AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i089_Sugar_Transport_1_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pspA 151 phage shock protein, inner membrane protein #2 pspB 53 phage shock protein #3 pspE 74 phage shock protein #4 ycjM 185 putative polysaccharide hydrolase #5 ugpA 21 sn-glycerol 3-phosphate transport system, integral membrane protein #6 BIME167 47 BIME #7 ugpB 238 sn-glycerol 3-phosphate transport system; periplasmic binding protein #8 BIME168 126 BIME #9 livH 47 high-affinity branched-chain amino acid transport system; membrane component #10 livK 300 high-affinity leucine-specific transport system; periplasmic binding protein Motif number 1 ACAGCAACATGCCAGGATGAGTTAGCGAATTA 1 20 0 GCAGATGAGT 0.801088 -132 AAGTACTCCTTAGACGATGAGCGGCGGCGCGT 2 32 0 TAAGATGAGC 0.900057 -22 AAAATTGCCATCCATTATACGCCTGAGATTTA 3 32 0 TCATATACGC 0.686185 -43 ACCATGAGCGGCGCTTATGCGCCGTTTTTTTT 4 19 1 GCCTATGCGC 0.700384 -167 TTGCGTCAGCTCACAAATACGCTTTTTCCCTG 4 85 1 TCCAATACGC 0.915939 -101 GAAAATAAACTGTCAATTGAGCACAAGGGTTT 4 143 0 TGCATTGAGC 0.678263 -43 TCAGTGTAATGTCGGATGCGTTTCGCTTATC 6 10 1 TGCGATGCGT 0.933382 -38 CGCGATGCCAGGTCAGATAAGCGAAACGCATC 6 25 0 GGCGATAAGC 0.97764 -23 ATGAAACGATGAGCAATCTGTAGA 7 3 1 GAAGATGAGC 0.925607 -236 GGGAGATGGGGCACGGATAAGCGGGAAAATAT 7 53 0 GCCGATAAGC 0.97777 -186 TCTCTTGTTGTACCGAATGCGCGAATTCACGC 7 209 0 TACAATGCGC 0.914691 -30 AATGTAAAATTGCCTGATGCGCTGCGCTTATC 8 61 1 TGCGATGCGC 0.99105 -66 TCACCCAGTAGGCCTGATAAGCGCAGCGCATC 8 76 0 GGCGATAAGC 0.97778 -51 ** * ******* Masking position 8 Map Score: 12.755 Number of sites scoring better than the average of aligned sites = 2773 Number in coding regions = 2469 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 ATGCGCCGTTTTTTTTTCTGTCACACCTTAT 4 35 1 TTTTTTCTGT 0.984467 -151 TGGTAAAAAATGATTTCCTGCGTGACTAAAA 4 115 1 TATTTCCTGC 0.95678 -71 AATTGACAGTTTATTTTCTGCGGAGTAGTCT 4 157 1 TATTTTCTGC 0.968839 -29 AGACCTTCTATATTTTCCCGCTTATCCGTGC 7 44 1 TTTTTCCCGC 0.919503 -195 ACAAAAAAGTTATTTTTCTGTAATTCGAGCA 7 151 1 TTTTTTCTGT 0.984467 -88 CTTTGTGCCGTTATTTTATGCTGACAAAGGC 10 71 1 TATTTTATGC 0.843133 -230 GACAAAGGCACTTTTTTCTGTTTATCTATCA 10 93 1 CTTTTTCTGT 0.929664 -208 TTAAAATCCCTATTTTTCAGTCGATTAAGAA 10 145 0 TTTTTTCAGT 0.909017 -156 TACTGCACTGTTTTTGCCTGTCTGATTAAGG 10 206 0 TTTTGCCTGT 0.903946 -95 TGTGTTGCTTTGTTTTTATGTGTTAACAAAT 10 255 0 TTTTTTATGT 0.916362 -46 * ********* Masking position 5 Map Score: 10.6016 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 413 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 CCAGGATGAGTTAGCGAATTACACTAACAA 1 11 0 TTAGCGAATT 0.778219 -141 CGTATAATGGATGGCAATTTTCATCCATAG 3 43 1 ATGGCAATTT 0.840813 -32 AGCGCCGCTCATGGTGAATTCTT 4 4 0 ATGGTGAATT 0.965293 -182 CAAATAATCTATGGGGATGTAAATAAGGTG 4 58 0 ATGGGGATGT 0.926409 -128 GAGTGGCAATATGTTGAATTTGCACGATCT 8 106 1 ATGTTGAATT 0.731655 -21 CCCCTGAATGATAGTGAATTATTCCGCCCT 10 43 1 ATAGTGAATT 0.934019 -258 CGACTGAAAAATAGGGATTTTAATCGCTAT 10 153 1 ATAGGGATTT 0.964816 -148 TTTTGTGATAATAGCGATTAAAATCCCTAT 10 163 0 ATAGCGATTA 0.812126 -138 AACATCACGAATGGGGATTTTTGACT 10 285 1 ATGGGGATTT 0.981778 -16 ********** Masking position 7 Map Score: 5.58891 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 424 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 CGCTTATCCGTGCCCCATCTCCCATTTTCCCTCA 7 62 1 TCCCATCCCA 0.97996 -177 CCATCTCCCATTTTCCCTCACCCACGCCGTCACC 7 76 1 TTCCCTCCCA 0.982743 -163 GCATGTCATGTTACCCCGCGAGCATAAAACGCGT 7 179 1 TCCCCGCACA 0.989716 -60 ATTTTACATTTGTCACCTGTCTCAAAGGAGTCTT 8 37 0 TCACCTGCCA 0.94887 -90 ATTCAACATATTGCCACTCACCCAGTAGGCCTGA 