AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i325_not_clear_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 tldD 47 suppresses inhibitory activity of CsrA #2 BIME161 74 BIME #3 yhdR 67 orf, hypothetical protein #4 mreC 65 rod shape-determining protein #5 mreB 244 regulator of ftsI, penicillin binding protein 3, septation function #6 yhdA 151 orf, hypothetical protein Motif number 1 TTGCCGGATGGCGGCCCAGCATCTGT 3 7 0 GCGGCCCAGC 0.960483 -61 GGGCCGCCATCCGGCAAAGGGTTTTTGAGT 3 20 1 CCGGCAAAGG 0.937769 -48 CACATTTTTAGCAGACAAGGAGTGACGG 3 50 1 GCAGACAAGG 0.988928 -18 TCGGATGCAGGCAGGGGAAGTGTCTG 4 7 1 GCAGGCAGGG 0.992168 -59 TCGTATCAGACCAGGCAGGGTAAACAGACA 4 31 0 CCAGGCAGGG 0.986052 -35 AATCTGGCGAGCAGACAAGCACACTCCCAT 5 58 0 GCAGACAAGC 0.991007 -187 TTACGCGGTTGCAAACAGGCGAGGAATGCT 5 116 1 GCAAACAGGC 0.977224 -129 CTGCCTGAGTCCAGAAAGGCTTAATGCATC 5 149 0 CCAGAAAGGC 0.973554 -96 ACGCAGCAGCGACAAGGCGCAAAAATCA 5 227 0 GCGACAAGGC 0.93339 -18 ********** Masking position 2 Map Score: 14.3856 Number of sites scoring better than the average of aligned sites = 2016 Number in coding regions = 1915 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 2 ATTGGGGCAATTACGCGCCCTCGTCAAA 2 8 0 TTACCGCCCT 0.982562 -67 AAACAGACACTTCCCCTGCCTGCATCCGA 4 9 0 TTCCCTGCCT 0.990937 -57 AAGTGTCTGTTTACCCTGCCTGGTCTGATAC 4 28 1 TTACCTGCCT 0.982347 -38 TGAAAACGGATTAAACGGCAGG 5 2 0 TTAACGGCAG 0.949488 -243 CGTAAGGTCATTCATCTGCATATGTGCTGCA 5 90 0 TTCACTGCAT 0.957964 -155 ATGAATGACCTTACGCGGTTGCAAACAGGCG 5 106 1 TTACCGGTTG 0.849004 -139 ATCAGCAGCATTCCTCGCCTGTTTGCAACCG 5 121 0 TTCCCGCCTG 0.983071 -124 AGAAATTATTTTCCAATCCATCATGCACATG 6 21 0 TTCCATCCAT 0.778417 -131 TTTATTGCGCTTCATCGGCTTTGCTTTTCCA 6 70 0 TTCACGGCTT 0.978153 -82 **** ****** Masking position 2 Map Score: 8.33424 Number of sites scoring better than the average of aligned sites = 1979 Number in coding regions = 1852 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 GTTGGCCTTTGGCAACGATTATCCTATGAG 2 39 0 GGCAACGATT 0.957992 -36 GTTGCCAAAGGCCAACGAGCCAGAACATAA 2 53 1 GCCAACGAGC 0.951075 -22 GCCGCCATCCGGCAAAGGGTTTTTGAGTCA 3 22 1 GGCAAAGGGT 0.9611 -46 ATTTTTAGCAGACAAGGAGTGACGG 3 53 1 GACAAGGAGT 0.943559 -15 TCGGATGCAGGCAGGGGAAGTGTCTGTTT 4 10 1 GGCAGGGGAA 0.842006 -56 TATTCTACGTGAAAACGGATTAAACGGCAG 5 12 0 GAAAACGGAT 0.71597 -233 TCCCATGAGACGCAGCGCGCATTATTCTAC 5 34 0 CGCAGCGCGC 0.868915 -211 GTTGCAAACAGGCGAGGAATGCTGCTGATG 5 123 1 GGCGAGGAAT 0.831774 -122 TCTGGACTCAGGCAGAGATTTGTAACAAAG 5 164 1 GGCAGAGATT 0.811002 -81 TTGTAACAAAGGAAACGAACTGCACTAATT 5 183 1 GGAAACGAAC 0.926498 -62 ACGCAGCAGCGACAAGGCGCAAAAATCATC 5 225 0 GACAAGGCGC 0.927029 -20 CCGATAGTGAGGAAGCGGGCATACTAGCAA 6 119 0 GGAAGCGGGC 0.963395 -33 ********** Masking position 7 Map Score: 7.3353 Number of sites scoring better than the average of aligned sites = 5394 Number in coding regions = 5113 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 4 GTTTTTGCTACTCGTTAGTTACTGCAGTAG 1 27 0 CTCGTTAGTT 0.971986 -21 GGTTATGTTCTGGCTCGTTGGCCTTTGGC 2 56 0 CTGGCTCGTT 0.960284 -19 TTTACCCTGCCTGGTCTGATACGAGAATAC 4 37 1 CTGGTCTGAT 0.842967 -29 TGCTTGTCTGCTCGCCAGATTGTTGCAGCA 5 67 1 CTCGCCAGAT 0.98862 -178 AGCAGCATTCCTCGCCTGTTTGCAACCGCG 5 119 0 CTCGCCTGTT 0.990757 -126 GAAGACTATACTCGCTAATGGAAAAGCAAA 6 52 1 CTCGCTAATG 0.858256 -100 TCAGATTTATCTCGCAATTTATTGCGCTTC 6 88 0 CTCGCAATTT 0.88621 -64 ********** Masking position 2 Map Score: 3.49882 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 773 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 CAACGATTATCCTATGAGATTGGGGCAATT 2 27 0 CCTATGAGAT 0.948495 -48 TGCGTATTCTCGTATCAGACCAGGCAGGGT 4 40 0 CGTATCAGAC 0.966898 -26 CAAGCACACTCCCATGAGACGCAGCGCGCA 5 43 0 CCCATGAGAC 0.928799 -202 AGATTTGTAACAAAGGAAACGAACTGCACT 5 179 1 CAAAGGAAAC 0.763417 -66 TAATTTTCACCGTAGCAGATGATTTTTGCG 5 208 1 CGTAGCAGAT 0.966898 -37 AATGGAAAAGCAAAGCCGATGAAGCGCAAT 6 68 1 CAAAGCCGAT 0.892772 -84 GGCATACTAGCAAATCAGATTTATCTCGCA 6 102 0 CAAATCAGAT 0.957278 -50 ********** Masking position 4 Map Score: 1.17556 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 523 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 TACTCGTTAGTTACTGCAGTAGAGGATTTTT 1 18 0 TTATGCAGTA 0.9904 -30 GCTCGCCAGATTGTTGCAGCACATATGCAGA 5 76 1 TTGTGCAGCA 0.989429 -169 CCAGAAAGGCTTAATGCATCAGCAGCATTCC 5 138 0 TTATGCATCA 0.975705 -107 ACGGTGAAAATTAGTGCAGTTCGTTTCCTTT 5 190 0 TTATGCAGTT 0.976093 -55 *** ******* Masking position 5 Map Score: 0.962863 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 63 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: -1.16996e-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 8 ********** No masking Map Score: -1.16996e-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 9 ********** No masking Map Score: -1.16996e-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