AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_ecoli_hinf_reg_100.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 ybaD 90 orf, hypothetical protein #2 ribH 88 riboflavin synthase, beta chain #3 ribA 169 GTP cyclohydrolase II #4 ribE 214 riboflavin synthase, alpha chain #5 ribB 300 3,4 dihydroxy-2-butanone-4-phosphate synthase #6 HI0212 44 GTP cyclohydrolase II (ribA) #7 HI0764 218 3,4-dihydroxy-2-butanone 4-phosphate synthase (ribB) #8 HI0938 200 H. influenzae predicted coding region HI0938 #9 HI0942 45 exodeoxyribonuclease V, gamma chain (recC) #10 HI0943 54 conserved hypothetical protein #11 HI1303 147 riboflavin synthase, beta chain (ribH) #12 HI1613 43 riboflavin synthase, alpha chain (ribE) Motif number 1 ACGCCAGTTCCAGGAAAAATTGACAGATTT 3 51 1 CAGGAAAAAT 0.938639 -119 CCAGCATTATCTGGAGAATTTC 3 158 1 CTGGAGAATT 0.986446 -12 AAAGAAGAAGCAGGGGAAATTCAGTCTATT 4 71 1 CAGGGGAAAT 0.903498 -144 TATTTTTTCACTGGAGAATTAATAAATCCT 4 107 0 CTGGAGAATT 0.986446 -108 TTTACCGCCGGTGGGGAATTTCGCCCCGCC 5 71 0 GTGGGGAATT 0.894823 -230 GACAATTTCGCAGGAAAAATTTGCCAAAAA 7 33 0 CAGGAAAAAT 0.938639 -186 AAGTGAAAATCAGGACAATTTCGCAGGAAA 7 46 0 CAGGACAATT 0.933521 -173 TTTTAAAGAACAGAAAAATTCCGTGCCATT 8 23 1 CAGAAAAATT 0.751615 -178 TTAAAGTGCGGTGGAAAATTGGAGCGTTTT 8 181 1 GTGGAAAATT 0.932888 -20 ACACCCTTTTATGGAGAATTATCT 10 41 1 ATGGAGAATT 0.934772 -14 CTATATTTTTATGGAAAATTTCCTTCATTA 11 34 0 ATGGAAAATT 0.899865 -114 ********** Masking position 7 Map Score: 14.3403 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 347 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 CGCAGGGGGGCGGATTTTAGCATAATATTTC 2 40 0 CGGATTTTGC 0.945601 -49 TCTGTATTGGCTTATTTTGCCATAACGAGAA 3 126 0 CTTATTTTCC 0.952391 -44 TCCCCTGCTTCTTCTTTTTGCTGCCCATTCA 4 57 0 CTTCTTTTGC 0.83785 -158 CTACAATAGACTGAATTTCCCCTGCTTCTTC 4 74 0 CTGAATTTCC 0.863805 -141 ACCGCCGGTGGGGAATTTCGCCCCGCCCTGA 5 67 0 GGGAATTTGC 0.72402 -234 ACCCGCTCACGTTATTTTGGCTATATGCCGC 5 224 1 GTTATTTTGC 0.968844 -77 TAAGACTGCCCTGATTCTGGTAACCATAATT 5 261 1 CTGATTCTGT 0.897371 -40 TTTTAGTGAGGTTTTTTTACC 5 290 1 GTTTTTTTCC 0.633494 -11 GAATGCGCGCGTTATTTTTGTTATCAAGGGG 6 16 0 GTTATTTTGT 0.908524 -29 CGAAATTGTCCTGATTTTCACTTTTAAAGTC 7 53 1 CTGATTTTAC 0.849778 -166 TTTCTCAGCCCTGATTCTGGTATTTAATTGA 7 176 1 CTGATTCTGT 0.897371 -43 TTTTCAACTAGTTATTTTGGCAAATCTCGCT 8 55 0 GTTATTTTGC 0.968844 -146 ATCACTTGATCTGATTTTGCGATCTGTATC 8 128 0 CTGATTTTGC 0.984791 -73 ATCAGATCAAGTGATTTTTCTACCCATTCAT 8 144 1 GTGATTTTCT 0.911136 -57 ATAAAAGGGTGTTATTCTACTAAAAAATAGG 10 22 0 GTTATTCTCT 0.703396 -33 ******** ** Masking position 6 Map Score: 15.3318 Number of sites scoring better than the average of aligned sites = 1198 Number in coding