AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_fla_operon_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 flgB 154 flagellar biosynthesis, cell-proximal portion of basal-body rod #2 flgE 24 flagellar biosynthesis, hook protein #3 BIME65 28 BIME #4 flgG 44 flagellar biosynthesis, cell-distal portion of basal-body rod #5 flhB 130 putative part of export apparatus for flagellar proteins #6 BIME88 37 BIME #7 tap 45 methyl-accepting chemotaxis protein IV, peptide sensor receptor #8 tar 144 methyl-accepting chemotaxis protein II, aspartate sensor receptor #9 motA 126 proton conductor component of motor; no effect on switching #10 flhD 300 regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor #11 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #12 BIME89 108 BIME #13 fliC 265 flagellar biosynthesis; flagellin, filament structural protein #14 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #15 fliL 104 flagellar biosynthesis #16 fliO 62 flagellar biosynthesis Motif number 1 TAGGGCTTTTGCTGCCACACATCAAGCATAGTG 5 18 0 GCTGCCACCC 0.993513 -113 CTTTATTGCTGATGCCACCCGCCGCGAAATTGA 8 69 0 GATGCCACCC 0.979765 -76 CAGCAATAAAGTTTCCCCCCTCCTTGCCGATAA 8 91 1 GTTTCCCCCC 0.997185 -54 CTGCTGGAATGTTGCGCCTCACCGTATCAG 9 8 0 GTTGCGCCCC 0.988232 -119 ATTGAAAATCGCAGCCCCCCTCCGTTGTATGTG 10 63 1 GCAGCCCCCC 0.993532 -238 TTTTACCGGGGCTTCCCGGCGACATCACGGGGT 10 240 1 GCTTCCCGCC 0.987849 -61 TTTTTATGCGGTTTCACCGCACCCCGTGATGTC 10 260 0 GTTTCACCCC 0.975238 -41 TCAGCAACGTGCTTCCCCGCCACCGGCGGGGTT 11 29 1 GCTTCCCCCC 0.998201 -150 TACGTATTGGGTTTCCACCCGTCGGCTCAATCG 13 212 0 GTTTCCACCC 0.990099 -54 GCCGGTTTCTGCTGCGCCACTGCTGCAG 16 45 1 GCTGCGCCCC 0.974716 -18 ******** * * Masking position 5 Map Score: 23.0333 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 138 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 CGTTTATTCCGCCGATAACGCGCGCGTAAAG 1 91 1 GCCGTAACGC 0.99657 -64 TATGCACTTTGTCACTAATCCACTACAGGAC 4 19 1 GTCATAATCC 0.779008 -26 GTCGCCAATCCTGGAAAGAGT 5 120 0 GTCGCAATCC 0.928019 -11 CTCCCCATCAGGCGGCAATGACCGCGTTAGT 7 20 0 GGCGCAATGA 0.662046 -26 CCCCCTCCTTGCCGATAACGAGATCAACTTG 8 106 1 GCCGTAACGA 0.971218 -39 GCAGCGGTACGTCGTTACCGCTGCTGGAATG 9 30 0 GTCGTACCGC 0.968718 -97 TCAGTCGTCAGGCGTTAACGCGCGATTGGGG 9 70 0 GGCGTAACGC 0.988819 -57 GGATAATCATGCCGATAACTCATATAACGCA 11 146 1 GCCGTAACTC 0.966082 -33 AACTGAGACTGACGGCAACGCCAAATTGCCT 12 27 1 GACGCAACGC 0.955581 -82 CGCAATTCAGACCGATAACCCCGGTATTCGT 13 41 0 ACCGTAACCC 0.918082 -225 CGGCTCAATCGCCGTCAACCCTGTTATCGTC 13 192 0 GCCGCAACCC 0.991872 -74 