AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00780_hinf_reg_100.orf -o00780_hinf_100.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 HI0151 109 hflK protein (hflK) #2 HI0419 168 protease, putative #3 HI0587 99 peptidase E (pepE) #4 HI1022 112 biotin synthetase (bioB) #5 HI1445 102 dethiobiotin synthase (bioD-1) #6 HI1541 97 protease IV (sppA) #7 HI1556 59 2-hydroxyacid dehydrogenase #8 HI1560 22 H. influenzae predicted coding region HI1560 #9 HI1561 106 peptide chain release factor 1 (prfA) #10 HI1682 197 protease, putative (sohB) Motif number 1 TAAGAATTTAACCGCACTTTCCTTTACAAG 2 67 1 ACCGCACTTT 0.999065 -102 GGTTAAAAACACCACGCTTTTTATACTTTC 4 74 0 ACCACGCTTT 0.977331 -39 GGTGTTTTTAACCGCACTTTCAAAGGAAAA 4 91 1 ACCGCACTTT 0.999065 -22 TTTAAAATCCACCGCACTTTTTAAAGGAGA 5 78 1 ACCGCACTTT 0.999065 -25 GCTATAATCCACCGCACTTTTACTTATAAG 6 21 0 ACCGCACTTT 0.999065 -77 GTCAAAATTAACCGCACTTTTGATGAAAT 7 10 0 ACCGCACTTT 0.999065 -50 GTTAATTTTGACCGCACTTTGTATATAAAA 7 28 1 ACCGCACTTT 0.999065 -32 ********** Masking position 1 Map Score: 31.5923 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AAGAATTTAACCGCACTTTCCTTTACAAGC 2 68 1 CCGCACTTTC 0.998536 -101 GTTAAAAACACCACGCTTTTTATACTTTCT 4 73 0 CCACGCTTTT 0.970452 -40 GTGTTTTTAACCGCACTTTCAAAGGAAAAA 4 92 1 CCGCACTTTC 0.998536 -21 TTAAAATCCACCGCACTTTTTAAAGGAGAA 5 79 1 CCGCACTTTT 0.998786 -24 CTATAATCCACCGCACTTTTACTTATAAGG 6 20 0 CCGCACTTTT 0.998786 -78 TCAAAATTAACCGCACTTTTGATGAAAT 7 9 0 CCGCACTTTT 0.998786 -51 TTAATTTTGACCGCACTTTGTATATAAAAA 7 29 1 CCGCACTTTG 0.99731 -31 ********** Masking position 7 Map Score: 24.9408 Number of sites scoring better than the average of aligned sites = 1040 Number in coding regions = 687 Number in noncoding regions = 353 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 3 TTATATAAGGATTTTTTTGA 1 1 0 ATTTTTTTGA 0.736888 -109 AAAAATCCTTGATTTTATATAAGGATTTTT 1 15 0 GATTTTATAT 0.690574 -95 TAAAATCAAGGATTTTTTATTGCCTAAAAA 1 28 1 GATTTTTTAT 0.92244 -82 AACTCTTAACAATTTTTTGACAA 1 97 1 AATTTTTTGA 0.966051 -13 TAAGCGGTTAAATTTTATATAAAATTCCAC 2 37 1 AATTTTATAT 0.81553 -132 TGATACGGTTTATTTTTTGATATTCGTCAA 3 21 1 TATTTTTTGA 0.783343 -79 GAAAAATTATAATTGTTTGACGAATATCAA 3 37 0 AATTGTTTGA 0.929053 -63 AAACAATTATAATTTTTCGTTGAAAATTAA 3 49 1 AATTTTTCGT 0.879195 -51 CATAACGTTGAATTGATTGTTTCTACCATA 4 24 1 AATTGATTGT 0.693224 -89 ATTTTAAAGGAATTTTTTATTTAATAATTT 5 56 0 AATTTTTTAT 0.959282 -47 CGCTAGCACAAATTTTTTAAAGGTAATTTG 6 77 1 AATTTTTTAA 0.930734 -21 ATTAATTTAAAATTTTTTGTTATAAATAGC 10 86 1 AATTTTTTGT 0.98035 -112 AAAACATTGTGATTGTTTGTGCTATTTATA 