AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_1_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0658 160 ABC transporter, ATP-binding protein #2 HI0660 269 H. influenzae predicted coding region HI0660 #3 HI0661 300 hemoglobin-binding protein #4 HI1560 22 H. influenzae predicted coding region HI1560 #5 HI1561 106 peptide chain release factor 1 (prfA) #6 HI1562 252 H. influenzae predicted coding region HI1562 #7 HI1563 32 conserved hypothetical protein #8 HI1564 32 H. influenzae predicted coding region HI1564 #9 HI1564.1 284 H. influenzae predicted coding region HI1564.1 Motif number 1 TACCGCACTTTTGATTTTAGATAGGT 2 5 0 TTGTTTAGAT 0.943186 -265 CAATAAGTTATTGATTTTTGATGTGTAATCAT 2 215 0 TTGTTTTGAT 0.985241 -55 CAATAACTTATTGGTTATTGAAATAAGTAGAT 2 234 1 TTGTTTTGAA 0.955783 -36 CGTACTTCTTTTTATTTTAGGAGTAATCATTA 3 39 0 TTTTTTAGGA 0.669195 -262 TATCTTACGATTGTTTGATGGTGGGCTGAAGC 3 123 1 TTGTTATGGT 0.797126 -178 ATGCGAGCCGTTGATTGTTGATATTAGTAATT 3 164 0 TTGTTTTGAT 0.985241 -137 AGAATAGTTTTTATTTCTTGATTTTGATCAAA 3 233 1 TTATTTTGAT 0.920256 -68 ATACTAAAAGTGTATTTTTGATCAAAATCAAG 3 249 0 TGTTTTTGAT 0.894991 -52 TCTCAGACGCTTTATTTGTGATTTACCCA 5 8 0 TTTTTGTGAT 0.822418 -99 ATACGCCGATTTTATTTTCGGTGACTTACAA 5 86 1 TTTTTTCGGT 0.785612 -21 CTTGTTTTAGTGTGTTTTTGATTTGCCAAAAC 6 187 1 TGTTTTTGAT 0.894991 -66 ATTGCTTCAATTTTTTCTTGAAGATCAGGCTG 6 218 0 TTTTTTTGAA 0.922029 -35 TATTATTATTTTTTTTATAGGACTAAATATGA 9 65 0 TTTTTTAGGA 0.669195 -220 ACAATAAAGATTGATTTTTGATAAAAATCAAG 9 137 1 TTGTTTTGAT 0.985241 -148 AGAATAGTTTTTATTTCTTGATTTTTATCAAA 9 153 0 TTATTTTGAT 0.920256 -132 ATGCGAGCCGTTGATTGTTGATTAGTAGTTGT 9 222 1 TTGTTTTGAT 0.985241 -63 TATCTCTCGATTGTTTTTTGGTGGGCTAAAGC 9 261 0 TTGTTTTGGT 0.978687 -24 *** ** ***** Masking position 6 Map Score: 29.8811 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 237 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 TACTTAATGTAGGGTGGGCTTCAGCCCACC 3 89 1 AGGGTGGGCT 0.998599 -212 GTAAGATATTTTGGTGGGCTGAAGCCCACC 3 101 0 TTGGTGGGCT 0.997782 -200 CGATTGTTTGATGGTGGGCTGAAGCCCACC 3 130 1 ATGGTGGGCT 0.997782 -171 TAGTAATTGTAGGGTGGGCTTCAGCCCACC 3 142 0 AGGGTGGGCT 0.998599 -159 TAGGAGGGAATTGGAGGGCTTAAGACTGAA 6 42 0 TTGGAGGGCT 0.987746 -211 TATTCCGTTATGCTTGGGCTAACGGCAA 9 9 0 TGCTTGGGCT 0.929505 -276 TAGTAGTTGTAGGGTGGGCTTTAGCCCACC 9 244 1 AGGGTGGGCT 0.998599 -41 CGATTGTTTTTTGGTGGGCTAAAGCCCACC 9 256 0 TTGGTGGGCT 0.997782 -29 ********** Masking position 10 Map Score: 26.2491 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 18 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 GTGGGCTGAAGCCCACCCTACATTAAGTAC 3 88 0 GCCCACCCTA 0.998287 -213 GTGGGCTTCAGCCCACCAAAATATCTTACG 3 102 1 GCCCACCAAA 0.99731 -199 GTGGGCTTCAGCCCACCATCAAACAATCGT 3 129 0 GCCCACCATC 0.994366 -172 GTGGGCTGAAGCCCACCCTACAATTACTAA 