8 91 0 TCCACTCCCA 0.980012 -36 TCATCCCACCGCCCGTAAAATGCGGGC 9 4 1 TCACCGCCTA 0.916612 -44 GTAACCTTTCTAAACCCGCCCGCATTTTACGGGC 9 21 0 TACCCGCCCA 0.982395 -27 AATACTGCGCTAACCCCTTAATCAGACAGGCAAA 10 191 1 TCCCCTTACA 0.928693 -110 * ****** * ** Masking position 14 Map Score: 4.49605 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 335 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 GCTAACTCATCCTGGCATGTTGCTGTTGATTCT 1 26 1 CTGCATGTTC 0.987934 -126 ATACAATTTGCGTGCCAATTTTTTATCTTTTTG 1 79 0 CTGCAATTTT 0.832618 -73 CCATTATACGCCTGAGATTTAACAATTTTTGCG 3 20 0 CTGGATTTAC 0.807399 -55 GCGTATAATGGATGGCAATTTTCATCCATAGAA 3 42 1 GTGCAATTTC 0.880563 -33 CCGTCACCGCCTTGTCATCTTTCTGACACCTTA 7 102 1 CTGCATCTTC 0.978018 -137 GTAATTCGAGCATGTCATGTTACCCCGCGAGCA 7 170 1 CTGCATGTTC 0.987934 -69 CGCAGCGCATCAGGCAATTTTACATTTGTCACC 8 54 0 CGGAATTTTC 0.899371 -73 GGGGATTATGCTGGACATTTTTCATTCTCTAAT 10 14 0 CGGCATTTTC 0.985695 -287 * ** ****** * Masking position 7 Map Score: 3.48716 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 262 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 CGCGTTCGGACGCCGCCTGGATGTTA 2 7 0 CGCCGCCTGG 0.992508 -47 CGTCCGAACGCGCCGCCGCTCATCGTCTAA 2 25 1 CGCCGCCGCT 0.970074 -29 GGCGCATAAGCGCCGCTCATGGTGAATTCT 4 12 0 CGCCGCTCAT 0.952288 -174 GGCGCTTATGCGCCGTTTTTTTTTCTGTCA 4 28 1 CGCCGTTTTT 0.920516 -158 CCCACGCCGTCACCGCCTTGTCATCTTTCT 7 96 1 CACCGCCTTG 0.941289 -143 TCATCCCACCGCCCGTAAAATGCGGG 9 7 1 CACCGCCCGT 0.978107 -41 TGAATTATTCCGCCCTTTGTGCCGTTATTT 10 57 1 CGCCCTTTGT 0.833788 -244 ********** Masking position 4 Map Score: 2.44359 Number of sites scoring better than the average of aligned sites = 2850 Number in coding regions = 2739 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 7 ATCAGATCTTTATAAATCAAAAAGATAAAA 1 62 1 TATAAATCAA 0.878998 -90 CTTACAAATGTAACAAAAAAGTTATTTTTC 7 139 1 TAACAAAAAA 0.864822 -100 TTTGACTCCCTATCAATCAACGTGTTA 8 8 0 TATCAATCAA 0.955553 -119 TCTGTTTATCTATCAATAAATTCAGAATAT 10 109 1 TATCAATAAA 0.962865 -192 TAATCGCTATTATCACAAAATACTGCGCTA 10 173 1 TATCACAAAA 0.904598 -128 AACAGTGCAGTATAAAAAAAGAACAGTCTG 10 225 1 TATAAAAAAA 0.897561 -76 ********** Masking position 5 Map Score: 1.23913 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 58 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 AATTGTATTAACAGTTCAGCAGGACAATCCT 1 104 1 ACAGTTCAGA 0.993771 -48 ACAGTTCAGGAATTAACCGTA 5 1 1 ACAGTTCAGA 0.993771 -21 ACAGGCAAAAACAGTGCAGTATAAAAAAAGA 10 216 1 ACAGTGCAGA 0.992598 -85 ********* * Masking position 8 Map Score: 0.904209 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 11 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: -9.21273e-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 10 TTTTTTTCTGTCACACCTTATTTACATCCCC 4 45 1 TCACACCTTT 0.911837 -141 AAAGCGTATTTGTGAGCTGACGCAAATAATC 4 79 0 TGTGAGCTGC 0.93183 -107 GTTTCGCTTATCTGACCTGGCATCGCGT 6 30 1 TCTGACCTGC 0.978443 -18 AGAGTTTGATTCAGACCTTCTATATTTTCCC 7 32 1 TCAGACCTTT 0.887314 -207 GTCACCGCCTTGTCATCTTTCTGACACCTTA 7 104 1 TGTCATCTTC 0.90935 -135 GTCATCTTTCTGACACCTTACTATCTTACAA 7 115 1 TGACACCTTC 0.980314 -124 ATTTTACATTTGTCACCTGTCTCAAAGGAGT 8 40 0 TGTCACCTGC 0.98739 -87 ********* * Masking position 5 Map Score: 2.22438 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 201 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 11 ********** No masking Map Score: -9.21273e-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 12 ********** No masking Map Score: -9.21273e-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: -9.21273e-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