AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ifur_hinf_opreg_100.orf -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 HI0190 28 ferric uptake regulation protein (fur) #2 HI0191 96 flavodoxin (fldA) #3 HI0253 168 biopolymer transport protein (exbB) #4 HI0262 300 heme-hemopexin utilization protein C #5 HI0866 300 H. influenzae predicted coding region HI0866 #6 HI1088 248 superoxide dismutase (sodA) Motif number 1 AGGCTTATCCAAATTTGGCGAACTATATCATAAAA 2 30 0 AAATTTCAAA 0.981627 -67 TCAATAGATTAAATTTAATATAAAAAAGGAAATAA 2 70 1 AAATTTTTAA 0.883203 -27 AAAAATTCAGAAATTTTTCAATTCAAGGTTTACGC 3 53 1 AAATTTCATA 0.916189 -116 ATTCTCAAAGAAATTTCTCAAATAACAAGGAAAAA 3 142 1 AAATTTCAAA 0.981643 -27 GTACCTGCAAAAATTGGACTAAATAAGCGAGAGAT 4 138 0 AAATTGCAAA 0.988323 -163 TAAGTTACCGAAATCGGTTGAACGAGGCACAACCC 5 17 0 AAATCGTAAA 0.842996 -284 GGAAGTGCCTAAATTGACCATACAATGAACCTGAT 5 113 0 AAATTGCTAA 0.968211 -188 TCACCCATACAGATTGTTTTAAGAACTGGCGTTTT 5 164 0 AGATTGTAAA 0.842996 -137 GTATGGGTGAAAATTATACTAAGGAGATGACAGAA 5 189 1 AAATTACAAA 0.917437 -112 GTTGTTCACGAAATTGATCCGAAGAAAAAAGATTT 5 269 1 AAATTGCGAA 0.946992 -32 TGAGTTGCGAAAATTTCATCAAATATTAGAATACT 6 38 0 AAATTTTAAA 0.955071 -211 TGAATTTATTAAATTTTGTTTTAAATCAATAAACC 6 103 0 AAATTTTTTA 0.606989 -146 TCTATAACCAAAATTGAGCAAATAATAGCAAAAAA 6 178 0 AAATTGCAAA 0.988175 -71 ****** * ** * Masking position 3 Map Score: 15.1602 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 257 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 2 AATTTTCCTTCCTATTATGCAC 1 17 0 TTTTCCTTCC 0.971768 -12 TTTTATTTCCTTTTTTATATTAAA 2 83 0 ATTTCCTTTT 0.928293 -14 TTTTTTTCCTTGTTATTTGAGAA 3 156 0 TTTTCCTTGT 0.964686 -13 CTGTTTTCCTTATTGTAATAATT 4 288 0 TTTTCCTTAT 0.948537 -13 GCGACAGTGAATTTTCTTCTGTAGCGTTAT 5 85 1 ATTTTCTTCT 0.942146 -216 CAATTTAGGCACTTCCTTCTTTCTAGAGAT 5 132 1 ACTTCCTTCT 0.932022 -169 AAATATGTCTTTATTCTTCTGTCATCTCCT 5 210 0 TTATTCTTCT 0.838575 -91 AGTTAAATCTTTTTTCTTCGGATCAATTTC 5 278 0 TTTTTCTTCG 0.895028 -23 TCACTTTCTATTTTCCCTCTGTAATT 6 7 0 TTTTCCCTCT 0.968831 -242 CATTAAATGTTTTTCCTTTTTTAAAAAGTG 6 136 0 TTTTCCTTTT 0.97015 -113 AATGTATTCCTTCTATTGTTAAAA 6 235 0 TATTCCTTCT 0.958719 -14 ********** Masking position 4 Map Score: 13.1062 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 285 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 AATTTAATCTATTGATTATAAGGCTTATCCAAATTTG 2 48 0 ATGATTATAA 0.961325 -49 TAATCAATAGATTAAATTTAATATAAAAAAGGAAATA 2 67 1 