regions = 1063 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 3 TCAAAAGCGTTGCGCCTTTGTTGTATCGTCAGTTCAGGGTAA 1 23 1 TGGTTATCGG 0.882193 -68 TTTCGTGCGCTGCTTCCCTTTCGAGCCGGGAGA 2 2 0 TGTTTGCCGG 0.982187 -87 TCTTCCTTCGGGTTCGAGTATGGCCCCGCAGGGGGGCGGATT 2 55 0 GGTTTCCCGG 0.943064 -34 TTGACAGATTTGTGCCATTCCGTGAACGATCGACGCGTCGTG 3 70 1 TGGTCAACGG 0.936355 -100 TGTAGTTATATGAGAGACTAAAAAGCCGCCTGAATGGGCAGC 4 27 1 TGGTAGCCGG 0.983437 -188 GTTTTCCACCTGCTATTGTGCTGAACAGAATGTCTTAACTGA 4 166 1 TGTTCACAGG 0.787215 -49 GGCTTTCAACTGAGTTGATTTACCGCCGGTGGGGAATTTCGC 5 77 0 TGGTTGCCGG 0.994909 -224 CAGCAGATCCGGTGTAATTCCGGGGCCGACGGTTAGAGTCCG 5 149 1 GGGTCGCCGG 0.996355 -152 CAAAATAACGTGAGCGGGTCCATGCCCGACAGAATCGTTACT 5 201 0 TGGTCCCCGG 0.993855 -100 CAGCAGATTTGGTGAAATTCCAAAGCCGACAGTAAAGTCTGG 7 83 1 GGGTCGCCGG 0.996355 -136 ** * * * **** * Masking position 9 Map Score: 11.4098 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 328 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 GGAAATCTATTTTACCCTGAACTGACGATACAAC 1 42 0 TTACCCGATG 0.966304 -49 ATAGACTGAATTTCCCCTGCTTCTTCTTTTTGCT 4 66 0 TTCCCCGCCT 0.904186 -149 ATAGCCATTCTTACCCCTTCACTGGTAAGGGCGT 4 134 1 TTCCCCTCTG 0.959314 -81 TAAGGGCGTTTTCCACCTGCTATTGTGCTGAACA 4 159 1 TTCACCGCTT 0.978837 -56 GGTGGGGAATTTCGCCCCGCCCTGAGAATAAGCG 5 58 0 TTGCCCGCTG 0.957581 -243 GCTCGCGGGCTTTCAACTGAGTTGATTTACCGCC 5 92 0 TTCAACGATG 0.880834 -209 GGCCCCGGAATTACACCGGATCTGCTGTCCTTTG 5 142 0 TTCACCGATG 0.989453 -159 GGCTTTGGAATTTCACCAAATCTGCTGACTTTAA 7 76 0 TTCACCAATG 0.901929 -143 TTTATTCTCTTTCATCCAGACTTTACTGTCGGCT 7 106 0 TTATCCGATT 0.66876 -113 ATTTCCACCAGCTTTTAAAGAACAGA 8 3 1 TTCACCGCTT 0.978837 -198 TCCACCGCACTTTAACCATAAATGAATGGGTAGA 8 162 0 TTAACCTATG 0.820653 -39 ** **** ** ** Masking position 2 Map Score: 8.01501 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 906 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 TAGGTGAACCCCTTCTCGTTATGGCAAAATAAGCCAA 3 114 1 CTCTTTGGCA 0.990174 -56 GTGAACACCTTTTATTTGTAGTTATATGAGAGAC 4 8 1 CTATTTAGTA 0.9643 -207 TGCCGCTAATCATTAGCGTTATAGTGAATCCGCTTAT 5 28 1 CTCTTTAGTA 0.970255 -273 AAAAAAACCTCACTAAAATTATGGTTACCAGAATCAG 5 271 0 CTATTTGGTA 0.985735 -30 TTTAAAAGTGCGGTCAATTTTTGGCAAATTTTTCCTG 7 16 1 CTATTTGGCA 0.988158 -203 CAGAAAAATTCCGTGCCATTATAGCGAGATTTGCCAA 8 33 1 CTCTTTAGCA 0.975242 -168 ATTTTTCTACCCATTCATTTATGGTTAAAGTGCGGTG 8 157 1 CTATTTGGTA 0.985735 -44 CGCACCAACACTATATTTTTATGGAAAATTTCCTTCA 11 37 0 CTTTTTGGAA 0.864569 -111 * * * ** **** * Masking position 17 Map Score: 6.85842 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 64 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 AATATTATGCTAAAATCCGCCCCCCTGCGGG 2 42 1 TAAAATCGCC 0.854765 -47 