10 106 0 GATTGTTTGT 0.920574 -92 AAACAATCACAATGTTTTATTATGTTGGCG 10 118 1 AATGTTTTAT 0.774605 -80 ********** Masking position 3 Map Score: 15.5844 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 504 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 4 TTTGGCTTGTAAAGGAAAGTGCGGTTAAAT 2 72 0 AAAGGAAAGT 0.89486 -97 GGGACTTACTCAAGGTAAATCGTTAGGTGG 2 120 0 CAAGGTAAAT 0.713362 -49 GAAATCAGACAAAAGAGAATATT 2 156 1 AAAAGAGAAT 0.852466 -13 TACGCTTAGAAAAGGTTAATTTTCAACGAA 3 64 0 AAAGGTTAAT 0.728959 -36 CCGCACTTTCAAAGGAAAAAC 4 102 1 AAAGGAAAAA 0.968739 -11 ATAAGATAAAAAAAGTGAAAATTTGCGTTA 5 22 1 AAAAGTGAAA 0.647158 -81 GGTGGATTTTAAAGGAATTTTTTATTTAAT 5 61 0 AAAGGAATTT 0.686355 -42 CGCACTTTTTAAAGGAGAAAAAA 5 90 1 AAAGGAGAAA 0.969304 -13 CAAATTTTTTAAAGGTAATTTGT 6 85 1 AAAGGTAATT 0.887617 -13 TGTATATAAAAAAGGAGCAATTA 7 47 1 AAAGGAGCAA 0.908895 -13 TTGACAGCGAAAAGGAAATTAAGAATCTCA 9 35 0 AAAGGAAATT 0.949732 -72 CATTTATACCAAAGGAGCAATT 10 3 0 AAAGGAGCAA 0.908895 -195 CCTTTGGTATAAATGAAATACTCGCTTATG 10 18 1 AAATGAAATA 0.665917 -180 AAATTAGCCAAAATGAAAATAAAAAGTAAG 10 55 1 AAATGAAAAT 0.850083 -143 ********** Masking position 3 Map Score: 13.5991 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 419 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 5 AAATCCTTGATTTTATATAAGGATTTTTTT 1 13 0 TTTTATATAA 0.903906 -97 CTAAAAAGCCTTGTATTTTCATAGACGTGC 1 51 1 TTGTATTTTC 0.887434 -59 GCTTAATAGGTTGTATTTAATTCCTCAAAT 2 12 0 TTGTATTTAA 0.831003 -157 CTTAGTGGAATTTTATATAAAATTTAACCG 2 41 0 TTTTATATAA 0.903906 -128 AAGCCAAATATTTTCTCTACAATACCCCAC 2 94 1 TTTTCTCTAC 0.755694 -75 CGGTTTATTTTTTGATATTCGTCAAACAAT 3 26 1 TTTGATATTC 0.758439 -74 TTTTCACTTTTTTTATCTTATAAATAGACA 5 13 0 TTTTATCTTA 0.879 -90 TAAAGGAATTTTTTATTTAATAATTTGAGA 5 52 0 TTTTATTTAA 0.927448 -51 ATTGCTCCTTTTTTATATACAAAGTGCGGT 7 38 0 TTTTATATAC 0.951704 -22 AATACGCCGATTTTATTTTCGGTGACTTAC 9 85 1 TTTTATTTTC 0.953577 -22 AATTCTTACTTTTTATTTTCATTTTGGCTA 10 59 0 TTTTATTTTC 0.953577 -139 ********** Masking position 6 Map Score: 12.7791 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 197 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 TTTATTTAGCTAAACTCTTAACAATTTTTT 1 85 1 TAAACTCTTA 0.621525 -25 TATTAAGCGGTTAAATTTTATATAAAATTC 2 34 1 TTAAATTTTA 0.658522 -135 AAAGTGCGGTTAAATTCTTAGTGGAATTTT 2 57 0 TAAATTCTTA 0.88623 -112 TTAGAAAAGGTTAATTTTCAACGAAAAATT 3 59 0 TTAATTTTCA 0.93699 -41 TGAGATAACGCAAATTTTCACTTTTTTTAT 5 27 0 CAAATTTTCA 0.892798 -76 TGCGTTATCTCAAATTATTAAATAAAAAAT 5 45 1 CAAATTATTA 0.662451 -58 TACGCTAGCACAAATTTTTTAAAGGTAATT 6 75 1 CAAATTTTTT 