3 143 1 GCCCACCCTA 0.998287 -158 TCAGTCTTAAGCCCTCCAATTCCCTCCTAA 6 43 1 GCCCTCCAAT 0.949967 -210 GTGGGCTAAAGCCCACCCTACAACTACTAA 9 243 0 GCCCACCCTA 0.998287 -42 GTGGGCTTTAGCCCACCAAAAAACAATCGA 9 257 1 GCCCACCAAA 0.99731 -28 ********** Masking position 6 Map Score: 20.2724 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 20 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 AATAAGACGCAATAAAAACTATTTATAATATAACA 1 32 0 AATAACATTA 0.977022 -129 ATCTCCTTGAAAATCAAGCTATTTTCGCTATTTTT 2 124 1 AAAAACATTT 0.934366 -146 AATTTATCCTATTTATCTACTTATT 2 255 0 AATATCATTA 0.843817 -15 TGTTTCCTATAATGCGAGCCGTTGATTGTTGATAT 3 172 0 AATGACGTTA 0.956333 -129 AAAATCAAGAAATAAAAACTATTCTCATTATTTGC 3 223 0 AATAACATTT 0.972813 -78 AAGACTGAAAAAAGTGAGCAATTTTGATCACTTTC 6 16 0 AAAGACATTT 0.950306 -237 AAATGATTAAAAATTGAACTATTTAATTAGGAGGG 6 64 0 AAAGACATTA 0.957852 -189 TTCAAGAAAAAATTGAAGCAATTAAAGAAGAATTG 6 228 1 AATAACATTA 0.977023 -25 TATAGGACTAAATATGACCAATTTTAGATTAAACG 9 47 0 AATGACATTT 0.97959 -238 AAAATCAAGAAATAAAAACTATTCTTATTATTTTC 9 160 1 AATAACATTT 0.972813 -125 TGTTTCCTATAATGCGAGCCGTTGATTGTTGATTA 9 211 1 AATGACGTTA 0.956333 -74 *** ** * *** * Masking position 2 Map Score: 14.6678 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 75 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TTTTCTAGTCAAAAAAGCCACGTATAATAA 1 62 0 AAAAAAGCCA 0.655717 -99 GAAAATCGATAAAATCGGAATAGACTGTTC 1 87 1 AAAATCGGAA 0.736494 -74 AAAATATTGCAAAATAGCCTCAAATTAAGA 1 128 1 AAAATAGCCT 0.804047 -33 CCGATGTTTGAACATTGGCTTTGAAAGAGA 2 82 0 AACATTGGCT 0.868565 -188 CCAATGTTCAAACATCGGCATTTGTGCAAA 2 94 1 AACATCGGCA 0.968905 -176 GCATTTGTGCAAAATCTCCTTGAAAATCAA 2 111 1 AAAATCTCCT 0.656483 -159 ATGATGATAGATAAACGCCTAATTAACAC 3 10 0 ATAAACGCCT 0.887373 -291 AATATCAACAATCAACGGCTCGCATTATAG 3 171 1 ATCAACGGCT 0.926949 -130 AATTTTCCCTAAAATCGGCTAGAATACGCC 5 63 1 AAAATCGGCT 0.98317 -44 CACCGAAAATAAAATCGGCGTATTCTAGCC 5 79 0 AAAATCGGCG 0.939453 -28 ACAACAAAGCATAATTGGCAACTAGGATTA 6 141 1 ATAATTGGCA 0.751643 -112 TCGACTCCTAAAAAACCGCAAGATTATA 7 9 0 AAAAACCGCA 0.742505 -24 CTAATCAACAATCAACGGCTCGCATTATAG 9 217 0 ATCAACGGCT 0.926949 -68 ********** Masking position 4 Map Score: 9.69902 Number of sites scoring better than the average of aligned sites = 770 Number in coding regions = 680 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 TTATATTATAAATAGTTTTTATTGCGTCTT 1 34 1 AATAGTTTTT 0.924312 -127 GCTATTTTGCAATATTTTTTCTTTTCTCGG 1 116 0 AATATTTTTT 0.904633 -45 TCGCCAAATTTTTAGTTTCTATTTATGATT 2 191 1 TTTAGTTTCT 0.694215 -79 AAGTACGCATAATTCTTTCTATGCGTACTT 3 64 0 AATTCTTTCT 0.821518 -237 AACTATTCTCATTATTTGCTGTATTTAAAC 3 212 0 ATTATTTGCT 0.723266 -89 AAATAATGAGAATAGTTTTTATTTCTTGAT 3 225 1 AATAGTTTTT 0.924312 -76 ATTGTGAGAGAATACTTTCTCCTATAATAT 3 279 1 AATACTTTCT 