ATAAATTTAA 0.583337 -30 TATAATTGAGAATGAATTTCAATCATACGGGGGATTT 3 106 0 ATGAATTTAA 0.905852 -63 ACAGCAAGTTATTGATTTTTAACTTAAAAAAACTAAA 4 63 0 ATGATTTTAA 0.981706 -238 GACTAAATATAATTATTTTGACAGCAAGTTATTGATT 4 83 0 ATTATTTTAA 0.881809 -218 AGATTAAGGTATAGATTTTTATGACTAAATATAATTA 4 105 0 AAGATTTTAA 0.957353 -196 TTTTGCAGGTACAGATTGAAATCCAAAATTAGTTTGA 4 161 1 AAGATTGAAA 0.780365 -140 ATTAAATTCAAATGATTATAAATAAACCAATTGATTA 4 208 1 ATGATTATAC 0.78162 -93 AAATAAACCAATTGATTATTATTATTATTATTATTAT 4 227 1 ATGATTATAA 0.96123 -74 TCCTTATTGTAATAATTAAAAAGAGGAGAATGGCGAT 4 268 0 ATAATTAAAA 0.723961 -33 CCTTCTTTCTAGAGATTTAAAACGCCAGTTCTTAAAA 5 146 1 AAGATTTAAA 0.944584 -155 AAGAATAAAGACATATTTATATTGAAAATGTAGTCTC 5 222 1 AATATTTAAA 0.703085 -79 CGATAGGTTTATTGATTTAAAACAAAATTTAATAAAT 6 98 1 ATGATTTAAA 0.975982 -151 TAGCAAAAAAATTGATTTAGATCATTAAATGTTTTTC 6 151 0 ATGATTTAAA 0.976062 -98 * ******* * * Masking position 11 Map Score: 12.171 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 232 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 AAATTTAATCTATTGATTATAAGGCTTATC 2 56 0 TATTGATTAT 0.913762 -41 GACAGCAAGTTATTGATTTTTAACTTAAAA 4 71 0 TATTGATTTT 0.947282 -230 TGACTAAATATAATTATTTTGACAGCAAGT 4 91 0 TAATTATTTT 0.61539 -210 GAGATTAAGGTATAGATTTTTATGACTAAA 4 113 0 TATAGATTTT 0.816625 -188 AATTAAATTCAAATGATTATAAATAAACCA 4 207 1 AAATGATTAT 0.88128 -94 TAAATAAACCAATTGATTATTATTATTATT 4 226 1 AATTGATTAT 0.926423 -75 ATCCGAAGAAAAAAGATTTAACTGAG 5 285 1 AAAAGATTTA 0.64048 -16 TCGATAGGTTTATTGATTTAAAACAAAATT 6 97 1 TATTGATTTA 0.913757 -152 TTAAAAAGTGAATTTATTAAATTTTGTTTT 6 116 0 AATTTATTAA 0.533516 -133 TTAGATCATTAAATGTTTTTCCTTTTTTAA 6 142 0 AAATGTTTTT 0.615332 -107 ATAGCAAAAAAATTGATTTAGATCATTAAA 6 159 0 AATTGATTTA 0.926415 -90 ********** Masking position 2 Map Score: 7.57708 Number of sites scoring better than the average of aligned sites = 762 Number in coding regions = 623 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 5 TCATAAAAGCATTCTCACTTAAACTAC 2 5 0 ATTCCATAAA 0.936148 -92 ATAACCGCACTTTTCCACATAAAGTGCGGTAAA 3 22 1 TTTTCATAAA 0.975951 -147 AATTCAGAAATTTTTCAATTCAAGGTTTACGCA 3 56 1 TTTTCATCAA 0.958084 -113 ATTGAAATTCATTCTCAATTATATTCTCAAAGA 3 120 1 ATTCCATATA 0.673535 -49 CTCAAAGAAATTTCTCAAATAACAAGGAAAAAA 3 145 1 TTTCCATAAC 0.918261 -24 GACTTTAGTTTTTTTAAGTTAAAAATCAATAAC 4 60 1 TTTTAATAAA 0.861801 -241 TTAGTCCAATTTTTGCAGGTACAGATTGAAATC 4 151 1 TTTTCATACA 0.940059 -150 TTCAAACTAATTTTGGATTTCAATCTGTACCTG 4 166 