AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_ecoli_bsub_300.orf -o180_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 talB 278 transaldolase B #2 mog 114 required for the efficient incorporation of molybdate into molybdoproteins #3 moaA 300 molybdopterin biosynthesis, protein A #4 moaB 21 molybdopterin biosynthesis, protein B #5 moeA 203 molybdopterin biosynthesis #6 ydiG 125 similar to molybdopterin precursor biosynthesis #7 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #8 moeB 50 molybdopterin biosynthesis protein #9 narQ 245 alternate gene name: narAA #10 ywmE 93 ywmE #11 ywmD 300 similar to hypothetical proteins from B. subtilis Motif number 1 GCATATCCCTCTTATTGCCGGTCGCGATGACTTTCCTG 1 11 1 CTCGTGCGAT 0.981237 -268 CAGAAGTTATCAAGTACCTCGTAGCGTATATACTTCTT 1 70 0 CTTGTGCGTA 0.912597 -209 CGATAACCGTCTTGTCGGCGGTTGCGCTGACGTTGCGT 1 187 1 CTCGTGCGCT 0.991585 -92 GTAGCGTGACCGACTTCCCGGTCACGCTAAGAATGA 2 9 0 CTCGTACGCT 0.92033 -106 TCTGTCACTCCCTTCGCAGTGTATCATTCTGTTTAACG 2 62 1 CCGGTTCATT 0.827436 -53 AAGATTTTTCCGTTTAAACAGTCTCGTTAAACAGAATG 2 86 0 CTCGTTCGTT 0.983788 -29 CCGCCATTTTCCCTTATTCTGTAGCGAAATAGCACGAT 3 69 1 CTCGTGCGAA 0.943789 -232 GACTGTATGCCACCTCGGGCGTAGCGCTGGGTCCTGCC 5 118 0 CTGGTGCGCT 0.978676 -86 CCCGAGGTGGCATACAGTCTGTGGCGTTTTTCTGACAT 5 137 1 CCCGTGCGTT 0.994811 -67 CTTTAATAAACAGACAAGCAGTAGCGTTGAGCCTTTGC 7 71 1 CCCGTGCGTT 0.994811 -66 ATCATCTCACCTCTAGTTTCGTTAAAAGCATAG 7 114 0 CCTGTTCGTT 0.914452 -23 ATGTTCAACCCCTTTTTAGGGTATCATTCCCGCCCAAA 10 66 0 CTGGTTCATT 0.824732 -28 AACTAATTAGCTGTCTGCCTGTAGCATAGTAGCAGATT 11 42 1 CCCGTGCATA 0.924548 -259 * * * ** ***** Masking position 12 Map Score: 16.6753 Number of sites scoring better than the average of aligned sites = 919 Number in coding regions = 871 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 CAGAATGATACACTGCGAAGGGAGTGACAGACAGGC 2 57 0 CAGCAAGGAG 0.994021 -58 TACATGATTACATAGCGAAAGTGTGGATGGTAAAAA 3 119 1 CAGCAAAGGG 0.993093 -182 CGAGCATTGTCACGGCCAAAGCACCGTATCAGTTGA 3 213 0 CAGCAAAGAG 0.992241 -88 AGATTGCCACCAGGGCGAAGGAAGAAATGACTTCGC 3 252 1 CAGCAAGGAA 0.97968 -49 TTCTGATATTTATAGCAAAAGTGGCGAACCACCCTT 5 25 0 TAGCAAAGGG 0.975946 -179 CTTAACTTATTATAGCAGAGGTGAAATAAT 6 5 0 TAGCGAGGGA 0.86371 -121 CTATGTCTTATATGGCCAATGTATTGTTTGCTGACT 6 59 0 TAGCAATGAG 0.902288 -67 TCGTTAAAAGCATAGCAAAAGCAAAGGCTCAACGCT 7 93 0 CAGCAAAGAG 0.992468 -44 AAGGCAGGAACATTGCGGAGGGGAAGAGACA 9 225 1 CAGCGAGGGG 0.987589 -21 CTGTCATAATCAAGGCGAAAAAAGAATGAATGATCA 11 89 1 CAGCAAAAAA 0.765908 -212 ** ** **** * * Masking position 9 Map Score: 11.7797 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 317 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 