AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___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 HI1655 71 antigen #2 HI1658 56 hemolysin, putative #3 HI1659 179 ribonucleoside-diphosphate reductase, alpha chain (nrdA) #4 HI1660 141 ribonucleoside diphosphate reductase, beta chain (nrdB) Motif number 1 TTTAAGTTATGAGATAAGTAAGATCTGCTA 1 22 1 GAGATAAGTA 0.905307 -50 CAGGAAAATAAATCACTTTC 2 1 1 CAGGAAAATA 0.94439 -56 ATTTTTTATTTAGAAAAATAAGAAAAAGTG 3 51 0 TAGAAAAATA 0.853626 -129 CCCATAAGTTGGGGAAGACAATAGGGGCGT 4 11 0 GGGGAAGACA 0.97097 -131 CCCAACTTATGGGGAAGATAGCACGACATA 4 28 1 GGGGAAGATA 0.993063 -114 ATCAAAGACTGAGGAAAGTATCCTAATTCG 4 59 0 GAGGAAAGTA 0.983455 -83 CTGTTTATCAGGGGAAACTATCAAAGACTG 4 78 0 GGGGAAACTA 0.991509 -64 CTGATAAACAGGGAAAGCTAAATAAATGAT 4 97 1 GGGAAAGCTA 0.980011 -45 TTCTATTTAAAGGATAAATAAA 4 130 1 AGGATAAATA 0.783588 -12 ********** Masking position 6 Map Score: 9.88106 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 324 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 TTAGTTTGAAAGTGATTTATTTTCCTG 2 7 0 AGTATTTATT 0.979863 -50 TCAAACTAATAGTAATTTAATCTAAAAAGGA 2 29 1 AGTATTTAAT 0.908564 -28 AAAGTGCGGTAAAAATTTGTTGAATTTTTCA 3 26 0 AAAATTTGTT 0.903805 -154 TAAAAATTAAAATTTTTTATTTAGAAAAATA 3 61 0 AATTTTTATT 0.953211 -119 TAAAAAATTTTAATTTTTATTCTCACAAAAA 3 73 1 TAATTTTATT 0.834102 -107 TTTTTAAATAAGTTATCTATTGTCAAGAATC 3 111 1 AGTATCTATT 0.939844 -69 AATCAAATCAAAAAATTTATTACTTGCGATC 3 138 1 AAAATTTATT 0.896297 -42 AAATAGAACTTATCATTTATTTAGCTTTCCC 4 107 0 TATATTTATT 0.953614 -35 *** ******* Masking position 6 Map Score: 6.55628 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 200 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 3 ACTATTGTCTGTTTATGATGGAGCAAAG 1 54 1 GTTATGATGG 0.982918 -18 AAAATAAACGGTTTTTGTGAGAATAAAAATT 3 84 0 GTTTTGTGAG 0.981241 -96 AAGATAATGTGTTTGAGAAAAGATCGCAA 3 161 0 GTTTTGAGAA 0.970565 -19 ACTTTCCTCAGTCTTTGATAGTTTCCCCTGA 4 70 1 GTTTTGATAG 0.987007 -72 AGCTTTCCCTGTTTATCAGGGGAAACTATCA 4 85 0 GTTATCAGGG 0.973561 -57 ** ******** Masking position 6 Map Score: 2.08569 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 44 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 CATAACTTAAAAGCAAACAAAA 1 3 0 AAGCAAACAA 0.972515 -69 GCTCCATCATAAACAGACAATAGTCGTAGC 1 48 0 AAACAGACAA 0.941252 -24 ATAGTAATTTAATCTAAAAAGGAGTTAATT 2 37 1 AATCTAAAAA 0.953841 -20 TGCGGTGAAAAATTCAACAAATTTTTACCG 3 21 1 AATTCAACAA 0.781146 -159 TATTTAGAAAAATAAGAAAAAGTGCGGTAA 3 45 0 AATAAGAAAA 0.677614 -135 TTATTTTTCTAAATAAAAAATTTTAATTTT 3 60 1 AAATAAAAAA 0.853441 -120 TCAAGAATCAAATCAAAAAATTTATTACTT 3 133 1 AATCAAAAAA 0.970718 -47 TTATCAGGGGAAACTATCAAAGACTGAGGA 4 74 0 AAACTATCAA 0.763085 -68 TAAACAGGGAAAGCTAAATAAATGATAAGT 4 101 1 AAGCTAAATA 0.729752 -41 ********** Masking position 2 Map Score: 4.39132 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 788 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 5 AGTAATTTAATCTAAAAAGGAGTTAATT 2 39 1 TCTAAGAGTT 0.97331 -18 TTTGTTGAATTTTTCACCGCACTTTGAAGGA 3 8 0 TTTACGACTT 0.992205 -172 ATTCAACAAATTTTTACCGCACTTTTTCTTATTT 3 32 1 TTTACGACTT 0.992205 -148 AAACCGTTTATTTTTAAATAAGTTATCTATTGTC 3 101 1 TTTAATAGTT 0.939438 -79 TTATTTATCCTTTAAATAGAACTTATCATTTATT 4 117 0 TTTAAGACTT 0.991591 -25 *** * ** **** Masking position 6 Map Score: 1.79001 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 271 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 6 GAATTTTTCACCGCACTTTGAAGGA 3 6 0 CCGCACTTTG 0.99144 -174 CAAATTTTTACCGCACTTTTTCTTATTTTT 3 38 1 CCGCACTTTT 0.994961 -142 TTTATTACTTGCGATCTTTTCTCAAACACA 3 153 1 GCGATCTTTT 0.949615 -27 TATTGTCTTCCCCAACTTATGGGGAAGATA 4 18 1 CCCAACTTAT 0.949615 -124 ********** Masking position 7 Map Score: 0.711385 Number of sites scoring better than the average of aligned sites = 1504 Number in coding regions = 1000 Number in noncoding regions = 504 Number of orfs with sites within 600 bp upstream = 330 Fraction of orfs with sites within 600 bp upstream = 0.0530035 Motif number 7 ********** No masking Map Score: -5.51791e-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: -5.51791e-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 9 ********** No masking Map Score: -5.51791e-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