TTTTCTATCCGCCAATAAACCCGTTTTTTTG 14 83 0 GCCATAAACC 0.744651 -132 GTTCCACTTTGCCAATAACGCCGTCCATAAT 14 177 1 GCCATAACGC 0.981369 -38 GTCTTCCTGTGTCGCTACTGCTTATCGGCTA 15 76 0 GTCGTACTGC 0.899052 -29 **** ****** Masking position 7 Map Score: 19.5151 Number of sites scoring better than the average of aligned sites = 2071 Number in coding regions = 1827 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 3 TGAGTAAGGGGCAAAACAGGCGGGATTTAGG 5 47 0 GCAAACAGGC 0.957933 -84 CGTGGTCACGCCACATCAGGCAATACAAA 6 9 0 CCCATCAGGC 0.987904 -29 CAACGCTCCCCATCAGGCGGCAATGACC 7 28 0 CCCATCAGGC 0.987888 -18 CCGATGCGCAGATCATCGGGTTCATTTCAAT 8 28 0 GACATCGGGT 0.888883 -117 CCGATGATCTGCGCATCGGGTTTTTTATTTC 8 40 1 GCCATCGGGT 0.944239 -105 TTTTTTTTGCCCCAATCGCGCGTTAACGCCT 9 61 1 CCAATCGCGC 0.872559 -66 TTTGTGTGATCTGCATCACGCATTATTGAAA 10 39 1 CTCATCACGC 0.717275 -262 CGCAATTTGTCAGCAACGTGCTTCCCCGCCA 11 20 1 CACAACGTGC 0.540112 -159 TGCAGAAACGGATAATCATGCCGATAACTCA 11 137 1 GAAATCATGC 0.781102 -42 GATAAACAGCCCTGCGTTATA 11 168 0 GAAAACAGCC 0.787116 -11 GTCAGTCTCAGTTAATCAGGTTACAACGA 12 9 0 GTAATCAGGT 0.709077 -100 GATAAGCGCAGCGCATCAGGCAATTTGGCGT 12 44 0 GCCATCAGGC 0.9903 -65 GATGCGCTGCGCTTATCAGGCCTACAAGTTG 12 58 1 GCTATCAGGC 0.953594 -51 GAATTTTTTTCAAAAACAGCCATTTTTTGTT 13 142 0 CAAAACAGCC 0.743112 -124 TAACGCCGTCCATAATCAGCCACGAGGTGCG 14 192 1 CAAATCAGCC 0.892033 -23 TGTCGCTACTGCTTATCGGCTAATTATCCTG 15 67 0 GCTATCGGCT 0.534147 -38 ** ******** Masking position 5 Map Score: 14.5266 Number of sites scoring better than the average of aligned sites = 4148 Number in coding regions = 3389 Number in noncoding regions = 759 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 4 AAGGGGCAAAACAGGCGGGATTTAGGGCTT 5 43 0 ACAGGCGGGA 0.945859 -88 GCTGATGCCACCCGCCGCGAAATTGAAATA 8 65 0 CCCGCCGCGA 0.875051 -80 TCGTTATCGGCAAGGAGGGGGGAAACTTTA 8 97 0 CAAGGAGGGG 0.980513 -48 GCGCAACATTCCAGCAGCGGTAACGACGTA 9 24 1 CCAGCAGCGG 0.960812 -103 GGGGCAAAAAAAAGCAGCGGTACGTCGTTA 9 44 0 AAAGCAGCGG 0.962587 -83 ACGCACATACAACGGAGGGGGGCTGCGATT 10 69 0 AACGGAGGGG 0.986082 -232 CTTCCCCGCCACCGGCGGGGTTTTTTTCTG 11 40 1 ACCGGCGGGG 0.991801 -139 TTAGTGGGTGAAATGAGGGGTTATTTGGGG 11 89 0 AAATGAGGGG 0.828156 -90 TAACTCATATAACGCAGGGCTGTTTATC 11 161 1 AACGCAGGGC 0.842431 -18 AAAGCGGGGAAAAGACGCGGATTACGGTGC 15 22 0 AAAGACGCGG 0.887526 -83 TTGAGCGCAACAAAGCGGGGAAAAGACGCG 15 33 0 CAAAGCGGGG 0.863851 -72 CGCAGCAGAAACCGGCGCGGAAGATTGCAC 16 31 0 ACCGGCGCGG 0.989541 -32 ********** Masking position 7 Map Score: 12.9157 Number of sites scoring better than the average of aligned sites = 1844 Number in