CAATTGGTAACGTTTACACAGGAAAGTCATC 1 36 0 CGTTTAACAG 0.986241 -243 CGTTACCAATTGTTTAAGAAGTATATACGCT 1 55 1 TGTTTAGAAG 0.752465 -224 ATAGTATTTCTCTTTAAACAGCTTGTTAGGG 1 257 0 TCTTTAACAG 0.985708 -22 TTAAACAGTCTCGTTAAACAGAATGATACAC 2 80 0 TCGTTAACAG 0.948227 -35 AAGATTTTTCCGTTTAAACAGTCTCGTTAAA 2 93 0 CGTTTAACAG 0.986139 -22 ATTAAAACGCTCCTTAAACAGATCATACACT 6 105 0 TCCTTAACAG 0.948245 -21 AGTCCTTTATACAGAGGTGTCTCA 9 4 1 CCTTTAACAG 0.988862 -242 ATGACGGCGGTGTTTAGGCAGGACGCCTAAG 9 111 0 TGTTTAGCAG 0.964566 -135 CTGTAAAAGCCCTTTATATAGAGGGCTCTTT 9 148 1 CCTTTAATAG 0.908402 -98 ****** **** Masking position 6 Map Score: 9.82072 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 123 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GCATATCCCTCTTATTGCCGGTCGCG 1 7 1 CCCTCTTATT 0.627404 -272 GTTGATATCGCCCGCCATTTTTATACAAAA 1 124 0 CCCGCCATTT 0.878846 -155 GCGTCATGATCGTGCTATTTCGCTACAGAA 3 85 0 CGTGCTATTT 0.729131 -216 CTGATCTCTCCTTTTGACGTT 4 7 0 CTCTCCTTTT 0.879155 -15 AGCGCTGGGTCCTGCCTTTACATGCCATAT 5 104 0 CCTGCCTTTA 0.856501 -100 ATTTAGCCGCCGTTCCTTTTATAACACGTG 9 80 0 CGTTCCTTTT 0.956414 -166 TTATATAGAGGGCTCTTTTTGTGTCTCAGA 9 161 1 GGCTCTTTTT 0.855038 -85 CCGCAATGTTCCTGCCTTTATATTTTTTCA 9 213 0 CCTGCCTTTA 0.856501 -33 CGCTCCCCCAGGCGCCTTTTTTATTGGTTT 10 28 1 GGCGCCTTTT 0.930203 -66 AGCCTCTTTTTGTATGTAACA 11 2 1 GCCTCTTTTT 0.875542 -299 TGTGATCATTCATTCTTTTTTCGCCTTGAT 11 97 0 CATTCTTTTT 0.646138 -204 CTTGAAATGCCGTTCATTTTTAGCCATTTC 11 151 0 CGTTCATTTT 0.710179 -150 TATAGGACATGCTGCCTTTTGTGCTGCTTT 11 200 0 GCTGCCTTTT 0.928971 -101 TGATTACTTCCTTTCTTTTTCATATTTTCC 11 280 0 CTTTCTTTTT 0.763023 -21 ********** Masking position 9 Map Score: 9.11354 Number of sites scoring better than the average of aligned sites = 1225 Number in coding regions = 1011 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 5 CTCTTATTGCCGGTCGCGATGACTTTCCTG 1 19 1 CGGTCGCGAT 0.861731 -260 AAACAGTCTCGCCTGGCGATAACCGTCTTG 1 171 1 GCCTGGCGAT 0.958583 -108 CGCTGACGTTGCGTCGTGATATCATCAGGG 1 211 1 GCGTCGTGAT 0.959371 -68 AACCGGTCTGCCCTGATGATATCACGACGC 1 221 0 CCCTGATGAT 0.975121 -58 CGCTATGCCTCCCTGATGATGTATATCAAA 3 33 1 CCCTGATGAT 0.975121 -268 CATGTATATAGCGTCATGATCGTGCTATTT 3 95 0 GCGTCATGAT 0.960144 -206 GGTGCTTTGGCCGTGACAATGCTCGTAAAG 3 224 1 CCGTGACAAT 0.810964 -77 CGAACCATCTCCCTCATGATGTTAACACTA 7 12 1 CCCTCATGAT 0.975121 -125 ********** Masking position 9 Map Score: 6.17209 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 654 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 6 CTGGCGATAACCGTCTTGTCGGCGGTTGCG 1 183 1 CCGTCTTGTC 0.871841 -96 GGGGATGTAACCGGTCTGCCCTGATGATAT 1 229 0 CCGGTCTGCC 0.972389 -50 