0.418388 -23 AAAAGTGCGGTTAATTTTGACCGCACTTTG 7 19 1 TTAATTTTGA 0.77356 -41 ATTCTTACTTTTTATTTTCATTTTGGCTAA 10 58 0 TTTATTTTCA 0.633293 -140 AAATTTTAAATTAATTCTTACTTTTTATTT 10 71 0 TTAATTCTTA 0.8877 -127 TTTAATGGATTAAATTTTCACGACACTGGT 10 161 0 TAAATTTTCA 0.933973 -37 ATTTAATCCATTAAATATCAACGGGAGTAA 10 176 1 TTAAATATCA 0.538882 -22 ********** Masking position 4 Map Score: 4.44926 Number of sites scoring better than the average of aligned sites = 612 Number in coding regions = 425 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 7 ATAAAAAATCCTTGATTTTATATAAGGATT 1 18 0 CTTGATTTTA 0.859444 -92 TTCTCTTTTGTCTGATTTCAGGTCAGGGAC 2 145 0 TCTGATTTCA 0.946946 -24 AAAAAGTGCGGTGGATTTTAAAGGAATTTT 5 70 0 GTGGATTTTA 0.905791 -33 GATAGGGACATCTGATTTCAG 8 12 1 TCTGATTTCA 0.946946 -11 GCGTATTCTAGCCGATTTTAGGGAAAATTG 9 62 0 GCCGATTTTA 0.981261 -45 GCTAGAATACGCCGATTTTATTTTCGGTGA 9 80 1 GCCGATTTTA 0.981261 -27 ********** Masking position 5 Map Score: 2.91794 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 112 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 ATACAAGGCTTTTTAGGCAATAAAAAATCC 1 37 0 TTTTAGGCAA 0.976257 -73 TCTTAACAATTTTTTGACAA 1 100 1 TTTTTGACAA 0.960665 -10 AGGTGGGGTATTGTAGAGAAAATATTTGGC 2 96 0 TTGTAGAGAA 0.913807 -73 TATAGCATAGTTTTTGACAAGGCTTTGTGA 6 45 1 TTTTTGACAA 0.960665 -53 TTCTAGCCGATTTTAGGGAAAATTGACAGC 9 57 0 TTTTAGGGAA 0.966041 -50 ********** Masking position 4 Map Score: 2.91448 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 54 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 GTTGTATTTAATTCCTCAAATC 2 3 0 ATTCCTCAAA 0.974324 -166 ATTTTTTGATATTCGTCAAACAATTATAAT 3 32 1 ATTCGTCAAA 0.974324 -68 ATATACACTAATTCATCAATTAAGAAAGTA 4 51 1 ATTCATCAAT 0.915377 -62 ATTTCATCAAAAGTGCGGTTA 7 2 1 TTTCATCAAA 0.915377 -58 ********** Masking position 6 Map Score: 0.79304 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 47 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 TGATTTCAGGTCAGGGACTTACTCAAGGTAAA 2 131 0 TCGGACTTAC 0.991659 -38 AGACGCTTTATTTGTGATTTACCCA 9 4 0 TTGGATTTAC 0.980276 -103 GATTTTATTTTCGGTGACTTACAA 9 93 1 TCGGACTTAC 0.991661 -14 TTTTATTATGTTGGCGATCTACACACTAAACC 10 132 1 TTGGATCTAC 0.966833 -66 ** * ******* Masking position 7 Map Score: 0.0127337 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 ********** No masking Map Score: -4.94948e-13 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 ********** No masking Map Score: -4.94948e-13 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: -4.94948e-13 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