0.953581 -22 AGCAATTTTGATCACTTTCTGCCA 6 5 0 ATCACTTTCT 0.71924 -248 TAATTGCTTCAATTTTTTCTTGAAGATCAG 6 222 0 AATTTTTTCT 0.824435 -31 GAGAATTATTATTATTTTTTTTATAGGACT 9 73 0 ATTATTTTTT 0.873277 -212 AAATAATAAGAATAGTTTTTATTTCTTGAT 9 163 0 AATAGTTTTT 0.924312 -122 AACTATTCTTATTATTTTCTGTATTTAAAC 9 176 1 ATTATTTTCT 0.938365 -109 ********** Masking position 6 Map Score: 10.3132 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 279 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 CGGTAAAAATTTACCGCACTTTTGATTTTAG 2 17 0 TTACGCACTT 0.949391 -253 CGGTAAATTTTTACCGCACTTTTTCTTAAGA 2 32 1 TTACGCACTT 0.949391 -238 AATTTATCCTATTTATCTACTTAT 2 256 0 TTACCTATTT 0.688337 -14 TAATTCTTTCTATGCGTACTTCTTTTTATTT 3 54 0 TATCGTACTT 0.95854 -247 TAGAAAGAATTATGCGTACTTAATGTAGGGT 3 73 1 TATCGTACTT 0.95854 -228 TTGCTGTATTTAAACGTGCTTGTTTCCTATA 3 196 0 TAACGTGCTT 0.983699 -105 ATATGCTTGCTAATCCTAGTTGCCAATTATG 6 150 0 TAACCTAGTT 0.861883 -103 AATTTTAGATTAAACGTGCTTGCCTATTCCG 9 32 0 TAACGTGCTT 0.983699 -253 TTTCTGTATTTAAACCTGCTTGTTTCCTATA 9 191 1 TAACCTGCTT 0.968847 -94 *** ******* Masking position 10 Map Score: 8.01775 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 426 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 8 GTCAAAAAAGCCACGTATAATAAGACGCAA 1 55 0 CCACGTATAA 0.958026 -106 ATAAAAAGAAGTACGCATAGAAAGAATTAT 3 56 1 GTACGCATAG 0.840267 -245 CCTACATTAAGTACGCATAATTCTTTCTAT 3 72 0 GTACGCATAA 0.952115 -229 TAGGAAACAAGCACGTTTAAATACAGCAAA 3 198 1 GCACGTTTAA 0.958733 -103 GAGAGTACAACAAAGCATAATTGGCAACTA 6 135 1 CAAAGCATAA 0.69446 -118 ACTAGGATTAGCAAGCATATTGTCGCCTTG 6 161 1 GCAAGCATAT 0.859051 -92 TGCCGTTAGCCCAAGCATAACGGAATAGGC 9 12 1 CCAAGCATAA 0.945932 -273 GAATAGGCAAGCACGTTTAATCTAAAATTG 9 34 1 GCACGTTTAA 0.958733 -251 TAGGAAACAAGCAGGTTTAAATACAGAAAA 9 190 0 GCAGGTTTAA 0.841947 -95 ********** Masking position 3 Map Score: 4.61762 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 223 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 GATTTTATCGATTTTCTAGTCAAAAAAGCCACGT 1 69 0 ATTTTCTAAA 0.769651 -92 AATATTTTTTCTTTTCTCGGAACAGTCTATTCCG 1 102 0 CTTTTCTCAA 0.948297 -59 AAAGATAGATCCTTTCTTAAGAAAAAGTGCGGTA 2 43 0 CCTTTCTTAA 0.93371 -227 TCTATCTTTTACTCTCTCTTTCAAAGCCAATGTT 2 68 1 ACTCTCTCCA 0.920842 -202 GATTGAAATGACTATCTCGCCAAATTTTTAGTTT 2 175 1 ACTATCTCAA 0.926099 -95 AGGAGAAAGTATTCTCTCACAATACTAAAAGTGT 3 268 0 ATTCTCTCAA 0.955052 -33 GTGAGAGAATACTTTCTCCTATAATATGT 3 282 1 ACTTTCTCTA 0.904904 -19 TGGGTGTTGTACTCTCTTTACAGAGAGTACAACA 6 113 1 ACTCTCTTAA 0.942256 -140 TGAGAAAATACCTTTCTTCATATAATATGTTTGA 9 101 0 CCTTTCTTAA 0.933712 -184 GAAGAAAGGTATTTTCTCACAACAATAAAGATTG 9 116 1 ATTTTCTCAA 0.962631 -169 ******** * * Masking position 7 Map Score: 5.42372 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 99 