coding regions = 1694 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 5 TTCACGTTGTAGAAATGGCTGGGGGCGAAA 1 11 0 AGAAATGGCT 0.973471 -144 GGAATAAACGCAAAATGGGTCGCTATTTAT 1 71 0 CAAAATGGGT 0.932258 -84 ATTACTTAACATAAATGGGTA 10 2 0 ATAAATGGGT 0.946526 -299 CCTTACAAATAGAAATGGGTCTTTACACTT 10 143 0 AGAAATGGGT 0.985977 -158 AAAACCCTGCAGAAACGGATAATCATGCCG 11 130 1 AGAAACGGAT 0.900679 -49 GCGACTAACAAAAAATGGCTGTTTTTGAAA 13 136 1 AAAAATGGCT 0.958973 -130 ATAGCAACAAAAAAACGGGTTTATTGGCGG 14 76 1 AAAAACGGGT 0.967842 -139 ********** Masking position 5 Map Score: 6.71895 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 60 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 AAAATGGGTCGCTATTTATGCCGTTGATGG 1 60 0 GCTATTTATG 0.874666 -95 GAAGACATATGCACTTTGTCACTAATCCAC 4 12 1 GCACTTTGTC 0.865938 -33 CTATTCTAATGCTAATTATTTTTTACCGGG 10 220 1 GCTAATTATT 0.722444 -81 AACATAAAGCGCAATTTGTCAGCAACGTGC 11 11 1 GCAATTTGTC 0.960493 -168 ATAACGCAGGGCTGTTTATC 11 169 1 GCTGTTTATC 0.905968 -10 AGCGCATCAGGCAATTTGGCGTTGCCGTCA 12 36 0 GCAATTTGGC 0.92191 -73 AAGTTGAATTGCAATTTATTGAATTTGCAC 12 83 1 GCAATTTATT 0.870857 -26 TTTTTTTGTTGCTATTTAGCGCCTTTGTCT 14 61 0 GCTATTTAGC 0.818906 -154 CTGCTTATCGGCTAATTATCCTGCGTCTTG 15 60 0 GCTAATTATC 0.833956 -45 ********** Masking position 6 Map Score: 5.2664 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 398 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 GCGCGTTATCGGCGGAATAAACGCAAAATGG 1 83 0 GGCGGATAAA 0.960779 -72 CTTGATGTGTGGCAGCAAAAGCCCTAAATCC 5 25 1 GGCAGCAAAG 0.941221 -106 GCGCGATTGGGGCAAAAAAAAGCAGCGGTAC 9 51 0 GGCAAAAAAA 0.948794 -76 GTAAATTCCAGGCAGAAAAAAACCCCGCCGG 11 51 0 GGCAGAAAAA 0.99172 -128 GGGAATAAGGGGCAGAGAAAAGAGTATTTCG 13 105 1 GGCAGAAAAA 0.99172 -161 CGGGTTTATTGGCGGATAGAAAAAAACGAAA 14 91 1 GGCGGAAGAA 0.973195 -124 ****** **** Masking position 10 Map Score: 3.33068 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 181 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 TTGATGGTCATTGCGGACAGGTACAATTCA 1 37 0 TTGCGGACAG 0.963826 -118 ATTGAACGCTTTGCGCTCTGGCATCATTCA 5 82 1 TTGCGCTCTG 0.983538 -49 ATTAGAATAGTTGCGATAAGCTGCAATAAG 10 200 0 TTGCGATAAG 0.833966 -101 TGCTGACAAATTGCGCTTTATGTT 11 5 0 TTGCGCTTTA 0.716514 -174 CAATTTGGCGTTGCCGTCAGTCTCAGTTAA 12 25 0 TTGCCGTCAG 0.923579 -84 TCGGTCTGAATTGCGCAAAGTTTACGTTTA 13 57 1 TTGCGCAAAG 0.9056 -209 CCCCGCTTTGTTGCGCTCAAGACGCAGGAT 15 43 1 TTGCGCTCAA 0.936126 -62 GTGTTGCGGTCTTCCTGTGTCGC 15 92 0 TTGCGGTCTT 0.875841 -13 ********** Masking position 2 Map Score: 3.67012 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 