ACAATCATAACTGAAAACGCCAGTTCCAGGA 3 35 1 CTGAAACGCC 0.831919 -135 CTCGTTATGGCAAAATAAGCCAATACAGAAC 3 128 1 CAAAATAGCC 0.842478 -42 ATGAGAGACTAAAAAGCCGCCTGAATGGGCA 4 36 1 AAAAAGCGCC 0.972567 -179 TTCTCCAGTGAAAAAATAGCCATTCTTACCC 4 119 1 AAAAAAAGCC 0.934725 -96 GCCGCCACTCCTAAGACTGCCCTGATTCTGG 5 250 1 CTAAGATGCC 0.787405 -51 ATTTCGCAGGAAAAATTTGCCAAAAATTGAC 7 28 0 AAAAATTGCC 0.914991 -191 TAACCTAGAAAAAACAACGCCATT 9 4 0 AAAACACGCC 0.936011 -42 TTAAATCATCAAAAGGTCGCCATT 9 32 1 AAAAGGCGCC 0.938439 -14 ATAAAATTGCCGATAGTTTAC 11 1 1 ATAAAATGCC 0.923652 -147 GTTATGAACAATAAAATCGCCTTAAAAATGA 11 75 1 ATAAAACGCC 0.973624 -73 ****** **** Masking position 4 Map Score: 8.1173 Number of sites scoring better than the average of aligned sites = 989 Number in coding regions = 805 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 7 GCTTATTTTGCCATAACGAGAAGGGGTTCACCTA 3 114 0 CCATAAGAGG 0.958053 -56 TCTCATATAACTACAAATAAAAGGTGTTCAC 4 8 0 CTACAATAGG 0.94949 -207 AGCGGATTCACTATAACGCTAATGATTAGCGGCA 5 28 0 CTATAAGATG 0.952316 -273 ATTCTGGTAACCATAATTTTAGTGAGGTTTTTTT 5 274 1 CCATAATATG 0.940264 -27 GCAAATCTCGCTATAATGGCACGGAATTTTTCTG 8 33 0 CTATAAGAGG 0.986621 -168 CGCACTTTAACCATAAATGAATGGGTAGAAAAAT 8 157 0 CCATAATAGG 0.870754 -44 CGCACCAACACTATATTTTTATGGAAAATTTCCT 11 40 0 CTATATTAGG 0.798624 -108 ****** * * ** Masking position 5 Map Score: 3.94832 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 17 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 ACGGCGTCCTGACCAGGTGGTTA 1 78 0 GCGTCCTGAC 0.956369 -13 CTTCCCTTTCGAGCCGGGAGA 2 2 0 GAGCCGGGAG 0.890695 -87 AACGATCGACGCGTCGTGATTAGGTGAACC 3 94 1 GCGTCGTGAT 0.954974 -76 GAATTTCGCCCCGCCCTGAGAATAAGCGGA 5 56 0 CCGCCCTGAG 0.979885 -245 CCGACGGTTAGAGTCCGGATGGGAGAGAGT 5 174 1 GAGTCCGGAT 0.95573 -127 ACTCCTAAGACTGCCCTGATTCTGGTAACC 5 256 1 CTGCCCTGAT 0.969815 -45 TCCTGCGAAATTGTCCTGATTTTCACTTTT 7 48 1 TTGTCCTGAT 0.836022 -171 TTGCATTTCTCAGCCCTGATTCTGGTATTT 7 171 1 CAGCCCTGAT 0.978741 -48 ********** Masking position 9 Map Score: 4.3014 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 520 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 ACAACAAAGGCGCAACGCTTTTGAGATAAAGG 1 15 0 CCAACGCTTT 0.962778 -76 AGGTGGTTAACGGAAATCTATTTTACCCTGAA 1 55 0 CGAAATCTTT 0.942816 -36 CACGGAATGGCACAAATCTGTCAATTTTTCCT 3 62 0 CCAAATCTTC 0.963276 -108 CTTACAACTCCTGAAATCAGTTAAGACATTCT 4 192 0 CGAAATCATT 0.833646 -23 TGAGTTCGCACCCAAAGCGCTCGCGGGCTTTC 5 112 0 CCAAAGCGTC 0.968978 -189 GATTTGGGAACCCAACTCGTTTTATTCTCTTT 7 128 0 CCAACTCGTT 0.969575 -91 GAGTTGGGTTCCCAAATCGTTTATTTTATTTG 7 142 1 CCAAATCGTT 0.982541 -77 CGATCTGTATCGCAAAGTTTTTCTGAAAACCT 8 107 0 CCAAAGTTTT 0.836085 -94 * ******* ** Masking position 5 Map Score: 3.50122 