTGAATATTTTTCTGCGGGCTATTTTACATA 5 93 0 TTTCGCGGCT 0.938372 -54 ATTGTGCTGGTTGGCGTGGGGTTGGGACGCT 6 10 0 TTGGGTGGGT 0.927688 -291 ACCACGGTTATCGCGGCGCGGTGGCGTCTATT 6 72 0 TCGCGCGGGT 0.996382 -229 GATAACCGTGGTTGAGCGAGGTGGTCATAGTG 6 92 1 GTTGGCGGGT 0.911375 -209 TACGCTACTGTCGCAGCGTTGTGTCAGGCACG 6 236 1 TCGCGCGTGT 0.99275 -65 **** *** *** Masking position 12 Map Score: 2.30559 Number of sites scoring better than the average of aligned sites = 1045 Number in coding regions = 982 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 8 ATAGTAAAAACATGAATTGTTTGATTTCGC 1 48 1 CATGAATTGT 0.881496 -225 ATAATTCGAAAGTGAAACGTGATTTCATGC 1 90 1 AGTGAAACGT 0.953026 -183 AACATTCATAAATTAAATGTGAATTGCCGC 1 160 0 AATTAAATGT 0.908435 -113 ACGGTTAATTCCTGAACTGT 2 1 0 CCTGAACTGT 0.90137 -21 ACAGTTCAGGAATTAACCGTA 2 11 1 AATTAACCGT 0.846967 -11 TCAGTGTAATGTCGGATGCGTT 3 3 1 AGTGTAATGT 0.86221 -45 TGGTTAATGAAATGTTGATTTTATG 5 6 1 AATGAAATGT 0.973238 -141 ********** Masking position 6 Map Score: 0.421896 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 187 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 TTAAATGTGAATTGCCGCACACATTATTAA 1 148 0 ATTGCCGCAC 0.946242 -125 TTTTCTTAACATCGCGGCAACTCAAGAAAC 1 188 1 ATCGCGGCAA 0.977387 -85 GCGTTTTATGCTCGCGGGGTAACATGACAT 4 181 0 CTCGCGGGGT 0.867959 -58 GGTGGCGTCTATTGCTGGGCTTCAGACCGG 6 55 0 ATTGCTGGGC 0.948055 -246 AACCACGGTTATCGCGGCGCGGTGGCGTCT 6 75 0 ATCGCGGCGC 0.996231 -226 ACAGTAGCGTATTGTGGCACAAAAATAGAC 6 217 0 ATTGTGGCAC 0.889368 -84 TGCCTGACACAACGCTGCGACAGTAGCGTA 6 236 0 AACGCTGCGA 0.862386 -65 ********** Masking position 4 Map Score: 1.98759 Number of sites scoring better than the average of aligned sites = 2464 Number in coding regions = 2354 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 10 ********** No masking Map Score: -2.71184e-12 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 11 ********** No masking Map Score: -2.71184e-12 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 12 ********** No masking Map Score: -2.71184e-12 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