488 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 GCTATTTATGCCGTTGATGGTCATTGCGGACA 1 48 0 CCGTTTGGTC 0.930082 -107 AAAATGTCCTGTAGTGGATTAGTGACAAA 4 26 0 CCTGTTGGAT 0.854526 -19 GACTGAACATCCTGTCATGGTCAACAGTGGAA 9 95 1 CCTGTTGGTC 0.990451 -32 AATCGACGCAACTGTACTCGTCACTACACGCA 10 94 0 ACTGTTCGTC 0.946441 -207 CTCATTTCACCCACTAATCGTCCGATTAAAAA 11 102 1 CCACTTCGTC 0.904709 -77 ACCGATAACCCCGGTATTCGTTTTACGTGTCG 13 30 0 CCGGTTCGTT 0.968564 -236 CGCCGTCAACCCTGTTATCGTCTGTCGTAAAA 13 182 0 CCTGTTCGTC 0.992713 -84 ***** ***** Masking position 5 Map Score: 1.8419 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 223 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 CGCCTGTTTTGCCCCTTACTCAAACCATTGA 5 56 1 GCCCCTTATC 0.982616 -75 AAGGCACCTTCCTGAAAACAAGTT 8 131 0 GCACCTTCTG 0.928368 -14 ATAAGCAGAACCACCTTTTTGGTTTAATATG 10 174 0 CCACCTTTTG 0.809436 -127 TCTTTTCTCTGCCCCTTATTCCCGCTATTAA 13 97 0 GCCCCTTATC 0.982616 -169 TTGCTATTTAGCGCCTTTGTCTTATTGACTT 14 52 0 GCGCCTTTTC 0.982616 -163 GTCAGAGGTAGCACCGTAATCCGCGTCTTTT 15 12 1 GCACCGTATC 0.972402 -93 GCAATCTTCCGCGCCGGTTTCTGCTGCGCCA 16 33 1 GCGCCGGTTC 0.921279 -30 ******** ** Masking position 10 Map Score: 1.54028 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 249 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 ********** No masking Map Score: 7.21444e-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 ATCTCCTCCGCAGGTATCAAAATTCTGCCAT 1 134 0 CGGTATCAAA 0.792132 -21 TGCTTGATGTGTGGCAGCAAAAGCCCTAAAT 5 23 1 GGGCAGCAAA 0.985681 -108 GTTTGAGTAAGGGGCAAAACAGGCGGGATTT 5 50 0 GGGCAAAACA 0.812843 -81 ACGCGCGATTGGGGCAAAAAAAAGCAGCGGT 9 53 0 GGGCAAAAAA 0.954182 -74 CCGGGAAGCCCCGGTAAAAAATAATTAGCAT 10 228 0 CGGTAAAAAA 0.898861 -73 AGGTAAATTCCAGGCAGAAAAAAACCCCGCC 11 53 0 CGGCAGAAAA 0.984506 -126 GCGGGAATAAGGGGCAGAGAAAAGAGTATTT 13 103 1 GGGCAGAGAA 0.929833 -163 CGGATAATTTCTGGTAGCAAAGCCTACCAGT 14 21 1 CGGTAGCAAA 0.967082 -194 GGTTTATTGGCGGATAGAAAAAAACGAAAGC 14 93 1 CGATAGAAAA 0.726658 -122 ACTCACTCCCGGGTCAGCAAACTCGAAAAAT 14 143 0 GGTCAGCAAA 0.87095 -72 * ********* Masking position 6 Map Score: 7.41923 Number of sites scoring better than the average of aligned sites = 1187 Number in coding regions = 1075 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 13 ********** No masking Map Score: 7.21444e-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 14 ********** No masking Map Score: 7.21444e-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 15 ********** No masking Map Score: 7.21444e-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