AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_hinf_reg_300.orf -o00640_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #2 HI0408 171 ABC transporter, ATP-binding protein (yebM) #3 HI0774 205 acetate CoA-transferase, alpha subunit #4 HI0967 25 H. influenzae predicted coding region HI0967 #5 HI0970 57 3-dehydroquinase (aroQ) #6 HI0971 152 acetyl-CoA carboxylase, biotin carboxyl carrier protein (accB) #7 HI0972 174 acetyl-CoA carboxylase, biotin carboxylase (accC) #8 HI1194 300 glycine cleavage system transcriptional activator (gcvA) #9 HI1196 35 succinyl-CoA synthetase, beta subunit (sucC) #10 HI1204 214 acetate kinase (ackA) #11 HI1260 193 acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) Motif number 1 GCGGTCGATTTTTACGGTCTTTTTAGGATAACAA 1 65 1 TTTTCTTTTT 0.972759 -25 GGTTGGGGAAAATAACGCATTTTTATAGAATTCT 2 125 0 AATCATTTTT 0.66926 -47 TACGAAATTCTTTTTGCTATTTTTAATATCAATC 3 72 1 TTTTATTTTT 0.970517 -134 ATTATACTGGTTTTTTCGATTTTTGGTGGTCGAA 5 11 0 TTTGATTTTT 0.91941 -47 TTTTAATCCTTTTTGTGTGGCACA 5 44 0 TTTCCTTTTT 0.967028 -14 GAAAATCGAGTATTTTTGGCGAAATTC 6 4 1 AATTATTTTT 0.711448 -149 TGCGGTTAAAATTTCAATCTTTTTAGGAAGAACG 6 128 1 ATTTCTTTTT 0.920403 -25 TTTCCAATATTTTTGTCGGGCGGA 7 1 1 TTTTATTTTT 0.970517 -174 TCGGGCGGACTTTAGTCCGTATTTCATATACAAA 7 26 1 TTTCGTATTT 0.610232 -149 TCACTTGTCCTTTCCTACCCTTTTCCTTACAATA 8 204 0 TTTCCCTTTT 0.777352 -97 GCGGTCAATTTTTGAGGTGTTTTT 10 1 0 TTTTGTTTTT 0.926653 -214 TCATACGCTATTTTAAGTCTATTTTTAGTAAAAA 10 40 1 TTTTCTATTT 0.843453 -175 TTTTTGAAAAATTAAACTATTTTTACTAAAAATA 10 59 0 ATTTATTTTT 0.914232 -156 AAATACAAACTTTATCGTATTTTTTGAAAAATTA 10 79 0 TTTTATTTTT 0.970517 -136 AGGTGTATTCTATGTCTGATTTTTCAAACCATCT 10 147 1 TATGATTTTT 0.725188 -68 TTATTGAACATTTTTTTTATTTTTTTGTCTTACA 11 45 0 TTTTATTTTT 0.970517 -149 TTTTTGACCTTTTTATTGACTAGA 11 180 0 TTTCCTTTTT 0.967028 -14 *** ******* Masking position 3 Map Score: 20.361 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 461 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 2 CGTAAAAATCGACCGCACTTTATCAAGGAA 1 51 0 GACCGCACTT 0.995265 -39 GTTTATTCATAACCGCACTTTTTCCTTTAA 6 95 1 AACCGCACTT 0.996533 -58 TTGAAATTTTAACCGCACTTTTAAAGGAAA 6 115 0 AACCGCACTT 0.996533 -38 TAGTTCGGGAAACCGAACTTGAGTAACAAT 8 99 0 AACCGAACTT 0.979734 -202 CTTACAATACAACCATACTTAATGATTGGT 8 183 0 AACCATACTT 0.882279 -118 CAAATAAAAAAACGTCACTTGTCCTTTCCT 8 222 0 AACGTCACTT 0.903005 -79 CTCAAAAATTGACCGCACTTATCATACGCT 10 19 1 GACCGCACTT 0.995265 -196 ********** Masking position 7 Map Score: 13.9348 Number of sites scoring better than the average of aligned sites = 1471 Number in coding regions = 993 Number in noncoding regions = 478 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 3 TGAATAATGCTTTTTCCATAGGAATGAATT 2 59 0 TTTTTCCATA 0.824424 -113 TGGAAAAAGCATTATTCAAACGCTTAAATA 2 71 1 ATTATTCAAA 0.874108 -101 AAAATCGCCGTGTTTTCAACAATGGTTGGG 2 152 0 TGTTTTCAAC 0.879453 -20 TAAGTATCTTATATTTCAAATGGATATGTT 3 142 0 ATATTTCAAA 0.813977 -64 ATTACCTTAATTTTTTCAAATTTGCGATAA 6 46 0 TTTTTTCAAA 0.974117 -107 CAAAAGTAAGTTTATTCATAACCGCACTTT 6 86 1 TTTATTCATA 0.906756 -67 TGAGTGGCGTTTTTTTCATCCCGATTTTA 8 10 0 TTTTTTCATC 0.938617 -291 TGGACAAGATTTATTTCAAATTAGTTTTTC 8 260 0 TTATTTCAAA 0.89403 -41 GTGAACTGTTTTCATAACCAAAAAGG 9 7 1 TGTTTTCATA 0.904576 -29 AAATAGTTTAATTTTTCAAAAAATACGATA 10 71 1 ATTTTTCAAA 0.951289 -144 ATGAATTTATTTTATTCATCAAAAGGTGTA 10 124 1 TTTATTCATC 0.844636 -91 TCTATGTCTGATTTTTCAAACCATCTTAGA 10 155 1 ATTTTTCAAA 0.951289 -60 ********** Masking position 8 Map Score: 12.129 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 306 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 TTTGTTATCCTAAAAAGACCGTAAAA 1 74 0 ATCCTAAAAA 0.914982 -16 AATCTTGAGAATTCTATAAAAATGCGTTAT 2 118 1 ATTCTATAAA 0.800772 -54 GTTGATATTCTTTCTTTTAATCTCGTTATT 3 175 1 TTTCTTTTAA 0.78254 -31 AGAGACCTCCTAATAACGAGATTAAA 3 190 0 CTCCTAATAA 0.778855 -16 ATTTGATCCTTATAAAAGTGAGAAT 4 6 1 ATCCTTATAA 0.833214 -20 ACCGCACTTTTTCCTTTAAAAGTGCGGTTA 6 106 1 TTCCTTTAAA 0.938876 -47 ACGTTCTTCCTAAAAAGATTGAAATT 6 137 0 TTCCTAAAAA 0.953835 -16 AATATTGTTCTCCCTATAAAATTTGGCGTG 7 105 0 TCCCTATAAA 0.791303 -70 TCCTACCCTTTTCCTTACAATACAACCATA 8 196 0 TTCCTTACAA 0.778856 -105 TAAACTATTTTTACTAAAAATAGACTTAAA 10 51 0 TTACTAAAAA 0.668155 -164 AGATGATGGATTTCTATTAACCTCAATCAA 10 182 1 TTTCTATTAA 0.848008 -33 CTGCTCCGATTTCCTTTTAAACAAGATAAT 11 90 0 TTCCTTTTAA 0.917752 -104 CAAGTAGCAAATTCTATAAATTTATGTTCT 11 136 1 ATTCTATAAA 0.800772 -58 ********** Masking position 9 Map Score: 8.6872 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 169 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 5 ACTTATACCCGCCTAAGAAAGATGTATTTCTT 3 39 1 GCCAGAAAGA 0.930713 -167 AAAGAATTTCGTAAAAGAAATACATCTTTCTT 3 53 0 GTAAGAAATA 0.783283 -153 AGTATAATGTGCCACACAAAAAGGATTAAAA 5 37 1 GCCACAAAAA 0.986116 -21 GGTAATCTTTGCAACACAAAAGTAAGTTTATT 6 70 1 GCAACAAAAG 0.950608 -83 ACTAAAGTCCGCCCGACAAAAATATTGGAAA 7 10 0 