0 TTTTGATCAA 0.747457 -135 AGTTTGAATTTTACGCAATTAAATTCAAATGAT 4 191 1 TTACCATAAA 0.883446 -110 TTAGTATAATTTTCACCCATACAGATTGTTTTA 5 178 0 TTTCCCTACA 0.811731 -123 AGAGACTACATTTTCAATATAAATATGTCTTTA 5 227 0 TTTTAATAAA 0.86281 -74 TTGATGAAATTTTCGCAACTCAAACACATAACT 6 51 1 TTTCCATCAA 0.973393 -198 **** ** **** Masking position 10 Map Score: 7.23198 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 384 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 6 CATTTTGTGCATAATAGGAAGGA 1 4 1 TTTGTGCATA 0.845985 -25 GTGAGAATGCTTTTATGATATAGTTCGCCA 2 20 1 TTTTATGATA 0.849481 -77 AGTGCGGTTATTTTTTGAAATA 3 3 0 TTTTTTGAAA 0.924745 -166 TACCGCACTTTATGTGGAAAAGTGCGGTTA 3 23 0 TATGTGGAAA 0.76389 -146 ATACGGGGGATTTTAGCAAAGGCTAAATAA 3 89 0 TTTTAGCAAA 0.736903 -80 GAGAAATTTCTTTGAGAATATAATTGAGAA 3 131 0 TTTGAGAATA 0.689348 -38 TTGAAAGTTGTTTTTGGAAAGTAAGGACTT 4 35 1 TTTTTGGAAA 0.954673 -266 TATTCTAATATTTGATGAAATTTTCGCAAC 6 40 1 TTTGATGAAA 0.800123 -209 ATGTTTTTCCTTTTTTAAAAAGTGAATTTA 6 130 0 TTTTTTAAAA 0.681696 -119 CTAAATCAATTTTTTTGCTATTATTTGCTC 6 168 1 TTTTTTGCTA 0.65508 -81 ********** Masking position 3 Map Score: 2.97702 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 492 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 7 ATAATCAATAGATTAAATTTAATATAAAAA 2 66 1 GATTAAATTT 0.790991 -31 TTTTAGCAAAGGCTAAATAATGCGTAAACC 3 79 0 GGCTAAATAA 0.95301 -90 CTTTCAAGTTGGCTATATTAAAACCATCTA 4 12 0 GGCTATATTA 0.860416 -289 AGATTTTTATGACTAAATATAATTATTTTG 4 100 0 GACTAAATAT 0.960728 -201 GCAAAAATTGGACTAAATAAGCGAGAGATT 4 137 0 GACTAAATAA 0.960728 -164 AATACTTAGAGACTACATTTTCAATATAAA 5 237 0 GACTACATTT 0.916805 -64 ********** Masking position 5 Map Score: 1.27568 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 67 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 CATTTTGTGCATAATAGGAAGGAAAATT 1 11 1 ATAATAGGAA 0.950054 -18 AATAATAATAATAATAATAATAATAATCAA 4 238 0 ATAATAATAA 0.935403 -63 GAGAATGGCGATAATAATAATAATAATAAT 4 250 0 ATAATAATAA 0.935403 -51 AATTGAGCAAATAATAGCAAAAAAATTGAT 6 172 0 ATAATAGCAA 0.950054 -77 ********** Masking position 5 Map Score: 0.0127152 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ********** No masking Map Score: -2.49157e-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 10 ********** No masking Map Score: -2.49157e-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 11 ********** No masking Map Score: -2.49157e-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