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 188 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 CATAATATTTCGTGCGCTGCTTCCCTTTCG 2 21 0 CGTGCGCTGC 0.954108 -68 AATCCGCCCCCCTGCGGGGCCATACTCGAA 2 55 1 CCTGCGGGGC 0.972082 -34 TTTGCCATAACGAGAAGGGGTTCACCTAAT 3 112 0 CGAGAAGGGG 0.885917 -58 CGCCCTTACCAGTGAAGGGGTAAGAATGGC 4 137 0 AGTGAAGGGG 0.938426 -78 GCTTATTCTCAGGGCGGGGCGAAATTCCCC 5 59 1 AGGGCGGGGC 0.969808 -242 GCCAAAATAACGTGAGCGGGTCCATGCCCG 5 215 0 CGTGAGCGGG 0.979836 -86 TTATGGTTAAAGTGCGGTGGAAAATTGGAG 8 175 1 AGTGCGGTGG 0.969204 -26 ********** Masking position 4 Map Score: 2.32957 Number of sites scoring better than the average of aligned sites = 719 Number in coding regions = 654 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 AGCTATGCGTTGCTGCCGCTAATCATTAGC 5 15 1 TGCTGCCGCT 0.939952 -286 TGAGTTGATTTACCGCCGGTGGGGAATTTC 5 79 0 TACCGCCGGT 0.968771 -222 GTAATTCCGGGGCCGACGGTTAGAGTCCGG 5 162 1 GGCCGACGGT 0.982892 -139 TTTGGCTATATGCCGCCACTCCTAAGACTG 5 239 1 TGCCGCCACT 0.985159 -62 GAAATTCCAAAGCCGACAGTAAAGTCTGGA 7 96 1 AGCCGACAGT 0.96102 -123 ATAAAATTGCCGATAGTTTACCTTAAT 11 8 1 TGCCGATAGT 0.926195 -140 ********** Masking position 10 Map Score: 2.26609 Number of sites scoring better than the average of aligned sites = 1222 Number in coding regions = 1182 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 12 ATCTATTTTACCCTGAACTGACGATACAAC 1 42 0 CCCTGAACTG 0.899188 -49 GTCAATTTTTCCTGGAACTGGCGTTTTCAG 3 45 0 CCTGGAACTG 0.979835 -125 TCCAGATAATGCTGGTTCTGTATTGGCTTA 3 143 0 GCTGGTTCTG 0.960571 -27 CCGGAATTACACCGGATCTGCTGTCCTTTG 5 142 0 ACCGGATCTG 0.962116 -159 CTAAGACTGCCCTGATTCTGGTAACCATAA 5 260 1 CCTGATTCTG 0.959016 -41 ATTTCTCAGCCCTGATTCTGGTATTTAATT 7 175 1 CCTGATTCTG 0.959016 -44 TAGAAAAATCACTTGATCTGATTTTGCGA 8 136 0 ACTTGATCTG 0.911471 -65 ********** Masking position 9 Map Score: 5.14471 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 705 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 ********** No masking Map Score: -2.36368e-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: -2.36368e-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 TCTCCCGGCTCGAAAGGGAAGCAGCG 2 4 1 CCCGTCGAAG 0.930962 -85 GGGGCCATACTCGAACCCGAAGGAAGAAA 2 70 1 TCGACCGAAG 0.907927 -19 TTGTGCCATTCCGTGAACGATCGACGCGTCGTG 3 79 1 CCGGACGATG 0.953442 -91 CGGTGTAATTCCGGGGCCGACGGTTAGAGTCCG 5 158 1 CCGGCCGACG 0.996341 -143 GTGAGCGGGTCCATGCCCGACAGAATCGTTACT 5 201 0 CCAGCCGACG 0.994721 -100 TGGTGAAATTCCAAAGCCGACAGTAAAGTCTGG 7 92 1 CCAACCGACG 0.984544 -127 *** * ***** * Masking position 10 Map Score: 0.793253 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 173 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274