GCCACAAAAA 0.986116 -165 TTTATTTGAGGTATTAGAAAAACTAATTTGAA 8 244 1 GTAAGAAAAA 0.94568 -57 AACGTGGTCTGTAAGACAAAAAAATAAAAAAA 11 36 1 GTAACAAAAA 0.965899 -158 GGAAATCGGAGCAGTACAAAAACGGTCTTACA 11 106 1 GCAACAAAAA 0.986387 -88 *** ******* Masking position 6 Map Score: 5.9324 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 136 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 TGAATAATGCTTTTTCCATAGGAATGAATT 2 59 0 TTTTTCCATA 0.705508 -113 TCTCAAGATTTTCTCTCTTATGTCGAATAT 2 98 0 TTCTCTCTTA 0.8804 -74 AAAGAAATACATCTTTCTTAGGCGGGTATA 3 42 0 ATCTTTCTTA 0.623176 -164 TTTGTTGATATTCTTTCTTTTAATCTCGTT 3 172 1 TTCTTTCTTT 0.873891 -34 ATTCTCACTTTTATAAGGATC 4 15 0 TTCTCACTTT 0.751796 -11 ATAACCGCACTTTTTCCTTTAAAAGTGCGG 6 103 1 TTTTTCCTTT 0.917469 -50 ACGTTCTTCCTAAAAAGATTGAA 6 140 0 TTCTTCCTAA 0.934572 -13 TGAAATATTGTTCTCCCTATAAAATTTGGC 7 108 0 TTCTCCCTAT 0.840632 -67 CTTTCCTACCCTTTTCCTTACAATACAACC 8 199 0 CTTTTCCTTA 0.797246 -102 AATTAAACTATTTTTACTAAAAATAGACTT 10 54 0 TTTTTACTAA 0.632043 -161 AAGTTTGTATTTTTTCCTTACCGATGAATT 10 101 1 TTTTTCCTTA 0.949634 -114 ********** Masking position 4 Map Score: 4.21647 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 257 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 7 AAGACCGTAAAAATCGACCGCACTTTATCAA 1 55 0 AAATGACCGC 0.966493 -35 TTGTTATCCTAAAAAGACCGTAAAAATCGAC 1 68 0 AAAAGACCGT 0.843524 -22 AACCATTGTTGAAAACACGGCGATTTT 2 155 1 GAAACACGGC 0.923756 -17 GCCTACATAAAAATTCACGTCTATCTGACTA 7 141 1 AAATCACGTC 0.944901 -34 AATCGGGATGAAAAAAACGCCACTCAATGAG 8 14 1 AAAAAACGCC 0.867313 -287 TACCTCAAATAAAAAAACGTCACTTGTCCTT 8 226 0 AAAAAACGTC 0.935526 -75 TTCATAACCAAAAAGGACGTCGCGA 9 21 1 AAAAGACGTC 0.977243 -15 AAAAACACCTCAAAAATTGAC 10 1 1 AAAACACCTC 0.963495 -214 AACACCTCAAAAATTGACCGCACTTATCATA 10 14 1 AAATGACCGC 0.966493 -201 **** ****** Masking position 7 Map Score: 6.04242 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 312 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 8 GCTGAAAACTTTTTTATTTTAGGG 2 5 0 TTTTTATTTT 0.923546 -167 AGGCGGGTATAAGTTATTTTGATAGTGTTT 3 23 0 AAGTTATTTT 0.738372 -183 AAGAAAGATGTATTTCTTTTACGAAATTCT 3 53 1 TATTTCTTTT 0.729968 -153 AAATATAAGATACTTATTTGTTGATATTCT 3 156 1 TACTTATTTG 0.703167 -50 AAGTGACGTTTTTTTATTTGAGGTATTAGA 8 232 1 TTTTTATTTG 0.822575 -69 TACAAACTTTATCGTATTTTTTGAAAAATT 10 80 0 ATCGTATTTT 0.626523 -135 TACGATAAAGTTTGTATTTTTTCCTTACCG 10 94 1 TTTGTATTTT 0.822575 -121 CTTACCGATGAATTTATTTTATTCATCAAA 10 117 1 AATTTATTTT 