TCTTCTGAAGCCTGTCTGTCACTCCCTTCG 2 48 1 CCTGTCTGTC 0.839343 -67 GAGTGTTTAGTGGTTATGCCGATACTAGCG 3 166 0 TGGTTATGCC 0.701459 -135 GCGTAGCGCTGGGTCCTGCCTTTACATGCC 5 108 0 GGGTCCTGCC 0.981142 -96 TAGGCAAATTCGATTTTGCCTCCGCAGGAG 5 177 1 CGATTTTGCC 0.8096 -27 CAACGAACGCGGGGTTTGTCGACACGCTGA 9 32 0 GGGGTTTGTC 0.909502 -214 AAATGCTTAGGCGTCCTGCCTAAACACCGC 9 106 1 GCGTCCTGCC 0.981142 -140 CACACTCCTCGGATTTTGTCGAATTCTGAG 9 185 0 GGATTTTGTC 0.739814 -61 CCCTCCGCAATGTTCCTGCCTTTATATTTT 9 217 0 TGTTCCTGCC 0.795921 -29 AAACTAATTAGCTGTCTGCCTGTAGCATAG 11 41 1 GCTGTCTGCC 0.944603 -260 AGCACAAAAGGCAGCATGTCCTATATCTTT 11 205 1 GCAGCATGTC 0.67159 -96 ********** Masking position 7 Map Score: 5.46537 Number of sites scoring better than the average of aligned sites = 2396 Number in coding regions = 2273 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 7 TTATCGCCAGGCGAGACTGTTTCGGATTTCT 1 162 0 GCGGACTGTT 0.99111 -117 ATTCTGTTTAACGAGACTGTTTAAACGGAAA 2 87 1 ACGGACTGTT 0.935308 -28 AGGTGCAGAGGCTAGAGTGTTTAGTGGTTAT 3 179 0 GCTGAGTGTT 0.986092 -122 TTTTGCCTCCGCAGGAGTGTTTTC 5 190 1 GCAGAGTGTT 0.96559 -14 CAACGCTACTGCTTGTCTGTTTATTAAAGAG 7 69 0 GCTGTCTGTT 0.968598 -68 AACAGTTTGGGCGGGAATGATACCCTAAAAA 10 61 1 GCGGAATGAT 0.924285 -33 AGCATAAACAGCTTGTGTGATCATTCATTCT 11 111 0 GCTGTGTGAT 0.930644 -190 *** ******* Masking position 8 Map Score: 4.48216 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 124 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 CTCTAGCCTCTGCACCTGGGTCAACTGATA 3 193 1 TGCACCTGGG 0.980417 -108 CGTAAAGATTGCCACCAGGGCGAAGGAAGA 3 247 1 GCCACCAGGG 0.973372 -54 CAGACTGTATGCCACCTCGGGCGTAGCGCT 5 128 0 GCCACCTCGG 0.993293 -76 ATTATTTCACCTCTGCTATAATAAG 6 6 1 TTCACCTCTG 0.861208 -120 GACACGCTGAGACACCTCTGTATAAAGGAC 9 12 0 GACACCTCTG 0.948355 -234 CAATAAAAAAGGCGCCTGGGGGAGCGCCTG 10 24 0 GGCGCCTGGG 0.981884 -70 ********** Masking position 5 Map Score: 2.42804 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 229 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 ACCGGCAATAAGAGGGATATGC 1 1 0 AGAGATATGC 0.976286 -278 CAATTGTTTAAGAAGTATATACGCTACGAGGT 1 61 1 AGAGATATAC 0.963211 -218 GAATATAGAAAGATGGATATGGCATGTAAAGG 5 88 1 AGAGATATGG 0.945569 -116 TTCTGACATAATAGGCAAATTCGATTTTGCCT 5 166 1 ATAGAAATTC 0.867247 -38 TAAGACATAGAGAAGAAAATAGTGTATGATCT 6 85 1 AGAGAAATAG 0.935004 -41 TAACACTACAATATGCAAATACTGAACAGCTA 7 34 1 ATAGAAATAC 0.942877 -103 TTATGCTAGAATACGAAAATGCAAAAAGATAT 11 227 0 ATAGAAATGC 0.962902 -74 *** * ****** Masking position 7 Map Score: 1.86316 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 70 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 ACGAGGTACTTGATAACTTCTGCGTAGCATA 1 86 1 TGATACTTCT 0.911708 -193 GACACTGCGTTGATATCGCCCGCCATTTTTA 1 131 0 TGATTCGCCC 0.871387 -148 CGTTGCGTCGTGATATCATCAGGGCAGACCG 1 217 1 TGATTCATCA 0.6993 -62 GGAGGCGAAGTCATTTCTTCCTTCGCCCTGG 3 261 0 TCATTCTTCC 0.947693 -40 CTGATCTCTCCTTTTGACGTT 4 10 0 TGATTCTCCT 0.942555 -12 ATTATTTCACCTCTGCTATAAT 6 2 1 TTATTCACCT 0.759511 -124 ATGTATTGTTTGCTGACTTCTGGTTCATAAG 6 46 0 TGCTACTTCT 0.639699 -80 ATCATCTCACCTCTAGTTTCGT 7 125 0 TCATTCACCT 0.903349 -12 TCCTTATCTTTTATGTCATCTTATCATGTTA 8 19 0 TTATTCATCT 0.792784 -32 AACACCGCCGTCATCACATCCTGTAAAAGCC 9 128 1 TCATACATCC 0.887717 -118 CCTTTCTTTTTCATATTTTCCAACTATATGT 11 270 0 TCATTTTTCC 0.565217 -31 ATGATTACTTCCTTTCTTTTTC 11 289 0 TGATACTTCC 0.932771 -12 **** ****** Masking position 4 Map Score: 4.66365 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 660 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 11 TTTCTCTTTAAACAGCTTGTTAGGGGGATG 1 252 0 AACAGCTTGT 0.964338 -27 ACGCTCCTTAAACAGATCATACACTATTTT 6 100 0 AACAGATCAT 0.874901 -26 GCAAATACTGAACAGCTATTCCTCTTTAAT 7 48 1 AACAGCTATT 0.867677 -89 GCTACAGGCAGACAGCTAATTAGTTTTGAA 11 37 0 GACAGCTAAT 0.900084 -264 AGAAAGCATAAACAGCTTGTGTGATCATTC 11 116 0 AACAGCTTGT 0.964338 -185 AGCGATTTTGGACAGATCGTGAAAGCAGCA 11 179 1 GACAGATCGT 0.933057 -122 AGAAGAATCCAACATATAGTTGGAAAATAT 11 259 1 AACATATAGT 0.713349 -42 ********** Masking position 4 Map Score: 1.30544 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 141 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 TCGGATTTCTGACACTGCGTTGATATCGCCC 1 141 0 GACCTGCGTT 0.920293 -138 CGGTTGCGCTGACGTTGCGTCGTGATATCAT 1 205 1 GACTTGCGTC 0.637796 -74 TCATTCTTAGCGTGACCGGGAAGT 2 4 1 TTCTAGCGTG 0.868235 -111 GGCTTCAGAAGAGGTAGCGTGACCGACTTCC 2 29 0 GAGTAGCGTG 0.947689 -86 TCATCAGGGAGGCATAGCGTGCATCGTCCTT 3 21 0 GGCTAGCGTG 0.977025 -280 GTAAAGGCAGGACCCAGCGCTACGCCCGAGG 5 113 1 GACCAGCGCT 0.917769 -91 ATACAGAGGTGTCTCAGCGTGTCGACAAACC 9 19 1 GTCCAGCGTG 0.983407 -227 *** ******* Masking position 7 Map Score: 0.384481 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 426 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 GAGACTGTTTCGGATTTCTGACACTGCGTT 1 151 0 CGGATTTCTG 0.943842 -128 CGCCATTTTCCCTTATTCTGTAGCGAAATA 3 70 1 CCTTATTCTG 0.917322 -231 CAGTCTGTGGCGTTTTTCTGACATAATAGG 5 151 1 CGTTTTTCTG 0.986876 -53 AGCAGATTTCCGTTTTTCTGTCATAATCAA 11 72 1 CGTTTTTCTG 0.986876 -229 ********** Masking position 6 Map Score: 0.178204 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 86 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 ********** No masking Map Score: -4.56636e-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: -4.56636e-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