AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i137_Potential_Transporter_hinf_reg_100.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 AGCATATTACAACTTATAAAAGATTGTTTTG 1 17 0 ACTTATAAAA 0.888616 -284 TAATAAGGTTAAATGATGAAAATATAAGCAT 1 43 0 AATGATGAAA 0.956381 -258 ATTTAACCTTATTATATGAAAAATAAATGCC 1 60 1 ATATATGAAA 0.968494 -241 AAGTTGATCACATTTATGAAAAAACACTTCA 1 108 0 CTTTATGAAA 0.908493 -193 AGTAAAAAAACAAATTTAAAATAGTTTTACG 1 159 0 CAATTTAAAA 0.772676 -142 GTAAAACGCCATAATATAAAACGAATCACAT 3 27 1 AAATATAAAA 0.972747 -45 TTCACAATATGAAATATTATCACA 4 4 1 AAATATGAAA 0.985484 -172 TTATAAATCAATATGTTAAAATAATTTTACT 4 62 0 AATGTTAAAA 0.740955 -114 ATAATTTACAAAAATAAGAAAGCTCAGTCAA 4 116 0 AAATAAGAAA 0.896113 -60 TTATTTTTGTAAATTATGAAACGTAATTTTA 4 130 1 AATTATGAAA 0.982797 -46 ACGTAATTTTACTATATAAAATTAAGAGAGG 4 150 1 ATATATAAAA 0.941732 -26 * ********* Masking position 9 Map Score: 11.9359 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 323 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 CATTTTAAAGAATATTTTTGAAGTGTTTTT 1 90 1 AATATTTTTG 0.849708 -211 AGAAGTTGATCACATTTATGAAAAAACACT 1 111 0 CACATTTATG 0.884408 -190 TGATCAACTTCTCATTTTGGAAATAAAACT 1 129 1 CTCATTTTGG 0.971375 -172 GCTCTCGAATCCTATTTTGGGGGAGAAAAC 1 199 1 CCTATTTTGG 0.960224 -102 GGAGAAAACATACATTTTTGGCCTAAATTG 1 220 1 TACATTTTTG 0.891301 -81 AATTGATTCTCATATTACGGGGTTAATCTA 1 245 1 CATATTACGG 0.925262 -56 CCTGTGTGAACTTATGTTGGAAAGGGGCAT 1 274 0 CTTATGTTGG 0.876274 -27 TTACTGGAAACATATTGCTG 3 1 0 CATATTGCTG 0.922861 -71 TGATTCGTTTTATATTATGGCGTTTTACTG 3 25 0 TATATTATGG 0.816033 -47 TAAAACGAATCACATTTGTGATAATCAATT 3 43 1 CACATTTGTG 0.917781 -29 GATAATATTTCATATTGTGAA 4 2 0 CATATTGTGA 0.761655 -174 ACTGAGCTTTCTTATTTTTGTAAATTATGA 4 119 1 CTTATTTTTG 0.962642 -57 ********** Masking position 4 Map Score: 9.84986 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 600 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 TGAAAATATAAGCATATTACAACTTATAAA 1 28 0 AGCATATTAC 0.802722 -273 TTATATTTTCATCATTTAACCTTATTATAT 1 47 1 ATCATTTAAC 0.810459 -254 TAAAATGGCATTTATTTTTCATATAATAAG 1 67 0 TTTATTTTTC 0.722893 -234 CAAATTTAAAATAGTTTTACGAGTTTTATT 1 150 0 ATAGTTTTAC 0.933324 -151 TTTTAAATTTGTTTTTTTACTCTTAGAATT 1 169 1 GTTTTTTTAC 0.684266 -132 TAAATTGATTCTCATATTACGGGGTTAATC 1 243 1 CTCATATTAC 0.822573 -58 TTTATATTATGGCGTTTTACTGGAAACATA 3 17 0 GGCGTTTTAC 0.874518 -55 ACAAATGTGATTCGTTTTATATTATGGCGT 3 32 0 TTCGTTTTAT 0.698005 -40 TTTTCTTGTGATAATATTTCATATTGTGAA 4 11 0 ATAATATTTC 0.607379 -165 ATATGTTAAAATAATTTTACTGATTTTGTG 4 53 0 ATAATTTTAC 0.940405 -123 AAATAATTTATTTATTTTACATTTATTGAC 4 91 1 TTTATTTTAC 0.927084 -85 ATTATGAAACGTAATTTTACTATATAAAAT 4 142 1 GTAATTTTAC 0.832057 -34 TTTTCCTCTCTTAATTTTATATAGTAAAAT 4 155 0 TTAATTTTAT 0.719353 -21 ********** Masking position 5 Map Score: 8.41172 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 723 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 4 AAAAGATTGTTTTGTGTGGA 1 1 0 TTTGTGTGGA 0.958393 -300 ATTCGCTCCTGTGTGAACTTATGTTGG 1 284 0 CCTGTGTGAA 0.981097 -17 AAAAGTCTCCTTGTGTTAAGAAAGTCTGT 2 12 0 CTTGTGTTAA 0.990717 -19 ACGAATCACATTTGTGATAATCAATTGGAG 3 47 1 TTTGTGATAA 0.970636 -25 ATCCTATTTTCTTGTGATAATATTTCATAT 4 17 0 CTTGTGATAA 0.986752 -159 ********** Masking position 5 Map Score: 4.65376 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 27 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 GTAATATGAGAATCAATTTAGGCCAAAAAT 1 233 0 AATCAATTTA 0.936221 -68 CATTTGTGATAATCAATTGGAGGTGTA 3 55 1 AATCAATTGG 0.910943 -17 TAGATCACAAAATCAGTAAAATTATTTTAA 4 48 1 AATCAGTAAA 0.934852 -128 ATTATTTATAAATCAATATGTTAAAATAAT 4 68 0 AATCAATATG 0.957815 -108 ATAAATGTAAAATAAATAAATTATTTATAA 4 87 0 AATAAATAAA 0.858581 -89 AAGAAAGCTCAGTCAATAAATGTAAAATAA 4 102 0 AGTCAATAAA 0.934852 -74 ********** Masking position 5 Map Score: 1.44932 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 265 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 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