0.923534 -98 CGTTATCTGAAATTTATTTTGGAGTATTT 11 10 0 AATTTATTTT 0.923534 -184 TTGAACATTTTTTTTATTTTTTTGTCTTAC 11 46 0 TTTTTATTTT 0.923546 -148 AAATTCTATAAATTTATGTTCTAATACGCG 11 144 1 AATTTATGTT 0.694544 -50 ********** Masking position 5 Map Score: 3.86916 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 285 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 9 GCCACAGTTTAATTCCTTGATAAAGTGCGGTC 1 39 1 ATTCCTTATA 0.982529 -51 ATAGGAATGAATTTTCTTTATAATCTGTAGTC 2 40 0 ATTTCTTATA 0.938815 -132 ATATCAATCTAGTTCCTTTATTGCCTATCAAG 3 97 1 ATTCCTTATT 0.960724 -109 TGTTGCAAAGATTACCTTAATTTTTTCAAATT 6 54 0 ATACCTTATT 0.83547 -99 CACAAAAGTAAGTTTATTCATAACCGCACTTT 6 84 1 ATTTATTATA 0.665579 -69 TTACTCATTTACTTCCTGTATATTATTAAACC 8 64 0 ATTCCTGATA 0.945362 -237 AATGATTGGTAATTCCTTACTAGTTAATGAGT 8 161 0 ATTCCTTCTA 0.945374 -140 * ****** *** Masking position 1 Map Score: 0.988068 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 32 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 CAGTGAAAACCATTTGCGCCACAGTTTAAT 1 22 1 CATTTGCGCC 0.92778 -68 AATTTTTTCAAATTTGCGATAAAATTCTGT 6 38 0 AATTTGCGAT 0.934252 -115 GCCTACGATAAATTCGCTCTAATTGTTTGT 7 55 0 AATTCGCTCT 0.907873 -120 CTTGAGTAACAATTTGTTACTCATTTACTT 8 82 0 AATTTGTTAC 0.806555 -219 TAAACAAGATAATTTGCTCTCCTCTTATTG 11 73 0 AATTTGCTCT 0.964224 -121 AAATTTATAGAATTTGCTACTTGTAAGACC 11 129 0 AATTTGCTAC 0.964224 -65 ********** Masking position 4 Map Score: 0.71121 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 94 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 GACCGCACTTTATCAAGGAATTAAACTGTG 1 41 0 TATCAAGGAA 0.972586 -49 GACTACAGATTATAAAGAAAATTCATTCCT 2 40 1 TATAAAGAAA 0.892237 -132 CTTGATAGGCAATAAAGGAACTAGATTGAT 3 99 0 AATAAAGGAA 0.86644 -107 CTTTATTGCCTATCAAGGATCATCGCAAGA 3 112 1 TATCAAGGAT 0.864106 -94 AAAGAAAGAATATCAACAAATAAGTATCTT 3 162 0 TATCAACAAA 0.741685 -44 TAACCGCACTTTTAAAGGAAAAAGTGCGGT 6 106 0 TTTAAAGGAA 0.866438 -47 GGTTTAATAATATACAGGAAGTAAATGAGT 8 64 1 TATACAGGAA 0.917619 -237 TCTTGTCCATTATAGACGAAAATTTTATAA 8 281 1 TATAGACGAA 0.797605 -20 ********** Masking position 6 Map Score: 2.30879 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 84 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 12 ********** No masking Map Score: -4.67335e-15 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: -4.67335e-15 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: -4.67335e-15 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