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 CTTTGAAAGAGAGAGTAAAAGATAGATCCT 2 64 0 GAGAGTAAAA 0.980388 -206 ATCATAAATAGAAACTAAAAATTTGGCGAG 2 190 0 GAAACTAAAA 0.892202 -80 GTAAGTCACCGAAAATAAAATCGGCGTATT 5 85 0 GAAAATAAAA 0.848123 -22 TCTCTGTAAAGAGAGTACAACACCCAGTAT 6 109 0 GAGAGTACAA 0.981806 -144 TCTCTTTACAGAGAGTACAACAAAGCATAA 6 125 1 GAGAGTACAA 0.981806 -128 ********** Masking position 6 Map Score: 2.8371 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 4 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 TTAGTTTCTATTTATGATTACACATCAAAA 2 202 1 TTTATGATTA 0.684678 -68 AGGAGTAATCATTATGATGATAGATAAACG 3 23 0 ATTATGATGA 0.84516 -278 AATAAAAACTATTCTCATTATTTGCTGTAT 3 218 0 ATTCTCATTA 0.787902 -83 TTATTTCTTGATTTTGATCAAAAATACACT 3 243 1 ATTTTGATCA 0.936028 -58 AAAGTGAGCAATTTTGATCACTTTCTGCCA 6 11 0 ATTTTGATCA 0.936028 -242 ATGTTTGAGAATTATTATTATTTTTTTTAT 9 79 0 ATTATTATTA 0.854367 -206 TTATTTCTTGATTTTTATCAAAAATCAATC 9 145 0 ATTTTTATCA 0.876306 -140 AATAAAAACTATTCTTATTATTTTCTGTAT 9 170 1 ATTCTTATTA 0.86363 -115 ********** Masking position 7 Map Score: 1.95708 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 141 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 CTATTTTCGCTATTTTTGCGATCTAGATCG 2 142 1 TATTTTTGCG 0.931745 -128 TAGAAACTAAAAATTTGGCGAGATAGTCAT 2 182 0 AAATTTGGCG 0.941137 -88 GTGTTAATTAGGCGTTTATCTATC 3 5 1 TAATTAGGCG 0.980304 -296 CGCATAGAAAGAATTATGCGTACTTAATGT 3 69 1 GAATTATGCG 0.89808 -232 AATCGTAAGATATTTTGGTGGGCTGAAGCC 3 105 0 TATTTTGGTG 0.81349 -196 TTGAACTATTTAATTAGGAGGGAATTGGAG 6 56 0 TAATTAGGAG 0.885056 -197 TATAATCTTGCGGTTTTTTAGG 7 3 1 TAATCTTGCG 0.90615 -30 ********** Masking position 2 Map Score: 1.47902 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 216 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 ATTTTCGCTATTTTTGCGATCTAGATCGAA 2 144 1 TTTTTGCGAT 0.81218 -126 AGTCATTTCAATCTTTCGATCTAGATCGCA 2 158 0 ATCTTTCGAT 0.978079 -112 GTACGCATAATTCTTTCTATGCGTACTTCT 3 62 0 TTCTTTCTAT 0.800244 -239 CCACCAAAATATCTTACGATTGTTTGATGG 3 114 1 ATCTTACGAT 0.924432 -187 TATAATCTTGCGGTTTTTTAGGAG 7 5 1 ATCTTGCGGT 0.949686 -28 AATATCTCTCGATTGTTTTTTGG 9 272 0 ATCTCTCGAT 0.942124 -13 ********** Masking position 4 Map Score: 0.922538 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 46 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 TTTCCTATAATGCGAGCCGTTGATTGTTGA 3 175 0 TGCGAGCCGT 0.992588 -126 AATCGGCGTATTCTAGCCGATTTTAGGGAA 5 67 0 TTCTAGCCGA 0.956124 -40 AGATTAAACGTGCTTGCCTATTCCGTTATG 9 27 0 TGCTTGCCTA 0.896098 -258 TTTCCTATAATGCGAGCCGTTGATTGTTGA 9 213 1 TGCGAGCCGT 0.992588 -72 ********** Masking position 1 Map Score: 0.184713 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 ********** No masking Map Score: -8.85746e-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