AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i137_Potential_Transporter_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 HI0146 300 conserved hypothetical protein #2 HI1028 30 conserved hypothetical protein #3 HI1030 71 conserved hypothetical transmembrane protein #4 HI1031 175 conserved hypothetical protein Motif number 1 TAACCTTATTATATGAAAAATAAATGCCATTTTAA 1 63 1 ATATGAAAAT 0.990619 -238 TTGATCACATTTATGAAAAAACACTTCAAAAATAT 1 101 0 TTATGAAAAT 0.990621 -200 TTTATTTCCAAAATGAGAAGTTGATCACATTTATG 1 121 0 AAATGAAAGT 0.859605 -180 TAACCCCGTAATATGAGAATCAATTTAGGCCAAAA 1 235 0 ATATGAAAAT 0.990394 -66 AAAAGTCTCCTTGTGTTAAGAAAGTCTGTT 2 6 0 TTGTGTAAAT 0.953625 -25 CGAATCACATTTGTGATAATCAATTGGAGGTGTA 3 48 1 TTGTGAAAAT 0.978422 -24 ATATGAAATATTATCACAAGAAAATAGGATCTAGA 4 17 1 TTATCAAAAT 0.931862 -159 TTATAAATCAATATGTTAAAATAATTTTACTGATT 4 58 0 ATATGTAAAT 0.979517 -118 CTCAGTCAATAAATGTAAAATAAATAAATTATTTA 4 90 0 AAATGTAAAT 0.930039 -86 TTTTTGTAAATTATGAAACGTAATTTTACTATATA 4 133 1 TTATGAACAT 0.956571 -43 ****** ** * * Masking position 8 Map Score: 12.4856 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 104 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 TTATAAGTTGTAATATGCTTATATTTTCAT 1 29 1 TAATATGCTT 0.770874 -272 ATATTCTTTAAAATGGCATTTATTTTTCAT 1 75 0 AAATGGCATT 0.81928 -226 AACACTTCAAAAATATTCTTTAAAATGGCA 1 87 0 AAATATTCTT 0.90631 -214 GTTTTTTCATAAATGTGATCAACTTCTCAT 1 114 1 AAATGTGATC 0.942442 -187 AACAAATTTAAAATAGTTTTACGAGTTTTA 1 152 0 AAATAGTTTT 0.915767 -149 AAACTATTTTAAATTTGTTTTTTTACTCTT 1 163 1 AAATTTGTTT 0.831157 -138 TTCTCCCCCAAAATAGGATTCGAGAGCAAT 1 196 0 AAATAGGATT 0.977626 -105 CAGCAATATGTTTCCAGTAAAAC 3 4 1 CAATATGTTT 0.856847 -68 TGATTATCACAAATGTGATTCGTTTTATAT 3 40 0 AAATGTGATT 0.966963 -32 TCACAATATGAAATATTATCACAAGAAAAT 4 12 1 AAATATTATC 0.90569 -164 TATCACAAGAAAATAGGATCTAGATCACAA 4 28 1 AAATAGGATC 0.960705 -148 CAATATGTTAAAATAATTTTACTGATTTTG 4 55 0 AAATAATTTT 0.675484 -121 ********** Masking position 3 Map Score: 10.4091 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 446 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 TTGTAATATGCTTATATTTTCATCATTTAACCT 1 36 1 CTATTTTTAT 0.910941 -265 AGAAGTTGATCACATTTATGAAAAAACACTTCA 1 108 0 CAATTATGAA 0.744091 -193 TGATCAACTTCTCATTTTGGAAATAAAACTCGT 1 129 1 CTATTTGGAA 0.991257 -172 CCTGTGTGAACTTATGTTGGAAAGGGGCATAGA 1 271 0 CTATTTGGAA 0.991257 -30 GTGATAATATTTCATATTGTGAA 4 1 0 TTATTTGTAA 0.94158 -175 AATAATTTTACTGATTTTGTGATCTAGATCCTA 4 41 0 CTATTTGTAT 0.963192 -135 ACTGAGCTTTCTTATTTTTGTAAATTATGAAAC 4 119 1 CTATTTTGAA 0.977934 -57 CTCTCTTAATTTTATATAGTAAAATTACGTTTC 4 147 0 TTATTAGTAA 0.856134 -29 ** ** **** ** Masking position 4 Map Score: 7.25527 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 173 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 TTTTATAAGTTGTAATATGCTTATATTTTC 1 27 1 TGTAATATGC 0.827778 -274 AAATAAAACTCGTAAAACTATTTTAAATTT 1 149 1 CGTAAAACTA 0.93883 -152 CAATTCTAAGAGTAAAAAAACAAATTTAAA 1 170 0 AGTAAAAAAA 0.825684 -131 AGATTAACCCCGTAATATGAGAATCAATTT 1 244 0 CGTAATATGA 0.929225 -57 ATATGTTTCCAGTAAAACGCCATAATATAA 3 16 1 AGTAAAACGC 0.942805 -56 TCACAAAATCAGTAAAATTATTTTAACATA 4 52 1 AGTAAAATTA 0.964926 -124 AGTCAATAAATGTAAAATAAATAAATTATT 4 92 0 TGTAAAATAA 0.911429 -84 AATTTTATATAGTAAAATTACGTTTCATAA 4 143 0 AGTAAAATTA 0.964926 -33 ********** Masking position 5 Map Score: 5.93118 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 207 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 AAACAATCTTTTATAAGTTGTAATATGCTT 1 19 1 TTATAAGTTG 0.787221 -282 TATAATAAGGTTAAATGATGAAAATATAAG 1 46 0 TTAAATGATG 0.955533 -255 TCATTTAACCTTATTATATGAAAAATAAAT 1 58 1 TTATTATATG 0.906499 -243 TATTACGGGGTTAATCTATGCCCCTTTCCA 1 257 1 TTAATCTATG 0.890696 -44 GTGATTCGTTTTATATTATGGCGTTTTACT 3 26 0 TTATATTATG 0.962853 -46 TCTTATTTTTGTAAATTATGAAACGTAATT 4 128 1 GTAAATTATG 0.904556 -48 ********** Masking position 3 Map Score: 0.365398 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 154 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ********** No masking Map Score: 8.40873e-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 7 ********** No masking Map Score: 8.40873e-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 8 ********** No masking Map Score: 8.40873e-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